snRNA-seq of marmoset (Callithrix jacchus) adult testis

Experiment ID:ERP132588
Technology:scRNA-Seq
Description:Single-nucleus RNA sequencing (snRNA-seq) was used to profile the transcriptome of 7,318 nuclei in marmoset adult testis. This dataset includes two samples from two 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:ERP132588 ENA
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scRNA-Seq droplet-based processed expression values per cell population in Callithrix jacchusscRNA-Seq droplet-based H5AD data per cell in Callithrix jacchus

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Showing 1 to 16 of 16 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
ERX6700543CL:0002371 somatic cellOther_somaticUBERON:0000473 testistestisUBERON:0007222 late adult stage10 yearsmaleNANANACallithrix jacchusNA10X Genomics V2NextSeq 550THREE_PRIMENUCLEUS0paired252465439123185548092215350916553Browse results
ERX6700543CL:0000216 Sertoli cellSertoliUBERON:0000473 testistestisUBERON:0007222 late adult stage10 yearsmaleNANANACallithrix jacchusNA10X Genomics V2NextSeq 550THREE_PRIMENUCLEUS0paired2524654391231855480102960384316467Browse results
ERX6700543CL:0000020 spermatogoniumDifferentiated_SpermatogoniaUBERON:0000473 testistestisUBERON:0007222 late adult stage10 yearsmaleNANANACallithrix jacchusNA10X Genomics V2NextSeq 550THREE_PRIMENUCLEUS0paired2524654391231855480250397438517804Browse results
ERX6700543CL:0000017 spermatocyteLeptotene_SpermatocytesUBERON:0000473 testistestisUBERON:0007222 late adult stage10 yearsmaleNANANACallithrix jacchusNA10X Genomics V2NextSeq 550THREE_PRIMENUCLEUS0paired2524654391231855480163849391217101.5Browse results
ERX6700543CL:4030036 early spermatidEarly_Round_spermatidsUBERON:0000473 testistestisUBERON:0007222 late adult stage10 yearsmaleNANANACallithrix jacchusNA10X Genomics V2NextSeq 550THREE_PRIMENUCLEUS0paired2524654391231855480577593519718819Browse results
ERX6700543CL:4030037 late spermatidElongated_spermatidsUBERON:0000473 testistestisUBERON:0007222 late adult stage10 yearsmaleNANANACallithrix jacchusNA10X Genomics V2NextSeq 550THREE_PRIMENUCLEUS0paired2524654391231855480491555469718549Browse results
ERX6700543CL:0000000 cellNAUBERON:0000473 testistestisUBERON:0007222 late adult stage10 yearsmaleNANANACallithrix jacchusNA10X Genomics V2NextSeq 550THREE_PRIMENUCLEUS0paired2524654391231855480290835429817678.5Browse results
ERX6700543CL:0000016 male germ line stem cellUndifferentiated_SpermatogoniaUBERON:0000473 testistestisUBERON:0007222 late adult stage10 yearsmaleNANANACallithrix jacchusNA10X Genomics V2NextSeq 550THREE_PRIMENUCLEUS0paired2524654391231855480173657457217385.5Browse results
ERX6700544CL:0000000 cellNAUBERON:0000473 testistestisUBERON:0007222 late adult stage10 yearsmaleNANANACallithrix jacchusNA10X Genomics V2NextSeq 550THREE_PRIMENUCLEUS0paired2896209871355156820416817447917921Browse results
ERX6700544CL:4030037 late spermatidElongated_spermatidsUBERON:0000473 testistestisUBERON:0007222 late adult stage10 yearsmaleNANANACallithrix jacchusNA10X Genomics V2NextSeq 550THREE_PRIMENUCLEUS0paired2896209871355156820352096429117801Browse results
ERX6700544CL:4030036 early spermatidLate_Round_spermatidsUBERON:0000473 testistestisUBERON:0007222 late adult stage10 yearsmaleNANANACallithrix jacchusNA10X Genomics V2NextSeq 550THREE_PRIMENUCLEUS0paired2896209871355156820415285461718004.5Browse results
ERX6700544CL:0000017 spermatocyteZygotene_SpermatocytesUBERON:0000473 testistestisUBERON:0007222 late adult stage10 yearsmaleNANANACallithrix jacchusNA10X Genomics V2NextSeq 550THREE_PRIMENUCLEUS0paired2896209871355156820366514480817793.5Browse results
ERX6700544CL:0000020 spermatogoniumDifferentiated_SpermatogoniaUBERON:0000473 testistestisUBERON:0007222 late adult stage10 yearsmaleNANANACallithrix jacchusNA10X Genomics V2NextSeq 550THREE_PRIMENUCLEUS0paired2896209871355156820203664423517195Browse results
ERX6700544CL:0000216 Sertoli cellSertoliUBERON:0000473 testistestisUBERON:0007222 late adult stage10 yearsmaleNANANACallithrix jacchusNA10X Genomics V2NextSeq 550THREE_PRIMENUCLEUS0paired2896209871355156820420933505417924.5Browse results
ERX6700544CL:0002371 somatic cellOther_somaticUBERON:0000473 testistestisUBERON:0007222 late adult stage10 yearsmaleNANANACallithrix jacchusNA10X Genomics V2NextSeq 550THREE_PRIMENUCLEUS0paired289620987135515682083162385716447.5Browse results
ERX6700544CL:0000016 male germ line stem cellUndifferentiated_SpermatogoniaUBERON:0000473 testistestisUBERON:0007222 late adult stage10 yearsmaleNANANACallithrix jacchusNA10X Genomics V2NextSeq 550THREE_PRIMENUCLEUS0paired2896209871355156820546812535618693Browse results

Showing 1 to 16 of 16 entries

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