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Series GSE65748 Query DataSets for GSE65748
Status Public on Jun 11, 2015
Title Genome-wide binding and mechanistic analyses of Smchd1 mediated epigenetic regulation [ChIP-Seq, MBD-Seq]
Organism Mus musculus
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Methylation profiling by high throughput sequencing
Summary Purpose: The aim of this study is (1) to identify the chromatin occupancy of the epigenetic regulator Smchd1 in neural stem cells (NSCs) derived from E14.5 mouse brain; (2) to profile key epigenetic marks H3K4me3, H3K27me3 and DNA methylation in wild type and Smchd1 null NSCs; (3) to identify the chromatin occupancy of Ctcf in wild type and Smchd1 null NSCs.
Methods: Chromatin immunoprecipitation for Smchd1, H3K4me3, H3K27me3 and Ctcf was performed essentially as in (Nelson et al. 2006). Briefly, nuclei were isolated from formaldehyde crosslinked NSCs and chromatin was fragmented by sonication. Chromatin immunoprecipitation was performed with corresponding antibodies for Smchd1, H3K4me3 and H3K27me3. DNA was extracted from the immunoprecipitated fraction following reverse-crosslinking. Isolated DNA was used to generate sequencing libraries with Illumina's TruSeq DNA Sample Preparation Kit or Ovation Ultralow system (NuGen) according to manufacturer's instruction. Libraries were pooled and sequenced on the Illumina HiSeq 2000 platform for 100 bp single-end reads. Image analysis was performed in real time by the HiSeq Control Software (HCS) v1.4.8 and Real Time Analysis (RTA) v1.12.4.2, running on the instrument computer. Real-time base calling on the HiSeq instrument computer was performed with the RTA software. Illumina CASAVA1.8 pipeline was used to generate the sequence data. To examine the level of DNA methylation, genomic DNA was extracted using an AllPrep DNA/RNA Mini Kit (Qiagen) and methylated DNA was isolated via binding to the methyl-CpG binding domain of human MBD2 protein coupled beads using the MethylMiner methylated DNA enrichment kit (Life Technologies) according to the manufacturer’s instructions. Isolated DNA was used to generate sequencing libraries as for the ChIP-seq experiment with Illumina’s TruSeq DNA Sample Preparation Kit according to manufacturer's instruction and sequenced on the Illumina HiSeq 2000 platform for 49 bp single-end reads. Sequencing analysis was performed as described for the ChIP-seq experiments.
 
Overall design Chromatin occupancy of the epigenetic regulator Smchd1 in neural stem cells (NSCs) derived from E14.5 mouse brain was determined by Smchd1 ChIP-seq. Enrichment of H3K4me3 and H3K27me3 in wild type and Smchd1 null NSCs were assessed by H3K4me3 and H3K27me3 ChIP-seq, respectively. DNA methylation in wild type and Smchd1 null NSCs was assessed by MBD-seq. Chromatin occupancy of Ctcf in wild type and Smchd1 null NSCs was determined by by Ctcf ChIP-seq.
 
Contributor(s) Liu R
Citation(s) 26091879
Submission date Feb 09, 2015
Last update date May 15, 2019
Contact name Ruijie Liu
E-mail(s) cynthia.liu@adelaide.edu.au
Organization name the university of Adelaide
Street address Mudla Wirra Rd
City Roseworthy
State/province South Australia
ZIP/Postal code 5371
Country Australia
 
Platforms (1)
GPL13112 Illumina HiSeq 2000 (Mus musculus)
Samples (28)
GSM1604019 Smchd1 ChIP in wild type NSCs replicate 1
GSM1604020 H3K4me3 ChIP in wild type NSCs replicate 1
GSM1604021 H3K27me3 ChIP in wild type NSCs replicate 1
This SubSeries is part of SuperSeries:
GSE65749 Genome-wide binding and mechanistic analyses of Smchd1 mediated epigenetic regulation
Relations
SRA SRP053353
BioProject PRJNA275206

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SOFT formatted family file(s) SOFTHelp
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Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE65748_macs2D1H3K27me3_5e-4_summits.bed.gz 1.1 Kb (ftp)(http) BED
GSE65748_macs2D1H3K27me3_5e-4_treat_pileup.bedgraph.gz 446.4 Mb (ftp)(http) BEDGRAPH
GSE65748_macs2D1H3K4me3_5e-4_summits.bed.gz 319.3 Kb (ftp)(http) BED
GSE65748_macs2D1H3K4me3_5e-4_treat_pileup.bedgraph.gz 102.8 Mb (ftp)(http) BEDGRAPH
GSE65748_macs2D1MBD_5e-4_summits.bed.gz 1.5 Mb (ftp)(http) BED
GSE65748_macs2D1MBD_5e-4_treat_pileup.bedgraph.gz 328.1 Mb (ftp)(http) BEDGRAPH
GSE65748_macs2WTH3K27me3_5e-4_summits.bed.gz 8.3 Kb (ftp)(http) BED
GSE65748_macs2WTH3K27me3_5e-4_treat_pileup.bedgraph.gz 372.7 Mb (ftp)(http) BEDGRAPH
GSE65748_macs2WTH3K4me3_5e-4_summits.bed.gz 310.4 Kb (ftp)(http) BED
GSE65748_macs2WTH3K4me3_5e-4_treat_pileup.bedgraph.gz 305.8 Mb (ftp)(http) BEDGRAPH
GSE65748_macs2WTMBD_5e-4_summits.bed.gz 1.9 Mb (ftp)(http) BED
GSE65748_macs2WTMBD_5e-4_treat_pileup.bedgraph.gz 310.1 Mb (ftp)(http) BEDGRAPH
GSE65748_macs2WTsmchd1_5e-3_summits.bed.gz 14.8 Kb (ftp)(http) BED
GSE65748_macs2WTsmchd1_5e-3_treat_pileup.bedgraph.gz 1.5 Gb (ftp)(http) BEDGRAPH
GSE65748_macs2WTsmchd1_5e-4_summits.bed.gz 5.8 Kb (ftp)(http) BED
GSE65748_macs2WTsmchd1_5e-4_treat_pileup.bedgraph.gz 1.5 Gb (ftp)(http) BEDGRAPH
GSE65748_macs2ctcfD1UnVS67_5e-4_summits.bed.gz 150.5 Kb (ftp)(http) BED
GSE65748_macs2ctcfD1UnVS67_5e-4_treat_pileup.bedgraph.gz 90.7 Mb (ftp)(http) BEDGRAPH
GSE65748_macs2ctcfWTNonsVS67_5e-4_summits.bed.gz 263.3 Kb (ftp)(http) BED
GSE65748_macs2ctcfWTNonsVS67_5e-4_treat_pileup.bedgraph.gz 109.8 Mb (ftp)(http) BEDGRAPH
GSE65748_macs2ctcfWTUnVS67_5e-4_summits.bed.gz 107.5 Kb (ftp)(http) BED
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