|
| Status |
Public on Oct 05, 2015 |
| Title |
5hmc-MeDIP-MCF7-normoxia |
| 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: normoxia
|
| 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 normoxia 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 |
SAMN02990968 |
| SRA |
SRX681548 |
