The landscape of accessible chromatin in mouse and human primordial germ cells (PGC) [human DNase-Hypersensitivity]
Ontology highlight
ABSTRACT:
ORGANISM(S): Homo sapiens
PROVIDER: GSE109768 | GEO | 2018/06/26
REPOSITORIES: GEO
Similar Datasets
Project description:We mapped and systematically annotated the cis-regulatory elements in moue human primordial germ cells (PGCs).
2018-06-26 | GSE109767 | GEO
Project description:We mapped and systematically annotated the cis-regulatory elements in moue human primordial germ cells (PGCs).
2018-06-26 | GSE109769 | GEO
Project description:Purpose: To identify molecular pathways underlying epigenetic reprogramming in early germ cell precursors, we examined global gene expression of wild type primordial germ cells using mRNA sequencing. Methods: Given the limited number of PGCs collected from E9.5 to E13.5 (ranging from 300 to 5000), we used a low-input RNA sequencing method, Smart-Seq. RNA libraries were pooled and sequenced by Illumina Hiseq. Results: We generated >22 million uniquely mapped reads per sample and identified >10 thousand transcripts per genotype (RPKM>0.1). Hierarchical clustering and correlation analysis on gene expression indicates samples were clearly separated according to their genotypes with Spearman correlation coefficient of 0.98/0.99 within biological replicates. Compared with E9.5 PGCs, 479 genes were significantly up-regulated and 248 genes were down-regulated in E11.5 PGCs. When compared with E11.5 PGCs, male E13.5 PGCs had 362 up-regulated, and 239 down-regulated genes, whereas female E13.5 PGCs had 1163 up-regulated and 333 down-regulated genes. Overall, the number of up-regulated genes was greater than that of the down-regulated genes in every comparison, suggesting that gene expression is generally activated during PGC reprogramming. mRNA profiles of primordial germ cells derived from developmental embryos stages (E9.5, E11.5 and E13.5) were generated by deep sequencing, in duplicates (E9.5 and E11.5) or triplicates (E13.5f and E13.5m), using Illumina Hiseq.
2012-10-31 | E-GEOD-41908 | biostudies-arrayexpress
Project description:The landscape of accessible chromatin in mouse and human primordial germ cells (PGC) [human DNase-Hypersensitivity]
| PRJNA431995 | ENA
Project description:The landscape of accessible chromatin in mouse and human primordial germ cells (PGC) [mouse DNase-Hypersensitivity]
| PRJNA431996 | ENA
Project description:Purpose: To identify molecular pathways underlying epigenetic reprogramming in early germ cell precursors, we examined global gene expression of wild type primordial germ cells using mRNA sequencing. Methods: Given the limited number of PGCs collected from E9.5 to E13.5 (ranging from 300 to 5000), we used a low-input RNA sequencing method, Smart-Seq. RNA libraries were pooled and sequenced by Illumina Hiseq. Results: We generated >22 million uniquely mapped reads per sample and identified >10 thousand transcripts per genotype (RPKM>0.1). Hierarchical clustering and correlation analysis on gene expression indicates samples were clearly separated according to their genotypes with Spearman correlation coefficient of 0.98/0.99 within biological replicates. Compared with E9.5 PGCs, 479 genes were significantly up-regulated and 248 genes were down-regulated in E11.5 PGCs. When compared with E11.5 PGCs, male E13.5 PGCs had 362 up-regulated, and 239 down-regulated genes, whereas female E13.5 PGCs had 1163 up-regulated and 333 down-regulated genes. Overall, the number of up-regulated genes was greater than that of the down-regulated genes in every comparison, suggesting that gene expression is generally activated during PGC reprogramming.
