GSM1835808: RRBS_E8.5 G9aKO-Rep3; Mus musculus; Bisulfite-Seq - SRA

SRX1123788: GSM1835808: RRBS_E8.5 G9aKO-Rep3; Mus musculus; Bisulfite-Seq
1 ILLUMINA (Illumina HiSeq 2500) run: 23M spots, 3.5G bases, 1.6Gb downloads

Submitted by: Gene Expression Omnibus (GEO)

Study: Study of the impact of G9a on DNA methylation in mouse embryonic cells [seq]

PRJNA291405 • SRP061767 • All experiments • All runs

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We explored the role of the lysine-methyltrasferase G9a in the control of DNA methylation during mouse embryogenesis. We provide maps of cytosine methylation by MeDIP and RRBS in G9a-deficient mouse embryos and ES cells, as well as ChIP-Seq profiles for H3K9me2 in embryos and RNA-Seq expression profiles in G9a-deficient embryos. Overall design: We prepared RRBS libraries from single embryos and mapped DNA methylation by RRBS in four WT and three G9aKO E8.5 embryos. We prepared RNA-Seq libraries from RNAs of single embryos and mapped the transcriptome of two WT and two G9aKO E8.5 embryos. We prepared H3K9me2 ChIP-Seq libraries from three independant ChIP experiments on eight pooled E8.5 embryos.

Sample: RRBS_E8.5 G9aKO-Rep3

SAMN03943751 • SRS1016199 • All experiments • All runs

Organism: Mus musculus

Library:

Instrument: Illumina HiSeq 2500

Strategy: Bisulfite-Seq

Source: GENOMIC

Selection: Reduced Representation

Layout: PAIRED

Construction protocol: Genomic DNA was extracted by proteinase K digestion followed by phenol/chloroform extraction. We prepared RRBS libraries using a published protocol (Gu et al., Nat Protoc 6:468-81, 2011) with some modifications. Briefly, we digested 70 ng of genomic DNA 5 hours with MspI (Thermo Scientific), followed by end-repair and A-tailing (Klenow fragment, Thermo Scientific) and ligation to methylated adapters (T4 DNA ligase, Thermo Scientific) in Tango 1X buffer. Fragments between 150 and 400 bp were excised from a 3% agarose 0.5X TBE gel with the MinElute kit (Qiagen) and bisulfite-converted with the EpiTect Bisulfite kit (Qiagen) using two consecutive rounds of conversion. Final RRBS libraries were amplified with 14-16 cycles of PCR.

Experiment attributes:

GEO Accession: GSM1835808

Links:

NCBI link: NCBI Entrez (gds)

Runs: 1 run, 23M spots, 3.5G bases, 1.6Gb

Run	# of Spots	# of Bases	Size	Published
SRR2133431	23,032,908	3.5G	1.6Gb	2015-11-13

ID:: 1639593

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