{
 "cells": [
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "[![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/saketkc/pysradb/blob/develop/notebooks/01.Python-API_demo.ipynb)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# Python API Demo\n",
    "\n",
    "This notebook demonstrates the core functionality of pysradb Python API for querying SRA metadata."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {
    "execution": {
     "iopub.execute_input": "2025-11-01T13:07:15.972370Z",
     "iopub.status.busy": "2025-11-01T13:07:15.972015Z",
     "iopub.status.idle": "2025-11-01T13:07:16.357927Z",
     "shell.execute_reply": "2025-11-01T13:07:16.356676Z"
    }
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "pysradb 3.0.0.dev0 is already installed\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "/data/github/pysradb/pysradb/utils.py:16: TqdmExperimentalWarning: Using `tqdm.autonotebook.tqdm` in notebook mode. Use `tqdm.tqdm` instead to force console mode (e.g. in jupyter console)\n",
      "  from tqdm.autonotebook import tqdm\n"
     ]
    }
   ],
   "source": [
    "# Install pysradb if not already installed\n",
    "try:\n",
    "    import pysradb\n",
    "\n",
    "    print(f\"pysradb {pysradb.__version__} is already installed\")\n",
    "except ImportError:\n",
    "    print(\"Installing pysradb from GitHub...\")\n",
    "    import sys\n",
    "\n",
    "    !{sys.executable} -m pip install -q git+https://github.com/saketkc/pysradb\n",
    "    print(\"pysradb installed successfully!\")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {
    "colab": {
     "base_uri": "https://localhost:8080/"
    },
    "execution": {
     "iopub.execute_input": "2025-11-01T13:07:16.423567Z",
     "iopub.status.busy": "2025-11-01T13:07:16.423041Z",
     "iopub.status.idle": "2025-11-01T13:07:16.426702Z",
     "shell.execute_reply": "2025-11-01T13:07:16.425713Z"
    },
    "id": "D-CWF0xjKhxJ",
    "outputId": "b639c586-2a2b-4ecd-ae4a-55643c276cda"
   },
   "outputs": [],
   "source": [
    "# pip install git+https://github.com/saketkc/pysradb"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {
    "colab": {
     "base_uri": "https://localhost:8080/"
    },
    "execution": {
     "iopub.execute_input": "2025-11-01T13:07:16.428767Z",
     "iopub.status.busy": "2025-11-01T13:07:16.428621Z",
     "iopub.status.idle": "2025-11-01T13:07:17.350867Z",
     "shell.execute_reply": "2025-11-01T13:07:17.349172Z"
    },
    "id": "Tyd8Sjv3KpMa",
    "outputId": "9480b87f-a3bd-4507-fac4-c03ee2ad1c8f"
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "pysradb 3.0.0.dev0\r\n"
     ]
    }
   ],
   "source": [
    "!pysradb --version"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {
    "colab": {
     "base_uri": "https://localhost:8080/"
    },
    "execution": {
     "iopub.execute_input": "2025-11-01T13:07:17.354299Z",
     "iopub.status.busy": "2025-11-01T13:07:17.353950Z",
     "iopub.status.idle": "2025-11-01T13:07:17.358832Z",
     "shell.execute_reply": "2025-11-01T13:07:17.357663Z"
    },
    "id": "3h9Wlv3lKb7b",
    "outputId": "d3cf89f7-f059-41bd-9767-2bb2a0679dbf"
   },
   "outputs": [],
   "source": [
    "from pysradb.sraweb import SRAweb"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "metadata": {
    "execution": {
     "iopub.execute_input": "2025-11-01T13:07:17.361533Z",
     "iopub.status.busy": "2025-11-01T13:07:17.361250Z",
     "iopub.status.idle": "2025-11-01T13:07:17.365279Z",
     "shell.execute_reply": "2025-11-01T13:07:17.364056Z"
    },
    "id": "0iOHm8wUKb8G"
   },
   "outputs": [],
   "source": [
    "db = SRAweb()"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {
    "id": "CDyWgOqzdn6d"
   },
   "source": [
    "## Get metadata of one project"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "metadata": {
    "colab": {
     "base_uri": "https://localhost:8080/",
     "height": 3152
    },
    "execution": {
     "iopub.execute_input": "2025-11-01T13:07:17.368102Z",
     "iopub.status.busy": "2025-11-01T13:07:17.367803Z",
     "iopub.status.idle": "2025-11-01T13:07:19.140051Z",
     "shell.execute_reply": "2025-11-01T13:07:19.139033Z"
    },
    "id": "pXJ6WhsjKb_x",
    "outputId": "dfcb2624-7e85-487c-9550-0d7b7887ed68"
   },
   "outputs": [
    {
     "data": {
      "text/html": [
       "<div>\n",
       "<style scoped>\n",
       "    .dataframe tbody tr th:only-of-type {\n",
       "        vertical-align: middle;\n",
       "    }\n",
       "\n",
       "    .dataframe tbody tr th {\n",
       "        vertical-align: top;\n",
       "    }\n",
       "\n",
       "    .dataframe thead th {\n",
       "        text-align: right;\n",
       "    }\n",
       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>study_accession</th>\n",
       "      <th>study_title</th>\n",
       "      <th>experiment_accession</th>\n",
       "      <th>experiment_title</th>\n",
       "      <th>experiment_desc</th>\n",
       "      <th>organism_taxid</th>\n",
       "      <th>organism_name</th>\n",
       "      <th>library_name</th>\n",
       "      <th>library_strategy</th>\n",
       "      <th>library_source</th>\n",
       "      <th>...</th>\n",
       "      <th>biosample</th>\n",
       "      <th>bioproject</th>\n",
       "      <th>instrument</th>\n",
       "      <th>instrument_model</th>\n",
       "      <th>instrument_model_desc</th>\n",
       "      <th>total_spots</th>\n",
       "      <th>total_size</th>\n",
       "      <th>run_accession</th>\n",
       "      <th>run_total_spots</th>\n",
       "      <th>run_total_bases</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>133</th>\n",
       "      <td>SRP016501</td>\n",
       "      <td>Evolutionary dynamics of gene and isoform regu...</td>\n",
       "      <td>SRX196264</td>\n",
       "      <td>GSM1020640: mouse_a_brain; Mus musculus; RNA-Seq</td>\n",
       "      <td>GSM1020640: mouse_a_brain; Mus musculus; RNA-Seq</td>\n",
       "      <td>10090</td>\n",
       "      <td>Mus musculus</td>\n",
       "      <td></td>\n",
       "      <td>RNA-Seq</td>\n",
       "      <td>TRANSCRIPTOMIC</td>\n",
       "      <td>...</td>\n",
       "      <td>SAMN01766814</td>\n",
       "      <td>PRJNA177791</td>\n",
       "      <td>Illumina HiSeq 2000</td>\n",
       "      <td>Illumina HiSeq 2000</td>\n",
       "      <td>ILLUMINA</td>\n",
       "      <td>87264604</td>\n",
       "      <td>5927043102</td>\n",
       "      <td>SRR594393</td>\n",
       "      <td>87264604</td>\n",
       "      <td>8726460400</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>132</th>\n",
       "      <td>SRP016501</td>\n",
       "      <td>Evolutionary dynamics of gene and isoform regu...</td>\n",
       "      <td>SRX196265</td>\n",
       "      <td>GSM1020641: mouse_a_colon; Mus musculus; RNA-Seq</td>\n",
       "      <td>GSM1020641: mouse_a_colon; Mus musculus; RNA-Seq</td>\n",
       "      <td>10090</td>\n",
       "      <td>Mus musculus</td>\n",
       "      <td></td>\n",
       "      <td>RNA-Seq</td>\n",
       "      <td>TRANSCRIPTOMIC</td>\n",
       "      <td>...</td>\n",
       "      <td>SAMN01766815</td>\n",
       "      <td>PRJNA177791</td>\n",
       "      <td>Illumina HiSeq 2000</td>\n",
       "      <td>Illumina HiSeq 2000</td>\n",
       "      <td>ILLUMINA</td>\n",
       "      <td>101816491</td>\n",
       "      <td>6835402318</td>\n",
       "      <td>SRR594394</td>\n",
       "      <td>101816491</td>\n",
       "      <td>10181649100</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>131</th>\n",
       "      <td>SRP016501</td>\n",
       "      <td>Evolutionary dynamics of gene and isoform regu...</td>\n",
       "      <td>SRX196266</td>\n",
       "      <td>GSM1020642: mouse_a_heart; Mus musculus; RNA-Seq</td>\n",
       "      <td>GSM1020642: mouse_a_heart; Mus musculus; RNA-Seq</td>\n",
       "      <td>10090</td>\n",
       "      <td>Mus musculus</td>\n",
       "      <td></td>\n",
       "      <td>RNA-Seq</td>\n",
       "      <td>TRANSCRIPTOMIC</td>\n",
       "      <td>...</td>\n",
       "      <td>SAMN01766816</td>\n",
       "      <td>PRJNA177791</td>\n",
       "      <td>Illumina Genome Analyzer IIx</td>\n",
       "      <td>Illumina Genome Analyzer IIx</td>\n",
       "      <td>ILLUMINA</td>\n",
       "      <td>35175982</td>\n",
       "      <td>1502674440</td>\n",
       "      <td>SRR594395</td>\n",
       "      <td>35175982</td>\n",
       "      <td>2532670704</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>130</th>\n",
       "      <td>SRP016501</td>\n",
       "      <td>Evolutionary dynamics of gene and isoform regu...</td>\n",
       "      <td>SRX196267</td>\n",
       "      <td>GSM1020643: mouse_a_kidney; Mus musculus; RNA-Seq</td>\n",
       "      <td>GSM1020643: mouse_a_kidney; Mus musculus; RNA-Seq</td>\n",
