Command-line Download¶
This notebook demonstrates how to use pysradb from the command line to download SRA data.
[1]:
# Install pysradb if not already installed
try:
import pysradb
print(f"pysradb {pysradb.__version__} is already installed")
except ImportError:
print("Installing pysradb from GitHub...")
import sys
!{sys.executable} -m pip install -q git+https://github.com/saketkc/pysradb
print("pysradb installed successfully!")
pysradb 3.0.0.dev0 is already installed
/home/runner/work/pysradb/pysradb/pysradb/download.py:15: TqdmExperimentalWarning: Using `tqdm.autonotebook.tqdm` in notebook mode. Use `tqdm.tqdm` instead to force console mode (e.g. in jupyter console)
from tqdm.autonotebook import tqdm
[2]:
# pip install -U pysradb
[3]:
!pysradb --version
pysradb 3.0.0.dev0
Get metadata for SRX (SRRs/SRS etc)¶
[4]:
!pysradb srx-to-srr SRX4720625
Displaying 24 columns in chunks of 5
Columns 1-5:
experimen
t_accessi run_acce study_acc
on ssion ession study_title experiment_title
SRX472062 SRR78820 SRP162234 Transcriptomic profile of GSM3396533:
5 15 zebrafish cardiomyocytes wt_GFPpos_24hpf_r
throughout heart ep1; Danio rerio;
development RNA-Seq
Columns 6-10:
organism_t organism_ library_na library_s
experiment_desc axid name me trategy
GSM3396533: 7955 Danio RNA-Seq
wt_GFPpos_24hpf_rep1; Danio rerio
rerio; RNA-Seq
Columns 11-15:
library_selecti library_layou sample_accessi
library_source on t on sample_title
TRANSCRIPTOMIC cDNA PAIRED SRS3805811
Columns 16-20:
instrument_mode instrument_model_de
biosample bioproject instrument l sc
SAMN1009572 PRJNA492280 NextSeq 500 NextSeq 500 ILLUMINA
3
Columns 21-24:
total_spots total_size run_total_spots run_total_bases
47867961 3470385670 47867961 7230485009
Get detailed metadata¶
[5]:
!pysradb srx-to-srr SRX4720625 --detailed
Displaying 57 columns in chunks of 5
Columns 1-5:
experimen
t_accessi run_acce study_acc
on ssion ession study_title experiment_title
SRX472062 SRR78820 SRP162234 Transcriptomic profile of GSM3396533:
5 15 zebrafish cardiomyocytes wt_GFPpos_24hpf_r
throughout heart ep1; Danio rerio;
development RNA-Seq
Columns 6-10:
organism_t organism_ library_na library_s
experiment_desc axid name me trategy
GSM3396533: 7955 Danio - RNA-Seq
wt_GFPpos_24hpf_rep1; Danio rerio
rerio; RNA-Seq
Columns 11-15:
library_selecti library_layou sample_accessi
library_source on t on sample_title
TRANSCRIPTOMIC cDNA PAIRED SRS3805811 -
Columns 16-20:
instrument_mode instrument_model_de
biosample bioproject instrument l sc
SAMN1009572 PRJNA492280 NextSeq 500 NextSeq 500 ILLUMINA
3
Columns 21-25:
total_spots total_size run_total_spots run_total_bases run_alias
47867961 3470385670 47867961 7230485009 GSM3396533_r1
Columns 26-30:
public_filen public_vers
ame public_size public_date public_md5 ion
SRR7882015.s 1881003321 2020-06-14 8161154ca4e9cf674e3f0e 1
ralite 12:02:25 4af74c8455
Columns 31-35:
public_sem public_sup public_srat aws_free_eg
antic_name ertype oolkit aws_url ress
SRA Lite Primary 1 s3://sra-pub-zq-8/SRR78820 s3.us-east-
ETL 15/SRR7882015.sralite.1 1
Columns 36-40:
ncbi_ac
aws_acce ncbi_fre cess_ty
ss_type public_url ncbi_url e_egress pe
aws https://sra-downloadb.b https://sra-downloadb. worldwid anonymo
identity e-md.ncbi.nlm.nih.gov/s be-md.ncbi.nlm.nih.gov e us
os12/sra-pub-zq-1211/SR /sos12/sra-pub-zq-1211
R007/882/SRR7882015/SRR /SRR007/882/SRR7882015
7882015.sralite.1 /SRR7882015.sralite.1
Columns 41-45:
gcp_free_e gcp_access_ experiment
gcp_url gress type _alias source_name
gs://sra-pub-zq-107/SRR7 gs.us-east gcp GSM3396533 FACS-sorted
882015/SRR7882015.zq.1 1 identity embryo cells
Columns 46-50:
developmental genetic ena_fastq_h
tissue stage gfp status background ttp
FACS-sorted embryo 24 hpf GFP wild type -
cells positive
Columns 51-55:
ena_fastq_http ena_fastq_http ena_fastq_f ena_fastq_ftp_
