snRNA-seq of opossum (Monodelphis domestica) adult testis

Experiment ID:ERP132579
Technology:scRNA-Seq
Description:Single-nucleus RNA sequencing (snRNA-seq) was used to profile the transcriptome of 9,926 nuclei in opossum 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:ERP132579 ENA
Download:
scRNA-Seq droplet-based processed expression values per cell population in Monodelphis domesticascRNA-Seq droplet-based H5AD data per cell in Monodelphis domestica

List of assays

Show

entries

Showing 1 to 18 of 18 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
ERX6700414CL:0000017 spermatocyteSpermatocytesUBERON:0000473 testistestisUBERON:0000113 post-juvenileadultmaleNANANAMonodelphis domesticaNA10X Genomics V2NextSeq 550THREE_PRIMENUCLEUS0paired3015366701086213290713944406117731Browse results
ERX6700414CL:4030036 early spermatidRound_spermatidsUBERON:0000473 testistestisUBERON:0000113 post-juvenileadultmaleNANANAMonodelphis domesticaNA10X Genomics V2NextSeq 550THREE_PRIMENUCLEUS0paired3015366701086213290475520350117236.5Browse results
ERX6700414CL:4030037 late spermatidElongated_spermatidsUBERON:0000473 testistestisUBERON:0000113 post-juvenileadultmaleNANANAMonodelphis domesticaNA10X Genomics V2NextSeq 550THREE_PRIMENUCLEUS0paired301536670108621329080536157114762Browse results
ERX6700414CL:0002371 somatic cellOther_somaticUBERON:0000473 testistestisUBERON:0000113 post-juvenileadultmaleNANANAMonodelphis domesticaNA10X Genomics V2NextSeq 550THREE_PRIMENUCLEUS0paired3015366701086213290804671367418170Browse results
ERX6700414CL:0000216 Sertoli cellSertoliUBERON:0000473 testistestisUBERON:0000113 post-juvenileadultmaleNANANAMonodelphis domesticaNA10X Genomics V2NextSeq 550THREE_PRIMENUCLEUS0paired3015366701086213290589778418317713.5Browse results
ERX6700414CL:0000020 spermatogoniumSpermatogoniaUBERON:0000473 testistestisUBERON:0000113 post-juvenileadultmaleNANANAMonodelphis domesticaNA10X Genomics V2NextSeq 550THREE_PRIMENUCLEUS0paired3015366701086213290107002237915763.5Browse results
ERX6700415CL:4030037 late spermatidElongated_spermatidsUBERON:0000473 testistestisMdomDv:0000019 15-month-old stage (opossum)15.5 monthsmaleNANANAMonodelphis domesticaNA10X Genomics V2NextSeq 550THREE_PRIMENUCLEUS0paired2750516351059202750232173277816297Browse results
ERX6700415CL:0000216 Sertoli cellSertoliUBERON:0000473 testistestisMdomDv:0000019 15-month-old stage (opossum)15.5 monthsmaleNANANAMonodelphis domesticaNA10X Genomics V2NextSeq 550THREE_PRIMENUCLEUS0paired2750516351059202750366792400517063.5Browse results
ERX6700415CL:0002371 somatic cellOther_somaticUBERON:0000473 testistestisMdomDv:0000019 15-month-old stage (opossum)15.5 monthsmaleNANANAMonodelphis domesticaNA10X Genomics V2NextSeq 550THREE_PRIMENUCLEUS0paired2750516351059202750589190372118217Browse results
ERX6700415CL:4030036 early spermatidRound_spermatidsUBERON:0000473 testistestisMdomDv:0000019 15-month-old stage (opossum)15.5 monthsmaleNANANAMonodelphis domesticaNA10X Genomics V2NextSeq 550THREE_PRIMENUCLEUS0paired2750516351059202750877871462518351Browse results
ERX6700415CL:0000017 spermatocyteSpermatocytesUBERON:0000473 testistestisMdomDv:0000019 15-month-old stage (opossum)15.5 monthsmaleNANANAMonodelphis domesticaNA10X Genomics V2NextSeq 550THREE_PRIMENUCLEUS0paired2750516351059202750807954484318264.5Browse results
ERX6700415CL:0000020 spermatogoniumSpermatogoniaUBERON:0000473 testistestisMdomDv:0000019 15-month-old stage (opossum)15.5 monthsmaleNANANAMonodelphis domesticaNA10X Genomics V2NextSeq 550THREE_PRIMENUCLEUS0paired2750516351059202750118369267816112Browse results
ERX6700416CL:0000020 spermatogoniumSpermatogoniaUBERON:0000473 testistestisUBERON:0000113 post-juvenileadultmaleNANANAMonodelphis domesticaNA10X Genomics V2NextSeq 550THREE_PRIMENUCLEUS0paired3578887111429720070143114239116519.5Browse results
ERX6700416CL:0000017 spermatocyteSpermatocytesUBERON:0000473 testistestisUBERON:0000113 post-juvenileadultmaleNANANAMonodelphis domesticaNA10X Genomics V2NextSeq 550THREE_PRIMENUCLEUS0paired3578887111429720070743071447117993Browse results
ERX6700416CL:4030036 early spermatidRound_spermatidsUBERON:0000473 testistestisUBERON:0000113 post-juvenileadultmaleNANANAMonodelphis domesticaNA10X Genomics V2NextSeq 550THREE_PRIMENUCLEUS0paired35788871114297200701243040456218615.5Browse results
ERX6700416CL:4030037 late spermatidElongated_spermatidsUBERON:0000473 testistestisUBERON:0000113 post-juvenileadultmaleNANANAMonodelphis domesticaNA10X Genomics V2NextSeq 550THREE_PRIMENUCLEUS0paired3578887111429720070516927304317210Browse results
ERX6700416CL:0002371 somatic cellOther_somaticUBERON:0000473 testistestisUBERON:0000113 post-juvenileadultmaleNANANAMonodelphis domesticaNA10X Genomics V2NextSeq 550THREE_PRIMENUCLEUS0paired3578887111429720070416810278517680.5Browse results
ERX6700416CL:0000216 Sertoli cellSertoliUBERON:0000473 testistestisUBERON:0000113 post-juvenileadultmaleNANANAMonodelphis domesticaNA10X Genomics V2NextSeq 550THREE_PRIMENUCLEUS0paired3578887111429720070665359409917850.5Browse results

Showing 1 to 18 of 18 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