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Sample GSM1264229 Query DataSets for GSM1264229
Status Public on Nov 17, 2013
Title Bcells_untreated_ChIPseq_Cebpa
Sample type SRA
 
Source name primary Bcells untreated
Organism Mus musculus
Characteristics cell type: primary B cells
treatment: untreated
chip antibody: anti-Cebpa (Santa Cruz, catalog: sc-61, lot: k1009)
Treatment protocol Cells were trypsinized and FACS-sorted to remove feeder and dead cells
Growth protocol ESCs and iPSCs were cultured on mitomycin C treated MEF feeder cells in KO-DMEM (Invitrogen) supplemented withL-glutamine, penicillin/streptomycin, nonessential amino acids, β-mercaptoethanol, 1,000 U/ml LIF (ESC medium) and 15% fetal bovine serum (FBS, Invitrogen). MEF cultures were established by trypsin digestion of mouse embryos (embryonic day 13.5) and the resulting cells cultured in DMEM supplemented with 10% FBS, L-glutamine and penicillin/streptomycin. CD19+ pro-B and pre-B cells were isolated from bone marrow using monoclonal antibodies to CD19 (1D3), obtained from BD Pharmingen, using MACS (Miltenyi Biotech). After isolation B cells were grown in RPMI medium supplemented with 10% FBS and IL-7. cell reprogramming experiments were conducted in gelatinized plates seeded with a feeder layer of the OP9 stromal cell line, using ESC medium supplemented with 2μg/ml of doxycycline and 15% FBS. For the reprogramming of B cells, IL-4 (10ng/ml), IL-7 (10ng/ml) and IL-15 (2ng/ml) were added to the medium.
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 enriched chromatin fragments were prepared using Illumina's reagents and instructions.
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina HiSeq 2000
 
Description Sample 1
Data processing Basecalls: Images obtained from high throughput sequencing were processed using the Illumina pipeline to generate raw sequence files
Reads alignement: performed with bowtie v2.1.0 (option: -–very-sensitive, other default), on mm9
Filtering: Reads were filter to keep only reads that map, with a quality score (from bowtie2) higher than 10 (samtools -F4 -q10), that map only a unique position (removing reads with tag "XS:i:", using grep -v) and remove duplicates that match the same position (samtools rmdup)
Peak calling: performed with HOMER v4.3 (option: -style factor, other default), using Bcell untreated as control dataset
Genome_build: mm9
Supplementary_files_format_and_content: BED file (chromosome, start, strand, name, score, strand=+)
 
Submission date Nov 14, 2013
Last update date May 15, 2019
Contact name Bruno Di Stefano
E-mail(s) distefanob@gmail.com
Organization name Harvard University
Department Harvard Dept. of Stem Cell and Regenerative Biology
Street address 185 Cambridge Street
City Boston
State/province Ma
ZIP/Postal code 02114
Country USA
 
Platform ID GPL13112
Series (2)
GSE52373 C/EBPα poises B cells for rapid reprogramming into iPS cells [ChIP-Seq]
GSE52397 C/EBPα poises B cells for rapid reprogramming into iPS cells
Relations
BioSample SAMN02402448
SRA SRX377483

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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