 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Sep 09, 2011 |
| Title |
human_1_MspI |
| Sample type |
SRA |
| |
|
| Source name |
whole blood
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: neutrophil
gender: male
age: young adult
|
| Growth protocol |
Whole-blod samples were obtained from healthy, young adult males.
|
| 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-insensitive enyzme MspI (in contrast to HpaII, MspI cuts CCGG sites independently of their methylation state). MspI fragments of 50-300Â bp in length were isolated from an agarose gel, and used to construct single read sequencing libraries using the standard Illumina protocol.
|
| |
|
| Library strategy |
MRE-Seq |
| Library source |
genomic |
| Library selection |
Restriction Digest |
| Instrument model |
Illumina Genome Analyzer |
| |
|
| Description |
MspI digest
MethylSeq
|
| Data processing |
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.
|
| |
|
| Submission date |
Aug 01, 2011 |
| Last update date |
May 15, 2019 |
| Contact name |
Dario Boffelli |
| E-mail(s) |
dario.boffelli@cshs.org
|
| Organization name |
Cedars Sinai
|
| Department |
Pediatrics
|
| Lab |
Boffelli
|
| Street address |
700 N San Vicente Blvd
|
| City |
Los Angeles |
| State/province |
CA |
| ZIP/Postal code |
90069 |
| Country |
USA |
| |
|
| Platform ID |
GPL9052 |
| Series (1) |
| GSE22376 |
Phyloepigenetic comparison of apes |
|
| Relations |
| SRA |
SRX092373 |
| BioSample |
SAMN00710342 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM770500_h1_msp_CGG_bwtout.txt.gz |
151.4 Mb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
|
|
|
|
 |
