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Series GSE117473 Query DataSets for GSE117473
Status Public on Oct 01, 2018
Title Tracing the transitions from pluripotency to germ cell fate with CRISPR screening
Organisms Mus musculus; unidentified plasmid
Experiment type Expression profiling by high throughput sequencing
Summary Early mammalian development entails a series of cell fate transitions that includes transit through naïve pluripotency to post-implantation epiblast. This can subsequently give rise to primordial germ cells (PGC), the founding population of the germline lineage. To investigate the gene regulatory networks that control these critical cell fate decisions, we developed a compound-reporter system to track cellular identity in a model of PGC specification (PGC-like cells; PGCLC), and coupled it with unbiased genome-wide CRISPR screening. This enabled identification of key genes both for exit from pluripotency and for acquisition of PGC fate, with further characterisation revealing a central role for the transcription regulators Nr5a2 and Zfp296 in germline ontogeny. Abrogation of these genes results in significantly impaired PGCLC development accompanied with widespread activation (Nr5a2-/-) or inhibition (Zfp296-/-) of WNT pathway components. This leads to aberrant upregulation of the somatic programme or failure to appropriately activate germline genes in PGCLC, respectively, and consequently loss of germ cell identity. Overall our study places Zfp296 and Nr5a2 as key components of an expanded PGC gene regulatory network, and outlines a transferable strategy for identifying critical regulators of complex cell fate transitions.
Overall design Sample1-36: mRNA-seq of epiblast-like cells (EpiLC), and PGCLC at day (D) 2 and D6 of differentiation; 3 biological independent replicates for following genotypes in a Stella-GFP; Esg1-tdTomato background: wild-type, Nr5a2-/-, or Zfp296-/-; Sample37-42: mRNA-seq of infected? embryonic stem cells (ESC), EpiLC and D6 PGCLC; 2 biological replicates; Sample 43-52: gRNA amplicon libraries from embryonic stem cells (ESC), EpiLC or D6 PGCLC from CRISPR screen; 2 biological independent replicates
Contributor(s) Hackett JA, Huang Y, Günesdogan U, Holm-Gretarsson K, Kobayashi T, Surani A
Citation(s) 30327475
Submission date Jul 22, 2018
Last update date Mar 21, 2019
Contact name Jamie Hackett
Organization name European Molecular Biology Laboratory (EMBL)
Department Epigenetics & Neurobiology
Street address via Ramarini 32
City Rome
ZIP/Postal code 00015
Country Italy
Platforms (4)
GPL17021 Illumina HiSeq 2500 (Mus musculus)
GPL18480 Illumina HiSeq 1500 (Mus musculus)
GPL21103 Illumina HiSeq 4000 (Mus musculus)
Samples (52)
GSM3301574 wild type parental EpiLC
GSM3301575 wild type clone #45 EpiLC
GSM3301576 wild type clone #72 EpiLC
BioProject PRJNA482361
SRA SRP154866

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SOFT formatted family file(s) SOFTHelp
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Supplementary file Size Download File type/resource
GSE117473_RPKM_RNAseq_Hackett.xlsx 13.1 Mb (ftp)(http) XLSX
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Raw data are available in SRA
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