|
| Status |
Public on Sep 15, 2023 |
| Title |
MAFHD_MAF |
| Sample type |
SRA |
| |
|
| Source name |
MCF7
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: MCF7
cell type: breast cancer
type: IP
condition: MAFHD
antibody: c-MAF (E-7) antibodies (sc-518062. Santa Cruz Biotechnology)
|
| Treatment protocol |
E2 (10 nM, Sigma-Aldrich) or ethanol (vehicle) was added 1h prior to fixation
|
| Growth protocol |
Four 15 cm plates of control and MAF-overexpressing MCF7 cells per condition were prepared at 70-80% confluency. Cells were cultured in hormone-deprived medium [phenol-red free DMEM (Gibco) supplemented with 5% charcoal-stripped FBS (Capricorn Scientific), glutamine 0.29 mg/mL, penicillin 100 units/mL and streptomycin 0.1 mg/mL for 72 h before E2 (10 nM, Sigma-Aldrich) or ethanol (vehicle) addition.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Cells were crosslinked in 1% formaldehyde in DMEM for 10 min at RT. Next, glycine was added to a final concentration of 0.125 M and cells were incubated for 5 min at RT to stop the fixation. After two washes with ice-cold PBS, cells were harvested by gently scrapping on ice and centrifuged at 3,000 x g for 5 min. Cell pellets were stored at 80ºC until use.
Chromatin preparation and ChIP experiments were performed with the ChIP-IT High Sensitivity Kit (Active Motif) according to manufacturer’s protocol.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
ChIP-seq alignment: Sequence of the reads of the samples with spike-in were mapped to a synthetic genome containing the human and the fruit fly chromosomes (hg19+dm3) using BOWTIE (PubMed ID 19261174) with the option -m 1.
SeqCode (PubMed ID 34599234) was used to generate the genome-wide profiles of each ChIP-seq experiment. Height of the profiles is normalized by the total number of reads mapped over the fly spike-in genome
ChIP-seq analysis: Peak detection of every sample against its corresponding Input was performed with MACS (PubMed ID: 18798982). Peaks were reported in BED format.
Assembly: hg19
Supplementary files format and content: BedGraph format for ChIP-seq genome-wide profiles
Supplementary files format and content: BED files format for ChIP vs Input peak calling
|
| |
|
| Submission date |
Aug 05, 2022 |
| Last update date |
Sep 15, 2023 |
| Contact name |
Adria Caballe |
| E-mail(s) |
adria.caballe@irbbarcelona.org
|
| Organization name |
IRB
|
| Department |
biostatistics
|
| Street address |
C/ Baldiri Reixac 10
|
| City |
Barcelona |
| ZIP/Postal code |
08028 |
| Country |
Spain |
| |
|
| Platform ID |
GPL16791 |
| Series (2) |
| GSE210605 |
MAF Amplification licenses Estrogen Receptor α to Drive Breast Cancer Metastasis [MAF ChIP-seq] |
| GSE210608 |
MAF Amplification licenses Estrogen Receptor α to Drive Breast Cancer Metastasis |
|
| Relations |
| BioSample |
SAMN30166088 |
| SRA |
SRX16940293 |
