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| Status |
Public on Sep 09, 2011 |
| Title |
chimp_3 |
| Sample type |
SRA |
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| Source name |
whole blood
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| Organism |
Pan troglodytes |
| Characteristics |
cell type: neutrophil
gender: male
age: young adult
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| Growth protocol |
Whole-blod samples were obtained from healthy, young adult males.
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Neutrophils were isolated immediately after phlebotomy with CD-16 microbeads. An aliquot of each specimen was Wright-Giemsa stained and examined microscopically; all specimens contained >99% neutrophils. DNA was extracted by standard methods, and digested overnight with the methylation-sensitive enyzme HpaII (HpaII cuts CCGG sites when the central C is unmethylated). HpaII fragments of 50-300 bp in length were isolated from an agarose gel, and used to construct single read sequencing libraries using the standard Illumina protocol.
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| Library strategy |
MRE-Seq |
| Library source |
genomic |
| Library selection |
Restriction Digest |
| Instrument model |
Illumina Genome Analyzer |
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| Description |
HpaII digest
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| Data processing |
Raw sequencing data were quality-filtered using the Illumina Pipeline CHASTITY filter with default parameter (0.6).
Alignment ('_bwtout.txt' files): sequencing data were quality-filtered using the Illumina Pipeline CHASTITY filter with default parameter (0.6) and aligned using Bowtie v0.9.9.2 (bowtie-bio.sourceforge.net) to their respective reference genomes. Parameters used to run bowtie: --all -m 1. These parameters allow up to 2 mismatches in the first 28nt. In v 0.9.9.2, hits are "stratified" by default: if a read has 1 zero mismatch hit, and 2 1-mismatch hits, the 1 zero mismatch hit is reported when-m 1 is specified.
Determination of metylation status ('_metmap.wig' files): reads that aligned to HpaII sites (CCGG) were analyzed with MetMap (http://www.cs.berkeley.edu/~meromit/MetMap) to infer methylation states. Results are reported for each CCGG site that can generate a sequenceable fragment (ie, the fragment is of a length that can pass the size selection step during library construction). Results are expressed as the probability p(U) that the site in unmethylated, and vary between 0 (methylated site) and 1 (unmethylated site).
Processed data file build: PanTro2
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| Submission date |
Jun 16, 2010 |
| Last update date |
Jun 11, 2013 |
| Contact name |
Dario Boffelli |
| E-mail(s) |
dario.boffelli@cshs.org
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| Organization name |
Cedars Sinai
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| Department |
Pediatrics
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| Lab |
Boffelli
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| Street address |
700 N San Vicente Blvd
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| City |
Los Angeles |
| State/province |
CA |
| ZIP/Postal code |
90069 |
| Country |
USA |
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| Platform ID |
GPL10547 |
| Series (1) |
| GSE22376 |
Phyloepigenetic comparison of apes |
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| Relations |
| BioSample |
SAMN02196068 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM556673_chimp3_30061AAXX_readsPF.txt.gz |
45.2 Mb |
(ftp)(http) |
TXT |
| GSM556673_chimp3_bwtout.txt.gz |
72.3 Mb |
(ftp)(http) |
TXT |
| GSM556673_chimp3_metmap.wig.gz |
6.6 Mb |
(ftp)(http) |
WIG |
| Processed data provided as supplementary file |
| Raw data not provided for this record |
| Raw data provided as supplementary file |
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