|
|
GEO help: Mouse over screen elements for information. |
|
Status |
Public on Jan 13, 2016 |
Title |
H3K27ac Rhesus Brain WhiteMatter RM3 |
Sample type |
SRA |
|
|
Source name |
Rhesus macaque female white matter tissue
|
Organism |
Macaca mulatta |
Characteristics |
tissue: White matter gender: Female age: 10 Cause of death: Euthanasia postmortem delay: 12 hrs experiment type: ChIP-Seq chip antibody: H3K27ac (Abcam, ab4729)
|
Treatment protocol |
NA
|
Growth protocol |
NA
|
Extracted molecule |
genomic DNA |
Extraction protocol |
Crosslink, Lyse and Immunoprecipitate Illumina Truseq DNA library protocol
|
|
|
Library strategy |
ChIP-Seq |
Library source |
genomic |
Library selection |
ChIP |
Instrument model |
Illumina HiSeq 2000 |
|
|
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
|
|
|
Submission date |
Apr 16, 2015 |
Last update date |
May 15, 2019 |
Contact name |
Menno P Creyghton |
E-mail(s) |
m.creyghton@hubrecht.eu
|
Organization name |
Hubrecht Institute
|
Lab |
Creyghton
|
Street address |
Uppsalalaan 8
|
City |
Utrecht |
ZIP/Postal code |
3584 CT |
Country |
Netherlands |
|
|
Platform ID |
GPL14954 |
Series (1) |
GSE67978 |
Epigenomic annotation of gene regulatory alterations during evolution of the primate brain |
|
Relations |
BioSample |
SAMN03487967 |
SRA |
SRX998258 |
Supplementary file |
Size |
Download |
File type/resource |
GSM1660009_H3K27ac_Rhesus_Brain_WhiteMatter_RM3_rheMac3.bw |
270.4 Mb |
(ftp)(http) |
BW |
GSM1660009_H3K27ac_Rhesus_Brain_WhiteMatter_RM3_rheMac3_peaks.narrowPeak.gz |
1.5 Mb |
(ftp)(http) |
NARROWPEAK |
GSM1660009_H3K27ac_Rhesus_Brain_WhiteMatter_RM3_rheMac3_peaks.txt.gz |
1.7 Mb |
(ftp)(http) |
TXT |
GSM1660009_H3K27ac_Rhesus_Brain_WhiteMatter_RM3_rheMac3_treat_pileup.bedgraph.gz |
323.9 Mb |
(ftp)(http) |
BEDGRAPH |
SRA Run Selector |
Raw data are available in SRA |
Processed data provided as supplementary file |
|
|
|
|
|