       "      <td>10090</td>\n",
       "      <td>Mus musculus</td>\n",
       "      <td></td>\n",
       "      <td>RNA-Seq</td>\n",
       "      <td>TRANSCRIPTOMIC</td>\n",
       "      <td>...</td>\n",
       "      <td>SAMN01766817</td>\n",
       "      <td>PRJNA177791</td>\n",
       "      <td>Illumina HiSeq 2000</td>\n",
       "      <td>Illumina HiSeq 2000</td>\n",
       "      <td>ILLUMINA</td>\n",
       "      <td>119274786</td>\n",
       "      <td>7555854784</td>\n",
       "      <td>SRR594396</td>\n",
       "      <td>119274786</td>\n",
       "      <td>11927478600</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>129</th>\n",
       "      <td>SRP016501</td>\n",
       "      <td>Evolutionary dynamics of gene and isoform regu...</td>\n",
       "      <td>SRX196268</td>\n",
       "      <td>GSM1020644: mouse_a_liver; Mus musculus; RNA-Seq</td>\n",
       "      <td>GSM1020644: mouse_a_liver; Mus musculus; RNA-Seq</td>\n",
       "      <td>10090</td>\n",
       "      <td>Mus musculus</td>\n",
       "      <td></td>\n",
       "      <td>RNA-Seq</td>\n",
       "      <td>TRANSCRIPTOMIC</td>\n",
       "      <td>...</td>\n",
       "      <td>SAMN01766818</td>\n",
       "      <td>PRJNA177791</td>\n",
       "      <td>Illumina HiSeq 2000</td>\n",
       "      <td>Illumina HiSeq 2000</td>\n",
       "      <td>ILLUMINA</td>\n",
       "      <td>116292478</td>\n",
       "      <td>7481554926</td>\n",
       "      <td>SRR594397</td>\n",
       "      <td>116292478</td>\n",
       "      <td>11629247800</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>...</th>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>SRP016501</td>\n",
       "      <td>Evolutionary dynamics of gene and isoform regu...</td>\n",
       "      <td>SRX196393</td>\n",
       "      <td>GSM1020769: chicken_c_liver; Gallus gallus; RN...</td>\n",
       "      <td>GSM1020769: chicken_c_liver; Gallus gallus; RN...</td>\n",
       "      <td>9031</td>\n",
       "      <td>Gallus gallus</td>\n",
       "      <td></td>\n",
       "      <td>RNA-Seq</td>\n",
       "      <td>TRANSCRIPTOMIC</td>\n",
       "      <td>...</td>\n",
       "      <td>SAMN01766943</td>\n",
       "      <td>PRJNA177791</td>\n",
       "      <td>Illumina HiSeq 2000</td>\n",
       "      <td>Illumina HiSeq 2000</td>\n",
       "      <td>ILLUMINA</td>\n",
       "      <td>18978066</td>\n",
       "      <td>562367072</td>\n",
       "      <td>SRR594522</td>\n",
       "      <td>18978066</td>\n",
       "      <td>1366420752</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>SRP016501</td>\n",
       "      <td>Evolutionary dynamics of gene and isoform regu...</td>\n",
       "      <td>SRX196394</td>\n",
       "      <td>GSM1020770: chicken_c_lung; Gallus gallus; RNA...</td>\n",
       "      <td>GSM1020770: chicken_c_lung; Gallus gallus; RNA...</td>\n",
       "      <td>9031</td>\n",
       "      <td>Gallus gallus</td>\n",
       "      <td></td>\n",
       "      <td>RNA-Seq</td>\n",
       "      <td>TRANSCRIPTOMIC</td>\n",
       "      <td>...</td>\n",
       "      <td>SAMN01766944</td>\n",
       "      <td>PRJNA177791</td>\n",
       "      <td>Illumina HiSeq 2000</td>\n",
       "      <td>Illumina HiSeq 2000</td>\n",
       "      <td>ILLUMINA</td>\n",
       "      <td>26604280</td>\n",
       "      <td>931417024</td>\n",
       "      <td>SRR594523</td>\n",
       "      <td>26604280</td>\n",
       "      <td>1862299600</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>SRP016501</td>\n",
       "      <td>Evolutionary dynamics of gene and isoform regu...</td>\n",
       "      <td>SRX196395</td>\n",
       "      <td>GSM1020771: chicken_c_skm; Gallus gallus; RNA-Seq</td>\n",
       "      <td>GSM1020771: chicken_c_skm; Gallus gallus; RNA-Seq</td>\n",
       "      <td>9031</td>\n",
       "      <td>Gallus gallus</td>\n",
       "      <td></td>\n",
       "      <td>RNA-Seq</td>\n",
       "      <td>TRANSCRIPTOMIC</td>\n",
       "      <td>...</td>\n",
       "      <td>SAMN01766945</td>\n",
       "      <td>PRJNA177791</td>\n",
       "      <td>Illumina HiSeq 2000</td>\n",
       "      <td>Illumina HiSeq 2000</td>\n",
       "      <td>ILLUMINA</td>\n",
       "      <td>25606436</td>\n",
       "      <td>986287075</td>\n",
       "      <td>SRR594524</td>\n",
       "      <td>25606436</td>\n",
       "      <td>1792450520</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>SRP016501</td>\n",
       "      <td>Evolutionary dynamics of gene and isoform regu...</td>\n",
       "      <td>SRX196396</td>\n",
       "      <td>GSM1020772: chicken_c_spleen; Gallus gallus; R...</td>\n",
       "      <td>GSM1020772: chicken_c_spleen; Gallus gallus; R...</td>\n",
       "      <td>9031</td>\n",
       "      <td>Gallus gallus</td>\n",
       "      <td></td>\n",
       "      <td>RNA-Seq</td>\n",
       "      <td>TRANSCRIPTOMIC</td>\n",
       "      <td>...</td>\n",
       "      <td>SAMN01766946</td>\n",
       "      <td>PRJNA177791</td>\n",
       "      <td>Illumina HiSeq 2000</td>\n",
       "      <td>Illumina HiSeq 2000</td>\n",
       "      <td>ILLUMINA</td>\n",
       "      <td>24401708</td>\n",
       "      <td>1201671888</td>\n",
       "      <td>SRR594525</td>\n",
       "      <td>24401708</td>\n",
       "      <td>1756922976</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>SRP016501</td>\n",
       "      <td>Evolutionary dynamics of gene and isoform regu...</td>\n",
       "      <td>SRX196397</td>\n",
       "      <td>GSM1020773: chicken_c_testes; Gallus gallus; R...</td>\n",
       "      <td>GSM1020773: chicken_c_testes; Gallus gallus; R...</td>\n",
       "      <td>9031</td>\n",
       "      <td>Gallus gallus</td>\n",
       "      <td></td>\n",
       "      <td>RNA-Seq</td>\n",
       "      <td>TRANSCRIPTOMIC</td>\n",
       "      <td>...</td>\n",
       "      <td>SAMN01766947</td>\n",
       "      <td>PRJNA177791</td>\n",
       "      <td>Illumina HiSeq 2000</td>\n",
       "      <td>Illumina HiSeq 2000</td>\n",
       "      <td>ILLUMINA</td>\n",
       "      <td>37423394</td>\n",
       "      <td>1980545796</td>\n",
       "      <td>SRR594526</td>\n",
       "      <td>37423394</td>\n",
       "      <td>2993871520</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>134 rows × 24 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "    study_accession                                        study_title  \\\n",
       "133       SRP016501  Evolutionary dynamics of gene and isoform regu...   \n",
       "132       SRP016501  Evolutionary dynamics of gene and isoform regu...   \n",
       "131       SRP016501  Evolutionary dynamics of gene and isoform regu...   \n",
       "130       SRP016501  Evolutionary dynamics of gene and isoform regu...   \n",
       "129       SRP016501  Evolutionary dynamics of gene and isoform regu...   \n",
       "..              ...                                                ...   \n",
       "4         SRP016501  Evolutionary dynamics of gene and isoform regu...   \n",
       "3         SRP016501  Evolutionary dynamics of gene and isoform regu...   \n",
       "2         SRP016501  Evolutionary dynamics of gene and isoform regu...   \n",
       "1         SRP016501  Evolutionary dynamics of gene and isoform regu...   \n",
       "0         SRP016501  Evolutionary dynamics of gene and isoform regu...   \n",
       "\n",
       "    experiment_accession                                   experiment_title  \\\n",
       "133            SRX196264   GSM1020640: mouse_a_brain; Mus musculus; RNA-Seq   \n",
       "132            SRX196265   GSM1020641: mouse_a_colon; Mus musculus; RNA-Seq   \n",
       "131            SRX196266   GSM1020642: mouse_a_heart; Mus musculus; RNA-Seq   \n",
       "130            SRX196267  GSM1020643: mouse_a_kidney; Mus musculus; RNA-Seq   \n",
       "129            SRX196268   GSM1020644: mouse_a_liver; Mus musculus; RNA-Seq   \n",
       "..                   ...                                                ...   \n",
       "4              SRX196393  GSM1020769: chicken_c_liver; Gallus gallus; RN...   \n",
       "3              SRX196394  GSM1020770: chicken_c_lung; Gallus gallus; RNA...   \n",
       "2              SRX196395  GSM1020771: chicken_c_skm; Gallus gallus; RNA-Seq   \n",
       "1              SRX196396  GSM1020772: chicken_c_spleen; Gallus gallus; R...   \n",
       "0              SRX196397  GSM1020773: chicken_c_testes; Gallus gallus; R...   \n",
       "\n",
       "                                       experiment_desc organism_taxid  \\\n",
       "133   GSM1020640: mouse_a_brain; Mus musculus; RNA-Seq          10090   \n",
       "132   GSM1020641: mouse_a_colon; Mus musculus; RNA-Seq          10090   \n",
