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Sample GSM1154506 Query DataSets for GSM1154506
Status Public on Aug 13, 2013
Title IMR90_MeCP2_GA1580_replicate_ChIPseq
Sample type SRA
 
Source name IMR90_MeCP2
Organism Homo sapiens
Characteristics cell line: IMR90
chip antibody: MeCP2 (Abcam; ab2828)
Growth protocol Human IMR90 cells (American Type Culture Collection; ATCC) were cultured under optimal growth conditions as specified by ATCC, and only cells at early passage were used for experiments. HCT116 cells were generous gifts from Dr. B. Vogelstein (Johns Hopkins University). These cells were cultured in McCoy's 5A medium with 10% FBS.
Extracted molecule genomic DNA
Extraction protocol Chromatin from 5 million cells per ChIP was prepared by formaldehyde cross-linking and sonication as described previously. Antibodies against MeCP2 (Abcam; ab2828) and ser2p-PolII (Abcam; ab5095) were added in manufacturer-recommended amounts per ChIP. For input control samples, DNA was isolated from 10% (vol.) of chromatin material used for ChIP by phenol/chloroform extraction and ethanol purification procedures.
ChIP-Seq was carried out according to established protocols and prepared libraries were sequenced with the Illumina Genome Analyzer II or HiSeq 2000 sequencer according to the manufacturer’s instructions.
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina Genome Analyzer II
 
Description phred+64 fastq
Data processing BED files were generated by aligning ChIP-seq reads to hg18 genome using Bowtie algorithm (version 0.12.5). UCSC genome browser displayable bedGraph files for ChIP-Seq data were generated by counting shifted tags in 200-bp windows across the genome and normalizing window tag counts by 5 million total sequenced reads to make different libraries directly comparable.
Genome_build: hg18
Supplementary_files_format_and_content: The bed files report alignments. Most of the results reported in our manuscript were obtained by processing BED files (however, too many and too heterogeneous, making it difficult to deposit them all).
Supplementary_files_format_and_content: The bedGraph files report the number of ChIP-Seq sequencing reads in a genomic interval, normalized to 5 million uniquely aligned sequenced reads.
 
Submission date Jun 05, 2013
Last update date May 15, 2019
Contact name Iouri Chepelev
E-mail(s) ichepelev@gmail.com
Organization name US Department of Veterans Affairs Medical Center
Street address 3200 Vine St
City Cincinnati
State/province OH
ZIP/Postal code 45220
Country USA
 
Platform ID GPL9115
Series (2)
GSE47677 Intragenic DNA methylation modulates alternative splicing by recruiting MeCP2 to promote exon recognition [ChIP-Seq]
GSE47678 Intragenic DNA methylation modulates alternative splicing by recruiting MeCP2 to promote exon recognition
Relations
BioSample SAMN02191544
SRA SRX295036

Supplementary file Size Download File type/resource
GSM1154506_IMR90_MeCP2_GA1580_replicate_ChIPseq.bed.gz 125.4 Mb (ftp)(http) BED
GSM1154506_IMR90_MeCP2_GA1580_replicate_ChIPseq_norm.bedgraph.gz 20.0 Mb (ftp)(http) BEDGRAPH
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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