|
| Status |
Public on Oct 04, 2012 |
| Title |
Genomic DNA of the cell line K562_IHK002004_GAII |
| Sample type |
SRA |
| |
|
| Source name |
Pleural effusion of a 53-year-old woman with chronic myeloid leukemia (CML) in blast crisis
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: K562
tumor type: chronic myeloid leukemia
cell type: myeloid blast cells
|
| Treatment protocol |
no treatment
|
| 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 |
Illumina Genome Analyzer II |
| |
|
| Description |
genomic structural variations
genomic DNA hydrosheared in 1.1 kb fragments (std dev: 76.3bp below median; 71.1 above median), 2x25bp paired-end (mate pair) sequences, tag 1 and tag 2 sequence, IHK002
Deviation from 'library construction protocol' for the K562_GenomeAnalyzerII-samples: Illumina sequencing adaptors were ligated to the PET constructs, which were then amplified by PCR and sequenced by an Illumina Genome Analyzer II. For the above menioned study, 36 bp tags were trimmed to 27 bp tags for further analysis.
Processed data file generated from Samples K562_IHK002004_GAII and K562_IHK002004_SOLiDv2:
IHK002004_880_1320.dist.covsmooth.gff [hg18, NCBI build 36; clusters, gff]
Linked as supplementary file on Series record.
|
| 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 (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
|
| |
|
| Submission date |
Oct 06, 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 |
GPL9115 |
| Series (1) |
| GSE32674 |
Long Span DNA Paired-End-Tag (DNA-PET) Sequencing Strategy for the Interrogation of Genomic Structural Mutations |
|
| Relations |
| SRA |
SRX101491 |
| BioSample |
SAMN00739489 |
