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| Status |
Public on May 06, 2010 |
| Title |
EBF1_ChIPSeq |
| Sample type |
SRA |
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| Source name |
pre B-cells, ChIP
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| Organism |
Mus musculus |
| Characteristics |
cell line: 38B9
cell type: A-MuLV pre B-cells
antibody: anti-EBF1b
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| Treatment protocol |
At a density of 10^6 per ml, the cells were crosslinked with 1% Formaldehyde for 5 minutes at 37°C. The reaction was stopped by the addition of 1/10 volumes of ice cold 1M glycine solution. Cells were washed three times with ice cold PBS and lysed in 50mM Tris pH 8.0, 5mM EDTA, 1% (w/v) SDS (10^7 cell per ml). The chromatin was sheared to an average size of 500bp by sonication.
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| Growth protocol |
RPMI 1640 + 10% fetal calf serum + 4µl/l 2-mercapto-ethanol + penicillin/streptomycin/glutamine, 37°C, 5% CO2.
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
10ng of Ebf1 ChIP material and input DNA, respectively, as per manufacturer's protocol. Briefly, using the Solexa ChIP Seq DNA sample preparation kit, universal linkers were added to the chromatin fragments and DNA was PCR amplified for 15 cycles. DNA was gel-purified and fragments between 200-300bp were selected for sequencing.
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina Genome Analyzer |
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| Description |
ChIP was performed using custom-made polyclonal rabbit antibody against murine EBF1b.
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| Data processing |
The raw images have been processed using the Solexa Pipeline and mapped to the reference genome (NCBI Build 36, mm8) using Eland software with maximal 2 mis-matches.
Peak detection was performed using CCAT (Xu et al., manuscript under revision). The sequence tag density generated from the input library was used as background. Regions enriched in the Ebf1 ChIP sample were identified as peaks. Peaks with FDR <0.01 were considered significant. The peaks data is available in the 'GSE19971_EBF1_mm8_significant.peaks.txt' file, which is linked to the Series GSE19971 record as a supplementary file.
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| Submission date |
Jan 20, 2010 |
| Last update date |
May 15, 2019 |
| Contact name |
Sebastian Pott |
| E-mail(s) |
spott@uchicago.edu
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| Organization name |
University of Chicago
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| Department |
Human Genetics
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| Street address |
920 58th Street
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| City |
Chicago |
| State/province |
Il |
| ZIP/Postal code |
60637 |
| Country |
USA |
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| Platform ID |
GPL9185 |
| Series (1) |
| GSE19971 |
Genome-wide mapping of EBF1 binding sites in murine pre B-cells |
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| Relations |
| SRA |
SRX018714 |
| BioSample |
SAMN00010859 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM499030_CHB003_R00061_lane5_s5_sorted.txt.gz |
601.5 Mb |
(ftp)(http) |
TXT |
| GSM499030_CHB003_R00061_lane6_s6_sorted.txt.gz |
596.0 Mb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Processed data provided as supplementary file |
| Processed data are available on Series record |
| Raw data are available in SRA |
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