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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Jun 22, 2010 |
| Title |
p300_ChIPSeq |
| Sample type |
SRA |
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| Source name |
mouse ES cells
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| Organism |
Mus musculus |
| Characteristics |
strain: R1
cell type: ES cells
chip antibody: p300
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| Growth protocol |
R-1 ES cells were cultured under feeder free conditions according to standard procotols.
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
ChIP, DNA purification, and library preparation for Illumina sequencing were performed as described (Schmidt D, Wilson MD, Spyrou C, Brown GD, Hadfield J, et al. (2009) ChIP-seq: using high throughput sequencing to discover protein-DNA interactions. Methods 48: 240-248) . ChIP was performed using commercially available antibodies to CHD7 (Abcam, ab31824, batch #215651) and P300 (Santa Cruz, sc-585, batch # unknown). Sequencing was done on an Illumina GAII instrument according to the manufacturer’s protocol.
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina Genome Analyzer II |
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| Description |
Chromatin IP against p300
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| Data processing |
The Eland software (Illumina) was used to align reads with up to two mismatches against the mm8 reference genome. Regions significantly enriched for CHD7 or p300 binding were identified using F-seq, a feature density estimator for high-throughput sequence tags. Genomic regions found to have an unexpectedly high percentage of reads aligning to the sample positions, indicating PCR artifacts, were eliminated from the analysis. Also excluded from the analysis were CHD7 and p300 peaks in which the midpoint overlapped a repetitive region.
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| Submission date |
Jun 22, 2010 |
| Last update date |
May 15, 2019 |
| Contact name |
Mike Paul Schnetz |
| E-mail(s) |
mps35@case.edu
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| Phone |
216.368.1256
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| Organization name |
Case Western Reserve University
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| Department |
Genetics
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| Lab |
Scacheri
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| Street address |
10900 Eulid Ave
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| City |
Cleveland |
| State/province |
OH |
| ZIP/Postal code |
44106 |
| Country |
USA |
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| Platform ID |
GPL9250 |
| Series (1) |
| GSE22341 |
CHD7 targets active gene enhancer elements to modulate ES cell-specific gene expression. |
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| Relations |
| SRA |
SRX022493 |
| BioSample |
SAMN00016533 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM558675_p300_Aligned.sgr.gz |
96.8 Mb |
(ftp)(http) |
SGR |
| GSM558675_p300_peak_High_thresh.txt.gz |
18.2 Kb |
(ftp)(http) |
TXT |
| GSM558675_p300_peak_Low_thresh.txt.gz |
118.2 Kb |
(ftp)(http) |
TXT |
| GSM558675_p300_peak_Middle_thresh.txt.gz |
35.2 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Processed data provided as supplementary file |
| Raw data are available in SRA |
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