       "131   GSM1020642: mouse_a_heart; Mus musculus; RNA-Seq          10090   \n",
       "130  GSM1020643: mouse_a_kidney; Mus musculus; RNA-Seq          10090   \n",
       "129   GSM1020644: mouse_a_liver; Mus musculus; RNA-Seq          10090   \n",
       "..                                                 ...            ...   \n",
       "4    GSM1020769: chicken_c_liver; Gallus gallus; RN...           9031   \n",
       "3    GSM1020770: chicken_c_lung; Gallus gallus; RNA...           9031   \n",
       "2    GSM1020771: chicken_c_skm; Gallus gallus; RNA-Seq           9031   \n",
       "1    GSM1020772: chicken_c_spleen; Gallus gallus; R...           9031   \n",
       "0    GSM1020773: chicken_c_testes; Gallus gallus; R...           9031   \n",
       "\n",
       "     organism_name library_name library_strategy  library_source  ...  \\\n",
       "133   Mus musculus                       RNA-Seq  TRANSCRIPTOMIC  ...   \n",
       "132   Mus musculus                       RNA-Seq  TRANSCRIPTOMIC  ...   \n",
       "131   Mus musculus                       RNA-Seq  TRANSCRIPTOMIC  ...   \n",
       "130   Mus musculus                       RNA-Seq  TRANSCRIPTOMIC  ...   \n",
       "129   Mus musculus                       RNA-Seq  TRANSCRIPTOMIC  ...   \n",
       "..             ...          ...              ...             ...  ...   \n",
       "4    Gallus gallus                       RNA-Seq  TRANSCRIPTOMIC  ...   \n",
       "3    Gallus gallus                       RNA-Seq  TRANSCRIPTOMIC  ...   \n",
       "2    Gallus gallus                       RNA-Seq  TRANSCRIPTOMIC  ...   \n",
       "1    Gallus gallus                       RNA-Seq  TRANSCRIPTOMIC  ...   \n",
       "0    Gallus gallus                       RNA-Seq  TRANSCRIPTOMIC  ...   \n",
       "\n",
       "        biosample   bioproject                    instrument  \\\n",
       "133  SAMN01766814  PRJNA177791           Illumina HiSeq 2000   \n",
       "132  SAMN01766815  PRJNA177791           Illumina HiSeq 2000   \n",
       "131  SAMN01766816  PRJNA177791  Illumina Genome Analyzer IIx   \n",
       "130  SAMN01766817  PRJNA177791           Illumina HiSeq 2000   \n",
       "129  SAMN01766818  PRJNA177791           Illumina HiSeq 2000   \n",
       "..            ...          ...                           ...   \n",
       "4    SAMN01766943  PRJNA177791           Illumina HiSeq 2000   \n",
       "3    SAMN01766944  PRJNA177791           Illumina HiSeq 2000   \n",
       "2    SAMN01766945  PRJNA177791           Illumina HiSeq 2000   \n",
       "1    SAMN01766946  PRJNA177791           Illumina HiSeq 2000   \n",
       "0    SAMN01766947  PRJNA177791           Illumina HiSeq 2000   \n",
       "\n",
       "                 instrument_model instrument_model_desc total_spots  \\\n",
       "133           Illumina HiSeq 2000              ILLUMINA    87264604   \n",
       "132           Illumina HiSeq 2000              ILLUMINA   101816491   \n",
       "131  Illumina Genome Analyzer IIx              ILLUMINA    35175982   \n",
       "130           Illumina HiSeq 2000              ILLUMINA   119274786   \n",
       "129           Illumina HiSeq 2000              ILLUMINA   116292478   \n",
       "..                            ...                   ...         ...   \n",
       "4             Illumina HiSeq 2000              ILLUMINA    18978066   \n",
       "3             Illumina HiSeq 2000              ILLUMINA    26604280   \n",
       "2             Illumina HiSeq 2000              ILLUMINA    25606436   \n",
       "1             Illumina HiSeq 2000              ILLUMINA    24401708   \n",
       "0             Illumina HiSeq 2000              ILLUMINA    37423394   \n",
       "\n",
       "     total_size run_accession run_total_spots run_total_bases  \n",
       "133  5927043102     SRR594393        87264604      8726460400  \n",
       "132  6835402318     SRR594394       101816491     10181649100  \n",
       "131  1502674440     SRR594395        35175982      2532670704  \n",
       "130  7555854784     SRR594396       119274786     11927478600  \n",
       "129  7481554926     SRR594397       116292478     11629247800  \n",
       "..          ...           ...             ...             ...  \n",
       "4     562367072     SRR594522        18978066      1366420752  \n",
       "3     931417024     SRR594523        26604280      1862299600  \n",
       "2     986287075     SRR594524        25606436      1792450520  \n",
       "1    1201671888     SRR594525        24401708      1756922976  \n",
       "0    1980545796     SRR594526        37423394      2993871520  \n",
       "\n",
       "[134 rows x 24 columns]"
      ]
     },
     "execution_count": 6,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "df = db.sra_metadata(\"SRP016501\")\n",
    "df"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {
    "id": "gl-3e2L9Kb_7"
   },
   "source": [
    "## Get detailed metadata"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "metadata": {
    "colab": {
     "base_uri": "https://localhost:8080/",
     "height": 1000
    },
    "execution": {
     "iopub.execute_input": "2025-11-01T13:07:19.143434Z",
     "iopub.status.busy": "2025-11-01T13:07:19.143150Z",
     "iopub.status.idle": "2025-11-01T13:07:26.352948Z",
     "shell.execute_reply": "2025-11-01T13:07:26.351467Z"
    },
    "id": "JBUcbaxlKb_9",
    "outputId": "57afe1b5-cb98-4cdd-b452-69527cbd695d"
   },
   "outputs": [
    {
     "data": {
      "text/html": [
       "<div>\n",
       "<style scoped>\n",
       "    .dataframe tbody tr th:only-of-type {\n",
       "        vertical-align: middle;\n",
       "    }\n",
       "\n",
       "    .dataframe tbody tr th {\n",
       "        vertical-align: top;\n",
       "    }\n",
       "\n",
       "    .dataframe thead th {\n",
       "        text-align: right;\n",
       "    }\n",
       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>run_accession</th>\n",
       "      <th>study_accession</th>\n",
       "      <th>study_title</th>\n",
       "      <th>experiment_accession</th>\n",
       "      <th>experiment_title</th>\n",
       "      <th>experiment_desc</th>\n",
       "      <th>organism_taxid</th>\n",
       "      <th>organism_name</th>\n",
       "      <th>library_name</th>\n",
       "      <th>library_strategy</th>\n",
       "      <th>...</th>\n",
       "      <th>experiment_alias</th>\n",
       "      <th>source_name</th>\n",
       "      <th>tissue</th>\n",
       "      <th>strain</th>\n",
       "      <th>ena_fastq_http</th>\n",
       "      <th>ena_fastq_http_1</th>\n",
       "      <th>ena_fastq_http_2</th>\n",
       "      <th>ena_fastq_ftp</th>\n",
       "      <th>ena_fastq_ftp_1</th>\n",
       "      <th>ena_fastq_ftp_2</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>SRR594393</td>\n",
       "      <td>SRP016501</td>\n",
       "      <td>Evolutionary dynamics of gene and isoform regu...</td>\n",
       "      <td>SRX196264</td>\n",
       "      <td>GSM1020640: mouse_a_brain; Mus musculus; RNA-Seq</td>\n",
       "      <td>GSM1020640: mouse_a_brain; Mus musculus; RNA-Seq</td>\n",
       "      <td>10090</td>\n",
       "      <td>Mus musculus</td>\n",
       "      <td>&lt;NA&gt;</td>\n",
       "      <td>RNA-Seq</td>\n",
       "      <td>...</td>\n",
       "      <td>GSM1020640_1</td>\n",
       "      <td>mouse_brain</td>\n",
       "      <td>brain</td>\n",
       "      <td>DBA/2J</td>\n",
       "      <td>&lt;NA&gt;</td>\n",
       "      <td>http://ftp.sra.ebi.ac.uk/vol1/fastq/SRR594/SRR...</td>\n",
       "      <td>http://ftp.sra.ebi.ac.uk/vol1/fastq/SRR594/SRR...</td>\n",
       "      <td>&lt;NA&gt;</td>\n",
       "      <td>era-fasp@fasp.sra.ebi.ac.uk:vol1/fastq/SRR594/...</td>\n",
       "      <td>era-fasp@fasp.sra.ebi.ac.uk:vol1/fastq/SRR594/...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>SRR594394</td>\n",
       "      <td>SRP016501</td>\n",
       "      <td>Evolutionary dynamics of gene and isoform regu...</td>\n",
       "      <td>SRX196265</td>\n",
       "      <td>GSM1020641: mouse_a_colon; Mus musculus; RNA-Seq</td>\n",
       "      <td>GSM1020641: mouse_a_colon; Mus musculus; RNA-Seq</td>\n",
       "      <td>10090</td>\n",
       "      <td>Mus musculus</td>\n",
       "      <td>&lt;NA&gt;</td>\n",
       "      <td>RNA-Seq</td>\n",
       "      <td>...</td>\n",
       "      <td>GSM1020641_1</td>\n",
       "      <td>mouse_colon</td>\n",
       "      <td>colon</td>\n",
       "      <td>DBA/2J</td>\n",
       "      <td>&lt;NA&gt;</td>\n",
       "      <td>http://ftp.sra.ebi.ac.uk/vol1/fastq/SRR594/SRR...</td>\n",
       "      <td>http://ftp.sra.ebi.ac.uk/vol1/fastq/SRR594/SRR...</td>\n",
       "      <td>&lt;NA&gt;</td>\n",
       "      <td>era-fasp@fasp.sra.ebi.ac.uk:vol1/fastq/SRR594/...</td>\n",