_1 _2 tp 1 ena_fastq_ftp_2
http://ftp.sra http://ftp.sra - era-fasp@fasp. [email protected]
.ebi.ac.uk/vol .ebi.ac.uk/vol sra.ebi.ac.uk: ra.ebi.ac.uk:vo
1/fastq/SRR788 1/fastq/SRR788 vol1/fastq/SRR l1/fastq/SRR788
/005/SRR788201 /005/SRR788201 788/005/SRR788 /005/SRR7882015
5/SRR7882015_1 5/SRR7882015_2 2015/SRR788201 /SRR7882015_2.f
.fastq.gz .fastq.gz 5_1.fastq.gz astq.gz
Columns 56-57:
study_geo_accession experiment_geo_accession
GSE120236 GSM3396533
Download all runs for a particular experiment¶
[6]:
print("pysradb srx-to-srr SRX4720625 --detailed | pysradb download")
pysradb srx-to-srr SRX4720625 --detailed | pysradb download
Get metadata for entire project¶
[7]:
!pysradb metadata SRP162234 --detailed
Displaying 57 columns in chunks of 5
Columns 1-5:
experime
run_acce study_ac nt_acces
ssion cession study_title sion experiment_title
SRR78820 SRP16223 Transcriptomic profile of SRX47206 GSM3396532:
14 4 zebrafish cardiomyocytes 24 wt_GFPneg_24hpf_re
throughout heart p1; Danio rerio;
development RNA-Seq
SRR78820 SRP16223 Transcriptomic profile of SRX47206 GSM3396533:
15 4 zebrafish cardiomyocytes 25 wt_GFPpos_24hpf_re
throughout heart p1; Danio rerio;
development RNA-Seq
SRR78820 SRP16223 Transcriptomic profile of SRX47206 GSM3396534:
16 4 zebrafish cardiomyocytes 26 wt_GFPpos_24hpf_re
throughout heart p2; Danio rerio;
development RNA-Seq
SRR78820 SRP16223 Transcriptomic profile of SRX47206 GSM3396535:
17 4 zebrafish cardiomyocytes 27 wt_GFPneg_48hpf_re
throughout heart p1; Danio rerio;
development RNA-Seq
SRR78820 SRP16223 Transcriptomic profile of SRX47206 GSM3396536:
18 4 zebrafish cardiomyocytes 28 wt_GFPpos_48hpf_re
throughout heart p1; Danio rerio;
development RNA-Seq
SRR78820 SRP16223 Transcriptomic profile of SRX47206 GSM3396537:
19 4 zebrafish cardiomyocytes 29 wt_GFPpos_48hpf_re
throughout heart p2; Danio rerio;
development RNA-Seq
SRR78820 SRP16223 Transcriptomic profile of SRX47206 GSM3396538:
20 4 zebrafish cardiomyocytes 30 wt_GFPneg_72hpf_re
throughout heart p1; Danio rerio;
development RNA-Seq
SRR78820 SRP16223 Transcriptomic profile of SRX47206 GSM3396539:
21 4 zebrafish cardiomyocytes 31 wt_GFPpos_72hpf_re
throughout heart p1; Danio rerio;
development RNA-Seq
SRR78820 SRP16223 Transcriptomic profile of SRX47206 GSM3396540:
22 4 zebrafish cardiomyocytes 32 wt_GFPpos_72hpf_re
throughout heart p2; Danio rerio;
development RNA-Seq
SRR78820 SRP16223 Transcriptomic profile of SRX47206 GSM3396541:
23 4 zebrafish cardiomyocytes 33 gata5_GFPneg_72hpf
throughout heart _rep1; Danio
development rerio; RNA-Seq
SRR78820 SRP16223 Transcriptomic profile of SRX47206 GSM3396542:
24 4 zebrafish cardiomyocytes 34 gata5_GFPpos_72hpf
throughout heart _rep1; Danio
development rerio; RNA-Seq
SRR78820 SRP16223 Transcriptomic profile of SRX47206 GSM3396543:
25 4 zebrafish cardiomyocytes 35 gata5_GFPpos_72hpf
throughout heart _rep2; Danio
development rerio; RNA-Seq
SRR78820 SRP16223 Transcriptomic profile of SRX47206 GSM3396544:
26 4 zebrafish cardiomyocytes 36 tbx5_GFPneg_72hpf_
throughout heart rep1; Danio rerio;
development RNA-Seq
SRR78820 SRP16223 Transcriptomic profile of SRX47206 GSM3396545:
27 4 zebrafish cardiomyocytes 37 tbx5_GFPpos_72hpf_
throughout heart rep1; Danio rerio;
development RNA-Seq
SRR78820 SRP16223 Transcriptomic profile of SRX47206 GSM3396546:
28 4 zebrafish cardiomyocytes 38 tbx5_GFPpos_72hpf_
throughout heart rep2; Danio rerio;
development RNA-Seq
SRR78820 SRP16223 Transcriptomic profile of SRX47206 GSM3396547:
29 4 zebrafish cardiomyocytes 39 hand2_GFPneg_72hpf
throughout heart _rep1; Danio
development rerio; RNA-Seq
SRR78820 SRP16223 Transcriptomic profile of SRX47206 GSM3396548:
30 4 zebrafish cardiomyocytes 40 hand2_GFPpos_72hpf
throughout heart _rep1; Danio
development rerio; RNA-Seq
SRR78820 SRP16223 Transcriptomic profile of SRX47206 GSM3396549:
