|
| Status |
Public on Aug 23, 2018 |
| Title |
jc2835_MDA-MB-231-ERb_Input_Full_24_hrs_Dox_3_hrs_1nM_LY500307 |
| Sample type |
SRA |
| |
|
| Source name |
MDA-MB-231-ERb_Input_Full_24_hrs_Dox_3_hrs_1nM_LY500307
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: MDA-MB-231-ER-beta
cell type: Triple Negative Breast Cancer Cell Line
passages: 20-25
treated with: 10 nM LY500307 for 3 h
chip antibody: None
|
| Treatment protocol |
MDA-MB-231-ER-beta cells were plated in 15 cm dishes and allowed to grow to approximately 80% confluence in DMEM/F12 medium containing 10% charcoal stripped FBS and Doxycycline (100 ng/ml, to induce ER-beta expression). Cells were subsequently treated in triplicate with ethanol vehicle, 1 nM estradiol or 10 nM LY500307 for 3 hours.
|
| Growth protocol |
Doxycycline-inducible ER-beta expressing MDA-MB-231cells were maintained in phenol red-free DMEM/F12 medium supplemented with 10% fetal bovine serum (FBS), 1% antibiotic-antimycotic (AA), 5 mg/L blasticidin S and 500 mg/L zeocin.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Nuclear lysates were prepared and ER-beta bound chromatin was purified using the Flag-specific antibody.
DNA was prepared for Illumina sequencing on the HiSeq 2500 using the ThruPLEX DNA-seq kit according to the manufacturer's instructions.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
jc2835_MDA-MB-231-ERb_Input_Full_24_hrs_Dox_3_hrs_1nM_LY500307_CRI07
|
| Data processing |
Reads were mapped to hg38 genome using Bowtie2 version 2.2.6 (Langmead B and Salzberg S., 2012).
Aligned reads with the mapping quality less than 5 were filtered out.
The read alignments from three replicates were combined into single library and peaks were called with MACS2 version 2.1.1.20160309 (Zhang Y1 at al., 2008) using sequences from MCF7 chromatin extracts as a background input control.
The peaks yielded with MACS2 q value <= 1e-4 were selected for downstream analysis.
Meme version 4.9.1 (Timothy et al., 2009) was used to detect known and discover novel binding motifs amongst tag-enriched sequences.
For visualizing tag density and signal distribution heatmap the read coverage in a window of +/- 2.5 or 5 kb region flanking the tag midpoint was generated using the bin size of 1/100 of the window length.
Differential binding analysis (Diffbind) was performed as described previously (Brown and Stark, 2011).
Genome_build: GRCh38
Supplementary_files_format_and_content: bed/text
|
| |
|
| Submission date |
Jan 09, 2018 |
| Last update date |
Aug 23, 2018 |
| Contact name |
Jason Carroll |
| E-mail(s) |
Jason.Carroll@cruk.cam.ac.uk
|
| Phone |
+44 1223 769649
|
| Organization name |
Cancer Research UK, Cambridge Institute
|
| Street address |
Li Ka Shing Centre, Robinson Way
|
| City |
Cambridge |
| ZIP/Postal code |
CB2 ORE |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL16791 |
| Series (2) |
| GSE108979 |
Identification of the ER-beta cistrome in ER-beta expressing MDA-MB-231 cells [ChIP-seq] |
| GSE108981 |
Identification of the ERĪ² transcriptome in ER-beta expressing MDA-MB-231 cells |
|
| Relations |
| BioSample |
SAMN08334988 |
| SRA |
SRX3546811 |
