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Sample GSM1305208 Query DataSets for GSM1305208
Status Public on Sep 29, 2014
Title EC_H3K4ME3_TNF
Sample type SRA
 
Source name HUVEC
Organism Homo sapiens
Characteristics chip antibody: H3K4me3
antibody catalog number: ab8580
cell type: endothelium
agent: TNF alpha
duration: 1 hour TNF alpha treatment
Treatment protocol Cells were stimulated with human TNFalpha (25 ng/mL, hr) in the presence or absence of JQ1 (500 nM, 1 hour pretreatment)
Growth protocol M199 + 20% FBS + 0.1% heparin + 50 micrograms/mL endothelial cell growth factors (ECGF).
Extracted molecule genomic DNA
Extraction protocol Whole cell extracts were sonicated to solubilize the chromatin. The chromatin extracts containing DNA fragments with an average size of 500 bp were immunoprecipitated using different antibodies. Purified immunoprecipitated DNA were prepared for sequencing according to a modified version of the Solexa Genomic DNA protocol. Fragmented DNA was end repaired and subjected to 18 cycles of LM-PCR using oligos provided by Illumina. Amplified fragments between 150 and 300bp (representing shear fragments between 50 and 200nt in length and ~100bp of primer sequence) were isolated by agarose gel electrophoresis and purified.
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina HiSeq 2000
 
Description endothelium stimulated with TNF alpha
Data processing Images analysis and base calling was done using the solexa pipeline.
For all samples reads were aligned to their indicated build using bowtie with parameters -e 70 -k 2 -m 2 -n 2 --best --concise. Seed length (-l) was set to read length for each dataset.
Genome_build: hg18
Supplementary_files_format_and_content: WIG files: For all samples aligned sequences were extended 150bp upstream and 0bp downstream (with respect to read strand) and allocated into 25bp bins. Counts were normalized to reads per million, and bins with at least 1 read per million are shown.
 
Submission date Jan 10, 2014
Last update date May 15, 2019
Contact name James Bradner
E-mail(s) bradner_computation@dfci.harvard.edu
Organization name Dana-Farber Cancer Institute
Department Medical Oncology
Lab Bradner Lab
Street address 450 Brookline
City Boston
State/province MA
ZIP/Postal code 02215
Country USA
 
Platform ID GPL11154
Series (2)
GSE53998 NF-kB coordinates rapid, BRD4-dependent remodeling of proinflammatory super-enhancers [ChIP-Seq]
GSE54000 NF-kB coordinates rapid, BRD4-dependent remodeling of proinflammatory super-enhancers
Relations
BioSample SAMN02581492
SRA SRX425260

Supplementary file Size Download File type/resource
GSM1305208_EC_H3K4ME3_TNF.wig.gz 67.9 Mb (ftp)(http) WIG
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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