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Sample GSM801508 Query DataSets for GSM801508
Status Public on May 28, 2012
Title input_stim_DC
Sample type SRA
Source name input_stim_DC
Organism Mus musculus
Characteristics cell type: dendritic cells
chip antibody: none
Treatment protocol stimulated for 2h with 100ng/ml LPS
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 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 dendritic cells, 2h after stimulation with 100ng/ml LPS
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 (3)
GSE32377 Analysis of H3K9 trimethylation in unstimulated and stimulated dendritic cells and fibroblasts
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 SRX099239
BioSample SAMN00727970

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data not provided for this record

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