|
| Status |
Public on Dec 17, 2015 |
| Title |
mm_rep1_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
mBMDM_GC_ChIP_control_combined_ucsc.bedGrapg
mBMDM_GR_ChIP_dex100nM_2h_combined_peaks.txt
|
| 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 |
| E-mail(s) |
alasdair.jubb@ed.ac.uk
|
| 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 |
|
| Relations |
| BioSample |
SAMN03084129 |
| SRA |
SRX716928 |
