|
| Status |
Public on Jan 04, 2017 |
| Title |
UCD4 E2 replicate 3 input |
| Sample type |
SRA |
| |
|
| Source name |
Breast tumor xenograft
|
| Organism |
Homo sapiens |
| Characteristics |
xenograft: UCD4
treatment: estrogen
chip antibody: input
|
| Treatment protocol |
Chronic E2/E2+P4 treatment upon transplant
|
| Growth protocol |
Xenografts were grown in NOD/SCID/Il2rgnull mice
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Tissue was pulverized and crosslinked. Lysates were produced from sonicated nuclei and ER or PR were isolated with antibody.
Libraries were prepared at the University of Colorado Denver Genomics and Microarray Core facility using the NuGEN Ovation Ultralow Library System v2 .
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
ChIPseq reads were processed with cutadapt (https://code.google.com/p/cutadapt/) to remove 3’ adaptor sequences and 3’ bases with QUAL < 13.
Trimmed reads were aligned to the human genome (grch37/hg19 build) using bowtie2 (http://bowtie-bio.sourceforge.net/bowtie2/index.shtml).
Peaks were called on aligned reads using HOMER-IDR (https://github.com/karmel/homer-idr), an implementation of the Irreproducible Discovery Rate (IDR) framework (https://sites.google.com/site/anshulkundaje/projects/idr) using the HOMER peak caller (http://homer.salk.edu/homer/index.html).
Genome_build: hg19
Supplementary_files_format_and_content: BED file with HOMER-IDR peak calls for all four experimental groups (IgG control).
|
| |
|
| Submission date |
Jan 04, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Jessica Finlay-Schultz |
| E-mail(s) |
[email protected]
|
| Organization name |
University of Colorado Denver Anschutz Medical Campus
|
| Department |
Pathology
|
| Street address |
12801 E 17th Ave
|
| City |
Aurora |
| State/province |
CO |
| ZIP/Postal code |
80045 |
| Country |
USA |
| |
|
| Platform ID |
GPL16791 |
| Series (2) |
| GSE93108 |
ChIPseq analysis of patient-derived luminal breast cancer xenografts with progestins |
| GSE93109 |
Patient-derived luminal breast cancer xenografts with progestins |
|
| Relations |
| BioSample |
SAMN06200167 |
| SRA |
SRX2460053 |
