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Sample GSM3587793 Query DataSets for GSM3587793
Status Public on Jul 17, 2020
Title jc5857_Input Veh MCF7
Sample type SRA
 
Source name MCF7
Organism Homo sapiens
Characteristics cell type: Breast cancer
passages: 22
Treatment protocol Cells were treated with human recombinant IL6 (206-IL-200, R&D systems) for 30 min.
Growth protocol MCF7 cell were grown in DMEM supplemented with 10% FBS, 2mM L-glutamine, 50 U/ml penicillin, 50 ug/ml streptomycin. T47D cells were grown in RPMI supplemented with 10% FBS, 2mM L-glutamine and 50 U/ml penicillin and 50 ug/ml streptomycin.
Extracted molecule genomic DNA
Extraction protocol Cells were crosslinked with 2mM DSG for 20 min followed by crosslinking in 1% formaldehyde for 10 min and then quenched in 100mM glycine. Nuclear enrichment was performed followed by sonication for 15 minutes (Bioruptor plus, Diagenode). Chromatin was immunoprecipitated over night using specific antibodies. Beads were washed six times in RIPA buffer and eluted from beads using SDS buffer. After RNase and proteinase K treatment, DNA was purified by phenol/chloroform extraction.
Libraries were prepared using the Thruplex kit (Illumina) according to the manufacturer's instructions.
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina HiSeq 4000
 
Description none
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 2.1.1.2016 (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 Feb 01, 2019
Last update date Jul 17, 2020
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 GPL20301
Series (2)
GSE126004 IL6/STAT3 co-opts ER/FOXA1 regulatory elements to drive metastasis in breast cancer (ChIP-Seq)
GSE126006 IL6/STAT3 co-opts ER/FOXA1 regulatory elements to drive metastasis in breast cancer
Relations
BioSample SAMN10861370
SRA SRX5323879

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

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