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Sample GSM1479831 Query DataSets for GSM1479831
Status Public on Oct 05, 2015
Title 5hmc-MeDIP-MCF7-hypoxia
Sample type SRA
 
Source name MCF7 (human breast cancer cell line)
Organism Homo sapiens
Characteristics chip antibody: 5hmC (#39769, Active Motif, Lot No: 1031001)
treatment: hypoxia
Treatment protocol For hypoxia treatment, cells were cultured in hypoxia chamber (1% oxygen tension) for 24 hr.
Growth protocol MCF7 cells were cultured in the DMEM medium supplemented with 10% FBS at 37℃ in the presence of 5% CO2.
Extracted molecule genomic DNA
Extraction protocol genomic DNA was prepared with genomic DNA extraction kit (Promega) and sonicated into fragments ranging ~500bp.
Libraries were prepared according to Illumina's instructions. Illumina barcode adapters were ligated before hMeDIP. Adaptor-ligated DNA was denatured, followed by incubation with 5-hmC antibody (Active Motif). The immunoprecipitated DNA was purified and sequenced followed by standard Illumina protocols.
 
Library strategy MeDIP-Seq
Library source genomic
Library selection 5-methylcytidine antibody
Instrument model Illumina HiSeq 2500
 
Description hMeDIP-Seq in MCF7 cells under hypoxia conditions
Data processing Basecalls performed using CASAVA version 1.8.2
hMeDIP-Seq reads were aligned to the human genome (hg19) using bowtie2 (v2.1.0), keeping only reads that mapped to a unique genomic location (MAPQ > 10).
HOMER (v4.6) was used to process alignment files to generate normalized bedGraphs and bigwigs for the UCSC Genome Browser and quantify 5hmC levels at promoters.
Genome_build: hg19
Supplementary_files_format_and_content: bigwig format. Initial reads were extended to approximately 150 bp and normalized coverage bedGraphs were generated using HOMER. The bedGraphToBigWig utility from the UCSC Genome Browser was then used to generate the bigwig files.
 
Submission date Aug 14, 2014
Last update date May 15, 2019
Contact name Christopher Benner
E-mail(s) cbenner@ucsd.edu
Organization name University of California, San Diego (UCSD)
Department Medicine
Street address 9500 Gilman Dr. MC 0640
City La Jolla
State/province California
ZIP/Postal code 92093-0640
Country USA
 
Platform ID GPL16791
Series (1)
GSE60434 Hypoxia-induced TET-TNFa-p38-MAPK signaling axis drives tumor malignancy of human breast cancer
Relations
BioSample SAMN02990967
SRA SRX681547

Supplementary file Size Download File type/resource
GSM1479831_sample1.hMEDIP1.bigwig 199.2 Mb (ftp)(http) BIGWIG
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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