       "      <td>era-fasp@fasp.sra.ebi.ac.uk:vol1/fastq/SRR594/...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>SRR594395</td>\n",
       "      <td>SRP016501</td>\n",
       "      <td>Evolutionary dynamics of gene and isoform regu...</td>\n",
       "      <td>SRX196266</td>\n",
       "      <td>GSM1020642: mouse_a_heart; Mus musculus; RNA-Seq</td>\n",
       "      <td>GSM1020642: mouse_a_heart; Mus musculus; RNA-Seq</td>\n",
       "      <td>10090</td>\n",
       "      <td>Mus musculus</td>\n",
       "      <td>&lt;NA&gt;</td>\n",
       "      <td>RNA-Seq</td>\n",
       "      <td>...</td>\n",
       "      <td>GSM1020642_1</td>\n",
       "      <td>mouse_heart</td>\n",
       "      <td>heart</td>\n",
       "      <td>DBA/2J</td>\n",
       "      <td>&lt;NA&gt;</td>\n",
       "      <td>http://ftp.sra.ebi.ac.uk/vol1/fastq/SRR594/SRR...</td>\n",
       "      <td>http://ftp.sra.ebi.ac.uk/vol1/fastq/SRR594/SRR...</td>\n",
       "      <td>&lt;NA&gt;</td>\n",
       "      <td>era-fasp@fasp.sra.ebi.ac.uk:vol1/fastq/SRR594/...</td>\n",
       "      <td>era-fasp@fasp.sra.ebi.ac.uk:vol1/fastq/SRR594/...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>SRR594396</td>\n",
       "      <td>SRP016501</td>\n",
       "      <td>Evolutionary dynamics of gene and isoform regu...</td>\n",
       "      <td>SRX196267</td>\n",
       "      <td>GSM1020643: mouse_a_kidney; Mus musculus; RNA-Seq</td>\n",
       "      <td>GSM1020643: mouse_a_kidney; Mus musculus; RNA-Seq</td>\n",
       "      <td>10090</td>\n",
       "      <td>Mus musculus</td>\n",
       "      <td>&lt;NA&gt;</td>\n",
       "      <td>RNA-Seq</td>\n",
       "      <td>...</td>\n",
       "      <td>GSM1020643_1</td>\n",
       "      <td>mouse_kidney</td>\n",
       "      <td>kidney</td>\n",
       "      <td>DBA/2J</td>\n",
       "      <td>&lt;NA&gt;</td>\n",
       "      <td>http://ftp.sra.ebi.ac.uk/vol1/fastq/SRR594/SRR...</td>\n",
       "      <td>http://ftp.sra.ebi.ac.uk/vol1/fastq/SRR594/SRR...</td>\n",
       "      <td>&lt;NA&gt;</td>\n",
       "      <td>era-fasp@fasp.sra.ebi.ac.uk:vol1/fastq/SRR594/...</td>\n",
       "      <td>era-fasp@fasp.sra.ebi.ac.uk:vol1/fastq/SRR594/...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>SRR594397</td>\n",
       "      <td>SRP016501</td>\n",
       "      <td>Evolutionary dynamics of gene and isoform regu...</td>\n",
       "      <td>SRX196268</td>\n",
       "      <td>GSM1020644: mouse_a_liver; Mus musculus; RNA-Seq</td>\n",
       "      <td>GSM1020644: mouse_a_liver; Mus musculus; RNA-Seq</td>\n",
       "      <td>10090</td>\n",
       "      <td>Mus musculus</td>\n",
       "      <td>&lt;NA&gt;</td>\n",
       "      <td>RNA-Seq</td>\n",
       "      <td>...</td>\n",
       "      <td>GSM1020644_1</td>\n",
       "      <td>mouse_liver</td>\n",
       "      <td>liver</td>\n",
       "      <td>DBA/2J</td>\n",
       "      <td>&lt;NA&gt;</td>\n",
       "      <td>http://ftp.sra.ebi.ac.uk/vol1/fastq/SRR594/SRR...</td>\n",
       "      <td>http://ftp.sra.ebi.ac.uk/vol1/fastq/SRR594/SRR...</td>\n",
       "      <td>&lt;NA&gt;</td>\n",
       "      <td>era-fasp@fasp.sra.ebi.ac.uk:vol1/fastq/SRR594/...</td>\n",
       "      <td>era-fasp@fasp.sra.ebi.ac.uk:vol1/fastq/SRR594/...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>...</th>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>129</th>\n",
       "      <td>SRR594522</td>\n",
       "      <td>SRP016501</td>\n",
       "      <td>Evolutionary dynamics of gene and isoform regu...</td>\n",
       "      <td>SRX196393</td>\n",
       "      <td>GSM1020769: chicken_c_liver; Gallus gallus; RN...</td>\n",
       "      <td>GSM1020769: chicken_c_liver; Gallus gallus; RN...</td>\n",
       "      <td>9031</td>\n",
       "      <td>Gallus gallus</td>\n",
       "      <td>&lt;NA&gt;</td>\n",
       "      <td>RNA-Seq</td>\n",
       "      <td>...</td>\n",
       "      <td>GSM1020769_1</td>\n",
       "      <td>chicken_liver</td>\n",
       "      <td>liver</td>\n",
       "      <td>&lt;NA&gt;</td>\n",
       "      <td>&lt;NA&gt;</td>\n",
       "      <td>http://ftp.sra.ebi.ac.uk/vol1/fastq/SRR594/SRR...</td>\n",
       "      <td>http://ftp.sra.ebi.ac.uk/vol1/fastq/SRR594/SRR...</td>\n",
       "      <td>&lt;NA&gt;</td>\n",
       "      <td>era-fasp@fasp.sra.ebi.ac.uk:vol1/fastq/SRR594/...</td>\n",
       "      <td>era-fasp@fasp.sra.ebi.ac.uk:vol1/fastq/SRR594/...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>130</th>\n",
       "      <td>SRR594523</td>\n",
       "      <td>SRP016501</td>\n",
       "      <td>Evolutionary dynamics of gene and isoform regu...</td>\n",
       "      <td>SRX196394</td>\n",
       "      <td>GSM1020770: chicken_c_lung; Gallus gallus; RNA...</td>\n",
       "      <td>GSM1020770: chicken_c_lung; Gallus gallus; RNA...</td>\n",
       "      <td>9031</td>\n",
       "      <td>Gallus gallus</td>\n",
       "      <td>&lt;NA&gt;</td>\n",
       "      <td>RNA-Seq</td>\n",
       "      <td>...</td>\n",
       "      <td>GSM1020770_1</td>\n",
       "      <td>chicken_lung</td>\n",
       "      <td>lung</td>\n",
       "      <td>&lt;NA&gt;</td>\n",
       "      <td>&lt;NA&gt;</td>\n",
       "      <td>http://ftp.sra.ebi.ac.uk/vol1/fastq/SRR594/SRR...</td>\n",
       "      <td>http://ftp.sra.ebi.ac.uk/vol1/fastq/SRR594/SRR...</td>\n",
       "      <td>&lt;NA&gt;</td>\n",
       "      <td>era-fasp@fasp.sra.ebi.ac.uk:vol1/fastq/SRR594/...</td>\n",
       "      <td>era-fasp@fasp.sra.ebi.ac.uk:vol1/fastq/SRR594/...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>131</th>\n",
       "      <td>SRR594524</td>\n",
       "      <td>SRP016501</td>\n",
       "      <td>Evolutionary dynamics of gene and isoform regu...</td>\n",
       "      <td>SRX196395</td>\n",
       "      <td>GSM1020771: chicken_c_skm; Gallus gallus; RNA-Seq</td>\n",
       "      <td>GSM1020771: chicken_c_skm; Gallus gallus; RNA-Seq</td>\n",
       "      <td>9031</td>\n",
       "      <td>Gallus gallus</td>\n",
       "      <td>&lt;NA&gt;</td>\n",
       "      <td>RNA-Seq</td>\n",
       "      <td>...</td>\n",
       "      <td>GSM1020771_1</td>\n",
       "      <td>chicken_skm</td>\n",
       "      <td>skeletal muscle</td>\n",
       "      <td>&lt;NA&gt;</td>\n",
       "      <td>&lt;NA&gt;</td>\n",
       "      <td>http://ftp.sra.ebi.ac.uk/vol1/fastq/SRR594/SRR...</td>\n",
       "      <td>http://ftp.sra.ebi.ac.uk/vol1/fastq/SRR594/SRR...</td>\n",
       "      <td>&lt;NA&gt;</td>\n",
       "      <td>era-fasp@fasp.sra.ebi.ac.uk:vol1/fastq/SRR594/...</td>\n",
       "      <td>era-fasp@fasp.sra.ebi.ac.uk:vol1/fastq/SRR594/...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>132</th>\n",
       "      <td>SRR594525</td>\n",
       "      <td>SRP016501</td>\n",
       "      <td>Evolutionary dynamics of gene and isoform regu...</td>\n",
       "      <td>SRX196396</td>\n",
       "      <td>GSM1020772: chicken_c_spleen; Gallus gallus; R...</td>\n",
       "      <td>GSM1020772: chicken_c_spleen; Gallus gallus; R...</td>\n",
       "      <td>9031</td>\n",
       "      <td>Gallus gallus</td>\n",
       "      <td>&lt;NA&gt;</td>\n",
       "      <td>RNA-Seq</td>\n",
       "      <td>...</td>\n",
       "      <td>GSM1020772_1</td>\n",
       "      <td>chicken_spleen</td>\n",
       "      <td>spleen</td>\n",
       "      <td>&lt;NA&gt;</td>\n",
       "      <td>&lt;NA&gt;</td>\n",
       "      <td>http://ftp.sra.ebi.ac.uk/vol1/fastq/SRR594/SRR...</td>\n",
       "      <td>http://ftp.sra.ebi.ac.uk/vol1/fastq/SRR594/SRR...</td>\n",
       "      <td>&lt;NA&gt;</td>\n",
       "      <td>era-fasp@fasp.sra.ebi.ac.uk:vol1/fastq/SRR594/...</td>\n",
       "      <td>era-fasp@fasp.sra.ebi.ac.uk:vol1/fastq/SRR594/...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>133</th>\n",
       "      <td>SRR594526</td>\n",
       "      <td>SRP016501</td>\n",
       "      <td>Evolutionary dynamics of gene and isoform regu...</td>\n",
       "      <td>SRX196397</td>\n",
       "      <td>GSM1020773: chicken_c_testes; Gallus gallus; R...</td>\n",
       "      <td>GSM1020773: chicken_c_testes; Gallus gallus; R...</td>\n",
       "      <td>9031</td>\n",
       "      <td>Gallus gallus</td>\n",
       "      <td>&lt;NA&gt;</td>\n",
       "      <td>RNA-Seq</td>\n",
       "      <td>...</td>\n",
       "      <td>GSM1020773_1</td>\n",
       "      <td>chicken_testes</td>\n",
       "      <td>testes</td>\n",
       "      <td>&lt;NA&gt;</td>\n",
       "      <td>&lt;NA&gt;</td>\n",
       "      <td>http://ftp.sra.ebi.ac.uk/vol1/fastq/SRR594/SRR...</td>\n",
       "      <td>http://ftp.sra.ebi.ac.uk/vol1/fastq/SRR594/SRR...</td>\n",
       "      <td>&lt;NA&gt;</td>\n",
       "      <td>era-fasp@fasp.sra.ebi.ac.uk:vol1/fastq/SRR594/...</td>\n",
