The Transcriptome and DNA Methylome Landscapes of Human Primordial Germ Cells

Experiment ID:SRP050499
Technology:scRNA-Seq
Description:Overall design: In total, we analyzed the transcriptomes of 233 individual male and female human PGCs from 15 embryos at between 4 and 19 weeks of gestation as well as 86 neighboring somatic cells from 13 of these embryos using a single-cell RNA-Seq method that we developed. Furthermore, we analyzed the DNA methylomes of both male and female human gonadal PGCs as well as the neighboring somatic cells of eleven of these embryos at between 7 and 19 weeks of gestation using whole-genome bisulfite sequencing (WGBS). In total, we generated 1.3 billion 100 bp paired-end reads for transcriptome analyses and 4.1 billion 100 bp or 150 bp paired-end reads for DNA methylome analyses.
Cell count:57
DOI:10.1016/j.cell.2015.05.015
Source:SRP050499  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 57 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
SRX1021339CL:0000670 primordial germ cellPrimordial Germ CellsUBERON:0000991 gonadfetal gonadHsapDv:0000055 18th week post-fertilization stage (human)19 week gestationmale(Missing)NANAHomo sapiensNASmart-seq2Illumina HiSeq 2500FULL_LENGTHCELL101paired222785417758300078767885Browse results
SRX1021340CL:0000670 primordial germ cellPrimordial Germ CellsUBERON:0000991 gonadfetal gonadHsapDv:0000055 18th week post-fertilization stage (human)19 week gestationmale(Missing)NANAHomo sapiensNASmart-seq2Illumina HiSeq 2500FULL_LENGTHCELL101paired187066915034480084518467Browse results
SRX1021341CL:0000670 primordial germ cellPrimordial Germ CellsUBERON:0000991 gonadfetal gonadHsapDv:0000055 18th week post-fertilization stage (human)19 week gestationmale(Missing)NANAHomo sapiensNASmart-seq2Illumina HiSeq 2500FULL_LENGTHCELL101paired294125123335780082388256.5Browse results
SRX1021342CL:0000670 primordial germ cellPrimordial Germ CellsUBERON:0000991 gonadfetal gonadHsapDv:0000055 18th week post-fertilization stage (human)19 week gestationmale(Missing)NANAHomo sapiensNASmart-seq2Illumina HiSeq 2500FULL_LENGTHCELL101paired311050824051600075347542.5Browse results
SRX1021343CL:0000670 primordial germ cellPrimordial Germ CellsUBERON:0000991 gonadfetal gonadHsapDv:0000055 18th week post-fertilization stage (human)19 week gestationmale(Missing)NANAHomo sapiensNASmart-seq2Illumina HiSeq 2500FULL_LENGTHCELL101paired213808516692850077687783Browse results
SRX1021344CL:0000670 primordial germ cellPrimordial Germ CellsUBERON:0000991 gonadfetal gonadHsapDv:0000055 18th week post-fertilization stage (human)19 week gestationmale(Missing)NANAHomo sapiensNASmart-seq2Illumina HiSeq 2500FULL_LENGTHCELL101paired197393915232040080468056Browse results
SRX1021345CL:0000670 primordial germ cellPrimordial Germ CellsUBERON:0000991 gonadfetal gonadHsapDv:0000055 18th week post-fertilization stage (human)19 week gestationmale(Missing)NANAHomo sapiensNASmart-seq2Illumina HiSeq 2500FULL_LENGTHCELL101paired337033927475590082788287.5Browse results
SRX1021346CL:0000670 primordial germ cellPrimordial Germ CellsUBERON:0000991 gonadfetal gonadHsapDv:0000055 18th week post-fertilization stage (human)19 week gestationmale(Missing)NANAHomo sapiensNASmart-seq2Illumina HiSeq 2500FULL_LENGTHCELL101paired253757019810040084618482.5Browse results
