|
| Status |
Public on Feb 01, 2016 |
| Title |
Input_ERRa_ChIP-seq |
| Sample type |
SRA |
| |
|
| Source name |
Input DNA from BT474 breast cancer cell line
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: BT474
tissue type: Breast tumor
chip antibody: none
|
| Treatment protocol |
Reagents were simply added to the media for cell treatment in regular 6cm culture dish.
|
| Growth protocol |
Cells were cultured in regular DMEM. 24h after seeding, media was changed and fresh media with vehicle or AICAR 0.5mM
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
After 90min treatment with vehicle or AICAR, nuclei were isolated and subjected to chromatin immunoprecipitation. Following ERRa ChIP, genomic DNA was purified with QIAGEN DNA extraction kit.
Libraries were performed at the Génome Québec Innovation Centre (McGill University) using standard protocol for HiSeq - Illumina Single reads 50bp sequencing lane
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
input genomic DNA from BT474 cells
|
| Data processing |
Sequences were aligned to the human genome database (Hg19) using BWA v0.5.9 (Li and Durbin, 2009)
Significant DNA binding (peak) was determined using MACS v1.4.1 software (Zhang et al., 2008).
Peak annotation, tag directory, bed file generation, and de novo motif discovery were performed with the Homer package v3.18.
Genome_build: hg19
Supplementary_files_format_and_content: data are presented as bigwig and annotated peak lists in excel from the merged of two samples for control condition and two samples for AICAR-treated cells. Additionnally, we included fastq data for each sample. All samples were run twice so there is 2 fastq files per sample (except ERRa_ChIP_AICAR_replicate 1 that has 3 fastq files).
|
| |
|
| Submission date |
Dec 10, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Etienne Audet-Walsh |
| E-mail(s) |
etienne.audet-walsh@crchudequebec.ulaval.ca
|
| Organization name |
Université Laval
|
| Department |
Molecular Medicine
|
| Street address |
2705 boulevard Laurier
|
| City |
Québec City |
| State/province |
QC |
| ZIP/Postal code |
G1V 4G2 |
| Country |
Canada |
| |
|
| Platform ID |
GPL11154 |
| Series (2) |
| GSE75876 |
The PGC-1α/ERRα Axis Represses One-Carbon Metabolism and Promotes Sensitivity to Anti-Folate Therapy in Breast Cancer [ChIP-Seq] |
| GSE75877 |
The PGC-1α/ERRα Axis Represses One-Carbon Metabolism and Promotes Sensitivity to Anti-Folate Therapy in Breast Cancer |
|
| Relations |
| BioSample |
SAMN04329919 |
| SRA |
SRX1473611 |
