snRNA-seq of chimpanzee (Pan troglodytes) adult testis

Experiment ID:ERP132583
Technology:scRNA-Seq
Description:Single-nucleus RNA sequencing (snRNA-seq) was used to profile the transcriptome of 12,352 nuclei in chimpanzee adult testis. This dataset includes three samples from three different individuals. This dataset is part of a larger evolutionary study of adult testis at the single-nucleus level (97,521 single-nuclei in total) across mammals including 10 representatives of the three main mammalian lineages: human, chimpanzee, bonobo, gorilla, gibbon, rhesus macaque, marmoset, mouse (placental mammals); grey short-tailed opossum (marsupials); and platypus (egg-laying monotremes). Corresponding data were generated for a bird (red junglefowl, the progenitor of domestic chicken), to be used as an evolutionary outgroup.
DOI:10.1038/s41586-022-05547-7
Source:ERP132583 ENA
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scRNA-Seq droplet-based processed expression values per cell population in Pan troglodytesscRNA-Seq droplet-based H5AD data per cell in Pan troglodytes

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Library ID
Identifier of the RNA-Seq library
Cell type ID
ID of the cell type of the sample
Cell type name
Name of the cell type of the sample
Cell type author annotation
Free text annotation of cell type as provided by authors
Anat. entity ID
ID of the anatomical localization of the sample
Anat. entity name
Name of the anatomical localization of the sample
Anat. entity author annotation
Free text annotation of anatomical localization of the sample as provided by authors
Stage ID
ID of the developmental and life stage of the sample
Stage name
Name of the developmental and life stage of the sample
Stage author annotation
Free text annotation of the developmental and life stage of the sample as provided by authors
Sex
Annotation of the sex of the sample
Strain
Annotation of the strain of the sample
Time
Free text annotation of the time of sampling as provided by authors
Time unit
Unit for the time of sampling as provided by authors
Species
Physiological status
Physiological status of the organism at time of sampling
Technology
Sequencing platform
Sequenced transcript part
Possible values are: full length, all parts of the transcript are sequenced; 3': only the 3' end of the transcript is sequenced; 5': only the 5' end of the transcript is sequenced.
Fractionation
Possible values are: cell, transcripts are extracted from the cell; nuclei, transcripts are extracted from the nucleus.
Fragmentation
Size of the RNA fragmentation
Run sequencing type
Paired-end or single-read run
Total read count
Total number of reads for the library.
Mapped read count
Number of reads that could be mapped to the transcriptome.
Total UMI count
Total number of individual RNA molecules (UMI) for the annotated sample. Only applicable for libraries producing UMIs.
Mapped UMI count
Number of UMIs that could be mapped to the transcriptome. Only applicable for libraries producing UMIs.
Distinct rank count
When performing a fractional ranking of the genes in the annotated sample, based on their expression level, number of distinct ranks observed, to have a value of the power for distinguishing expression levels. Used as a weight to compute a weighted mean rank accross samples for each gene and compute expression scores in Bgee.
Max rank
When performing a fractional ranking of the genes in the annotated sample, based on their expression level, maximum rank attained in the sample. Used to normalize ranks accross samples and compute expression scores in Bgee.
Link to processed expression values
See the processed expression value results for this assay
ERX6700427CL:0000017 spermatocyteLeptotene_SpermatocytesUBERON:0000473 testistestisPtroDv:0000026 21-year-old stage (chimpanzee)21 yearsmaleNANANAPan troglodytesNA10X Genomics V2NextSeq 550THREE_PRIMENUCLEUS0paired3217185671641293420165790368817756.5Browse results
ERX6700427CL:4030036 early spermatidEarly_Round_spermatidsUBERON:0000473 testistestisPtroDv:0000026 21-year-old stage (chimpanzee)21 yearsmaleNANANAPan troglodytesNA10X Genomics V2NextSeq 550THREE_PRIMENUCLEUS0paired32171856716412934201198023525519470.5Browse results
ERX6700427CL:4030037 late spermatidElongated_spermatidsUBERON:0000473 testistestisPtroDv:0000026 21-year-old stage (chimpanzee)21 yearsmaleNANANAPan troglodytesNA10X Genomics V2NextSeq 550THREE_PRIMENUCLEUS0paired32171856716412934202378880571719986.5Browse results
ERX6700427CL:0000000 cellNAUBERON:0000473 testistestisPtroDv:0000026 21-year-old stage (chimpanzee)21 yearsmaleNANANAPan troglodytesNA10X Genomics V2NextSeq 550THREE_PRIMENUCLEUS0paired321718567164129342010369173013928.5Browse results

Showing 21 to 24 of 24 entries

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