The Human Testis Cell Atlas via Single-cell RNA-seq (Healthy men scRNA-seq data set)

Experiment ID:SRP135999
Technology:scRNA-Seq
Description:Overall design: We isolated single testicular cell from three healthy men of peak reproductive age. Two technical replicates were performed for each individual.
DOI:10.1038/s41422-018-0099-2
Source:SRP135999 SRA
Download:
scRNA-Seq droplet-based processed expression values per cell population in Homo sapiensscRNA-Seq droplet-based H5AD data per cell in Homo sapiens

List of assays

Show

entries

Showing 1 to 20 of 60 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
SRX3815586CL:0000656 primary spermatocyteLate primary S'cytesUBERON:0000473 testistestisUBERON:0000113 post-juvenilehealthy men of peak reproductive agemaleNANANAHomo sapiensNA10X Genomics V2Illumina HiSeq 2500THREE_PRIMECELL0paired2977453882326655770382081215824830Browse results
SRX3815586CL:0000019 spermSpermUBERON:0000473 testistestisUBERON:0000113 post-juvenilehealthy men of peak reproductive agemaleNANANAHomo sapiensNA10X Genomics V2Illumina HiSeq 2500THREE_PRIMECELL0paired29774538823266557701316662146226067.5Browse results
SRX3815586CL:0000020 spermatogoniumDifferentiating S'goniaUBERON:0000473 testistestisUBERON:0000113 post-juvenilehealthy men of peak reproductive agemaleNANANAHomo sapiensNA10X Genomics V2Illumina HiSeq 2500THREE_PRIMECELL0paired2977453882326655770875181314826114Browse results
SRX3815586CL:0002481 peritubular myoid cellmyoid cellUBERON:0000473 testistestisUBERON:0000113 post-juvenilehealthy men of peak reproductive agemaleNANANAHomo sapiensNA10X Genomics V2Illumina HiSeq 2500THREE_PRIMECELL0paired2977453882326655770727109147925068Browse results
SRX3815586CL:0000178 Leydig cellLeydig cellUBERON:0000473 testistestisUBERON:0000113 post-juvenilehealthy men of peak reproductive agemaleNANANAHomo sapiensNA10X Genomics V2Illumina HiSeq 2500THREE_PRIMECELL0paired2977453882326655770714201130524982Browse results
SRX3815586CL:0000235 macrophageMacrophagesUBERON:0000473 testistestisUBERON:0000113 post-juvenilehealthy men of peak reproductive agemaleNANANAHomo sapiensNA10X Genomics V2Illumina HiSeq 2500THREE_PRIMECELL0paired2977453882326655770473051108224228.5Browse results
SRX3815586CL:0000115 endothelial cellEndothelial CellsUBERON:0000473 testistestisUBERON:0000113 post-juvenilehealthy men of peak reproductive agemaleNANANAHomo sapiensNA10X Genomics V2Illumina HiSeq 2500THREE_PRIMECELL0paired29774538823266557701481242270825760.5Browse results
SRX3815586CL:0000216 Sertoli cellSertoli CellsUBERON:0000473 testistestisUBERON:0000113 post-juvenilehealthy men of peak reproductive agemaleNANANAHomo sapiensNA10X Genomics V2Illumina HiSeq 2500THREE_PRIMECELL0paired29774538823266557704059329320813Browse results
SRX3815586CL:0000089 male germ line stem cell (sensu Vertebrata)SSCsUBERON:0000473 testistestisUBERON:0000113 post-juvenilehealthy men of peak reproductive agemaleNANANAHomo sapiensNA10X Genomics V2Illumina HiSeq 2500THREE_PRIMECELL0paired2977453882326655770702736327726269.5Browse results
SRX3815586CL:0000018 spermatidRound S'tidsUBERON:0000473 testistestisUBERON:0000113 post-juvenilehealthy men of peak reproductive agemaleNANANAHomo sapiensNA10X Genomics V2Illumina HiSeq 2500THREE_PRIMECELL0paired2977453882326655770446227206025724.5Browse results
SRX3815587CL:0002481 peritubular myoid cellmyoid cellUBERON:0000473 testistestisUBERON:0000113 post-juvenilehealthy men of peak reproductive agemaleNANANAHomo sapiensNA10X Genomics V2Illumina HiSeq 2500THREE_PRIMECELL0paired300255669211720713020853273223766.5Browse results
SRX3815587CL:0000019 spermSpermUBERON:0000473 testistestisUBERON:0000113 post-juvenilehealthy men of peak reproductive agemaleNANANAHomo sapiensNA10X Genomics V2Illumina HiSeq 2500THREE_PRIMECELL0paired30025566921172071302482739195727574.5Browse results
SRX3815587CL:0000020 spermatogoniumDifferentiating S'goniaUBERON:0000473 testistestisUBERON:0000113 post-juvenilehealthy men of peak reproductive agemaleNANANAHomo sapiensNA10X Genomics V2Illumina HiSeq 2500THREE_PRIMECELL0paired30025566921172071301495880379426828Browse results
SRX3815587CL:0000178 Leydig cellLeydig cellUBERON:0000473 testistestisUBERON:0000113 post-juvenilehealthy men of peak reproductive agemaleNANANAHomo sapiensNA10X Genomics V2Illumina HiSeq 2500THREE_PRIMECELL0paired3002556692117207130773043137025113.5Browse results
SRX3815587CL:0000235 macrophageMacrophagesUBERON:0000473 testistestisUBERON:0000113 post-juvenilehealthy men of peak reproductive agemaleNANANAHomo sapiensNA10X Genomics V2Illumina HiSeq 2500THREE_PRIMECELL0paired3002556692117207130469568102523997Browse results
SRX3815587CL:0000115 endothelial cellEndothelial CellsUBERON:0000473 testistestisUBERON:0000113 post-juvenilehealthy men of peak reproductive agemaleNANANAHomo sapiensNA10X Genomics V2Illumina HiSeq 2500THREE_PRIMECELL0paired3002556692117207130402243116924435.5Browse results
SRX3815587CL:0000089 male germ line stem cell (sensu Vertebrata)SSCsUBERON:0000473 testistestisUBERON:0000113 post-juvenilehealthy men of peak reproductive agemaleNANANAHomo sapiensNA10X Genomics V2Illumina HiSeq 2500THREE_PRIMECELL0paired30025566921172071301502928423027396.5Browse results
SRX3815587CL:0000018 spermatidRound S'tidsUBERON:0000473 testistestisUBERON:0000113 post-juvenilehealthy men of peak reproductive agemaleNANANAHomo sapiensNA10X Genomics V2Illumina HiSeq 2500THREE_PRIMECELL0paired3002556692117207130840980298226788.5Browse results
SRX3815587CL:0000656 primary spermatocyteEarly primary S'cytesUBERON:0000473 testistestisUBERON:0000113 post-juvenilehealthy men of peak reproductive agemaleNANANAHomo sapiensNA10X Genomics V2Illumina HiSeq 2500THREE_PRIMECELL0paired30025566921172071301901455429127172.5Browse results
SRX3815587CL:0000216 Sertoli cellSertoli CellsUBERON:0000473 testistestisUBERON:0000113 post-juvenilehealthy men of peak reproductive agemaleNANANAHomo sapiensNA10X Genomics V2Illumina HiSeq 2500THREE_PRIMECELL0paired300255669211720713011096260422654.5Browse results

Showing 1 to 20 of 60 entries

This website requires cookies, and limited processing of your personal data in order to function. By using the site you are agreeing to this as outlined in our privacy notice.
Do not show this banner again