|
| Status |
Public on Feb 27, 2012 |
| Title |
Genomic DNA of patient P440 blood [SOLiD v2] |
| Sample type |
SRA |
| |
|
| Source name |
mononuclear blood cells
|
| Organism |
Homo sapiens |
| Characteristics |
tumor type: chronic myelogenous leukemia, remission, same patient as P145
tissue: blood
|
| Treatment protocol |
no treatment
|
| Growth protocol |
mononuclear cells extracted by standard protocol from patient blood samples
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA was hydrosheared, EcoP15I recognition sites were methylated and EcoP15I CAP adaptors were ligated to the ends of DNA fragments. The methylated DNA constructs were separated on agarose gel and 5, 7, or 9 Kb sized fragments were selected for ligation resulting in circularized products where 5' and 3' ends of the DNA fragments were connected by an internal biotinylated adaptor with two flanking non-methylated EcoP15I CAP adaptors. Constructs were digested by methylation sensitive EcoP15I to release 5' and 3' paired-end tag (PET) constructs. Sequencing adaptors were ligated to the PET constructs, which were then amplified by PCR and sequenced by the Applied Biosystems SOLiD system.
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
PCR |
| Instrument model |
AB SOLiD System 2.0 |
| |
|
| Description |
genomic DNA hydrosheared in 9.2 kb fragments (std dev: 560 bp below median; 502 above median), 2x25bp paired-end (mate pair) sequences
GSM700323 and GSM700324 contain identical processed data files since 2 GEO Sample records have been generated based on sequencers.
|
| Data processing |
Raw data provided. For the project, sequence tags were mapped to the human reference sequence (NCBI Build 36) allowing 2 color code mismatches and paired using SOLiD System Analysis Pipeline Tool, Corona Lite v0.31 (Applied Biosystems) except for library DHH014 which was mapped/paired by Bioscope v1.0.1 (Applied Biosystems). If sequence tags had multiple mapping locations and one of them was located in the expected distance and orientation to its mate, this location was chosen by a process termed 'rescue'. Discordant paired-end tags (PETs) were defined and clustered to call structural variations as described in the readme file.
|
| |
|
| Submission date |
Mar 31, 2011 |
| Last update date |
May 15, 2019 |
| Contact name |
Axel HILLMER |
| E-mail(s) |
ahillmer@uni-koeln.de
|
| Organization name |
University of Cologne
|
| Department |
Institute of Pathology
|
| Street address |
Kerpener Str. 62
|
| City |
Cologne |
| ZIP/Postal code |
50937 |
| Country |
Germany |
| |
|
| Platform ID |
GPL9138 |
| Series (1) |
| GSE28303 |
An East-Asian polymorphism underlies BCR-ABL mutation-independent resistance to tyrosine kinase inhibitors in chronic myelogenous leukemia |
|
| Relations |
| SRA |
SRX060148 |
| BioSample |
SAMN00262782 |
