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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Jan 13, 2016 |
| Title |
H3K4me3 Human Brain Putamen HS1 |
| Sample type |
SRA |
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| Source name |
Human female putamen tissue
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| Organism |
Homo sapiens |
| Characteristics |
tissue: Putamen
gender: Female
age: 68
Cause of death: Myocardial decompensation with sepsis
postmortem delay: 4.2 hrs
experiment type: ChIP-Seq
chip antibody: H3K4me3 (Millipore 07-473)
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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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| 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 |
Jul 14, 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
|
| Lab |
Creyghton
|
| 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 |
| BioSample |
SAMN03857995 |
| SRA |
SRX1096826 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1821390_H3K4me3_Human_Brain_Putamen_HS1_hg38.bw |
103.3 Mb |
(ftp)(http) |
BW |
| GSM1821390_H3K4me3_Human_Brain_Putamen_HS1_hg38_peaks.narrowPeak.gz |
747.0 Kb |
(ftp)(http) |
NARROWPEAK |
| GSM1821390_H3K4me3_Human_Brain_Putamen_HS1_hg38_peaks.txt.gz |
840.4 Kb |
(ftp)(http) |
TXT |
| GSM1821390_H3K4me3_Human_Brain_Putamen_HS1_hg38_treat_pileup.bedGraph.gz |
123.8 Mb |
(ftp)(http) |
BEDGRAPH |
SRA Run Selector |
| Processed data provided as supplementary file |
| Raw data are available in SRA |
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