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Status |
Public on Jan 13, 2016 |
Title |
H3K27ac Human Brain PrefrontalCortex HS1 |
Sample type |
SRA |
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Source name |
Human female prefrontal cortex tissue
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Organism |
Homo sapiens |
Characteristics |
tissue: Gyrus rectus gender: Female age: 68 Cause of death: Myocardial decompensation with sepsis postmortem delay: 4.2 hrs experiment type: ChIP-Seq chip antibody: H3K27ac (Abcam, ab4729)
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Treatment protocol |
NA
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Growth protocol |
NA
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Extracted molecule |
genomic DNA |
Extraction protocol |
Crosslink, Lyse and Immunoprecipitate Illumina Truseq DNA library protocol
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Library strategy |
ChIP-Seq |
Library source |
genomic |
Library selection |
ChIP |
Instrument model |
Illumina HiSeq 2000 |
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Description |
GSM1119166
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Data processing |
Mapping Illumina: Bowtie (1.1.0), parameters: -m 1 --best --strata --chunkmbs 512 -S --phred64-quals -q -l 40/45 -n 1 Mapping SOLiD: Bowtie (1.1.0), parameters: -m 1 --best --strata --chunkmbs 512 -S -l 50 -n 3 -C -Q -f Peak calling: MACS2 (2.1.0), parameters: callpeak -B -p 1e-5 -g hs --nomodel --extsize 400 --llocal 100000 genome build: hg38, rheMac3, panTro4, mm10 processed data files format and content: txt files contain called peaks processed data files format and content: narrowPeak files contain called peaks in BED format processed data files format and content: bedGraph files contain treat pileup processed data files format and content: bw files contain treat pileup read per million (RPM) normalized in bigWig format
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Submission date |
Apr 16, 2015 |
Last update date |
May 15, 2019 |
Contact name |
Menno P Creyghton |
E-mail(s) |
m.creyghton@hubrecht.eu
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Organization name |
Hubrecht Institute
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Lab |
Creyghton
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Street address |
Uppsalalaan 8
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City |
Utrecht |
ZIP/Postal code |
3584 CT |
Country |
Netherlands |
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Platform ID |
GPL11154 |
Series (1) |
GSE67978 |
Epigenomic annotation of gene regulatory alterations during evolution of the primate brain |
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Relations |
Reanalysis of |
GSM1119166 |
BioSample |
SAMN03487948 |
SRA |
SRX998298 |
Supplementary file |
Size |
Download |
File type/resource |
GSM1660049_H3K27ac_Human_Brain_PrefrontalCortex_HS1_hg38.bw |
167.5 Mb |
(ftp)(http) |
BW |
GSM1660049_H3K27ac_Human_Brain_PrefrontalCortex_HS1_hg38_peaks.narrowPeak.gz |
1.1 Mb |
(ftp)(http) |
NARROWPEAK |
GSM1660049_H3K27ac_Human_Brain_PrefrontalCortex_HS1_hg38_peaks.txt.gz |
1.2 Mb |
(ftp)(http) |
TXT |
GSM1660049_H3K27ac_Human_Brain_PrefrontalCortex_HS1_hg38_treat_pileup.bedGraph.gz |
199.1 Mb |
(ftp)(http) |
BEDGRAPH |
SRA Run Selector |
Raw data are available in SRA |
Processed data provided as supplementary file |
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