|
| Status |
Public on Dec 21, 2015 |
| Title |
MBD3_rep2 |
| Sample type |
SRA |
| |
|
| Source name |
MDA-MB-231
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: Breast
chip antibody: MBD3
cell line: MDA-MB-231
|
| Treatment protocol |
none
|
| Growth protocol |
Cells were grown on 15 cm plates in DMEM medium with 10% FBS
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Tagmentation and PCR amplification were performed using Nextera XT kit (Illumina).
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
Reads were filtered based on a mean base quality score >20. Reads were mapped to hg19 genome using Bowtie 0.12.8
Duplicate reads were removed using MarkDuplicates.jar from picard-tools-1.107 package.
Non-duplicate, uniquely mapped paired-end reads were converted to a single fragment. BigWig files were generated to visualize the genomic coverage.
Genome_build: hg19
Supplementary_files_format_and_content: bigWig
|
| |
|
| Submission date |
Dec 17, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Takashi Shimbo |
| E-mail(s) |
shimbot@niehs.nih.gov
|
| Organization name |
NIH/NIEHS
|
| Street address |
111 TW Alexander Dr.
|
| City |
RTP |
| ZIP/Postal code |
27709 |
| Country |
USA |
| |
|
| Platform ID |
GPL18573 |
| Series (1) |
| GSE76116 |
ChIP-seq analysis of MBD3 in human breast cancer cells |
|
| Relations |
| BioSample |
SAMN04348740 |
| SRA |
SRX1489434 |
