"The living contents of a cell; the matter contained within (but not including) the plasma membrane, usually taken to exclude large vacuoles and masses of secretory or ingested material. In eukaryotes it includes the nucleus and cytoplasm [goid 5622] [pmid 11256614] [evidence IDA]; That fraction of cells, prepared by disruptive biochemical methods, that includes the plasma and other membranes [goid 5624] [evidence ISS]; A cytoplasmic, membrane-bounded organelle that is found in most animal cells and that contains a variety of hydrolases, most of which have their maximal activities in the pH range 5-6. The contained enzymes display latency if properly isolated. About 40 different lysosomal hydrolases are known and lysosomes have a great variety of morphologies and functions [goid 5764] [evidence ISS]; Small irregularly shaped intracellular vesicles to which endocytosed molecules are initially delivered [goid 5769] [evidence ISS]; A prelysosomal endocytic organelle differentiated from early endosomes by lower lumenal pH and different protein composition. Late endosomes are more spherical than early endosomes and are mostly juxtanuclear, being concentrated near the microtubule organizing center [goid 5770] [evidence ISS]; The rough (or granular) endoplasmic reticulum (ER) has ribosomes adhering to the outer surface; the ribosomes are the site of translation of the mRNA for those proteins which are either to be retained within the cisternae (ER-resident proteins), the proteins of the lysosomes, or the proteins destined for export from the cell. Glycoproteins undergo their initial glycosylation within the cisternae [goid 5791] [evidence ISS]; The set of thin, flattened membrane-bounded compartments, called cisternae, that form the central portion of the Golgi complex. The stack usually comprises cis, medial, and trans cisternae; the cis- and trans-Golgi networks are not considered part of the stack [goid 5795] [evidence ISS]; That part of the cytoplasm that does not contain membranous or particulate subcellular components [goid 5829] [evidence ISS]; The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins [goid 5886] [evidence ISS]; A vesicle that mediates transport between the trans-Golgi network and other parts of the cell [goid 30140] [evidence ISS]; The continuous network of membranes encompassing the outer nuclear membrane and the endoplasmic reticulum [goid 42175] [evidence ISS]; Cytoplasm situated near, or occurring around, the nucleus [goid 48471] [evidence ISS]"