       "      <td>era-fasp@fasp.sra.ebi.ac.uk:vol1/fastq/SRR594/...</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>134 rows × 53 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "    run_accession study_accession  \\\n",
       "0       SRR594393       SRP016501   \n",
       "1       SRR594394       SRP016501   \n",
       "2       SRR594395       SRP016501   \n",
       "3       SRR594396       SRP016501   \n",
       "4       SRR594397       SRP016501   \n",
       "..            ...             ...   \n",
       "129     SRR594522       SRP016501   \n",
       "130     SRR594523       SRP016501   \n",
       "131     SRR594524       SRP016501   \n",
       "132     SRR594525       SRP016501   \n",
       "133     SRR594526       SRP016501   \n",
       "\n",
       "                                           study_title experiment_accession  \\\n",
       "0    Evolutionary dynamics of gene and isoform regu...            SRX196264   \n",
       "1    Evolutionary dynamics of gene and isoform regu...            SRX196265   \n",
       "2    Evolutionary dynamics of gene and isoform regu...            SRX196266   \n",
       "3    Evolutionary dynamics of gene and isoform regu...            SRX196267   \n",
       "4    Evolutionary dynamics of gene and isoform regu...            SRX196268   \n",
       "..                                                 ...                  ...   \n",
       "129  Evolutionary dynamics of gene and isoform regu...            SRX196393   \n",
       "130  Evolutionary dynamics of gene and isoform regu...            SRX196394   \n",
       "131  Evolutionary dynamics of gene and isoform regu...            SRX196395   \n",
       "132  Evolutionary dynamics of gene and isoform regu...            SRX196396   \n",
       "133  Evolutionary dynamics of gene and isoform regu...            SRX196397   \n",
       "\n",
       "                                      experiment_title  \\\n",
       "0     GSM1020640: mouse_a_brain; Mus musculus; RNA-Seq   \n",
       "1     GSM1020641: mouse_a_colon; Mus musculus; RNA-Seq   \n",
       "2     GSM1020642: mouse_a_heart; Mus musculus; RNA-Seq   \n",
       "3    GSM1020643: mouse_a_kidney; Mus musculus; RNA-Seq   \n",
       "4     GSM1020644: mouse_a_liver; Mus musculus; RNA-Seq   \n",
       "..                                                 ...   \n",
       "129  GSM1020769: chicken_c_liver; Gallus gallus; RN...   \n",
       "130  GSM1020770: chicken_c_lung; Gallus gallus; RNA...   \n",
       "131  GSM1020771: chicken_c_skm; Gallus gallus; RNA-Seq   \n",
       "132  GSM1020772: chicken_c_spleen; Gallus gallus; R...   \n",
       "133  GSM1020773: chicken_c_testes; Gallus gallus; R...   \n",
       "\n",
       "                                       experiment_desc organism_taxid  \\\n",
       "0     GSM1020640: mouse_a_brain; Mus musculus; RNA-Seq          10090   \n",
       "1     GSM1020641: mouse_a_colon; Mus musculus; RNA-Seq          10090   \n",
       "2     GSM1020642: mouse_a_heart; Mus musculus; RNA-Seq          10090   \n",
       "3    GSM1020643: mouse_a_kidney; Mus musculus; RNA-Seq          10090   \n",
       "4     GSM1020644: mouse_a_liver; Mus musculus; RNA-Seq          10090   \n",
       "..                                                 ...            ...   \n",
       "129  GSM1020769: chicken_c_liver; Gallus gallus; RN...           9031   \n",
       "130  GSM1020770: chicken_c_lung; Gallus gallus; RNA...           9031   \n",
       "131  GSM1020771: chicken_c_skm; Gallus gallus; RNA-Seq           9031   \n",
       "132  GSM1020772: chicken_c_spleen; Gallus gallus; R...           9031   \n",
       "133  GSM1020773: chicken_c_testes; Gallus gallus; R...           9031   \n",
       "\n",
       "     organism_name library_name library_strategy  ... experiment_alias  \\\n",
       "0     Mus musculus         <NA>          RNA-Seq  ...     GSM1020640_1   \n",
       "1     Mus musculus         <NA>          RNA-Seq  ...     GSM1020641_1   \n",
       "2     Mus musculus         <NA>          RNA-Seq  ...     GSM1020642_1   \n",
       "3     Mus musculus         <NA>          RNA-Seq  ...     GSM1020643_1   \n",
       "4     Mus musculus         <NA>          RNA-Seq  ...     GSM1020644_1   \n",
       "..             ...          ...              ...  ...              ...   \n",
       "129  Gallus gallus         <NA>          RNA-Seq  ...     GSM1020769_1   \n",
       "130  Gallus gallus         <NA>          RNA-Seq  ...     GSM1020770_1   \n",
       "131  Gallus gallus         <NA>          RNA-Seq  ...     GSM1020771_1   \n",
       "132  Gallus gallus         <NA>          RNA-Seq  ...     GSM1020772_1   \n",
       "133  Gallus gallus         <NA>          RNA-Seq  ...     GSM1020773_1   \n",
       "\n",
       "        source_name           tissue  strain ena_fastq_http  \\\n",
       "0       mouse_brain            brain  DBA/2J           <NA>   \n",
       "1       mouse_colon            colon  DBA/2J           <NA>   \n",
       "2       mouse_heart            heart  DBA/2J           <NA>   \n",
       "3      mouse_kidney           kidney  DBA/2J           <NA>   \n",
       "4       mouse_liver            liver  DBA/2J           <NA>   \n",
       "..              ...              ...     ...            ...   \n",
       "129   chicken_liver            liver    <NA>           <NA>   \n",
       "130    chicken_lung             lung    <NA>           <NA>   \n",
       "131     chicken_skm  skeletal muscle    <NA>           <NA>   \n",
       "132  chicken_spleen           spleen    <NA>           <NA>   \n",
       "133  chicken_testes           testes    <NA>           <NA>   \n",
       "\n",
       "                                      ena_fastq_http_1  \\\n",
       "0    http://ftp.sra.ebi.ac.uk/vol1/fastq/SRR594/SRR...   \n",
       "1    http://ftp.sra.ebi.ac.uk/vol1/fastq/SRR594/SRR...   \n",
       "2    http://ftp.sra.ebi.ac.uk/vol1/fastq/SRR594/SRR...   \n",
       "3    http://ftp.sra.ebi.ac.uk/vol1/fastq/SRR594/SRR...   \n",
       "4    http://ftp.sra.ebi.ac.uk/vol1/fastq/SRR594/SRR...   \n",
       "..                                                 ...   \n",
       "129  http://ftp.sra.ebi.ac.uk/vol1/fastq/SRR594/SRR...   \n",
       "130  http://ftp.sra.ebi.ac.uk/vol1/fastq/SRR594/SRR...   \n",
       "131  http://ftp.sra.ebi.ac.uk/vol1/fastq/SRR594/SRR...   \n",
       "132  http://ftp.sra.ebi.ac.uk/vol1/fastq/SRR594/SRR...   \n",
       "133  http://ftp.sra.ebi.ac.uk/vol1/fastq/SRR594/SRR...   \n",
       "\n",
       "                                      ena_fastq_http_2 ena_fastq_ftp  \\\n",
       "0    http://ftp.sra.ebi.ac.uk/vol1/fastq/SRR594/SRR...          <NA>   \n",
       "1    http://ftp.sra.ebi.ac.uk/vol1/fastq/SRR594/SRR...          <NA>   \n",
       "2    http://ftp.sra.ebi.ac.uk/vol1/fastq/SRR594/SRR...          <NA>   \n",
       "3    http://ftp.sra.ebi.ac.uk/vol1/fastq/SRR594/SRR...          <NA>   \n",
       "4    http://ftp.sra.ebi.ac.uk/vol1/fastq/SRR594/SRR...          <NA>   \n",
       "..                                                 ...           ...   \n",
       "129  http://ftp.sra.ebi.ac.uk/vol1/fastq/SRR594/SRR...          <NA>   \n",
       "130  http://ftp.sra.ebi.ac.uk/vol1/fastq/SRR594/SRR...          <NA>   \n",
       "131  http://ftp.sra.ebi.ac.uk/vol1/fastq/SRR594/SRR...          <NA>   \n",
       "132  http://ftp.sra.ebi.ac.uk/vol1/fastq/SRR594/SRR...          <NA>   \n",
       "133  http://ftp.sra.ebi.ac.uk/vol1/fastq/SRR594/SRR...          <NA>   \n",
       "\n",
       "                                       ena_fastq_ftp_1  \\\n",
       "0    era-fasp@fasp.sra.ebi.ac.uk:vol1/fastq/SRR594/...   \n",
       "1    era-fasp@fasp.sra.ebi.ac.uk:vol1/fastq/SRR594/...   \n",
       "2    era-fasp@fasp.sra.ebi.ac.uk:vol1/fastq/SRR594/...   \n",
       "3    era-fasp@fasp.sra.ebi.ac.uk:vol1/fastq/SRR594/...   \n",
       "4    era-fasp@fasp.sra.ebi.ac.uk:vol1/fastq/SRR594/...   \n",
       "..                                                 ...   \n",
       "129  era-fasp@fasp.sra.ebi.ac.uk:vol1/fastq/SRR594/...   \n",
       "130  era-fasp@fasp.sra.ebi.ac.uk:vol1/fastq/SRR594/...   \n",
       "131  era-fasp@fasp.sra.ebi.ac.uk:vol1/fastq/SRR594/...   \n",
       "132  era-fasp@fasp.sra.ebi.ac.uk:vol1/fastq/SRR594/...   \n",
       "133  era-fasp@fasp.sra.ebi.ac.uk:vol1/fastq/SRR594/...   \n",
       "\n",
       "                                       ena_fastq_ftp_2  \n",
       "0    era-fasp@fasp.sra.ebi.ac.uk:vol1/fastq/SRR594/...  \n",
       "1    era-fasp@fasp.sra.ebi.ac.uk:vol1/fastq/SRR594/...  \n",
       "2    era-fasp@fasp.sra.ebi.ac.uk:vol1/fastq/SRR594/...  \n",
       "3    era-fasp@fasp.sra.ebi.ac.uk:vol1/fastq/SRR594/...  \n",
       "4    era-fasp@fasp.sra.ebi.ac.uk:vol1/fastq/SRR594/...  \n",
       "..                                                 ...  \n",
