|
| Status |
Public on Mar 21, 2016 |
| Title |
ER_LY2_Veh_01 |
| Sample type |
SRA |
| |
|
| Source name |
LY2 Breast Cancer Cell Line
|
| Organism |
Homo sapiens |
| Characteristics |
treatment: Untreated
cell line: LY2
chip antibody: ER
|
| Treatment protocol |
Cells were maintained in steroid depleted medium for 72 hours prior to treatment with Vehicle (10% ethanol) for 45minutes.
|
| Growth protocol |
LY2 cells were grown in phenol red-free MEM with 2mM L-glutamine, 10% charcoal dextrin stripped fetal bovine serum, 50U/ml penicillin and 50ug/ml streptomycin in 37C incubator with 5% CO2.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
no entry
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina Genome Analyzer II |
| |
|
| Data processing |
The DNA sequencing was carried out on the Illumina GAII and Illumina HiSeq 2000
ChIP-seq reads were aligned to the hg19 genome using Bowtie (v0.12.9) with parameters "-m 1 -v 2 --strata --best"
Peak calling was carried out by MACS2 with a p-value cut off of 1e-03 and by linearly scaling the smaller dataset to the larger dataset (via the "--to-large" parameter).
Using the MACS2 results, a reliable peakset was produced by applying the Irreproducible Discovery Rate tool to the LetR replicates of the androstenedione treated and vehicle samples. The peak sets for the LetR androstenedione and vehicle samples were then assessed for overlapping peaks using bedtools (by at least 1bp).
Genome_build: hg19
Supplementary_files_format_and_content: There are the ChIP-seq data files in bedgraph format from the MACS2 peak calling software.
|
| |
|
| Submission date |
Dec 02, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Leonie Young |
| Organization name |
Royal College of Surgeons, Ireland
|
| Department |
Surgery
|
| Lab |
Endocrine Oncology Research Group
|
| Street address |
York Street
|
| City |
Dublin |
| ZIP/Postal code |
Dublin 2 |
| Country |
Ireland |
| |
|
| Platform ID |
GPL9115 |
| Series (1) |
| GSE54592 |
ER ChIP-seq of Androstenedione treated Letrozole Resistant Breast Cancer Cell line |
|
| Relations |
| BioSample |
SAMN03247833 |
| SRA |
SRX792932 |
