WGS and WTS data of patients diagnosed with MEITL.
WGS from 4 patients, WTS from only 3 patients (insufficient tissue from 4th patient for WTS). Whole-genome sequencing (WGS) was performed for 60 pairs of tumor-normal samples from patients diagnosed with NKTL. Genomic DNA from tumor tissue was extracted with QIAamp DNA Mini Kit. The DNA for the matching normal was obtained from blood or buccal swabs and purified by Blood and Cell Culture DNA Mini kit or E.Z.N.A. Tissue DNA Kit (Omega Bio-tek) according to manufacturer’s instructions. The quantity and quality were assessed by Quant-iT PicoGreen dsDNA Assay Kit (Invitrogen) and agarose gel electrophoresis. All sequencing libraries were prepared using TruSeq Nano DNA Library Prep Kit (Illumina). Paired-end sequencing was performed on Illumina HiSeq 2000. Whole-transcriptome sequencing (WTS): Total RNA from snap frozen EITL tumor samples was extracted using TRIzol (Invitrogen) and purified with RNeasy Mini Kit (Qiagen) according to manufacturer’s instructions. The integrity of RNA was determined by electrophoresis using 2100 Bioanalyzer (Agilent Technologies). 500 ng of total RNA was reverse transcribed with iScript cDNA Synthesis Kit (Bio-Rad, Hercules, CA, USA). Quantification was performed using SsoFast EvaGreen Supermix and CFX96 Real-Time PCR System (both Bio-Rad). Sequencing libraries were prepared using the TruSeq Stranded Total RNA Library Prep Kit with Ribo-Zero (Illumina) and WTS was performed on Illumina HiSeq 2500 with 2x101 bp read length. Description of prefix used in filenames: T: Tumor samples N: Normal samples (Blood) P: PDX samples
- 20/09/2019
- 9 samples
- DAC: EGAC00001001323
- Technologies: Illumina HiSeq 2000, Illumina HiSeq 2500
DUO:0000006 version: 2019-01-07
health or medical or biomedical research
This data use permission indicates that use is allowed for health/medical/biomedical purposes; does not include the study of population origins or ancestry.
DUO:0000020 version: 2019-01-07
collaboration required
This data use modifier indicates that the requestor must agree to collaboration with the primary study investigator(s).
DUO:0000021 version: 2019-01-07
ethics approval required
This data use modifier indicates that the requestor must provide documentation of local IRB/ERB approval.
DUO:0000026 version: 2019-01-07
user specific restriction
This data use modifier indicates that use is limited to use by approved users.
Data access policy for MEITL study. National Cancer Centre Singapore.
Contact corresponding author for data access.
Studies are experimental investigations of a particular phenomenon, e.g., case-control studies on a particular trait or cancer research projects reporting matching cancer normal genomes from patients.
| Study ID | Study Title | Study Type |
|---|---|---|
| EGAS00001003876 | Other |
This table displays only public information pertaining to the files in the dataset. If you wish to access this dataset, please submit a request. If you already have access to these data files, please consult the download documentation.
| ID | File Type | Size | Quality Report |
Located in
i
|
|---|---|---|---|---|
| EGAF00002727668 | fastq.gz | 31.2 GB | Report |
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| EGAF00002727669 | fastq.gz | 38.0 GB | Report |
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| EGAF00002727670 | fastq.gz | 72.4 GB | Report |
|
| EGAF00002727671 | fastq.gz | 81.4 GB | Report |
|
| EGAF00002727672 | fastq.gz | 70.5 GB | Report |
|
| EGAF00002727673 | fastq.gz | 78.7 GB | Report |
|
| EGAF00002727674 | fastq.gz | 70.2 GB | Report |
|
| EGAF00002727675 | fastq.gz | 81.1 GB | Report |
|
| EGAF00002727676 | fastq.gz | 69.1 GB | Report |
|
| EGAF00002727677 | fastq.gz | 79.5 GB | Report |
|
| EGAF00002727678 | fastq.gz | 73.9 GB | Report |
|
| EGAF00002727679 | fastq.gz | 80.9 GB | Report |
|
| EGAF00002727680 | fastq.gz | 73.7 GB | Report |
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| EGAF00002727681 | fastq.gz | 81.3 GB | Report |
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| EGAF00002727682 | fastq.gz | 60.1 GB | Report |
|
| EGAF00002727683 | fastq.gz | 70.7 GB | Report |
|
| EGAF00002727684 | fq.gz | 3.1 GB | Report |
|
| EGAF00002727685 | fq.gz | 3.1 GB | Report |
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| EGAF00002727686 | fq.gz | 3.1 GB | Report |
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| EGAF00002727687 | fq.gz | 3.1 GB | Report |
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| EGAF00002727688 | fq.gz | 4.3 GB | Report |
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| EGAF00002727689 | fq.gz | 4.3 GB | Report |
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| EGAF00003449030 | fq.gz | 5.0 GB | Report |
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| EGAF00003449031 | fq.gz | 5.0 GB | Report |
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| EGAF00003449032 | fq.gz | 6.0 GB | Report |
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| EGAF00003449033 | fq.gz | 6.0 GB | Report |
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| EGAF00003449034 | fq.gz | 11.5 GB | Report |
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| EGAF00003449035 | fq.gz | 11.4 GB | Report |
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| EGAF00003988491 | fastq.gz | 4.0 GB | Report |
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| EGAF00003988492 | fastq.gz | 4.2 GB | Report |
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| EGAF00003988493 | fastq.gz | 4.1 GB | Report |
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| EGAF00003988494 | fastq.gz | 4.3 GB | Report |
|
| 32 Files (1.2 TB) | ||||