       "129  era-fasp@fasp.sra.ebi.ac.uk:vol1/fastq/SRR594/...  \n",
       "130  era-fasp@fasp.sra.ebi.ac.uk:vol1/fastq/SRR594/...  \n",
       "131  era-fasp@fasp.sra.ebi.ac.uk:vol1/fastq/SRR594/...  \n",
       "132  era-fasp@fasp.sra.ebi.ac.uk:vol1/fastq/SRR594/...  \n",
       "133  era-fasp@fasp.sra.ebi.ac.uk:vol1/fastq/SRR594/...  \n",
       "\n",
       "[134 rows x 53 columns]"
      ]
     },
     "execution_count": 7,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "df = db.sra_metadata(\"SRP016501\", detailed=True)\n",
    "df"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {
    "id": "unVsYJARdsfL"
   },
   "source": [
    "## Get metadata of multiple projects"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 8,
   "metadata": {
    "colab": {
     "base_uri": "https://localhost:8080/",
     "height": 1000
    },
    "execution": {
     "iopub.execute_input": "2025-11-01T13:07:26.356567Z",
     "iopub.status.busy": "2025-11-01T13:07:26.356317Z",
     "iopub.status.idle": "2025-11-01T13:07:28.115240Z",
     "shell.execute_reply": "2025-11-01T13:07:28.113903Z"
    },
    "id": "YzbKfVVOdvIE",
    "outputId": "8333cc13-a3af-446d-ffad-54caab6fa46a"
   },
   "outputs": [
    {
     "data": {
      "text/html": [
       "<div>\n",
       "<style scoped>\n",
       "    .dataframe tbody tr th:only-of-type {\n",
       "        vertical-align: middle;\n",
       "    }\n",
       "\n",
       "    .dataframe tbody tr th {\n",
       "        vertical-align: top;\n",
       "    }\n",
       "\n",
       "    .dataframe thead th {\n",
       "        text-align: right;\n",
       "    }\n",
       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>study_accession</th>\n",
       "      <th>study_title</th>\n",
       "      <th>experiment_accession</th>\n",
       "      <th>experiment_title</th>\n",
       "      <th>experiment_desc</th>\n",
       "      <th>organism_taxid</th>\n",
       "      <th>organism_name</th>\n",
       "      <th>library_name</th>\n",
       "      <th>library_strategy</th>\n",
       "      <th>library_source</th>\n",
       "      <th>...</th>\n",
       "      <th>biosample</th>\n",
       "      <th>bioproject</th>\n",
       "      <th>instrument</th>\n",
       "      <th>instrument_model</th>\n",
       "      <th>instrument_model_desc</th>\n",
       "      <th>total_spots</th>\n",
       "      <th>total_size</th>\n",
       "      <th>run_accession</th>\n",
       "      <th>run_total_spots</th>\n",
       "      <th>run_total_bases</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>25</th>\n",
       "      <td>SRP098789</td>\n",
       "      <td>Selective stalling of human translation throug...</td>\n",
       "      <td>SRX2536403</td>\n",
       "      <td>GSM2475997: 1.5 µM PF-067446846, 10 min, rep 1...</td>\n",
       "      <td>GSM2475997: 1.5 µM PF-067446846, 10 min, rep 1...</td>\n",
       "      <td>9606</td>\n",
       "      <td>Homo sapiens</td>\n",
       "      <td></td>\n",
       "      <td>OTHER</td>\n",
       "      <td>TRANSCRIPTOMIC</td>\n",
       "      <td>...</td>\n",
       "      <td>SAMN06293487</td>\n",
       "      <td>PRJNA369742</td>\n",
       "      <td>Illumina HiSeq 2000</td>\n",
       "      <td>Illumina HiSeq 2000</td>\n",
       "      <td>ILLUMINA</td>\n",
       "      <td>42082855</td>\n",
       "      <td>916745706</td>\n",
       "      <td>SRR5227288</td>\n",
       "      <td>42082855</td>\n",
       "      <td>2104142750</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>24</th>\n",
       "      <td>SRP098789</td>\n",
       "      <td>Selective stalling of human translation throug...</td>\n",
       "      <td>SRX2536404</td>\n",
       "      <td>GSM2475998: 1.5 µM PF-067446846, 10 min, rep 2...</td>\n",
       "      <td>GSM2475998: 1.5 µM PF-067446846, 10 min, rep 2...</td>\n",
       "      <td>9606</td>\n",
       "      <td>Homo sapiens</td>\n",
       "      <td></td>\n",
       "      <td>OTHER</td>\n",
       "      <td>TRANSCRIPTOMIC</td>\n",
       "      <td>...</td>\n",
       "      <td>SAMN06293486</td>\n",
       "      <td>PRJNA369742</td>\n",
       "      <td>Illumina HiSeq 2000</td>\n",
       "      <td>Illumina HiSeq 2000</td>\n",
       "      <td>ILLUMINA</td>\n",
       "      <td>41657461</td>\n",
       "      <td>1360366732</td>\n",
       "      <td>SRR5227289</td>\n",
       "      <td>41657461</td>\n",
       "      <td>2082873050</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>23</th>\n",
       "      <td>SRP098789</td>\n",
       "      <td>Selective stalling of human translation throug...</td>\n",
       "      <td>SRX2536405</td>\n",
       "      <td>GSM2475999: 1.5 µM PF-067446846, 10 min, rep 3...</td>\n",
       "      <td>GSM2475999: 1.5 µM PF-067446846, 10 min, rep 3...</td>\n",
       "      <td>9606</td>\n",
       "      <td>Homo sapiens</td>\n",
       "      <td></td>\n",
       "      <td>OTHER</td>\n",
       "      <td>TRANSCRIPTOMIC</td>\n",
       "      <td>...</td>\n",
       "      <td>SAMN06293485</td>\n",
       "      <td>PRJNA369742</td>\n",
       "      <td>Illumina HiSeq 2000</td>\n",
       "      <td>Illumina HiSeq 2000</td>\n",
       "      <td>ILLUMINA</td>\n",
       "      <td>40462973</td>\n",
       "      <td>1287284933</td>\n",
       "      <td>SRR5227290</td>\n",
       "      <td>40462973</td>\n",
       "      <td>2023148650</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>22</th>\n",
       "      <td>SRP098789</td>\n",
       "      <td>Selective stalling of human translation throug...</td>\n",
       "      <td>SRX2536406</td>\n",
       "      <td>GSM2476000: 0.3 µM PF-067446846, 10 min, rep 1...</td>\n",
       "      <td>GSM2476000: 0.3 µM PF-067446846, 10 min, rep 1...</td>\n",
       "      <td>9606</td>\n",
       "      <td>Homo sapiens</td>\n",
       "      <td></td>\n",
       "      <td>OTHER</td>\n",
       "      <td>TRANSCRIPTOMIC</td>\n",
       "      <td>...</td>\n",
       "      <td>SAMN06293484</td>\n",
       "      <td>PRJNA369742</td>\n",
       "      <td>Illumina HiSeq 2000</td>\n",
       "      <td>Illumina HiSeq 2000</td>\n",
       "      <td>ILLUMINA</td>\n",
       "      <td>41143319</td>\n",
       "      <td>843881081</td>\n",
       "      <td>SRR5227291</td>\n",
       "      <td>41143319</td>\n",
       "      <td>2057165950</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>21</th>\n",
       "      <td>SRP098789</td>\n",
       "      <td>Selective stalling of human translation throug...</td>\n",
       "      <td>SRX2536407</td>\n",
       "      <td>GSM2476001: 0.3 µM PF-067446846, 10 min, rep 2...</td>\n",
       "      <td>GSM2476001: 0.3 µM PF-067446846, 10 min, rep 2...</td>\n",
       "      <td>9606</td>\n",
       "      <td>Homo sapiens</td>\n",
       "      <td></td>\n",
       "      <td>OTHER</td>\n",
       "      <td>TRANSCRIPTOMIC</td>\n",
       "      <td>...</td>\n",
       "      <td>SAMN06293483</td>\n",
       "      <td>PRJNA369742</td>\n",
       "      <td>Illumina HiSeq 2000</td>\n",
       "      <td>Illumina HiSeq 2000</td>\n",
       "      <td>ILLUMINA</td>\n",
       "      <td>60552437</td>\n",
       "      <td>1875910244</td>\n",
       "      <td>SRR5227292</td>\n",
       "      <td>60552437</td>\n",
       "      <td>3027621850</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>...</th>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>30</th>\n",
       "      <td>SRP016501</td>\n",
       "      <td>Evolutionary dynamics of gene and isoform regu...</td>\n",
       "      <td>SRX196393</td>\n",
       "      <td>GSM1020769: chicken_c_liver; Gallus gallus; RN...</td>\n",
       "      <td>GSM1020769: chicken_c_liver; Gallus gallus; RN...</td>\n",
       "      <td>9031</td>\n",
       "      <td>Gallus gallus</td>\n",
       "      <td></td>\n",
       "      <td>RNA-Seq</td>\n",
       "      <td>TRANSCRIPTOMIC</td>\n",
       "      <td>...</td>\n",
       "      <td>SAMN01766943</td>\n",
       "      <td>PRJNA177791</td>\n",
       "      <td>Illumina HiSeq 2000</td>\n",
       "      <td>Illumina HiSeq 2000</td>\n",
       "      <td>ILLUMINA</td>\n",
       "      <td>18978066</td>\n",
       "      <td>562367072</td>\n",
       "      <td>SRR594522</td>\n",
       "      <td>18978066</td>\n",
       "      <td>1366420752</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>29</th>\n",
       "      <td>SRP016501</td>\n",
       "      <td>Evolutionary dynamics of gene and isoform regu...</td>\n",
       "      <td>SRX196394</td>\n",
       "      <td>GSM1020770: chicken_c_lung; Gallus gallus; RNA...</td>\n",
       "      <td>GSM1020770: chicken_c_lung; Gallus gallus; RNA...</td>\n",
       "      <td>9031</td>\n",
       "      <td>Gallus gallus</td>\n",
       "      <td></td>\n",
