|
| Status |
Public on Apr 06, 2011 |
| Title |
breast tumor 2 |
| Sample type |
SRA |
| |
|
| Source name |
Primary breast tumor
|
| Organism |
Homo sapiens |
| Characteristics |
tumor type: basal-like subgroup based on micro array expression data
tissue: mammary gland; breast
|
| Growth protocol |
standard growth conditions for cell lines
|
| 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 10 Kb sized fragments were selected for ligation resulting in circularized products where 5’ and 3’ ends of 10 Kb 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 |
other |
| Instrument model |
AB SOLiD System 2.0 |
| |
|
| Description |
genomic DNA hydrosheared in 9.4 kb fragments (std dev: 2,403 bp below median; 1,332 above median), 2x25bp paired-end (mate pair) sequences
|
| Data processing |
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 (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 by Hillmer et al.: Comprehensive Long Span Paired-End-Tag Mapping Reveals Characteristic Patterns of Structural Variations in Epithelial Cancer Genomes. The Readme file includes additional information about the supplementary cluster and gff files.
|
| |
|
| Submission date |
Jan 29, 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) |
| GSE26954 |
Comprehensive Long Span Paired-End-Tag Mapping Reveals Characteristic Patterns of Structural Variations in Epithelial Cancer Genomes |
|
| Relations |
| SRA |
SRX039761 |
| BioSample |
SAMN00199325 |