2012-10-31 | GSE41908 | GEO
Project description:In poultry, in vitro derived primordial germ cells (PGCs) represent an important tool for management of genetic resources. However, several studies have highlighted sexual differences exhibited by PGCs through in vitro steps, which may compromise their reproductive capacities. To understand this phenomenon, we compared the proteome of pregonadal chicken male (ZZ) and female (ZW) PGCs expanded in vitro by quantitative proteomic analysis using a GeLC-MS/MS strategy. The proteins found to be differentially abundant in chicken male and female PGCs indicated their early sexual identity. Many of the proteins up-accumulated in male PGCs were encoded by genes strongly enriched in the sexual chromosome Z. This suggests that the known lack of dosage compensation of the transcription of Z-linked genes between sexes persists at protein level in PGCs, and that this may be a key factor of their autonomous sex differentiation. Male and female PGCs up-accumulated protein sets were associated with differential biological processes, and contained proteins biologically relevant for male and female germ cell development respectively. This study presents first evidence on early predetermined sex specific cell fate of chicken PGCs that will help to understand their sexual physiological specificities and enable more precise sex-specific adaptation of in vitro culture conditions.
2021-11-03 | PXD022452 | Pride
Project description:Purpose: To investigate the effect of Tet1 depletion on global DNA methylation, we performed whole-genome bisulfite sequencing (WGBS). Methods: Starting with as little as 1400-5251 manually micro-dissected PGCs, we used an ultra-low input method, Tn5mC-seq. Results: We generated 945 million reads for Tet1Gt/Gt PGCs and 302 million reads for wild-type PGCs. We obtained 14-16 million CpG sites per genotype at 1.76-2.66x genome coverage, which enables a comprehensive view of genome-wide DNA methylation patterns in E13.5 PGCs. PGCs are almost completely unmethylated genome-wide. Loss of Tet1 led to a subtle increase of methylation level in various genomic elements including promoters, exons, introns and repetitive elements in Tet1Gt/Gt PGCs (p<0.01). Local analysis identified 4,337 differentially methylated regions (DMRs) between Tet1-/- PGCs and wild-type cells. These DMRs are associated with 5,261 genes, among which 271 genes also exhibited differential gene expression and enriched for the cell cycle pathway (FDR=0.02). Conclusions: This result revealed that demethylation of certain set of cell cycle genes is largely abolished in the Tet1-/- PGCs. Genome-wide methylation profiles of primordial germ cells derived from the wild type (WT) and Tet1-null female embryos at E13.5 were generated by whole genome bisulfite sequencing using Illumina Hiseq.
2012-11-20 | E-GEOD-41912 | biostudies-arrayexpress
Project description:Human germ cell development is a highly regulated process beginning soon after embryo implantation with the specification of primordial germ cells (PGCs) and ending in adulthood with the differentiation of gametes. Here, we show that fibroblast growth factor receptor 3 (FGFR3) is expressed by human PGCs during the first and second trimester, becoming repressed as PGCs differentiate into primordial oocytes. Using fluorescence activated cell sorting (FACS) with antibodies that recognize FGFR3 followed by single cell RNA sequencing, we show that isolating FGFR3-positive cells enriches for human PGCs. Taken together, FGFR3 could be used in future studies as a strategy to identify maturing hPGCs.
2022-05-19 | GSE193474 | GEO
Project description:Primordial germ cells (PGCs), the embryonic precursors of eggs and sperm, are a unique model for identifying and studying regulatory mechanisms in singly migrating cells. From their time of specification to eventual colonization of the gonad, mouse PGCs traverse through and interact with many different cell types, including epithelial cells and mesenchymal tissues. Work in drosophila and zebrafish have identified many genes and signaling pathways involved in PGC migration, but little is known about this process in mammals. We have generated a point mutation in the Ror2 gene that we know disrupts primordial germ cell migration in the developing mouse embryo. We used microarray analysis to determine if this defect is mediated through genome-wide or pathway-specific transcriptional changes. We analyzed primordial germ cells (PGCs) from 4 wild-type (WT) and 4 Ror2Y324C/Y324C mutant embryos using Oct4-DPE-EGFP. PGCs were collected during their active migratory state at embryonic day 9.5 (somite range 20-25).
2014-08-08 | E-GEOD-60179 | biostudies-arrayexpress