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Series GSE144500 Query DataSets for GSE144500
Status Public on Jan 20, 2021
Title VENTX gene expression marks a subset of human primordial germ cells
Organism Homo sapiens
Experiment type Expression profiling by high throughput sequencing
Summary The Ventx genes are a family of non-clustered homeobox transcription factors that confer a ventral phenotype on mesodermal cells in the Xenopus laevis embryo. Ventx genes are conserved in vertebrates, although they have been lost in rodents. We evaluated the expression of VENTX during differentiation of a human pluripotent stem cell (hPSC) line in which a GFP reporter marked the expression of VENTX (VENTXGFP/w), discovering that VENTX was expressed in a subset of early primordial germ cell-like cells (PGCLCs). We generated a dual reporter hPSC line in which mCHERRY marked the pluripotency gene OCT4 (VENTXGFP/wOCT42AmCHERRY/w), and further modified this to also create a VENTX knock out line by deleting the VENTX homeodomain (VENTXGFP/-OCT42AmCHERRY/w).
Transcriptional profiling experiments revealed two populations of PGCLCs, those that co expressed VENTX and OCT4 (GFP+mCHERRY+) and those that were VENTX-OCT4+ (GFP-mCHERRY+). Our analyses showed that VENTX+ and VENTX- PGCLCs clustered together, and also failed to reveal transcriptional consequences of VENTX deletion on commitment to PGCLCs. Evaluation of public databases confirmed expression of VENTX in populations of PGCLCs derived by others and in primary human embryonic germ cell samples. These results identify VENTX as a new PGC-associated gene in humans, however it does not seem to be required for initial human PGC commitment.
 
Overall design Undiferentiated hESCs and PGC-like cells derived from hESC. Biological replicates vary from 3 to 5 (refer to number at the end of sample title). Study performed in VENTX^GFP/w OCT4^mCHERRY/w (abreviated to VO) and VENTX^GFP/- OCT4^mCHERRY/w (abreviated to KO) cell lines.

 
Contributor(s) Leitoguinho AC, Elefanty AG
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Submission date Jan 29, 2020
Last update date Jan 23, 2021
Contact name Ana Rita Leitoguinho
E-mail(s) anaritacle@gmail.com
Phone 0426027559
Organization name Murdoch Children's Research Institute
Department Cell Biology
Lab Blood development
Street address 50 Flemington road
City Melbourne
State/province VIC
ZIP/Postal code 3052
Country Australia
 
Platforms (1)
GPL21697 NextSeq 550 (Homo sapiens)
Samples (44)
GSM4289699 hESC-KO-1
GSM4289700 hESC-KO-2
GSM4289701 hESC-KO-3
Relations
BioProject PRJNA603803
SRA SRP245922

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
GSE144500_RAW.tar 126.2 Mb (http)(custom) TAR (of TXT)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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