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Status |
Public on Apr 01, 2013 |
Title |
H3K4me2_9yr |
Sample type |
SRA |
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Source name |
prefrontal cortex
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Organism |
Macaca mulatta |
Characteristics |
tissue: prefrontal cortex age: 9 yr antibody: Anti-dimethyl-Histone H3 (Lys4) Antibody [Millipore, catalog# 07-030]
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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.
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Library strategy |
ChIP-Seq |
Library source |
genomic |
Library selection |
ChIP |
Instrument model |
Illumina Genome Analyzer II |
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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.
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Submission date |
Sep 25, 2012 |
Last update date |
May 15, 2019 |
Contact name |
Dali Han |
E-mail(s) |
handali294@gmail.com
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Organization name |
University of Chicago
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Department |
Department of Chemisty
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Street address |
5801 South Ellis Avenue
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City |
Chicago |
State/province |
IL |
ZIP/Postal code |
60637 |
Country |
USA |
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Platform ID |
GPL9160 |
Series (1) |
GSE41128 |
Stress-associated H3K4 methylation accumulates during postnatal development and aging of Rhesus macaque brain |
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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 Selector |
Raw data are available in SRA |
Processed data provided as supplementary file |
Processed data are available on Series record |
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