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Sample GSM801532 Query DataSets for GSM801532
Status Public on May 28, 2012
Title H3K4me1_unstim_DC
Sample type SRA
Source name H3K4me1_unstim_DC
Organism Mus musculus
Characteristics cell type: dendritic cells
chip antibody: anti-H3K4me1 (clone CMA302)
Treatment protocol unstimulated
Growth protocol Bone marrow-derived progenitor cells were cultured in 20ng/ml each of SCF, IL-3 and IL-6, retrovirally infected using the pSir-delta U6CHisD vector carrying a hairpin directed against the JmjD2d coding sequence, and selected using 2mM histidinol. Dendritic cells were differentiated from progenitor cells in GM-CSF (4% X63-GMCSF supernatant) + 5ng/ml SCF for 4 days, followed by GM-CSF alone for 4 days.
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 dendritic cells, 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 SRX099249
BioSample SAMN00727978
Named Annotation GSM801532_H3K4me1_unstim_DC.wig.gz
Named Annotation GSM801532_H3K4me1_unstim_DC_summits.bed.gz

Supplementary file Size Download File type/resource
GSM801532_H3K4me1_unstim_DC.wig.gz 16.1 Mb (ftp)(http) WIG
GSM801532_H3K4me1_unstim_DC_summits.bed.gz 840.4 Kb (ftp)(http) BED
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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