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Sample GSM1516129 Query DataSets for GSM1516129
Status Public on Dec 17, 2015
Title mm_rep2_cont_IP
Sample type SRA
Source name mouse bone marrow derived macrophages
Organism Mus musculus
Characteristics treatment: control
gender: male
age: 10 week old
strain: C57BL/6
antibody: BuGR2, monoclonal (Pierce/ThermoFisher)
Treatment protocol Treated with either 100nM dexamethasone (Sigma) or ethanol vehicle for 2h.
Growth protocol Bone marrow from 2x 10 week old male C57BL/6 was extracted and differentiated in culture with 10% fetal calf serum, penicillin/streptomycin, Glutamax and recombinant human CSF1 (10,000U/ml) for 1 week. They were then replated in fresh medium, supplemented as above, at 0.5M cells/ml.
Extracted molecule genomic DNA
Extraction protocol 10M Cells per condition were fixed in 1% formaldehyde for 10min at RT, lysed and sonicated. GR-DNA complexes were then isolated from soluble chromatin using BuGR2 monoclonal antibody (Pierce), crosslinks reversed at 65 degrees and DNA cleaned up using Minielute columns(Qiagen)
Multiplex libraries were prepared by Edinburgh Genomics using Illumina standard protocols and reagents. Libraries were sequenced on the Hiseq2500 following the manufacturer's protocols.
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina HiSeq 2500
Description ChIP DNA
Data processing Base calls were generated using CASAVA 1.8
Trimming of adapters, Trimmomatic v0.27, ILLUMINACLIP:TruSeq3-PE.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36
Alignment, Bowtie2 for PE sequencing (defaults)
Formation of tag directories, HOMER
peak calling(cmd = ./homer/bin/findPeaks ./homer/homer_out/combined_1119_dexAb_tags/ -style factor -o auto -i ./homer/homer_out/combined_dex_input_1119_tags/), production of bedGraphs, HOMER.
combination of replicates after checking for concordance (86% peak overlap) and formation of bedGraph for visualization, HOMER
Genome_build: mm9
Supplementary_files_format_and_content: bedGraphs for treated and untreated IP, an input bedGraph and a tab-delimited peak file
Submission date Sep 29, 2014
Last update date May 15, 2019
Contact name Alasdair W Jubb
Organization name University of Edinburgh
Department Roslin Institute
Lab Hume lab / Bickmore lab (MRC HGU)
Street address The Roslin Institute
City Easter Bush
State/province Midlothian
ZIP/Postal code EH25 9RG
Country United Kingdom
Platform ID GPL17021
Series (2)
GSE61877 Genome wide binding of glucocorticoid receptor in dexamethasone treated mouse bone marrow derived macrophages
GSE61881 Divergent transcriptional activation by glucocorticoids in mouse and human macrophages is the result of gain and loss of enhancers
BioSample SAMN03084133
SRA SRX716932

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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