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Series GSE63818 Query DataSets for GSE63818
Status Public on Jun 03, 2015
Title The Transcriptome and DNA Methylome Landscapes of Human Primordial Germ Cells
Organism Homo sapiens
Experiment type Expression profiling by high throughput sequencing
Methylation profiling by high throughput sequencing
Summary Germ cells are vital for transmitting genetic information from one generation to the next and for maintaining the continuation of species. Here, we analyze the transcriptome of human primordial germ cells (PGCs) from the migrating stage to the gonadal stage at single-cell and single-base resolutions. Human PGCs show unique transcription patterns involving the simultaneous expression of both pluripotency genes and germline-specific genes, with a subset of them displaying developmental stage-specific features. Furthermore, we analyze the DNA methylome of human PGCs and find global demethylation of their genomes. Approximately 10-11 weeks after gestation, the PGCs are nearly devoid of any DNA methylation; with only 7.8% and 6.0% of the median methylation levels in male and female PGCs, respectively. Our work paves the way toward deciphering the complex epigenetic reprogramming of the germline with the aim of restoring totipotency in fertilized oocytes.
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.
Contributor(s) Guo F, Guo H, Li L, Tang F
Citation(s) 26046443
Submission date Dec 03, 2014
Last update date May 15, 2019
Contact name Hongshan Guo
Organization name MGH cancer center
Street address 13th street
City Charlestown
State/province MA
ZIP/Postal code 02129
Country USA
Platforms (2)
GPL11154 Illumina HiSeq 2000 (Homo sapiens)
GPL16791 Illumina HiSeq 2500 (Homo sapiens)
Samples (364)
GSM1677473 M_PGC_4W_embryo3_sc1
GSM1677474 M_PGC_4W_embryo3_sc2
GSM1677475 M_PGC_4W_embryo3_sc3
BioProject PRJNA269154
SRA SRP050499

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Supplementary file Size Download File type/resource
GSE63818_Brain_5W_embryo1_methylation_calling.bed.gz 3.5 Gb (ftp)(http) BED
GSE63818_Heart_5W_embryo1_methylation_calling.bed.gz 2.8 Gb (ftp)(http) BED
GSE63818_PGC_10W_embryo1_F_rep1_methylation_calling.bed.gz 3.6 Gb (ftp)(http) BED
GSE63818_PGC_10W_embryo1_F_rep2_methylation_calling.bed.gz 3.0 Gb (ftp)(http) BED
GSE63818_PGC_10W_embryo1_M_methylation_calling.bed.gz 4.2 Gb (ftp)(http) BED
GSE63818_PGC_10W_embryo2_M_PBAT_methylation_calling.bed.gz 2.2 Gb (ftp)(http) BED
GSE63818_PGC_10W_embryo2_M_TA-PBAT_methylation_calling.bed.gz 2.4 Gb (ftp)(http) BED
GSE63818_PGC_11W_embryo1_F_methylation_calling.bed.gz 4.2 Gb (ftp)(http) BED
GSE63818_PGC_11W_embryo1_M_rep1_methylation_calling.bed.gz 3.9 Gb (ftp)(http) BED
GSE63818_PGC_11W_embryo1_M_rep2_methylation_calling.bed.gz 3.7 Gb (ftp)(http) BED
GSE63818_PGC_13W_embryo1_M_methylation_calling.bed.gz 4.1 Gb (ftp)(http) BED
GSE63818_PGC_17W_embryo1_F_methylation_calling.bed.gz 4.6 Gb (ftp)(http) BED
GSE63818_PGC_19W_embryo1_M_methylation_calling.bed.gz 3.4 Gb (ftp)(http) BED
GSE63818_PGC_19W_embryo2_M_methylation_calling.bed.gz 3.7 Gb (ftp)(http) BED
GSE63818_PGC_7W_embryo1_M_methylation_calling.bed.gz 3.6 Gb (ftp)(http) BED
GSE63818_PGC_7W_embryo2_M_methylation_calling.bed.gz 3.7 Gb (ftp)(http) BED
GSE63818_RAW.tar 30.6 Mb (http)(custom) TAR (of TXT)
GSE63818_Soma_10W_embryo1_M_methylation_calling.bed.gz 2.7 Gb (ftp)(http) BED
GSE63818_Soma_11W_embryo1_M_methylation_calling.bed.gz 3.7 Gb (ftp)(http) BED
GSE63818_Soma_17W_embryo1_F_methylation_calling.bed.gz 2.2 Gb (ftp)(http) BED
GSE63818_Soma_19W_embryo1_M_methylation_calling.bed.gz 2.5 Gb (ftp)(http) BED
GSE63818_Soma_7W_embryo1_M_methylation_calling.bed.gz 2.0 Gb (ftp)(http) BED
GSE63818_Soma_7W_embryo2_M_methylation_calling.bed.gz 1.7 Gb (ftp)(http) BED
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