31 4 zebrafish cardiomyocytes 41 hand2_GFPpos_72hpf
throughout heart _rep2; Danio
development rerio; RNA-Seq
Columns 6-10:
organism_ organism_ library_na library_s
experiment_desc taxid name me trategy
GSM3396532: 7955 Danio - RNA-Seq
wt_GFPneg_24hpf_rep1; Danio rerio
rerio; RNA-Seq
GSM3396533: 7955 Danio - RNA-Seq
wt_GFPpos_24hpf_rep1; Danio rerio
rerio; RNA-Seq
GSM3396534: 7955 Danio - RNA-Seq
wt_GFPpos_24hpf_rep2; Danio rerio
rerio; RNA-Seq
GSM3396535: 7955 Danio - RNA-Seq
wt_GFPneg_48hpf_rep1; Danio rerio
rerio; RNA-Seq
GSM3396536: 7955 Danio - RNA-Seq
wt_GFPpos_48hpf_rep1; Danio rerio
rerio; RNA-Seq
GSM3396537: 7955 Danio - RNA-Seq
wt_GFPpos_48hpf_rep2; Danio rerio
rerio; RNA-Seq
GSM3396538: 7955 Danio - RNA-Seq
wt_GFPneg_72hpf_rep1; Danio rerio
rerio; RNA-Seq
GSM3396539: 7955 Danio - RNA-Seq
wt_GFPpos_72hpf_rep1; Danio rerio
rerio; RNA-Seq
GSM3396540: 7955 Danio - RNA-Seq
wt_GFPpos_72hpf_rep2; Danio rerio
rerio; RNA-Seq
GSM3396541: 7955 Danio - RNA-Seq
gata5_GFPneg_72hpf_rep1; Danio rerio
rerio; RNA-Seq
GSM3396542: 7955 Danio - RNA-Seq
gata5_GFPpos_72hpf_rep1; Danio rerio
rerio; RNA-Seq
GSM3396543: 7955 Danio - RNA-Seq
gata5_GFPpos_72hpf_rep2; Danio rerio
rerio; RNA-Seq
GSM3396544: 7955 Danio - RNA-Seq
tbx5_GFPneg_72hpf_rep1; Danio rerio
rerio; RNA-Seq
GSM3396545: 7955 Danio - RNA-Seq
tbx5_GFPpos_72hpf_rep1; Danio rerio
rerio; RNA-Seq
GSM3396546: 7955 Danio - RNA-Seq
tbx5_GFPpos_72hpf_rep2; Danio rerio
rerio; RNA-Seq
GSM3396547: 7955 Danio - RNA-Seq
hand2_GFPneg_72hpf_rep1; Danio rerio
rerio; RNA-Seq
GSM3396548: 7955 Danio - RNA-Seq
hand2_GFPpos_72hpf_rep1; Danio rerio
rerio; RNA-Seq
GSM3396549: 7955 Danio - RNA-Seq
hand2_GFPpos_72hpf_rep2; Danio rerio
rerio; RNA-Seq
Columns 11-15:
library_selecti library_layou sample_accessi
library_source on t on sample_title
TRANSCRIPTOMIC cDNA PAIRED SRS3805810 -
TRANSCRIPTOMIC cDNA PAIRED SRS3805811 -
TRANSCRIPTOMIC cDNA PAIRED SRS3805812 -
TRANSCRIPTOMIC cDNA PAIRED SRS3805813 -
TRANSCRIPTOMIC cDNA PAIRED SRS3805814 -
TRANSCRIPTOMIC cDNA PAIRED SRS3805815 -
TRANSCRIPTOMIC cDNA PAIRED SRS3805816 -
TRANSCRIPTOMIC cDNA PAIRED SRS3805817 -
TRANSCRIPTOMIC cDNA PAIRED SRS3805818 -
TRANSCRIPTOMIC cDNA PAIRED SRS3805819 -
TRANSCRIPTOMIC cDNA PAIRED SRS3805820 -
TRANSCRIPTOMIC cDNA PAIRED SRS3805821 -
TRANSCRIPTOMIC cDNA PAIRED SRS3805822 -
TRANSCRIPTOMIC cDNA PAIRED SRS3805823 -
TRANSCRIPTOMIC cDNA PAIRED SRS3805824 -
TRANSCRIPTOMIC cDNA PAIRED SRS3805825 -
TRANSCRIPTOMIC cDNA PAIRED SRS3805826 -
TRANSCRIPTOMIC cDNA PAIRED SRS3805827 -
Columns 16-20:
instrument_mode instrument_model_de
biosample bioproject instrument l sc
SAMN1009572 PRJNA492280 NextSeq 500 NextSeq 500 ILLUMINA
4
SAMN1009572 PRJNA492280 NextSeq 500 NextSeq 500 ILLUMINA
3
SAMN1009580 PRJNA492280 NextSeq 500 NextSeq 500 ILLUMINA
3
SAMN1009580 PRJNA492280 NextSeq 500 NextSeq 500 ILLUMINA
1
SAMN1009582 PRJNA492280 NextSeq 500 NextSeq 500 ILLUMINA
3
SAMN1009582 PRJNA492280 NextSeq 500 NextSeq 500 ILLUMINA
2
SAMN1009582 PRJNA492280 NextSeq 500 NextSeq 500 ILLUMINA
1
SAMN1009581 PRJNA492280 NextSeq 500 NextSeq 500 ILLUMINA
9
SAMN1009581 PRJNA492280 NextSeq 500 NextSeq 500 ILLUMINA
7
SAMN1009581 PRJNA492280 NextSeq 500 NextSeq 500 ILLUMINA
1
SAMN1009580 PRJNA492280 NextSeq 500 NextSeq 500 ILLUMINA
9
SAMN1009580 PRJNA492280 NextSeq 500 NextSeq 500 ILLUMINA
7
SAMN1009581 PRJNA492280 NextSeq 500 NextSeq 500 ILLUMINA
6
SAMN1009587 PRJNA492280 NextSeq 500 NextSeq 500 ILLUMINA
9
SAMN1009587 PRJNA492280 NextSeq 500 NextSeq 500 ILLUMINA
8
SAMN1009581 PRJNA492280 NextSeq 500 NextSeq 500 ILLUMINA
4
SAMN1009581 PRJNA492280 NextSeq 500 NextSeq 500 ILLUMINA
3
SAMN1009580 PRJNA492280 NextSeq 500 NextSeq 500 ILLUMINA
5
Columns 21-25:
total_spots total_size run_total_spots run_total_bases run_alias
21439471 1549237734 21439471 3235130828 GSM3396532_r1
