GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
Sample GSM801506 Query DataSets for GSM801506
Status Public on May 28, 2012
Title H3K9me3_stim_3T3
Sample type SRA
Source name H3K9me3_stim_3T3
Organism Mus musculus
Characteristics cell type: 3T3 fibroblasts
chip antibody: anti-H3K9me3 (clone 2F3)
Treatment protocol stimulated for 2h with 10ng/ml TNF-alpha
Growth protocol 3T3 fibroblasts were cultured under standard conditions
Extracted molecule genomic DNA
Extraction protocol ChIP was performed using sonicated extracts from formaldehyde-fixed nuclei. Immunoprecipitated or input DNA was re-sonicated to obtain a mean fragment size of around 300bp, ligated to adapters using the NEBNext kit (New England Biolabs), and amplified by PCR (18 cycles). Sequencing was performed using paired-end reads of 36bp each. Average insert size was around 270bp (sd 100bp) based on the mapped distances between read-pairs.
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina Genome Analyzer IIx
Description 3T3 fibroblasts, 2h after stimulation with 10ng/ml TNF-alpha
Data processing Sequence reads were aligned to the mm9 reference genome using the bowtie program, allowing for up to 2 mismatches.
Fragment midpoints were summed in overlapping 2kb windows; the number of tags in ChIP samples was divided by the number of tags in the same window in the corresponding input sample (when this was greater than zero) to generate wig files.
Submission date Sep 26, 2011
Last update date May 15, 2019
Contact name Dominic van Essen
Organization name Institute for Research on Cancer & Aging, Nice (IRCAN)
Lab Transcription specificity
Street address 28 Avenue Valombrose
City Nice
ZIP/Postal code 06107
Country France
Platform ID GPL11002
Series (2)
GSE32377 Analysis of H3K9 trimethylation in unstimulated and stimulated dendritic cells and fibroblasts
GSE32381 Cell-type specific control of enhancer activity by H3K9 trimethylation
SRA SRX099237
BioSample SAMN00727968
Named Annotation GSM801506_H3K9me3_stim_3T3.wig.gz

Supplementary file Size Download File type/resource
GSM801506_H3K9me3_stim_3T3.wig.gz 40.7 Mb (ftp)(http) WIG
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap