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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Showing 1 to 20 of 24 entries

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
ERX6700425CL:4030036 early spermatidLate_Round_spermatidsUBERON:0000473 testistestisUBERON:0007222 late adult stage45 yearsmaleNANANAPan troglodytesNA10X Genomics V2NextSeq 550THREE_PRIMENUCLEUS0paired2877490331302920430669241444618775Browse results
ERX6700425CL:0000016 male germ line stem cellUndifferentiated_SpermatogoniaUBERON:0000473 testistestisUBERON:0007222 late adult stage45 yearsmaleNANANAPan troglodytesNA10X Genomics V2NextSeq 550THREE_PRIMENUCLEUS0paired28774903313029204301020584514119765.5Browse results
ERX6700425CL:0000000 cellNAUBERON:0000473 testistestisUBERON:0007222 late adult stage45 yearsmaleNANANAPan troglodytesNA10X Genomics V2NextSeq 550THREE_PRIMENUCLEUS0paired287749033130292043021075230114602.5Browse results
ERX6700425CL:4030037 late spermatidElongated_spermatidsUBERON:0000473 testistestisUBERON:0007222 late adult stage45 yearsmaleNANANAPan troglodytesNA10X Genomics V2NextSeq 550THREE_PRIMENUCLEUS0paired28774903313029204301030236465119204.5Browse results
ERX6700425CL:0000020 spermatogoniumDifferentiated_SpermatogoniaUBERON:0000473 testistestisUBERON:0007222 late adult stage45 yearsmaleNANANAPan troglodytesNA10X Genomics V2NextSeq 550THREE_PRIMENUCLEUS0paired2877490331302920430419558428918872.5Browse results
ERX6700425CL:0000017 spermatocyteZygotene_SpermatocytesUBERON:0000473 testistestisUBERON:0007222 late adult stage45 yearsmaleNANANAPan troglodytesNA10X Genomics V2NextSeq 550THREE_PRIMENUCLEUS0paired2877490331302920430545733462318960.5Browse results
ERX6700425CL:0000216 Sertoli cellSertoliUBERON:0000473 testistestisUBERON:0007222 late adult stage45 yearsmaleNANANAPan troglodytesNA10X Genomics V2NextSeq 550THREE_PRIMENUCLEUS0paired2877490331302920430740978480018835.5Browse results
ERX6700425CL:0002371 somatic cellOther_somaticUBERON:0000473 testistestisUBERON:0007222 late adult stage45 yearsmaleNANANAPan troglodytesNA10X Genomics V2NextSeq 550THREE_PRIMENUCLEUS0paired2877490331302920430159854353117844.5Browse results
ERX6700426CL:0000017 spermatocyteZygotene_SpermatocytesUBERON:0000473 testistestisPtroDv:0000019 14-year-old stage (chimpanzee)14 yearsmaleNANANAPan troglodytesNA10X Genomics V2NextSeq 550THREE_PRIMENUCLEUS0paired27843800915099130201210044546919342.5Browse results
ERX6700426CL:0000000 cellNAUBERON:0000473 testistestisPtroDv:0000019 14-year-old stage (chimpanzee)14 yearsmaleNANANAPan troglodytesNA10X Genomics V2NextSeq 550THREE_PRIMENUCLEUS0paired2784380091509913020203046212595.5Browse results
ERX6700426CL:4030037 late spermatidElongated_spermatidsUBERON:0000473 testistestisPtroDv:0000019 14-year-old stage (chimpanzee)14 yearsmaleNANANAPan troglodytesNA10X Genomics V2NextSeq 550THREE_PRIMENUCLEUS0paired27843800915099130201971940542819929Browse results
ERX6700426CL:4030036 early spermatidLate_Round_spermatidsUBERON:0000473 testistestisPtroDv:0000019 14-year-old stage (chimpanzee)14 yearsmaleNANANAPan troglodytesNA10X Genomics V2NextSeq 550THREE_PRIMENUCLEUS0paired27843800915099130202005271567420019.5Browse results
ERX6700426CL:0000020 spermatogoniumDifferentiated_SpermatogoniaUBERON:0000473 testistestisPtroDv:0000019 14-year-old stage (chimpanzee)14 yearsmaleNANANAPan troglodytesNA10X Genomics V2NextSeq 550THREE_PRIMENUCLEUS0paired2784380091509913020322824423518593Browse results
ERX6700426CL:0000216 Sertoli cellSertoliUBERON:0000473 testistestisPtroDv:0000019 14-year-old stage (chimpanzee)14 yearsmaleNANANAPan troglodytesNA10X Genomics V2NextSeq 550THREE_PRIMENUCLEUS0paired2784380091509913020368327447418665Browse results
ERX6700426CL:0002371 somatic cellOther_somaticUBERON:0000473 testistestisPtroDv:0000019 14-year-old stage (chimpanzee)14 yearsmaleNANANAPan troglodytesNA10X Genomics V2NextSeq 550THREE_PRIMENUCLEUS0paired278438009150991302041798265616037.5Browse results
ERX6700426CL:0000016 male germ line stem cellUndifferentiated_SpermatogoniaUBERON:0000473 testistestisPtroDv:0000019 14-year-old stage (chimpanzee)14 yearsmaleNANANAPan troglodytesNA10X Genomics V2NextSeq 550THREE_PRIMENUCLEUS0paired2784380091509913020747495523519542Browse results
ERX6700427CL:0000016 male germ line stem cellUndifferentiated_SpermatogoniaUBERON:0000473 testistestisPtroDv:0000026 21-year-old stage (chimpanzee)21 yearsmaleNANANAPan troglodytesNA10X Genomics V2NextSeq 550THREE_PRIMENUCLEUS0paired3217185671641293420364441480718908.5Browse results
ERX6700427CL:0002371 somatic cellOther_somaticUBERON:0000473 testistestisPtroDv:0000026 21-year-old stage (chimpanzee)21 yearsmaleNANANAPan troglodytesNA10X Genomics V2NextSeq 550THREE_PRIMENUCLEUS0paired3217185671641293420216480383718313.5Browse results
ERX6700427CL:0000216 Sertoli cellSertoliUBERON:0000473 testistestisPtroDv:0000026 21-year-old stage (chimpanzee)21 yearsmaleNANANAPan troglodytesNA10X Genomics V2NextSeq 550THREE_PRIMENUCLEUS0paired3217185671641293420381252460418673.5Browse results
ERX6700427CL:0000020 spermatogoniumDifferentiated_SpermatogoniaUBERON:0000473 testistestisPtroDv:0000026 21-year-old stage (chimpanzee)21 yearsmaleNANANAPan troglodytesNA10X Genomics V2NextSeq 550THREE_PRIMENUCLEUS0paired3217185671641293420353375439518661Browse results

Showing 1 to 20 of 24 entries

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