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Series GSE140021 Query DataSets for GSE140021
Status Public on Dec 29, 2019
Title Human Primordial Germ Cells are Specified from Lineage Primed Progenitors
Organism Homo sapiens
Experiment type Expression profiling by high throughput sequencing
Summary In vitro gametogenesis is the process of making germline cells from human pluripotent stem cells. The foundation of this model is the quality of the first progenitors called primordial germ cells (PGCs), which in vivo are specified during the peri-implantation window of human development. Here, we show using human embryo attachment culture that hPGC specification begins at day 12 post fertilization. Using single cell RNA-sequencing of hPGC-like cells (hPGCLCs) differentiated from pluripotent stem cells we discovered that hPGCLC specification involves resetting pluripotency towards a transitional state with shared characteristics between naïve and primed pluripotency followed by differentiation into lineage primed TFAP2A+ progenitors. Applying the germline trajectory to TFAP2C mutants reveals that TFAP2C functions in the TFAP2A+ progenitors upstream of PRDM1 to regulate the expression of SOX17. This serves to protect hPGCLCs from crossing the Weismann’s barrier to adopt somatic cell fates and therefore is an essential mechanism for successfully initiating in vitro gametogenesis.
Overall design We applied single cell RNA-sequencing (scRNA-seq) with 10x Genomics to hESCs, iMeLCs and aggregate cells at D1-4 with two biological replicates in UCLA1 and UCLA2 cell lines, respectively. In total, we sequenced 85,309 cells with high quality to uncover the germline trajectory and explored the progenitors involved in establishing germline cell fate. Moreover, we performed scRNA-seq of TFAP2C -/- cells at 6 time points (hESCs, iMeLCs, aggregates at D1, D2-D4, 19,808 cells sequenced) and compared this to the single cells from UCLA1 wild type cells which is the genetic background used to make TFAP2C mutant.

We applied ChIP-seq to hESCs, iMeLCs, and day 4 aggregates using anti-TFAP2C antibodies and to ITGA6/EPCAM-isolated day 4 hPGCLCs using anti-H3K27ac antibodies. Two biological replicates were included for each sample.
Contributor(s) Clark A, Sun N
Citation(s) 31875561
Submission date Nov 06, 2019
Last update date Jan 15, 2020
Contact name Manolis Kellis
Organization name MIT
Department EECS
Street address 32 Vassar St. D524
City Cambridge
State/province MA
ZIP/Postal code 02139
Country USA
Platforms (2)
GPL20301 Illumina HiSeq 4000 (Homo sapiens)
GPL24676 Illumina NovaSeq 6000 (Homo sapiens)
Samples (44)
GSM4202923 ucla1.batch1.PGCLCd1
GSM4202924 ucla1.batch1.PGCLCd2
GSM4202925 ucla1.batch1.PGCLCd3
BioProject PRJNA593526
SRA SRP234711

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE140021_RAW.tar 3.8 Gb (http)(custom) TAR (of BW, TXT)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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