|
| Status |
Public on Jul 29, 2015 |
| Title |
C/EBPa-60minutes-ChIPseq |
| Sample type |
SRA |
| |
|
| Source name |
Haftl pre-B cells
|
| Organism |
Mus musculus |
| Characteristics |
cell type: haftl derived C10 cells
time after induction: 60 minutes
chip antibody: C/EBPa (sc-61, 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 HiSeq 2000 |
| |
|
| 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 (http://biowhat.ucsd.edu/homer/ngs/index.html) (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 |
| E-mail(s) |
chrisvanoevelen@gmail.com
|
| 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 |
GPL13112 |
| Series (1) |
| GSE53362 |
Genome-wide maps of transcription factor and co-factor binding during B-cell to Macrophage lineage switching |
|
| Relations |
| BioSample |
SAMN02444872 |
| SRA |
SRX392731 |
