NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM2443985 Query DataSets for GSM2443985
Status Public on Jan 04, 2017
Title UCD4 E2 replicate 1 IgG ChIP
Sample type SRA
 
Source name Breast tumor xenograft
Organism Homo sapiens
Characteristics xenograft: UCD4
treatment: estrogen
chip antibody: IgG (sc-2027, Santa Cruz Biotechnology), lot # H2615
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) jessica.finlay-schultz@ucdenver.edu
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 SAMN06200172
SRA SRX2460048

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap