Genomic profiling of human spermatogonial stem cells [scRNA-Seq]

Experiment ID:SRP094958
Technology:scRNA-Seq
Description:To better understand human spermatogonial stem cells (SSCs), we profiled their transciptome and epigenome, which revealed the mechanism how human SSCs regulates their self-renewal versus differentiation dermination, as well as how latent pluripotency is established in human SSCs. Remarkly, we discovered signaling pathways (e.g. LIF, BMP, WNT) that differentially regulated self-renewal vesus differentiation in SSCs. We also discovered that SSCs repress core pluripotent factors (Sox2, Pou5f1 and Nanog) yet activate ancillary factors (e.g. Klf4, Mbd3, Tcf3, Sall4) transcriptionally and epigenetically. Overall design: Using SSEA4 as self-renewal marker and Kit as differentiating marker, we isolated self-renewal and differentiation SSCs by magnetic antibody cell sorting (MACS). SSEA4+ or Kit+ cells were loaded into 5-10 µm integrated fluidic circuits (IFCs) using Fluidigm C1 instrument. Single cells in IFCs were lysed and total RNA was harvested for polyadenylation selection, reverse transcription and PCR amplification. Library constructions were performed according to Fluidigm Library preparation with Nextera XT protocol and sequenced on a 50-cycle single end run.
DOI:10.1016/j.stem.2017.09.003
Source:SRP094958 SRA
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scRNA-Seq full-length processed expression values per cell population in Homo sapiensscRNA-Seq full-length H5AD data per cell in Homo sapiens

