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| Status |
Public on Apr 24, 2014 |
| Title |
ChIPseq_E2A_mast |
| Sample type |
SRA |
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| Source name |
ChIPseq_E2A_mast
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| Organism |
Mus musculus |
| Characteristics |
cell type: primary mast cells
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| Growth protocol |
Mast cells were derived from bone marrow cells collected from tibias and femurs of 3- to 5- month old adult mice. Cells were cultured in Iscove’s modified Dulbecco’s medium (IMDM) supplemented with 10% fetal bovine serum (Sigma), 1% penicillin/streptomycin (Sigma), 150 micromolar MTG (Sigma), 10% stem cell factor conditional media from BHK/MKL cells and 10ng/ml of recombinant mIL-3 (Peprotech). Cells were frequently transferred to new flasks to remove adherent cells and experiments were performed after 3 weeks, when cultures were homogenous. Homogeneity of culture was confirmed by presence of FcERI by FACS and toluidine blue staining of cytospins.
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
ChIP assays were performed as previously described (Wilson NK et al., 2010 Cell Stem Cell) using polyclonal antibodies against CTCF (Upstate, 07-729), E2A (Santa Cruz, sc-763x), Erg (Santa Cruz, sc354x), FLI-1 (Abcam, ab15289-500), GATA2 (Santa Cruz, sc9008x), LMO2 (R&D, AF2726), Meis1 (Santa Cruz, sc-10599x), PU.1 (Santa Cruz, sc-352x), RUNX1 (Abcam, ab23980-100), TAL1 (Santa Cruz, sc12984x), Mitf (Cosmo Bio Co., BAM-73-107-EX), cFos (Santa Cruz, sc-253x). Each ChIPseq sample was amplified and sequenced using the Illumina Genome Analyzer IIx, following manufacturer's instructions.
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina Genome Analyzer IIx |
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| Data processing |
ChIP-seq reads aligned to mm9 using Bowtie with default parameters.
bedGraphs were created with in-house script.
Genome_build: mm9
Supplementary_files_format_and_content: bedGraph – read density profiles
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| Submission date |
Jun 19, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Felicia Ng |
| Organization name |
Cambridge Institute for Medical Research
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| Street address |
Wellcome Trust/MRC Building, Addenbrooke's Hospital, Hills Road
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| City |
Cambridge |
| ZIP/Postal code |
CB3 9BB |
| Country |
United Kingdom |
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| Platform ID |
GPL11002 |
| Series (2) |
| GSE48085 |
Genome-scale analysis in blood progenitor and mast cells reveals how lineage-affiliated transcription factors control distinct regulatory programs [ChIP-Seq/RNA-Seq Experiments] |
| GSE48086 |
Genome-scale analysis in blood progenitor and mast cells reveals how lineage-affiliated transcription factors control distinct regulatory programs |
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| Relations |
| BioSample |
SAMN02207816 |
| SRA |
SRX310199 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1167575_ChIPseq_E2A_mast.bedgraph.gz |
53.0 Mb |
(ftp)(http) |
BEDGRAPH |
| GSM1167575_E2A_mast.bed.gz |
22.8 Kb |
(ftp)(http) |
BED |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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