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| Status |
Public on Nov 17, 2013 |
| Title |
Bcells_untreated_ChIPseq_Cebpa |
| Sample type |
SRA |
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| Source name |
primary Bcells untreated
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| Organism |
Mus musculus |
| Characteristics |
cell type: primary B cells
treatment: untreated
chip antibody: anti-Cebpa (Santa Cruz, catalog: sc-61, lot: k1009)
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| Treatment protocol |
Cells were trypsinized and FACS-sorted to remove feeder and dead cells
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| 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.
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| 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.
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2000 |
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| Description |
Sample 1
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| 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=+)
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| Submission date |
Nov 14, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Bruno Di Stefano |
| E-mail(s) |
distefanob@gmail.com
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| Organization name |
Baylor College of Medicine
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| Department |
Molecular and Cellular Biology
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| Street address |
1 Baylor Plaza
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| City |
Houston |
| State/province |
TX |
| ZIP/Postal code |
77030 |
| Country |
USA |
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| 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 |
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| Relations |
| BioSample |
SAMN02402448 |
| SRA |
SRX377483 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data not provided for this record |
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