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Showing 1 to 20 of 101 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
SRX2416091CL:0000089 male germ line stem cell (sensu Vertebrata)Spermatogonial Stem CellsUBERON:0000473 testistestesUBERON:0000104 life cycleNAmale(Missing)NANAHomo sapiensNASmart-seq2Illumina HiSeq 2500FULL_LENGTHCELL50single543029622500550093649382Browse results
SRX2416092CL:0000089 male germ line stem cell (sensu Vertebrata)Spermatogonial Stem CellsUBERON:0000473 testistestesUBERON:0000104 life cycleNAmale(Missing)NANAHomo sapiensNASmart-seq2Illumina HiSeq 2500FULL_LENGTHCELL50single415258316176130099249943Browse results
SRX2416093CL:0000089 male germ line stem cell (sensu Vertebrata)Spermatogonial Stem CellsUBERON:0000473 testistestesUBERON:0000104 life cycleNAmale(Missing)NANAHomo sapiensNASmart-seq2Illumina HiSeq 2500FULL_LENGTHCELL50single396201917954050079827999Browse results
SRX2416094CL:0000089 male germ line stem cell (sensu Vertebrata)Spermatogonial Stem CellsUBERON:0000473 testistestesUBERON:0000104 life cycleNAmale(Missing)NANAHomo sapiensNASmart-seq2Illumina HiSeq 2500FULL_LENGTHCELL50single35806881757590001191311949Browse results
SRX2416095CL:0000089 male germ line stem cell (sensu Vertebrata)Spermatogonial Stem CellsUBERON:0000473 testistestesUBERON:0000104 life cycleNAmale(Missing)NANAHomo sapiensNASmart-seq2Illumina HiSeq 2500FULL_LENGTHCELL50single33435651049066001189611929.5Browse results
SRX2416096CL:0000089 male germ line stem cell (sensu Vertebrata)Spermatogonial Stem CellsUBERON:0000473 testistestesUBERON:0000104 life cycleNAmale(Missing)NANAHomo sapiensNASmart-seq2Illumina HiSeq 2500FULL_LENGTHCELL50single37841542064218001129311324Browse results
SRX2416097CL:0000089 male germ line stem cell (sensu Vertebrata)Spermatogonial Stem CellsUBERON:0000473 testistestesUBERON:0000104 life cycleNAmale(Missing)NANAHomo sapiensNASmart-seq2Illumina HiSeq 2500FULL_LENGTHCELL50single3130694132188500998510003Browse results
SRX2416098CL:0000089 male germ line stem cell (sensu Vertebrata)Spermatogonial Stem CellsUBERON:0000473 testistestesUBERON:0000104 life cycleNAmale(Missing)NANAHomo sapiensNASmart-seq2Illumina HiSeq 2500FULL_LENGTHCELL50single3133900996250001266612701Browse results
SRX2416099CL:0000089 male germ line stem cell (sensu Vertebrata)Spermatogonial Stem CellsUBERON:0000473 testistestesUBERON:0000104 life cycleNAmale(Missing)NANAHomo sapiensNASmart-seq2Illumina HiSeq 2500FULL_LENGTHCELL50single29501871511572001231812363.5Browse results
SRX2416100CL:0000089 male germ line stem cell (sensu Vertebrata)Spermatogonial Stem CellsUBERON:0000473 testistestesUBERON:0000104 life cycleNAmale(Missing)NANAHomo sapiensNASmart-seq2Illumina HiSeq 2500FULL_LENGTHCELL50single4425004954475001583815905Browse results
SRX2416101CL:0000089 male germ line stem cell (sensu Vertebrata)Spermatogonial Stem CellsUBERON:0000473 testistestesUBERON:0000104 life cycleNAmale(Missing)NANAHomo sapiensNASmart-seq2Illumina HiSeq 2500FULL_LENGTHCELL50single38897141542323001273712774Browse results
SRX2416102CL:0000089 male germ line stem cell (sensu Vertebrata)Spermatogonial Stem CellsUBERON:0000473 testistestesUBERON:0000104 life cycleNAmale(Missing)NANAHomo sapiensNASmart-seq2Illumina HiSeq 2500FULL_LENGTHCELL50single40000072165570001136811387Browse results
SRX2416103CL:0000089 male germ line stem cell (sensu Vertebrata)Spermatogonial Stem CellsUBERON:0000473 testistestesUBERON:0000104 life cycleNAmale(Missing)NANAHomo sapiensNASmart-seq2Illumina HiSeq 2500FULL_LENGTHCELL50single41929912088184001213212157Browse results
SRX2416104CL:0000089 male germ line stem cell (sensu Vertebrata)Spermatogonial Stem CellsUBERON:0000473 testistestesUBERON:0000104 life cycleNAmale(Missing)NANAHomo sapiensNASmart-seq2Illumina HiSeq 2500FULL_LENGTHCELL50single43307751792090001139311424.5Browse results
SRX2416105CL:0000089 male germ line stem cell (sensu Vertebrata)Spermatogonial Stem CellsUBERON:0000473 testistestesUBERON:0000104 life cycleNAmale(Missing)NANAHomo sapiensNASmart-seq2Illumina HiSeq 2500FULL_LENGTHCELL50single34158711469475001139311421.5Browse results
SRX2416106CL:0000089 male germ line stem cell (sensu Vertebrata)Spermatogonial Stem CellsUBERON:0000473 testistestesUBERON:0000104 life cycleNAmale(Missing)NANAHomo sapiensNASmart-seq2Illumina HiSeq 2500FULL_LENGTHCELL50single263149912824850097719814Browse results
SRX2416107CL:0000089 male germ line stem cell (sensu Vertebrata)Spermatogonial Stem CellsUBERON:0000473 testistestesUBERON:0000104 life cycleNAmale(Missing)NANAHomo sapiensNASmart-seq2Illumina HiSeq 2500FULL_LENGTHCELL50single2558473977597001264912680.5Browse results
SRX2416108CL:0000089 male germ line stem cell (sensu Vertebrata)Spermatogonial Stem CellsUBERON:0000473 testistestesUBERON:0000104 life cycleNAmale(Missing)NANAHomo sapiensNASmart-seq2Illumina HiSeq 2500FULL_LENGTHCELL50single33629472076765001074310786Browse results
SRX2416109CL:0000089 male germ line stem cell (sensu Vertebrata)Spermatogonial Stem CellsUBERON:0000473 testistestesUBERON:0000104 life cycleNAmale(Missing)NANAHomo sapiensNASmart-seq2Illumina HiSeq 2500FULL_LENGTHCELL50single38457041394520001240212429.5Browse results
SRX2416110CL:0000089 male germ line stem cell (sensu Vertebrata)Spermatogonial Stem CellsUBERON:0000473 testistestesUBERON:0000104 life cycleNAmale(Missing)NANAHomo sapiensNASmart-seq2Illumina HiSeq 2500FULL_LENGTHCELL50single43348232017344001205112078.5Browse results

Showing 1 to 20 of 101 entries

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