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Sample GSM1290091 Query DataSets for GSM1290091
Status Public on Jul 29, 2015
Title C/EBPb-24hours-ChIPseq
Sample type SRA
Source name Haftl pre-B cells
Organism Mus musculus
Characteristics cell type: haftl derived C10 cells
time after induction: 24 hours
chip antibody: C/EBPb (sc-150, Santa Cruz)
Treatment protocol C10 cells were induced by the addition 100 nM of β-estradiol (Calbiochem) and grown with 10 nM of IL-3 and CSF-1 (Peprotech). Control cells were treated with 0.1% ethanol (solvent)
Growth protocol C10 cells were grown in RPMI 1640 without phenol red (Lonza) supplemented with 10% charcoal/dextran-treated FBS (Hyclone) and 50 μM 2-mercaptoethanol (GIBCO), incubated at 37°C in 5% CO2
Extracted molecule genomic DNA
Extraction protocol ChIP experiments were performed as described previously (van Oevelen et al, 2008, PMID:20956564). DNA libraries of C/EBPa and C/EBPb enriched chromatin fragments were prepared using Illumina's reagents and instructions. All other libraries were prepared according to manufacturer’s instructions with some modifications (Asp et al, 2011, PMID: 21551099). All libraries were sequenced on the Illumina 2AAIIx sequencer except C/EBPa and PU.1 libraries generated 10, 30 and 60 minutes post induction and pax5 (0 hours) and Foxo1 (0 hours) that were sequenced using the Illumina Hiseq2000 sequencer.
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina Genome Analyzer IIx
Data processing Images obtained from high throughput sequencing were processed using the Illumina pipeline to generate raw sequence files, which were subsequently aligned to the mouse genome (mm9) using either the Illumina Eland alignment tool or Bowtie (cmd: bowtie -n 0 -l 28 -m 1 mm9 INPUT OUTPUT, Langmead et al, 2009, PMID: 19261174) without mismatches. Aligned sequences were further filtered to remove identical sequence tags and sequence tags that do not align uniquely to the mouse genome
To detect regions enriched for factor binding relative to background, we used HOMER ( (Heinz et al, 2010, PMID: 23064439) with the peak localization/shape option set to region and the style option set to factor.
Genome_build: mm9
Supplementary_files_format_and_content: USCS bed format: chr start end strand
Submission date Dec 16, 2013
Last update date May 15, 2019
Contact name Chris van Oevelen
Phone 0034 933160128
Organization name Centre for Genomic Regulation (CRG)
Department Differentiation and Cancer
Lab Graf
Street address C/ Dr. Aiguader, 88
City Barcelona
State/province Catalunya
ZIP/Postal code 08003
Country Spain
Platform ID GPL11002
Series (1)
GSE53362 Genome-wide maps of transcription factor and co-factor binding during B-cell to Macrophage lineage switching
BioSample SAMN02444881
SRA SRX392739

Supplementary file Size Download File type/resource
GSM1290091_cebpb-24hours-ChIPseq.bed.gz 21.0 Mb (ftp)(http) BED
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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