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Sample GSM1516132 Query DataSets for GSM1516132
Status Public on Dec 17, 2015
Title hMDM_GR_IP
Sample type SRA
Source name human monoycte derived macrophages
Organism Homo sapiens
Characteristics pooled: yes
fully anonymized: yes
cell type: human monoycte derived macrophages
antibody: Sigma Imprint anti-GR, monoclonal
Treatment protocol They were treated with either 100nM dexamethasone (Sigma) or ethanol vehicle for 2h.
Growth protocol CD14+ monocytes were extracted from whole blood donated by healthy volunteers using MACS separation (Miltenyi). They were differentiated in culture for 1 week in the presence of recombinant human CSF1 (10000U/ml),penicillin/streptomycin, Glutamax and 10% fetal calf serum then replated in fresh medium, also supplemented as above, for the time series experiment.
Extracted molecule genomic DNA
Extraction protocol rinsed with PBS, fixed in 1% formaldehyde for 7.5min at RT, lysed and sonicated to fragment size 400-600bp. GR-DNA complexes were then isolated from soluble chromatin using Sigma Imprint anti GR monoclonal antibody , crosslinks reversed at 65 degrees and DNA cleaned up using Minielute columns(Qiagen)
ChIP DNA samples were split into 3 aliquots and blunt ended with Klenow (Roche), PNK (NEB) and T4 DNA polymerase (Roche). An overhanging A base was added using Klenow (-exo) (NEB) and Illumina adapters ligated overnight at 16 degrees C with T4 DNA ligase (NEB). The IP samples were recombined after ligation and then split again into 7 aliquots. Libraries were amplified from each of these aliquots using Illumina Tru-seq multiplex primers and Phusion high-fidelity DNA polymerase (NEB) and the resulting material pooled and sequenced by Edinburgh Genomics on a Hiseq-2500.
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 and removal of low absolute value peaks(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.
Formation of bedGraph for visualization, HOMER
Genome_build: hg19
Supplementary_files_format_and_content: bedGraph for visualization of treated IP data, 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 GPL16791
Series (2)
GSE61878 Genome wide binding of glucocorticoid receptor in dexamethasone treated human monocyte derived macrophages
GSE61881 Divergent transcriptional activation by glucocorticoids in mouse and human macrophages is the result of gain and loss of enhancers
BioSample SAMN03084136
SRA SRX716944

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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