|
| Status |
Public on May 22, 2015 |
| Title |
JC2573_Xenograft_MCF7_ER_E2 r10 |
| Sample type |
SRA |
| |
|
| Source name |
Xenograft_MCF7_ER_E2
|
| Organism |
Homo sapiens |
| Characteristics |
implated cell line/type: MCF7; MCF7-Luc2/YFP cells
host strain: age-matched female NOD/SCID/IL2Rg-/- (NSG)
tissue: xenografts tumors in vivo
treatment groupd: E2
chip antibody: ERα Antibody (HC-20)
chip antibody vendor: Santa Cruz
chip antibody cat. #: sc-543
chip antibody lot #: A2213
|
| Treatment protocol |
90 day slow-release 17b-estradiol (0.72 mg/pellet) and/or progesterone (10 mg/pellet) and/or placebo hormone pellets (Innovative Research of America) were implanted subcutaneously in recipient mice. Concomitantly, ovariectomisation was performed.
|
| Growth protocol |
Age matched female NOD/SCID/IL2Rg-/- (NSG) mice were injected subcutaneously into the No 4 inguinal mammary fat pad with a suspension of 10^5 MCF7-Luc2/YFP cells in 50% growth factor reduced MatrigelTM (BD Biosciences).
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
immunoprecipitated DNA was end-repaired, A-tailed, ligated to the sequencing adapters, amplified by 18 cycles of PCR and size selected (200-300 bp) followed by single end 4 sequencing on an Illumina HiSeq 2000 according to the manufacturer’s recommendationas described in Chandra, T. et al. Independence of Repressive Histone Marks and ChromatinCompaction during Senescent Heterochromatic Layer Formation. Mol Cell 47, 203–214 (2012)
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
ChIP for ER in xenograft (MCF7 cells grown in mouse) after E2 treatment [Tumour #10]
|
| Data processing |
Single-end reads were aligned against the Human Reference Genome (assembly hg19, NCBI GRCH37) using BWA version 0.5.5. Reads were filtered by removing those with a BWA alignment quality score less than 15. A further filtration was carried out by removing reads falling into the 'blacklist' regions identified by ENCODE.
Quality was confirmed using Biocnoductor package ChIPQC. Peaks we called using MACS v 1.4.1.
The Bioconductor package DiffBind was used to determine clustering, formulate consensus peaksets, and identify differentially bound sites.
Genome_build: hg19, Genome Reference Consortium GRCh37
Supplementary_files_format_and_content: MACS peaks in .csv file format (named as .txt as per MACS software)
|
| |
|
| Submission date |
Apr 28, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Chandra Chilamakuri |
| E-mail(s) |
datasubmissions@cruk.cam.ac.uk
|
| Organization name |
Cancer Research UK Cambridge Institute
|
| Street address |
Robinson Way
|
| City |
Cambridge |
| ZIP/Postal code |
CB2 0RE |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL11154 |
| Series (2) |
| GSE68357 |
ChIP-seq of ER and PR in xenografted MCF7 tumors grown in mice [xenograft] |
| GSE68359 |
Progesterone receptor directs a distinct estrogen receptor-alpha chromatin binding profile in breast cancer to elicit good clinical outcome |
|
| Relations |
| BioSample |
SAMN03570720 |
| SRA |
SRX1012746 |