SRX1021347CL:0000670 primordial germ cellPrimordial Germ CellsUBERON:0000991 gonadfetal gonadHsapDv:0000055 18th week post-fertilization stage (human)19 week gestationmale(Missing)NANAHomo sapiensNASmart-seq2Illumina HiSeq 2500FULL_LENGTHCELL101paired172623614026340087288735Browse results
SRX1021348CL:0000670 primordial germ cellPrimordial Germ CellsUBERON:0000991 gonadfetal gonadHsapDv:0000055 18th week post-fertilization stage (human)19 week gestationmale(Missing)NANAHomo sapiensNASmart-seq2Illumina HiSeq 2500FULL_LENGTHCELL101paired235100318013020068166824Browse results
SRX1021349CL:0000670 primordial germ cellPrimordial Germ CellsUBERON:0000991 gonadfetal gonadHsapDv:0000055 18th week post-fertilization stage (human)19 week gestationmale(Missing)NANAHomo sapiensNASmart-seq2Illumina HiSeq 2500FULL_LENGTHCELL101paired235134819097570082618276Browse results
SRX1021350CL:0000670 primordial germ cellPrimordial Germ CellsUBERON:0000991 gonadfetal gonadHsapDv:0000055 18th week post-fertilization stage (human)19 week gestationmale(Missing)NANAHomo sapiensNASmart-seq2Illumina HiSeq 2500FULL_LENGTHCELL101paired233761618330650088178832Browse results
SRX1021351CL:0000670 primordial germ cellPrimordial Germ CellsUBERON:0000991 gonadfetal gonadHsapDv:0000055 18th week post-fertilization stage (human)19 week gestationmale(Missing)NANAHomo sapiensNASmart-seq2Illumina HiSeq 2500FULL_LENGTHCELL101paired406196131169500091079141.5Browse results
SRX1021352CL:0000670 primordial germ cellPrimordial Germ CellsUBERON:0000991 gonadfetal gonadHsapDv:0000055 18th week post-fertilization stage (human)19 week gestationmale(Missing)NANAHomo sapiensNASmart-seq2Illumina HiSeq 2500FULL_LENGTHCELL101paired513575040786760089008916Browse results
SRX1021353CL:0000670 primordial germ cellPrimordial Germ CellsUBERON:0000991 gonadfetal gonadHsapDv:0000055 18th week post-fertilization stage (human)19 week gestationmale(Missing)NANAHomo sapiensNASmart-seq2Illumina HiSeq 2500FULL_LENGTHCELL101paired451456436151990091149150.5Browse results
SRX1021354CL:0000670 primordial germ cellPrimordial Germ CellsUBERON:0000991 gonadfetal gonadHsapDv:0000055 18th week post-fertilization stage (human)19 week gestationmale(Missing)NANAHomo sapiensNASmart-seq2Illumina HiSeq 2500FULL_LENGTHCELL101paired443104333787880089949004.5Browse results
SRX1021355CL:0000670 primordial germ cellPrimordial Germ CellsUBERON:0000991 gonadfetal gonadHsapDv:0000055 18th week post-fertilization stage (human)19 week gestationmale(Missing)NANAHomo sapiensNASmart-seq2Illumina HiSeq 2500FULL_LENGTHCELL101paired438163833925670099049934.5Browse results
SRX1021356CL:0000670 primordial germ cellPrimordial Germ CellsUBERON:0000991 gonadfetal gonadHsapDv:0000055 18th week post-fertilization stage (human)19 week gestationmale(Missing)NANAHomo sapiensNASmart-seq2Illumina HiSeq 2500FULL_LENGTHCELL101paired51535883576519002817829609Browse results
SRX1021357CL:0000670 primordial germ cellPrimordial Germ CellsUBERON:0000991 gonadfetal gonadHsapDv:0000055 18th week post-fertilization stage (human)19 week gestationmale(Missing)NANAHomo sapiensNASmart-seq2Illumina HiSeq 2500FULL_LENGTHCELL101paired404840929194960084258439Browse results
SRX1021358CL:0000670 primordial germ cellPrimordial Germ CellsUBERON:0000991 gonadfetal gonadHsapDv:0000055 18th week post-fertilization stage (human)19 week gestationmale(Missing)NANAHomo sapiensNASmart-seq2Illumina HiSeq 2500FULL_LENGTHCELL101paired548391046075420096599679.5Browse results

Showing 1 to 20 of 57 entries