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| Status |
Public on Oct 19, 2010 |
| Title |
H3K4me3_ChipSeq |
| Sample type |
SRA |
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| Source name |
prefrontal cortex
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| Organism |
Macaca mulatta |
| Characteristics |
gender: Male
age: 3389 days
antibody: H3K4me3
antibody catalog: ab8580
antibody vendor: Abcam
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
The rhesus macaque samples were obtained from the Suzhou Experimental Animal Center (Suzhou, China). Chromatin from the 9-year old frozen rhesus macaque prefrontal cortex tissue was fragmented by sonication and immunueprecipitated by the incubation with antibody against H3K4me3 (cat. ab8580), then DNA was purified for the next library construction. Fragmented genomic DNA without the immunueprecipitation procedure was purified for the next similar treatment as control. Sequencing tags of 36-mer were obtained from the Solexa single-end pipeline. Total RNA was extracted from the dissected frozen prefrontal cortex tissue using Trizol® reagent (Invitrogen, Carlsbad, CA) from five male individuals of 8, 9, 10, 11 and 14 years old and equal amount of them were pooled together. Low molecular weight RNA was isolated, ligated to the adapters, amplified, and sequenced following the paired-end sample preparation protocol (Illumina, USA) and sequenced as 75-mers X2 using the Illumina 1G Genome Analyzer paired-end pipeline.
Library construction was following Illumina's protocol.
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina Genome Analyzer II |
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| Description |
H3K4me3 Chip-sequencing raw reads from post-mortem superior frontal gyrus of a 3389 day old rhesus individual
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| Data processing |
For the H3K4me3 Chip-Seq and Input aligned file, it is in the bed format. Procressed by Soap2 with default parameters. Then filter the duplicate reads.
For the mRNA Sequenceing aligned file, it is in the wig format. Procressed by Tophat with following parameters: "-r 100 -a 8 -m 0 -g 100 --solexa1.3-quals --coverage-search --microexon-search --segment-mismatches 2 --segment-length 25"
For the peak calling file,The meaning of each clolumn is listed below:
Column 1: Chromosome number
Column 2: Start
Column 3: End
Column 4: FDR
The peak calling use SICER with following parameters: w=200 g=200 FDR cutoff=1e-3.
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| Submission date |
Oct 06, 2010 |
| 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) |
| GSE24538 |
Ab initio identification of transcription start sites (TSSs) in the Rhesus macaque genome by histone modification and RNA-Seq |
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| Relations |
| SRA |
SRX028175 |
| BioSample |
SAMN00115679 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM605077_H3K4me3.bed.gz |
90.9 Mb |
(ftp)(http) |
BED |
| GSM605077_H3K4me3_peaks.txt.gz |
233.9 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Processed data provided as supplementary file |
| Raw data are available in SRA |
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