47867961 3470385670 47867961 7230485009 GSM3396533_r1
45108524 3347127540 45108524 6811055984 GSM3396534_r1
25172776 1597637090 25172776 3804459726 GSM3396535_r1
68478641 4227037694 68478641 10362706101 GSM3396536_r1
72822775 4519247080 72822775 11019279496 GSM3396537_r1
17619161 1288448692 17619161 2643010914 GSM3396538_r1
62587832 4050860463 62587832 9407123202 GSM3396539_r1
67147971 4345146386 67147971 10142882964 GSM3396540_r1
27837896 1720418790 27837896 4201863748 GSM3396541_r1
56555130 3467480388 56555130 8562517609 GSM3396542_r1
60833762 3735673536 60833762 9212176075 GSM3396543_r1
49187957 3190641550 49187957 7431177314 GSM3396544_r1
96090300 6245453636 96090300 14525399561 GSM3396545_r1
62838564 4072100836 62838564 9494332347 GSM3396546_r1
30761676 2091196312 30761676 4675774752 GSM3396547_r1
66234287 4470573268 66234287 10067611624 GSM3396548_r1
80003290 5496499311 80003290 12160500080 GSM3396549_r1
Columns 26-30:
public_siz public_vers
public_filename e public_date public_md5 ion
RNA_cardio_neg_24hp 988272024 2020-02-13 7ac08a0b2f9d379f6 1
f_rep_1_R1.fq.gz 04:48:02 27c9d0523c27317
SRR7882015.sralite 1881003321 2020-06-14 8161154ca4e9cf674 1
12:02:25 e3f0e4af74c8455
SRR7882016.sralite 1780836154 2020-06-22 2b5e272ac8b85fb07 1
13:49:36 e89842b6fa1e7ff
SRR7882017.sralite 991847394 2020-06-14 26b25df3ca97659b7 1
11:47:21 7d69fb9a2514f07
SRR7882018.sralite 2687036341 2020-06-20 076044f1f92cd47d5 1
12:03:19 5c8a89e6860e005
RNA_cardio_pos_48hp 2681320768 2020-02-13 1debfc9a0c98e1966 1
f_rep_2_R2.fq.gz 05:32:38 a0fe50ea2e34eb2
SRR7882020.sralite 693263779 2020-06-24 8c1d6436606b28b95 1
02:36:29 450cb538ea2f066
SRR7882021.sralite 2460093865 2020-06-20 527dc540e148a7288 1
12:01:27 012b188ed11541c
SRR7882022.sralite 2649120145 2020-06-22 9d3fcc2b555af6946 1
14:03:06 43af35393bd9d1d
SRR7882023.sralite 1092395868 2020-06-14 db7d0a7737eb61630 1
11:46:37 1bd7f544c57f455
SRR7882024.sralite 2216823671 2020-06-21 cd4c4270d817343d2 1
14:15:12 f81b3ff711fb7e4
SRR7882025.sralite 2384360834 2020-06-24 d179a5c3889518879 1
02:53:43 eaaec1914404090
SRR7882026.sralite 1940747812 2020-06-21 7f896dfee5c74c558 1
14:07:10 c9d95cbaa047ca2
SRR7882027.sralite 3777195699 2021-06-15 111d6ca4fb0018969 1
02:20:27 7d543d0ca744c3a
SRR7882028.sralite 2472733302 2020-06-24 8e8f270cee4fc7a9c 1
02:54:40 5f450a34930de4f
SRR7882029.sralite 1179822118 2020-06-20 5a7f09aa682cdee98 1
11:39:34 a67673aaf2d205a
SRR7882030.sralite 2532332515 2020-06-22 40e79360fa3d4ea48 1
13:51:55 1b82928909b68b1
SRR7882031.sralite 3062201982 2020-06-22 9942effecf10d150a 1
13:56:01 d565339bf207f81
Columns 31-35:
public_se
mantic_na public_sup public_sr aws_free_
me ertype atoolkit aws_url egress
fastq Original 0 s3://sra-pub-src-3/SRR7882014/R -
NA_cardio_neg_24hpf_rep_1_R1.fq
.gz
SRA Lite Primary 1 s3://sra-pub-zq-8/SRR7882015/SR s3.us-eas
ETL R7882015.sralite.1 t-1
SRA Lite Primary 1 s3://sra-pub-zq-8/SRR7882016/SR s3.us-eas
ETL R7882016.sralite.1 t-1
SRA Lite Primary 1 s3://sra-pub-zq-8/SRR7882017/SR s3.us-eas
ETL R7882017.sralite.1 t-1
SRA Lite Primary 1 s3://sra-pub-zq-4/SRR7882018/SR s3.us-eas
ETL R7882018.sralite.1 t-1
fastq Original 0 s3://sra-pub-src-3/SRR7882019/R -
NA_cardio_pos_48hpf_rep_2_R2.fq
.gz
SRA Lite Primary 1 s3://sra-pub-zq-5/SRR7882020/SR s3.us-eas
ETL R7882020.sralite.1 t-1
SRA Lite Primary 1 s3://sra-pub-zq-4/SRR7882021/SR s3.us-eas
ETL R7882021.sralite.1 t-1
SRA Lite Primary 1 s3://sra-pub-zq-8/SRR7882022/SR s3.us-eas
ETL R7882022.sralite.1 t-1
SRA Lite Primary 1 s3://sra-pub-zq-8/SRR7882023/SR s3.us-eas
ETL R7882023.sralite.1 t-1
SRA Lite Primary 1 s3://sra-pub-zq-9/SRR7882024/SR s3.us-eas
ETL R7882024.sralite.1 t-1
SRA Lite Primary 1 s3://sra-pub-zq-8/SRR7882025/SR s3.us-eas
ETL R7882025.sralite.1 t-1
SRA Lite Primary 1 s3://sra-pub-zq-8/SRR7882026/SR s3.us-eas