       "      <td>RNA-Seq</td>\n",
       "      <td>TRANSCRIPTOMIC</td>\n",
       "      <td>...</td>\n",
       "      <td>SAMN01766944</td>\n",
       "      <td>PRJNA177791</td>\n",
       "      <td>Illumina HiSeq 2000</td>\n",
       "      <td>Illumina HiSeq 2000</td>\n",
       "      <td>ILLUMINA</td>\n",
       "      <td>26604280</td>\n",
       "      <td>931417024</td>\n",
       "      <td>SRR594523</td>\n",
       "      <td>26604280</td>\n",
       "      <td>1862299600</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>28</th>\n",
       "      <td>SRP016501</td>\n",
       "      <td>Evolutionary dynamics of gene and isoform regu...</td>\n",
       "      <td>SRX196395</td>\n",
       "      <td>GSM1020771: chicken_c_skm; Gallus gallus; RNA-Seq</td>\n",
       "      <td>GSM1020771: chicken_c_skm; Gallus gallus; RNA-Seq</td>\n",
       "      <td>9031</td>\n",
       "      <td>Gallus gallus</td>\n",
       "      <td></td>\n",
       "      <td>RNA-Seq</td>\n",
       "      <td>TRANSCRIPTOMIC</td>\n",
       "      <td>...</td>\n",
       "      <td>SAMN01766945</td>\n",
       "      <td>PRJNA177791</td>\n",
       "      <td>Illumina HiSeq 2000</td>\n",
       "      <td>Illumina HiSeq 2000</td>\n",
       "      <td>ILLUMINA</td>\n",
       "      <td>25606436</td>\n",
       "      <td>986287075</td>\n",
       "      <td>SRR594524</td>\n",
       "      <td>25606436</td>\n",
       "      <td>1792450520</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>27</th>\n",
       "      <td>SRP016501</td>\n",
       "      <td>Evolutionary dynamics of gene and isoform regu...</td>\n",
       "      <td>SRX196396</td>\n",
       "      <td>GSM1020772: chicken_c_spleen; Gallus gallus; R...</td>\n",
       "      <td>GSM1020772: chicken_c_spleen; Gallus gallus; R...</td>\n",
       "      <td>9031</td>\n",
       "      <td>Gallus gallus</td>\n",
       "      <td></td>\n",
       "      <td>RNA-Seq</td>\n",
       "      <td>TRANSCRIPTOMIC</td>\n",
       "      <td>...</td>\n",
       "      <td>SAMN01766946</td>\n",
       "      <td>PRJNA177791</td>\n",
       "      <td>Illumina HiSeq 2000</td>\n",
       "      <td>Illumina HiSeq 2000</td>\n",
       "      <td>ILLUMINA</td>\n",
       "      <td>24401708</td>\n",
       "      <td>1201671888</td>\n",
       "      <td>SRR594525</td>\n",
       "      <td>24401708</td>\n",
       "      <td>1756922976</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>26</th>\n",
       "      <td>SRP016501</td>\n",
       "      <td>Evolutionary dynamics of gene and isoform regu...</td>\n",
       "      <td>SRX196397</td>\n",
       "      <td>GSM1020773: chicken_c_testes; Gallus gallus; R...</td>\n",
       "      <td>GSM1020773: chicken_c_testes; Gallus gallus; R...</td>\n",
       "      <td>9031</td>\n",
       "      <td>Gallus gallus</td>\n",
       "      <td></td>\n",
       "      <td>RNA-Seq</td>\n",
       "      <td>TRANSCRIPTOMIC</td>\n",
       "      <td>...</td>\n",
       "      <td>SAMN01766947</td>\n",
       "      <td>PRJNA177791</td>\n",
       "      <td>Illumina HiSeq 2000</td>\n",
       "      <td>Illumina HiSeq 2000</td>\n",
       "      <td>ILLUMINA</td>\n",
       "      <td>37423394</td>\n",
       "      <td>1980545796</td>\n",
       "      <td>SRR594526</td>\n",
       "      <td>37423394</td>\n",
       "      <td>2993871520</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>160 rows × 24 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "   study_accession                                        study_title  \\\n",
       "25       SRP098789  Selective stalling of human translation throug...   \n",
       "24       SRP098789  Selective stalling of human translation throug...   \n",
       "23       SRP098789  Selective stalling of human translation throug...   \n",
       "22       SRP098789  Selective stalling of human translation throug...   \n",
       "21       SRP098789  Selective stalling of human translation throug...   \n",
       "..             ...                                                ...   \n",
       "30       SRP016501  Evolutionary dynamics of gene and isoform regu...   \n",
       "29       SRP016501  Evolutionary dynamics of gene and isoform regu...   \n",
       "28       SRP016501  Evolutionary dynamics of gene and isoform regu...   \n",
       "27       SRP016501  Evolutionary dynamics of gene and isoform regu...   \n",
       "26       SRP016501  Evolutionary dynamics of gene and isoform regu...   \n",
       "\n",
       "   experiment_accession                                   experiment_title  \\\n",
       "25           SRX2536403  GSM2475997: 1.5 µM PF-067446846, 10 min, rep 1...   \n",
       "24           SRX2536404  GSM2475998: 1.5 µM PF-067446846, 10 min, rep 2...   \n",
       "23           SRX2536405  GSM2475999: 1.5 µM PF-067446846, 10 min, rep 3...   \n",
       "22           SRX2536406  GSM2476000: 0.3 µM PF-067446846, 10 min, rep 1...   \n",
       "21           SRX2536407  GSM2476001: 0.3 µM PF-067446846, 10 min, rep 2...   \n",
       "..                  ...                                                ...   \n",
       "30            SRX196393  GSM1020769: chicken_c_liver; Gallus gallus; RN...   \n",
       "29            SRX196394  GSM1020770: chicken_c_lung; Gallus gallus; RNA...   \n",
       "28            SRX196395  GSM1020771: chicken_c_skm; Gallus gallus; RNA-Seq   \n",
       "27            SRX196396  GSM1020772: chicken_c_spleen; Gallus gallus; R...   \n",
       "26            SRX196397  GSM1020773: chicken_c_testes; Gallus gallus; R...   \n",
       "\n",
       "                                      experiment_desc organism_taxid  \\\n",
       "25  GSM2475997: 1.5 µM PF-067446846, 10 min, rep 1...           9606   \n",
       "24  GSM2475998: 1.5 µM PF-067446846, 10 min, rep 2...           9606   \n",
       "23  GSM2475999: 1.5 µM PF-067446846, 10 min, rep 3...           9606   \n",
       "22  GSM2476000: 0.3 µM PF-067446846, 10 min, rep 1...           9606   \n",
       "21  GSM2476001: 0.3 µM PF-067446846, 10 min, rep 2...           9606   \n",
       "..                                                ...            ...   \n",
       "30  GSM1020769: chicken_c_liver; Gallus gallus; RN...           9031   \n",
       "29  GSM1020770: chicken_c_lung; Gallus gallus; RNA...           9031   \n",
       "28  GSM1020771: chicken_c_skm; Gallus gallus; RNA-Seq           9031   \n",
       "27  GSM1020772: chicken_c_spleen; Gallus gallus; R...           9031   \n",
       "26  GSM1020773: chicken_c_testes; Gallus gallus; R...           9031   \n",
       "\n",
       "    organism_name library_name library_strategy  library_source  ...  \\\n",
       "25   Homo sapiens                         OTHER  TRANSCRIPTOMIC  ...   \n",
       "24   Homo sapiens                         OTHER  TRANSCRIPTOMIC  ...   \n",
       "23   Homo sapiens                         OTHER  TRANSCRIPTOMIC  ...   \n",
       "22   Homo sapiens                         OTHER  TRANSCRIPTOMIC  ...   \n",
       "21   Homo sapiens                         OTHER  TRANSCRIPTOMIC  ...   \n",
       "..            ...          ...              ...             ...  ...   \n",
       "30  Gallus gallus                       RNA-Seq  TRANSCRIPTOMIC  ...   \n",
       "29  Gallus gallus                       RNA-Seq  TRANSCRIPTOMIC  ...   \n",
       "28  Gallus gallus                       RNA-Seq  TRANSCRIPTOMIC  ...   \n",
       "27  Gallus gallus                       RNA-Seq  TRANSCRIPTOMIC  ...   \n",
       "26  Gallus gallus                       RNA-Seq  TRANSCRIPTOMIC  ...   \n",
       "\n",
       "       biosample   bioproject           instrument     instrument_model  \\\n",
       "25  SAMN06293487  PRJNA369742  Illumina HiSeq 2000  Illumina HiSeq 2000   \n",
       "24  SAMN06293486  PRJNA369742  Illumina HiSeq 2000  Illumina HiSeq 2000   \n",
       "23  SAMN06293485  PRJNA369742  Illumina HiSeq 2000  Illumina HiSeq 2000   \n",
       "22  SAMN06293484  PRJNA369742  Illumina HiSeq 2000  Illumina HiSeq 2000   \n",
       "21  SAMN06293483  PRJNA369742  Illumina HiSeq 2000  Illumina HiSeq 2000   \n",
       "..           ...          ...                  ...                  ...   \n",
       "30  SAMN01766943  PRJNA177791  Illumina HiSeq 2000  Illumina HiSeq 2000   \n",
       "29  SAMN01766944  PRJNA177791  Illumina HiSeq 2000  Illumina HiSeq 2000   \n",
       "28  SAMN01766945  PRJNA177791  Illumina HiSeq 2000  Illumina HiSeq 2000   \n",
       "27  SAMN01766946  PRJNA177791  Illumina HiSeq 2000  Illumina HiSeq 2000   \n",
       "26  SAMN01766947  PRJNA177791  Illumina HiSeq 2000  Illumina HiSeq 2000   \n",
       "\n",
       "   instrument_model_desc total_spots  total_size run_accession  \\\n",
       "25              ILLUMINA    42082855   916745706    SRR5227288   \n",
