|
| Status |
Public on Aug 13, 2013 |
| Title |
IMR90_Input_GA2460_replicate_ChIPseq |
| Sample type |
SRA |
| |
|
| Source name |
IMR90_Input
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: IMR90
chip antibody: none (input)
|
| 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) |
[email protected]
|
| 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 |
SAMN02191546 |
| SRA |
SRX295038 |