ETL R7882026.sralite.1 t-1
SRA Lite Primary 1 s3://sra-pub-zq-9/SRR7882027/SR s3.us-eas
ETL R7882027.sralite.1 t-1
SRA Lite Primary 1 s3://sra-pub-zq-8/SRR7882028/SR s3.us-eas
ETL R7882028.sralite.1 t-1
SRA Lite Primary 1 s3://sra-pub-zq-4/SRR7882029/SR s3.us-eas
ETL R7882029.sralite.1 t-1
SRA Lite Primary 1 s3://sra-pub-zq-8/SRR7882030/SR s3.us-eas
ETL R7882030.sralite.1 t-1
SRA Lite Primary 1 s3://sra-pub-zq-5/SRR7882031/SR s3.us-eas
ETL R7882031.sralite.1 t-1
Columns 36-40:
ncbi_ac
aws_acce ncbi_fre cess_ty
ss_type public_url ncbi_url e_egress pe
Use https://sra-downloadb.b https://sra-downloadb. worldwid anonymo
Cloud e-md.ncbi.nlm.nih.gov/s be-md.ncbi.nlm.nih.gov e us
Data os12/sra-pub-zq-1211/SR /sos12/sra-pub-zq-1211
Delivery R007/882/SRR7882014/SRR /SRR007/882/SRR7882014
7882014.sralite.1 /SRR7882014.sralite.1
aws https://sra-downloadb.b https://sra-downloadb. worldwid anonymo
identity e-md.ncbi.nlm.nih.gov/s be-md.ncbi.nlm.nih.gov e us
os12/sra-pub-zq-1211/SR /sos12/sra-pub-zq-1211
R007/882/SRR7882015/SRR /SRR007/882/SRR7882015
7882015.sralite.1 /SRR7882015.sralite.1
aws https://sra-downloadb.b https://sra-downloadb. worldwid anonymo
identity e-md.ncbi.nlm.nih.gov/s be-md.ncbi.nlm.nih.gov e us
os12/sra-pub-zq-1211/SR /sos12/sra-pub-zq-1211
R007/882/SRR7882016/SRR /SRR007/882/SRR7882016
7882016.sralite.1 /SRR7882016.sralite.1
aws https://sra-downloadb.b https://sra-downloadb. worldwid anonymo
identity e-md.ncbi.nlm.nih.gov/s be-md.ncbi.nlm.nih.gov e us
os9/sra-pub-zq-922/SRR0 /sos9/sra-pub-zq-922/S
07/882/SRR7882017.srali RR007/882/SRR7882017.s
te.1 ralite.1
aws https://sra-downloadb.b https://sra-downloadb. worldwid anonymo
identity e-md.ncbi.nlm.nih.gov/s be-md.ncbi.nlm.nih.gov e us
os12/sra-pub-zq-1211/SR /sos12/sra-pub-zq-1211
R007/882/SRR7882018/SRR /SRR007/882/SRR7882018
7882018.sralite.1 /SRR7882018.sralite.1
Use https://sra-pub-run-odp https://sra-downloadb. worldwid anonymo
Cloud .s3.amazonaws.com/sra/S be-md.ncbi.nlm.nih.gov e us
Data RR7882019/SRR7882019 /sos12/sra-pub-zq-1211
Delivery /SRR007/882/SRR7882019
/SRR7882019.sralite.1
aws https://sra-downloadb.b https://sra-downloadb. worldwid anonymo
identity e-md.ncbi.nlm.nih.gov/s be-md.ncbi.nlm.nih.gov e us
os12/sra-pub-zq-1214/SR /sos12/sra-pub-zq-1214
R007/882/SRR7882020.sra /SRR007/882/SRR7882020
lite.1 .sralite.1
aws https://sra-downloadb.b https://sra-downloadb. worldwid anonymo
identity e-md.ncbi.nlm.nih.gov/s be-md.ncbi.nlm.nih.gov e us
os12/sra-pub-zq-1211/SR /sos12/sra-pub-zq-1211
R007/882/SRR7882021/SRR /SRR007/882/SRR7882021
7882021.sralite.1 /SRR7882021.sralite.1
aws https://sra-downloadb.b https://sra-downloadb. worldwid anonymo
identity e-md.ncbi.nlm.nih.gov/s be-md.ncbi.nlm.nih.gov e us
os12/sra-pub-zq-1211/SR /sos12/sra-pub-zq-1211
R007/882/SRR7882022/SRR /SRR007/882/SRR7882022
7882022.sralite.1 /SRR7882022.sralite.1
aws https://sra-downloadb.b https://sra-downloadb. worldwid anonymo
identity e-md.ncbi.nlm.nih.gov/s be-md.ncbi.nlm.nih.gov e us
os9/sra-pub-zq-922/SRR0 /sos9/sra-pub-zq-922/S
07/882/SRR7882023.srali RR007/882/SRR7882023.s
te.1 ralite.1
aws https://sra-downloadb.b https://sra-downloadb. worldwid anonymo
identity e-md.ncbi.nlm.nih.gov/s be-md.ncbi.nlm.nih.gov e us
os12/sra-pub-zq-1211/SR /sos12/sra-pub-zq-1211
R007/882/SRR7882024/SRR /SRR007/882/SRR7882024
7882024.sralite.1 /SRR7882024.sralite.1
aws https://sra-downloadb.b https://sra-downloadb. worldwid anonymo
identity e-md.ncbi.nlm.nih.gov/s be-md.ncbi.nlm.nih.gov e us
os12/sra-pub-zq-1211/SR /sos12/sra-pub-zq-1211
R007/882/SRR7882025/SRR /SRR007/882/SRR7882025
7882025.sralite.1 /SRR7882025.sralite.1
aws https://sra-downloadb.b https://sra-downloadb. worldwid anonymo
identity e-md.ncbi.nlm.nih.gov/s be-md.ncbi.nlm.nih.gov e us
os12/sra-pub-zq-1211/SR /sos12/sra-pub-zq-1211
R007/882/SRR7882026/SRR /SRR007/882/SRR7882026
