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| Status |
Public on Dec 05, 2012 |
| Title |
Genomic DNA of gastric cancer patient NGCII092 tumour_SOLiDv2 |
| Sample type |
SRA |
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| Source name |
gastric adenocarcinoma of a patient without active H. pylori infection and microsatellite instability but with intestinal metaplasia
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| Organism |
Homo sapiens |
| Characteristics |
tumor type: stage 1b, intestinal Lauren classification, moderately differentiated and of tubular subtype
tissue: tumour
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| Treatment protocol |
no treatment
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| Growth protocol |
primary tissue, no growth conditions
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
For Illumina short insert libraries, genomic DNA was randomly fractionated using Roche Nebulizer following manufacturer's instructions. Fractionated DNA was then end-repaired, A-tailed at 3'end, ligated with Illumina paired end adaptors, PCR amplified followed by gel-selection of a range of 400-600 bp fragments as templates, and sequenced by Illumina GA from both ends to obtain 76 bp and 101 bp reads, respectively, at each end.
For Solid long insert libraries, 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 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.
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| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
AB SOLiD System 2.0 |
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| Description |
genomic DNA hydrosheared in 11.4 kb fragments (std dev: 1011 bp), 2x25bp paired-end (mate pair) sequences
Identification of SNVs, indels, and genomic structural variations
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| Data processing |
Paired-end Illumina reads were mapped to the reference human genome (NCBI Build 36) using ELAND (Illumina Inc.) and reads that failed pass-filter were removed from further analysis.
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 and v4.0 (Applied Biosystems). Discordant paired-end tags (PETs) were defined and clustered to call structural variations as described in the README file (linked as Supplementary file on Series record).
Processed data files linked below and on the Series record.
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| Submission date |
Jul 21, 2011 |
| Last update date |
May 15, 2019 |
| Contact name |
Axel HILLMER |
| E-mail(s) |
ahillmer@uni-koeln.de
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| Organization name |
University of Cologne
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| Department |
Institute of Pathology
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| Street address |
Kerpener Str. 62
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| City |
Cologne |
| ZIP/Postal code |
50937 |
| Country |
Germany |
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| Platform ID |
GPL9138 |
| Series (1) |
| GSE30833 |
Genome Sequencing of Gastric Cancer Reveals Diverse Mutational and Pathogen Signatures |
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| Relations |
| SRA |
SRX084845 |
| BioSample |
SAMN00672836 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM764986_IHG028.clusters.txt.gz |
93.7 Kb |
(ftp)(http) |
TXT |
| GSM764986_hillmer_IHG028_9372_13310.dist.covsmooth.gff.gz |
156.8 Mb |
(ftp)(http) |
GFF |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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