       "24              ILLUMINA    41657461  1360366732    SRR5227289   \n",
       "23              ILLUMINA    40462973  1287284933    SRR5227290   \n",
       "22              ILLUMINA    41143319   843881081    SRR5227291   \n",
       "21              ILLUMINA    60552437  1875910244    SRR5227292   \n",
       "..                   ...         ...         ...           ...   \n",
       "30              ILLUMINA    18978066   562367072     SRR594522   \n",
       "29              ILLUMINA    26604280   931417024     SRR594523   \n",
       "28              ILLUMINA    25606436   986287075     SRR594524   \n",
       "27              ILLUMINA    24401708  1201671888     SRR594525   \n",
       "26              ILLUMINA    37423394  1980545796     SRR594526   \n",
       "\n",
       "   run_total_spots run_total_bases  \n",
       "25        42082855      2104142750  \n",
       "24        41657461      2082873050  \n",
       "23        40462973      2023148650  \n",
       "22        41143319      2057165950  \n",
       "21        60552437      3027621850  \n",
       "..             ...             ...  \n",
       "30        18978066      1366420752  \n",
       "29        26604280      1862299600  \n",
       "28        25606436      1792450520  \n",
       "27        24401708      1756922976  \n",
       "26        37423394      2993871520  \n",
       "\n",
       "[160 rows x 24 columns]"
      ]
     },
     "execution_count": 8,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "df = db.sra_metadata([\"SRP016501\", \"SRP098789\"])\n",
    "df"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {
    "id": "UuKRorTWZoQQ"
   },
   "source": [
    "## Get metadata of a Run"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 9,
   "metadata": {
    "colab": {
     "base_uri": "https://localhost:8080/",
     "height": 214
    },
    "execution": {
     "iopub.execute_input": "2025-11-01T13:07:28.118706Z",
     "iopub.status.busy": "2025-11-01T13:07:28.118442Z",
     "iopub.status.idle": "2025-11-01T13:07:32.510732Z",
     "shell.execute_reply": "2025-11-01T13:07:32.509474Z"
    },
    "id": "V1bMg1W6ZqZL",
    "outputId": "9e6029ab-b0bf-4954-ada4-da4dc5ccb058"
   },
   "outputs": [
    {
     "data": {
      "text/html": [
       "<div>\n",
       "<style scoped>\n",
       "    .dataframe tbody tr th:only-of-type {\n",
       "        vertical-align: middle;\n",
       "    }\n",
       "\n",
       "    .dataframe tbody tr th {\n",
       "        vertical-align: top;\n",
       "    }\n",
       "\n",
       "    .dataframe thead th {\n",
       "        text-align: right;\n",
       "    }\n",
       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>run_accession</th>\n",
       "      <th>study_accession</th>\n",
       "      <th>study_title</th>\n",
       "      <th>experiment_accession</th>\n",
       "      <th>experiment_title</th>\n",
       "      <th>experiment_desc</th>\n",
       "      <th>organism_taxid</th>\n",
       "      <th>organism_name</th>\n",
       "      <th>library_name</th>\n",
       "      <th>library_strategy</th>\n",
       "      <th>...</th>\n",
       "      <th>host_disease</th>\n",
       "      <th>isolation_source</th>\n",
       "      <th>lat_lon</th>\n",
       "      <th>biosamplemodel</th>\n",
       "      <th>ena_fastq_http</th>\n",
       "      <th>ena_fastq_http_1</th>\n",
       "      <th>ena_fastq_http_2</th>\n",
       "      <th>ena_fastq_ftp</th>\n",
       "      <th>ena_fastq_ftp_1</th>\n",
       "      <th>ena_fastq_ftp_2</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>SRR11085797</td>\n",
       "      <td>SRP249482</td>\n",
       "      <td>Bat coronavirus RaTG13 Genome sequencing</td>\n",
       "      <td>SRX7724752</td>\n",
       "      <td>RNA-Seq of Rhinolophus affinis:Fecal swab</td>\n",
       "      <td>RNA-Seq of Rhinolophus affinis:Fecal swab</td>\n",
       "      <td>694135</td>\n",
       "      <td>unidentified coronavirus</td>\n",
       "      <td>RaTG13</td>\n",
       "      <td>RNA-Seq</td>\n",
       "      <td>...</td>\n",
       "      <td>not applicable</td>\n",
       "      <td>fecal swab</td>\n",
       "      <td>not collected</td>\n",
       "      <td>Pathogen.cl</td>\n",
       "      <td>&lt;NA&gt;</td>\n",
       "      <td>http://ftp.sra.ebi.ac.uk/vol1/fastq/SRR110/097...</td>\n",
       "      <td>http://ftp.sra.ebi.ac.uk/vol1/fastq/SRR110/097...</td>\n",
       "      <td>&lt;NA&gt;</td>\n",
       "      <td>era-fasp@fasp.sra.ebi.ac.uk:vol1/fastq/SRR110/...</td>\n",
       "      <td>era-fasp@fasp.sra.ebi.ac.uk:vol1/fastq/SRR110/...</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>1 rows × 60 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "  run_accession study_accession                               study_title  \\\n",
       "0   SRR11085797       SRP249482  Bat coronavirus RaTG13 Genome sequencing   \n",
       "\n",
       "  experiment_accession                           experiment_title  \\\n",
       "0           SRX7724752  RNA-Seq of Rhinolophus affinis:Fecal swab   \n",
       "\n",
       "                             experiment_desc organism_taxid  \\\n",
       "0  RNA-Seq of Rhinolophus affinis:Fecal swab         694135   \n",
       "\n",
       "              organism_name library_name library_strategy  ...  \\\n",
       "0  unidentified coronavirus       RaTG13          RNA-Seq  ...   \n",
       "\n",
       "     host_disease isolation_source        lat_lon biosamplemodel  \\\n",
       "0  not applicable       fecal swab  not collected    Pathogen.cl   \n",
       "\n",
       "  ena_fastq_http                                   ena_fastq_http_1  \\\n",
       "0           <NA>  http://ftp.sra.ebi.ac.uk/vol1/fastq/SRR110/097...   \n",
       "\n",
       "                                    ena_fastq_http_2 ena_fastq_ftp  \\\n",
       "0  http://ftp.sra.ebi.ac.uk/vol1/fastq/SRR110/097...          <NA>   \n",
       "\n",
       "                                     ena_fastq_ftp_1  \\\n",
       "0  era-fasp@fasp.sra.ebi.ac.uk:vol1/fastq/SRR110/...   \n",
       "\n",
       "                                     ena_fastq_ftp_2  \n",
       "0  era-fasp@fasp.sra.ebi.ac.uk:vol1/fastq/SRR110/...  \n",
       "\n",
       "[1 rows x 60 columns]"
      ]
     },
     "execution_count": 9,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "df = db.sra_metadata(\"SRR11085797\", detailed=True)\n",
    "df"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {
    "id": "cADqnvl0KcAn"
   },
   "source": [
    "## SRX to GSM"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 10,
   "metadata": {
    "colab": {
     "base_uri": "https://localhost:8080/",
     "height": 80
    },
    "execution": {
     "iopub.execute_input": "2025-11-01T13:07:32.514680Z",
     "iopub.status.busy": "2025-11-01T13:07:32.514374Z",
     "iopub.status.idle": "2025-11-01T13:07:33.931846Z",
     "shell.execute_reply": "2025-11-01T13:07:33.930414Z"
    },
    "id": "iCFhnY0FKcAp",
    "outputId": "7efff242-ca68-499a-ee9e-0ec1f1dff95a"
   },
   "outputs": [
    {
     "data": {
      "text/html": [
       "<div>\n",
       "<style scoped>\n",
       "    .dataframe tbody tr th:only-of-type {\n",
       "        vertical-align: middle;\n",
       "    }\n",
       "\n",
       "    .dataframe tbody tr th {\n",
       "        vertical-align: top;\n",
       "    }\n",
       "\n",
       "    .dataframe thead th {\n",
       "        text-align: right;\n",
       "    }\n",
       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>experiment_accession</th>\n",
       "      <th>experiment_alias</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>SRX1254413</td>\n",
       "      <td>GSM1887643</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "  experiment_accession experiment_alias\n",
       "0           SRX1254413       GSM1887643"
      ]
     },
     "execution_count": 10,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "df = db.srx_to_gsm(\"SRX1254413\")\n",
    "df"
   ]
  }
 ],
 "metadata": {
  "colab": {
   "collapsed_sections": [],
   "include_colab_link": true,
   "name": "01.Python-API_demo.ipynb",
   "provenance": []
  },
  "kernelspec": {
   "display_name": "Python 3",
   "language": "python",
   "name": "python3"
  },
  "language_info": {
   "codemirror_mode": {
    "name": "ipython",
    "version": 3
   },
   "file_extension": ".py",
   "mimetype": "text/x-python",
   "name": "python",
   "nbconvert_exporter": "python",
   "pygments_lexer": "ipython3",
   "version": "3.13.9"
  },
  "widgets": {
   "application/vnd.jupyter.widget-state+json": {
    "state": {},
    "version_major": 2,
    "version_minor": 0
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 },
 "nbformat": 4,
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