7882026.sralite.1 /SRR7882026.sralite.1
aws https://sra-downloadb.b https://sra-downloadb. worldwid anonymo
identity e-md.ncbi.nlm.nih.gov/s be-md.ncbi.nlm.nih.gov e us
os12/sra-pub-zq-1211/SR /sos12/sra-pub-zq-1211
R007/882/SRR7882027/SRR /SRR007/882/SRR7882027
7882027.sralite.1 /SRR7882027.sralite.1
aws https://sra-downloadb.b https://sra-downloadb. worldwid anonymo
identity e-md.ncbi.nlm.nih.gov/s be-md.ncbi.nlm.nih.gov e us
os12/sra-pub-zq-1211/SR /sos12/sra-pub-zq-1211
R007/882/SRR7882028/SRR /SRR007/882/SRR7882028
7882028.sralite.1 /SRR7882028.sralite.1
aws https://sra-downloadb.b https://sra-downloadb. worldwid anonymo
identity e-md.ncbi.nlm.nih.gov/s be-md.ncbi.nlm.nih.gov e us
os12/sra-pub-zq-1211/SR /sos12/sra-pub-zq-1211
R007/882/SRR7882029/SRR /SRR007/882/SRR7882029
7882029.sralite.1 /SRR7882029.sralite.1
aws https://sra-downloadb.b https://sra-downloadb. worldwid anonymo
identity e-md.ncbi.nlm.nih.gov/s be-md.ncbi.nlm.nih.gov e us
os12/sra-pub-zq-1211/SR /sos12/sra-pub-zq-1211
R007/882/SRR7882030/SRR /SRR007/882/SRR7882030
7882030.sralite.1 /SRR7882030.sralite.1
aws https://sra-downloadb.b https://sra-downloadb. worldwid anonymo
identity e-md.ncbi.nlm.nih.gov/s be-md.ncbi.nlm.nih.gov e us
os12/sra-pub-zq-1211/SR /sos12/sra-pub-zq-1211
R007/882/SRR7882031/SRR /SRR007/882/SRR7882031
7882031.sralite.1 /SRR7882031.sralite.1
Columns 41-45:
gcp_free_e gcp_access_ experiment
gcp_url gress type _alias source_name
gs://sra-pub-zq-107/SRR7 gs.us-east gcp GSM3396532 FACS-sorted
882014/SRR7882014.zq.1 1 identity embryo cells
gs://sra-pub-zq-107/SRR7 gs.us-east gcp GSM3396533 FACS-sorted
882015/SRR7882015.zq.1 1 identity embryo cells
gs://sra-pub-zq-107/SRR7 gs.us-east gcp GSM3396534 FACS-sorted
882016/SRR7882016.zq.1 1 identity embryo cells
gs://sra-pub-zq-107/SRR7 gs.us-east gcp GSM3396535 FACS-sorted
882017/SRR7882017.zq.1 1 identity embryo cells
gs://sra-pub-zq-107/SRR7 gs.us-east gcp GSM3396536 FACS-sorted
882018/SRR7882018.zq.1 1 identity embryo cells
gs://sra-pub-zq-107/SRR7 gs.us-east gcp GSM3396537 FACS-sorted
882019/SRR7882019.zq.1 1 identity embryo cells
gs://sra-pub-zq-105/SRR7 gs.us-east gcp GSM3396538 FACS-sorted
882020/SRR7882020.zq.1 1 identity embryo cells
gs://sra-pub-zq-107/SRR7 gs.us-east gcp GSM3396539 FACS-sorted
882021/SRR7882021.zq.1 1 identity embryo cells
gs://sra-pub-zq-107/SRR7 gs.us-east gcp GSM3396540 FACS-sorted
882022/SRR7882022.zq.1 1 identity embryo cells
gs://sra-pub-zq-107/SRR7 gs.us-east gcp GSM3396541 FACS-sorted
882023/SRR7882023.zq.1 1 identity embryo cells
gs://sra-pub-zq-107/SRR7 gs.us-east gcp GSM3396542 FACS-sorted
882024/SRR7882024.zq.1 1 identity embryo cells
gs://sra-pub-zq-107/SRR7 gs.us-east gcp GSM3396543 FACS-sorted
882025/SRR7882025.zq.1 1 identity embryo cells
gs://sra-pub-zq-107/SRR7 gs.us-east gcp GSM3396544 FACS-sorted
882026/SRR7882026.zq.1 1 identity embryo cells
gs://sra-pub-zq-105/SRR7 gs.us-east gcp GSM3396545 FACS-sorted
882027/SRR7882027.noqual 1 identity embryo cells
.1
gs://sra-pub-zq-107/SRR7 gs.us-east gcp GSM3396546 FACS-sorted
882028/SRR7882028.zq.1 1 identity embryo cells
gs://sra-pub-zq-107/SRR7 gs.us-east gcp GSM3396547 FACS-sorted
882029/SRR7882029.zq.1 1 identity embryo cells
gs://sra-pub-zq-107/SRR7 gs.us-east gcp GSM3396548 FACS-sorted
882030/SRR7882030.zq.1 1 identity embryo cells
gs://sra-pub-zq-105/SRR7 gs.us-east gcp GSM3396549 FACS-sorted
882031/SRR7882031.zq.1 1 identity embryo cells
Columns 46-50:
developmental genetic ena_fastq_h
tissue stage gfp status background ttp
FACS-sorted embryo 24 hpf GFP wild type -
cells negative
FACS-sorted embryo 24 hpf GFP wild type -
cells positive
FACS-sorted embryo 24 hpf GFP wild type -
cells positive
FACS-sorted embryo 48 hpf GFP wild type -
cells negative
FACS-sorted embryo 48 hpf GFP wild type -
cells positive
