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Sample GSM3502289 Query DataSets for GSM3502289
Status Public on Nov 26, 2019
Title WTKO_H3K27ac_WT6
Sample type SRA
 
Source name Cortex
Organism Mus musculus
Characteristics genotype: wild type
Sex: Male
strain: C57BL/6J
age: 7-8 weeks
Growth protocol Brain tissue was taken from MeCP2 knockout, overexpression and wild-type mice maintained under standard housing conditions.
Extracted molecule genomic DNA
Extraction protocol Cerebral cortex was dissected on ice in phosphate buffered saline from 1) MeCP2 knockout and wild-type male litter mates at 7-8 weeks old and 2) MeCP2 overexpression and wild-type male litter mates at 7-10 weeks old. The tissue was flash-frozen in liquid nitrogen and stored at -80°C. ChIP experiments were performed on half a cortex as previously described (Cohen et al., 2011), using an alternative chromatin fragmentation method. Chromatin were fragmented with Covaris E220 sonicator (5% Duty Factory, 140 Peak Incidence Power, 200 cycles per burst, milliTUBE 1mL AFA Fiber). ChIP was performed with H3K27ac (Abcam ab4729), H3K4me3 (Abcam ab1012), H3K36me3 (Active Motif 61101), and MeCP2 (rabbit polyclonal (Chen et al., 2003)).
ChIP libraries for H3K27ac, H3K4me3, and H3K36me3 were generated using Ovation Ultralow Library System V2 (NuGEN) and libraries for MeCP2 with Accel-NGS 2S Plus DNA Library Kit (Swift Biosciences).
Libraries were pooled to a final concentration of 8-10nM and sequenced using Illumina HiSeq 3000 with GTAC, yielding 15-20 million single-end reads per sample.
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina HiSeq 3000
 
Data processing Sequenced reads were mapped to the mm9 genome using bowtie2 alignment, and reads were deduplicated to consolidate PCR duplicate reads. Deduplicated reads were used to quantify read density normalized by the number of reads per sample and by read length in basepairs. Bedtools coverage –counts was used to quantify ChIP signal at the transcriptional start site (TSS), gene body (GB), and transcriptional end site (TES). For consistency with methylation analysis, the TSS was defined as a 1kb region surrounding the TSS (+/-500bp), the GB was defined as 3kb downstream of the TSS to the end of the transcript, and the TES was defined as 2kb upstream through 3kb downstream of the end of the transcript. edgeR was then used to determine differential ChIP-signal across genotypes.
Genome_build: mm9
Supplementary_files_format_and_content: Tab-separated table (with header) of H3K27ac peaks, identifiers, and various peak-associated ChIP signals, and methylation information
 
Submission date Dec 05, 2018
Last update date Nov 26, 2019
Contact name Harrison Wren Gabel
E-mail(s) gabelh@pcg.wustl.edu
Organization name Harvard Medical School
Department Neurbiology
Lab Michael Greenberg
Street address 220 longwood avenue
City brookline
State/province Massachusetts
ZIP/Postal code 02115
Country USA
 
Platform ID GPL21493
Series (2)
GSE123371 Chromosome topology shapes neuronal non-CG DNA methylation to influence MeCP2-mediated enhancer repression (ChIP-Seq)
GSE123373 Chromosome topology shapes neuronal non-CG DNA methylation to influence MeCP2-mediated enhancer repression
Relations
BioSample SAMN10524627
SRA SRX5098354

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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