|
Status |
Public on Oct 24, 2012 |
Title |
AHR_ChIP-Seq |
Sample type |
SRA |
|
|
Source name |
MCF-7 Breast Cancer Cells
|
Organism |
Homo sapiens |
Characteristics |
cell line: MCF-7 chip antibody: AHR antibody (Santa Cruz, H-211, catalog# sc-5579, lot# K1010)
|
Treatment protocol |
10 nM dioxin for 45 min
|
Growth protocol |
MCF-7 cells were grown in low glucose DMEM supplemented by steroid-free serum.
|
Extracted molecule |
genomic DNA |
Extraction protocol |
Cell extracts were sonicated and AHR/ARNT-DNA complexes are immunoprecipitated. Immunoprecipitated DNA was amplified using sigma aldrich SeqPlex whole-genome amplification kit. Library was prepared according to Illumina's instruction by BGI (Shenzhen, China).
|
|
|
Library strategy |
ChIP-Seq |
Library source |
genomic |
Library selection |
ChIP |
Instrument model |
Illumina HiSeq 2000 |
|
|
Description |
AHR Replicates 1 and 3
|
Data processing |
Basecalling were performed using CASAVA ChIP-Seq reads were aligned to the human genome version 19 using Short Oligo Analysis Package 2.21 (BGI, Shenzhen, China) (Li et al. 2009). AHR Replicates 1 and 3 were compared against IgG Replicate 1 and 3. ARNT Replicates 1 and 2 were compared against IgG Replicate 1 and 2. Peaks were called using CisGenome v2.0 with the following settings: Read Extension = 150 bp; Bin Size = 50 bp; Max Gap = 50 bp; Min Peak Length = 100 bp Genome_build: hg19 Supplementary_files_format_and_content: BED
|
|
|
Submission date |
Oct 24, 2012 |
Last update date |
Feb 14, 2021 |
Contact name |
Jason Matthews |
E-mail(s) |
jason.matthews@medisin.uio.no
|
Organization name |
University of Oslo
|
Department |
Nutrition
|
Street address |
Domus Medica Room 2201 Sognsvannsveien 9
|
City |
Oslo |
ZIP/Postal code |
0372 |
Country |
Norway |
|
|
Platform ID |
GPL11154 |
Series (1) |
GSE41820 |
High-resolution genome-wide mapping of AHR and ARNT binding sites by ChIP-Seq |
|
Relations |
SRA |
SRX201314 |
BioSample |
SAMN01780246 |