|
| Status |
Public on Oct 24, 2012 |
| Title |
IgG_negative_control [reps 1 and 3] |
| Sample type |
SRA |
| |
|
| Source name |
MCF-7 Breast Cancer Cells
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: MCF-7
chip antibody: IgG from rabbit serum (Sigma Aldrich, I5006)
|
| 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 |
IgG 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 |
SRX201316 |
| BioSample |
SAMN01780248 |
