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| Status |
Public on Jan 29, 2013 |
| Title |
human_fetal_cortex_p300 |
| Sample type |
SRA |
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| Source name |
human fetal (gestational week 20) cortex
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| Organism |
Homo sapiens |
| Characteristics |
tissue: human cortex
developmental stage: fetal (gestational week 20)
chip antibody: acCBP/p300 (rabbit polyclonal, Cell Signaling Technology, catalog number = 4771, lot number = 2)
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Tissue samples were cross linked and cells were dissociated and subject to chromatin isolation, sonication and immunoprecipitation using an anti-P300 or anti-acCBP/p300 antibody. ChIP DNA was sheared by sonication, end-repaired, ligated to illumina sequencing adapters. Gel purified amplified ChIP DNA between 300 and 500bp was sequenced on the Illumina GAII or Illumina HiSeq 2000 platforms
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2000 |
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| Description |
Tissue from a single individual. Chromatin IP against acCBP/p300 (rabbit polyclonal, Cell Signaling Technology, catalog number = 4771, lot number = 2)
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| Data processing |
Peaks: Sequence data in the file mouse_e11.5_forebrain_p300.fastq was supplemented with reads from a previously described forebrain p300 ChIP‐seq dataset (Visel et al, Nature 2009). P300 enriched regions were were identified using CCAT (Xu et al, bioinformatics 2010), using a previously described forebrain control sample (Visel et al, Nature 2009). CCAT was run using default parameters for ‘histone’ ChIP-Seq, except for minscore = 2. Enriched regions were filtered to remove those with: i)mapping to an unassembled genomic fragment, ii) an FDR < 0.2, iii) a CCAT enrichment score of <6.5, iv) a sample/control read depth ratio of <2, v) overlap with another CCAT peak with a higher-score region, and v) length >7kb. Finally, peaks within 5kb of the nearest transcript start site were excluded as likely promoters
Peaks: AcCBP/p300 enriched regions in mouse p0 cortex, and human fetal cortex p300 ChIP samples were identified from the intersection of peaks identified by MACS11 (version 1.4, with default settings except: bw = 300; P = 1 × 10−5; mfold = 10,30; local = 20,000; off-auto–shift size = 100) and a modified Grizzly Peak fitting algorithm. Peaks overlapping repeats, or duplicated regions of the genome were removed as likely mapping artifacts.
Alignment: Sequence data in the file mouse_e11.5_forebrain_p300.fastq was supplemented with reads from a previously described forebrain p300 ChIP‐seq dataset (Visel et al, Nature 2009) prior to alignment. Reads were mapped to the mouse genome (mm9) or human genome (hg18) using the Burrows‐ Wheeler Alignment (BWA) tool. Repetitively mapped reads (mapping to multiple sites) and likely PCR artifacts (multiple reads mapping with identical start sites) were removed.
Wig: Aligned read coordinates were extended to 300bp in the direction of the alignment. Coverage depth was calculated from extended reads at 25bp intervals throughout the genome.
Genome_build: mm9
Genome_build: hg18
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| Submission date |
Dec 12, 2012 |
| Last update date |
May 15, 2019 |
| Contact name |
Matthew James Blow |
| E-mail(s) |
mjblow@lbl.gov
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| Phone |
510-486-6590
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| Fax |
510-486-7004
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| Organization name |
Lawrence Berkeley National Laboratory
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| Department |
Genomics Division
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| Lab |
Rubin / Pennacchio
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| Street address |
1 Cyclotron Road
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| City |
Berkeley |
| State/province |
CA |
| ZIP/Postal code |
94720 |
| Country |
USA |
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| Platform ID |
GPL11154 |
| Series (1) |
| GSE42881 |
A High-Resolution Enhancer Atlas of the Developing Telencephalon |
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| Relations |
| SRA |
SRX209673 |
| BioSample |
SAMN01831013 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1052710_human_fetal_cortex_p300.peaks.txt.gz |
26.5 Kb |
(ftp)(http) |
TXT |
| GSM1052710_human_fetal_cortex_p300.wig.gz |
225.0 Mb |
(ftp)(http) |
WIG |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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