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SRX11664771: GSM5504896: ML-E12-5-Male__-ECKO___-E296-1-12; Mus musculus; RNA-Seq
1 ILLUMINA (Illumina NovaSeq 6000) run: 2.6M spots, 529.5M bases, 165.2Mb downloads

Submitted by: NCBI (GEO)
Study: EED is required for Mouse Primordial Germ Cell Differentiation in the Embryonic Gonad
show Abstracthide Abstract
Development of Primordial germ cells (PGCs) is required for reproduction. During PGC development in mammals, major epigenetic remodeling occurs which is hypothesized to establish an epigenetic landscape for sex-specific germ cell differentiation and gametogenesis. In order to address the role of Embryonic Ectoderm Development (EED) and Histone 3 lysine 27 trimethylation (H3K27me3) in this process, we created a conditional deletion in EED and show that EED is essential for regulating the timing of sex-specific PGC differentiation in both ovaries and testes, as well as X chromosome dosage decompensation in testes. Integrating chromatin and whole genome bisulfite sequencing of epiblast and PGCs, we identified a poised repressive signature of H3K27me3/DNA methylation which we propose is established in the epiblast where EED and DNMT1 interact. Thus, EED joins DNMT1 in regulating the timing of sex-specific PGC differentiation during the critical window when the gonadal niche cells specialize into an ovary or testis. Overall design: Examination of Transcription and DNA methylation in control and PGC-specific EED conditional knockout primordial germ cells
Sample: scRNA-seq_E12-5_XY_ECKO_Embryo_1_Rep_12
SAMN20603872 • SRS9697468 • All experiments • All runs
Organism: Mus musculus
Library:
Instrument: Illumina NovaSeq 6000
Strategy: RNA-Seq
Source: TRANSCRIPTOMIC
Selection: cDNA
Layout: PAIRED
Construction protocol: Female E12.5 gonads were extracted and digested in 0.05% trypsin. GFP positive single mPGCs were sorted into a 96 well skirtless plate, each well containing 3 µL of 0.2% Triton X-100 and 2U/µL RNaseOUT (Thermo Fisher Scientific). Single Cell RNA sequencing libraries were prepared according to the Smart Seq 2 single cell sequencing protocol (Picelli et al., 2014). The RNA was converted to cDNA in each well using Superscript II (Invitrogen). The cDNA was amplified in each well using a KAPA HiFI HotStart polymerase (KAPA Biosystems) in a PCR run for 18 cycles. cDNA was tagged via the Nextera Tagmentation kit (Illumina) using libraries A and C (Illumina). Indexed cDNA was pooled and run on a 2% agarose gel and the smear between 200-500 bp was extracted. Gel extract was cleaned with the Qiagen Gel Extraction Kit (Qiagen) and sent for sequencing.
Experiment attributes:
GEO Accession: GSM5504896
Links:
Runs: 1 run, 2.6M spots, 529.5M bases, 165.2Mb
Run# of Spots# of BasesSizePublished
SRR153623602,621,056529.5M165.2Mb2022-05-12

ID:
15580719

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