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Sample GSM1008953 Query DataSets for GSM1008953
Status Public on Apr 01, 2013
Title H3K4me2_9yr
Sample type SRA
 
Source name prefrontal cortex
Organism Macaca mulatta
Characteristics tissue: prefrontal cortex
age: 9 yr
antibody: Anti-dimethyl-Histone H3 (Lys4) Antibody [Millipore, catalog# 07-030]
Extracted molecule genomic DNA
Extraction protocol The Rhesus macaque tissue samples were obtained from the Suzhou Experimental Animal Center (Suzhou, China). The animals lived in a family setting in a spacious (H x L x W: 3x5x3m3) and clean environment with exercise equipment, and were adequately fed three times (rice, corn and vegetable and nutritional supplements) per day.
Around 200 mg of Rhesus macaque PFC tissues were used for each ChIP reaction using an antibody raised against H3K4me2 (Millipore, 07-030).
The genomic DNA was extracted using exactly the same buffers and procedures with ChIP except for the IP process. In detail, aliquot amount of tissue from seven individuals were pooled and grounded into powder in liquid nitrogen. Then tissue cells were suspended in PBS and chemically cross-linked by adding formaldehyde solution to a final concentration of 1% for 15 min at room temperature. Cells were rinsed twice with 1xPBS, resuspended, lysed (1% SDS, 50 mM Tris pH 8.0, 5 mM EDTA, proteinase inhibitors), and sonicated to gain DNA fragments of in 300-500bp length on average. Samples were then centrifuged at 14,000 rpm for 10 min. The supernatant was diluted (20 mM Tris pH 8.0, 2 mM EDTA, 1% Trion X-100, 150 mM NaCl, proteinase inhibitors) and de-cross-linked by incubation at 65°C water bath overnight. The input DNA were then purified by treatment with RNaseA, proteinase K and multiple phenol:chloroform:isoamyl and alcohol extraction.
Chromatin from the frozen rhesus macaque prefrontal cortex tissue was fragmented by sonication and immunoprecipitated by the incubation with antibody against H3K4me2 (Millipore, 07-030), then DNA was purified for the next library construction. Library construction was following Illumina's protocol. Genomic DNA extracted from a pool of 7 macaque individuals including the four used for ChIP-seq was also sequenced as a control “input” sample.
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina Genome Analyzer II
 
Data processing base-calling: Sequencing tags were obtained from the Solexa single-end pipeline.
alignment: Raw data were Procressed by Soap2 with default parameters. Duplicate reads were filtered.
peak calling: Summary islands were detected by SICER(w=200,g=400) using the combined sequence reads from all four samples.
Genome_build: Mmul 051212 (rheMac2)
Supplementary_files_format_and_content: bed file columns: Column 1: chromosome, Column 2: start, Column 3: end, Column 4: mismatch, Column 5: not use, Column 6: orientation.
Supplementary_files_format_and_content: peak file columns: Column 1: chromosome, Column 2: start position, Column 3: end position, Column 4: read count of input reads, Column 5: read count of control reads, Column 6: p-value as calculated by SICER, Column 7: fold change, Column 8: FDR. Peak file is linked as supplementary file on Series record.
 
Submission date Sep 25, 2012
Last update date May 15, 2019
Contact name Dali Han
E-mail(s) handali294@gmail.com
Organization name University of Chicago
Department Department of Chemisty
Street address 5801 South Ellis Avenue
City Chicago
State/province IL
ZIP/Postal code 60637
Country USA
 
Platform ID GPL9160
Series (1)
GSE41128 Stress-associated H3K4 methylation accumulates during postnatal development and aging of Rhesus macaque brain
Relations
SRA SRX189268
BioSample SAMN01729329

Supplementary file Size Download File type/resource
GSM1008953_H3K4me2_9yr.bed.gz 85.3 Mb (ftp)(http) BED
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

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