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Sample GSM801534 Query DataSets for GSM801534
Status Public on May 28, 2012
Title H3K4me1_unstim_3T3
Sample type SRA
Source name H3K4me1_unstim_3T3
Organism Mus musculus
Characteristics cell type: dendritic cells
chip antibody: anti-H3K4me1 (clone CMA302)
Treatment protocol unstimulated
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 single reads of 36bp.
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina Genome Analyzer IIx
Description 3T3 fibroblasts, unstimulated
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 200bp windows to generate wig files.
Summits (of peaks) were identified using MACS 1.4 with paramaters p=1e-4, nomodel, nolambda, shift=150, to generate bed 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)
GSE32380 Identification of candidate enhancer elements in unstimulated and stimulated dendritic cells and fibroblasts
GSE32381 Cell-type specific control of enhancer activity by H3K9 trimethylation
SRA SRX099251
BioSample SAMN00727980
Named Annotation GSM801534_H3K4me1_unstim_3T3.wig.gz
Named Annotation GSM801534_H3K4me1_unstim_3T3_summits.bed.gz

Supplementary file Size Download File type/resource
GSM801534_H3K4me1_unstim_3T3.wig.gz 18.0 Mb (ftp)(http) WIG
GSM801534_H3K4me1_unstim_3T3_summits.bed.gz 860.3 Kb (ftp)(http) BED
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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