FACS-sorted embryo 48 hpf GFP wild type -
cells positive
FACS-sorted embryo 72 hpf GFP wild type -
cells negative
FACS-sorted embryo 72 hpf GFP wild type -
cells positive
FACS-sorted embryo 72 hpf GFP wild type -
cells positive
FACS-sorted embryo 72 hpf GFP gata5 -
cells negative
FACS-sorted embryo 72 hpf GFP gata5 -
cells positive
FACS-sorted embryo 72 hpf GFP gata5 -
cells positive
FACS-sorted embryo 72 hpf GFP tbx5 -
cells negative
FACS-sorted embryo 72 hpf GFP tbx5 -
cells positive
FACS-sorted embryo 72 hpf GFP tbx5 -
cells positive
FACS-sorted embryo 72 hpf GFP hand2 -
cells negative
FACS-sorted embryo 72 hpf GFP hand2 -
cells positive
FACS-sorted embryo 72 hpf GFP hand2 -
cells positive
Columns 51-55:
ena_fastq_http ena_fastq_http ena_fastq_f ena_fastq_ftp_
_1 _2 tp 1 ena_fastq_ftp_2
http://ftp.sra http://ftp.sra - era-fasp@fasp. [email protected]
.ebi.ac.uk/vol .ebi.ac.uk/vol sra.ebi.ac.uk: ra.ebi.ac.uk:vo
1/fastq/SRR788 1/fastq/SRR788 vol1/fastq/SRR l1/fastq/SRR788
/004/SRR788201 /004/SRR788201 788/004/SRR788 /004/SRR7882014
4/SRR7882014_1 4/SRR7882014_2 2014/SRR788201 /SRR7882014_2.f
.fastq.gz .fastq.gz 4_1.fastq.gz astq.gz
http://ftp.sra http://ftp.sra - era-fasp@fasp. [email protected]
.ebi.ac.uk/vol .ebi.ac.uk/vol sra.ebi.ac.uk: ra.ebi.ac.uk:vo
1/fastq/SRR788 1/fastq/SRR788 vol1/fastq/SRR l1/fastq/SRR788
/005/SRR788201 /005/SRR788201 788/005/SRR788 /005/SRR7882015
5/SRR7882015_1 5/SRR7882015_2 2015/SRR788201 /SRR7882015_2.f
.fastq.gz .fastq.gz 5_1.fastq.gz astq.gz
http://ftp.sra http://ftp.sra - era-fasp@fasp. [email protected]
.ebi.ac.uk/vol .ebi.ac.uk/vol sra.ebi.ac.uk: ra.ebi.ac.uk:vo
1/fastq/SRR788 1/fastq/SRR788 vol1/fastq/SRR l1/fastq/SRR788
/006/SRR788201 /006/SRR788201 788/006/SRR788 /006/SRR7882016
6/SRR7882016_1 6/SRR7882016_2 2016/SRR788201 /SRR7882016_2.f
.fastq.gz .fastq.gz 6_1.fastq.gz astq.gz
http://ftp.sra http://ftp.sra - era-fasp@fasp. [email protected]
.ebi.ac.uk/vol .ebi.ac.uk/vol sra.ebi.ac.uk: ra.ebi.ac.uk:vo
1/fastq/SRR788 1/fastq/SRR788 vol1/fastq/SRR l1/fastq/SRR788
/007/SRR788201 /007/SRR788201 788/007/SRR788 /007/SRR7882017
7/SRR7882017_1 7/SRR7882017_2 2017/SRR788201 /SRR7882017_2.f
.fastq.gz .fastq.gz 7_1.fastq.gz astq.gz
http://ftp.sra http://ftp.sra - era-fasp@fasp. [email protected]
.ebi.ac.uk/vol .ebi.ac.uk/vol sra.ebi.ac.uk: ra.ebi.ac.uk:vo
1/fastq/SRR788 1/fastq/SRR788 vol1/fastq/SRR l1/fastq/SRR788
/008/SRR788201 /008/SRR788201 788/008/SRR788 /008/SRR7882018
8/SRR7882018_1 8/SRR7882018_2 2018/SRR788201 /SRR7882018_2.f
.fastq.gz .fastq.gz 8_1.fastq.gz astq.gz
http://ftp.sra http://ftp.sra - era-fasp@fasp. [email protected]
.ebi.ac.uk/vol .ebi.ac.uk/vol sra.ebi.ac.uk: ra.ebi.ac.uk:vo
1/fastq/SRR788 1/fastq/SRR788 vol1/fastq/SRR l1/fastq/SRR788
/009/SRR788201 /009/SRR788201 788/009/SRR788 /009/SRR7882019
9/SRR7882019_1 9/SRR7882019_2 2019/SRR788201 /SRR7882019_2.f
.fastq.gz .fastq.gz 9_1.fastq.gz astq.gz
http://ftp.sra http://ftp.sra - era-fasp@fasp. [email protected]
.ebi.ac.uk/vol .ebi.ac.uk/vol sra.ebi.ac.uk: ra.ebi.ac.uk:vo
1/fastq/SRR788 1/fastq/SRR788 vol1/fastq/SRR l1/fastq/SRR788
/000/SRR788202 /000/SRR788202 788/000/SRR788 /000/SRR7882020
0/SRR7882020_1 0/SRR7882020_2 2020/SRR788202 /SRR7882020_2.f
.fastq.gz .fastq.gz 0_1.fastq.gz astq.gz
http://ftp.sra http://ftp.sra - era-fasp@fasp. [email protected]
.ebi.ac.uk/vol .ebi.ac.uk/vol sra.ebi.ac.uk: ra.ebi.ac.uk:vo
1/fastq/SRR788 1/fastq/SRR788 vol1/fastq/SRR l1/fastq/SRR788
/001/SRR788202 /001/SRR788202 788/001/SRR788 /001/SRR7882021
1/SRR7882021_1 1/SRR7882021_2 2021/SRR788202 /SRR7882021_2.f
.fastq.gz .fastq.gz 1_1.fastq.gz astq.gz
http://ftp.sra http://ftp.sra - era-fasp@fasp. [email protected]
.ebi.ac.uk/vol .ebi.ac.uk/vol sra.ebi.ac.uk: ra.ebi.ac.uk:vo
1/fastq/SRR788 1/fastq/SRR788 vol1/fastq/SRR l1/fastq/SRR788
/002/SRR788202 /002/SRR788202 788/002/SRR788 /002/SRR7882022
2/SRR7882022_1 2/SRR7882022_2 2022/SRR788202 /SRR7882022_2.f
.fastq.gz .fastq.gz 2_1.fastq.gz astq.gz
http://ftp.sra http://ftp.sra - era-fasp@fasp. [email protected]
.ebi.ac.uk/vol .ebi.ac.uk/vol sra.ebi.ac.uk: ra.ebi.ac.uk:vo
1/fastq/SRR788 1/fastq/SRR788 vol1/fastq/SRR l1/fastq/SRR788
/003/SRR788202 /003/SRR788202 788/003/SRR788 /003/SRR7882023
3/SRR7882023_1 3/SRR7882023_2 2023/SRR788202 /SRR7882023_2.f
.fastq.gz .fastq.gz 3_1.fastq.gz astq.gz
http://ftp.sra http://ftp.sra - era-fasp@fasp. [email protected]
.ebi.ac.uk/vol .ebi.ac.uk/vol sra.ebi.ac.uk: ra.ebi.ac.uk:vo
1/fastq/SRR788 1/fastq/SRR788 vol1/fastq/SRR l1/fastq/SRR788
/004/SRR788202 /004/SRR788202 788/004/SRR788 /004/SRR7882024
4/SRR7882024_1 4/SRR7882024_2 2024/SRR788202 /SRR7882024_2.f
.fastq.gz .fastq.gz 4_1.fastq.gz astq.gz
http://ftp.sra http://ftp.sra - era-fasp@fasp. [email protected]
.ebi.ac.uk/vol .ebi.ac.uk/vol sra.ebi.ac.uk: ra.ebi.ac.uk:vo
1/fastq/SRR788 1/fastq/SRR788 vol1/fastq/SRR l1/fastq/SRR788
/005/SRR788202 /005/SRR788202 788/005/SRR788 /005/SRR7882025
5/SRR7882025_1 5/SRR7882025_2 2025/SRR788202 /SRR7882025_2.f
.fastq.gz .fastq.gz 5_1.fastq.gz astq.gz
http://ftp.sra http://ftp.sra - era-fasp@fasp. [email protected]
.ebi.ac.uk/vol .ebi.ac.uk/vol sra.ebi.ac.uk: ra.ebi.ac.uk:vo
1/fastq/SRR788 1/fastq/SRR788 vol1/fastq/SRR l1/fastq/SRR788
/006/SRR788202 /006/SRR788202 788/006/SRR788 /006/SRR7882026
6/SRR7882026_1 6/SRR7882026_2 2026/SRR788202 /SRR7882026_2.f
.fastq.gz .fastq.gz 6_1.fastq.gz astq.gz
http://ftp.sra http://ftp.sra - era-fasp@fasp. [email protected]
.ebi.ac.uk/vol .ebi.ac.uk/vol sra.ebi.ac.uk: ra.ebi.ac.uk:vo
1/fastq/SRR788 1/fastq/SRR788 vol1/fastq/SRR l1/fastq/SRR788
/007/SRR788202 /007/SRR788202 788/007/SRR788 /007/SRR7882027
7/SRR7882027_1 7/SRR7882027_2 2027/SRR788202 /SRR7882027_2.f
.fastq.gz .fastq.gz 7_1.fastq.gz astq.gz
http://ftp.sra http://ftp.sra - era-fasp@fasp. [email protected]
.ebi.ac.uk/vol .ebi.ac.uk/vol sra.ebi.ac.uk: ra.ebi.ac.uk:vo
1/fastq/SRR788 1/fastq/SRR788 vol1/fastq/SRR l1/fastq/SRR788
/008/SRR788202 /008/SRR788202 788/008/SRR788 /008/SRR7882028
8/SRR7882028_1 8/SRR7882028_2 2028/SRR788202 /SRR7882028_2.f
.fastq.gz .fastq.gz 8_1.fastq.gz astq.gz
http://ftp.sra http://ftp.sra - era-fasp@fasp. [email protected]
.ebi.ac.uk/vol .ebi.ac.uk/vol sra.ebi.ac.uk: ra.ebi.ac.uk:vo
1/fastq/SRR788 1/fastq/SRR788 vol1/fastq/SRR l1/fastq/SRR788
/009/SRR788202 /009/SRR788202 788/009/SRR788 /009/SRR7882029
9/SRR7882029_1 9/SRR7882029_2 2029/SRR788202 /SRR7882029_2.f
.fastq.gz .fastq.gz 9_1.fastq.gz astq.gz
http://ftp.sra http://ftp.sra - era-fasp@fasp. [email protected]
.ebi.ac.uk/vol .ebi.ac.uk/vol sra.ebi.ac.uk: ra.ebi.ac.uk:vo
1/fastq/SRR788 1/fastq/SRR788 vol1/fastq/SRR l1/fastq/SRR788
/000/SRR788203 /000/SRR788203 788/000/SRR788 /000/SRR7882030
0/SRR7882030_1 0/SRR7882030_2 2030/SRR788203 /SRR7882030_2.f
.fastq.gz .fastq.gz 0_1.fastq.gz astq.gz
http://ftp.sra http://ftp.sra - era-fasp@fasp. [email protected]
.ebi.ac.uk/vol .ebi.ac.uk/vol sra.ebi.ac.uk: ra.ebi.ac.uk:vo
1/fastq/SRR788 1/fastq/SRR788 vol1/fastq/SRR l1/fastq/SRR788
/001/SRR788203 /001/SRR788203 788/001/SRR788 /001/SRR7882031
1/SRR7882031_1 1/SRR7882031_2 2031/SRR788203 /SRR7882031_2.f
.fastq.gz .fastq.gz 1_1.fastq.gz astq.gz
Columns 56-57:
study_geo_accession experiment_geo_accession
GSE120236 GSM3396532
GSE120236 GSM3396533
GSE120236 GSM3396534
GSE120236 GSM3396535
GSE120236 GSM3396536
GSE120236 GSM3396537
GSE120236 GSM3396538
GSE120236 GSM3396539
GSE120236 GSM3396540
GSE120236 GSM3396541
GSE120236 GSM3396542
GSE120236 GSM3396543
GSE120236 GSM3396544
GSE120236 GSM3396545
GSE120236 GSM3396546
GSE120236 GSM3396547
GSE120236 GSM3396548
GSE120236 GSM3396549
Download an entire project!¶
[8]:
print("pysradb download -p SRP162234")
pysradb download -p SRP162234