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As the EGA is co-managed by the EMBL-EBI and CRG, files could be located in the UK and/or Spain, as indicated by their respective flags.

Alternatively, files could be located in one of the international Federated EGA nodes, as indicated next to the node's flag.
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13 WGS and 8 TCS data of ENKL patients treated with pembrolizumab.

Whole-genome sequencing (WGS) was performed for 13 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 or HiSeq X Ten as 2x101 bp or 2x151 bp, respectively. 8 NKTL FFPE specimens were screened for somatic mutations using deep targeted capture sequencing (TCS). FFPE rolls or slides were extracted using QIAamp DNA FFPE Tissue kit (QIAGEN). The FFPE genomic DNA was treated with NEBNext FFPE DNA Repair Mix and assessed by Quant-it PicoGreen dsDNA Assay Kit (Invitrogen). The library was generated from 10-200 ng DNA with SureSelectXT Low Input Target Enrichment System for Illumina Paired-End Sequencing Library (Agilent Technologies) according to manufacturer’s instructions. RNA based probe was designed with SureDesign (Agilent Technologies) to target-capture 140 genes. Next, the captured libraries were pooled in equimolar concentration and sequenced on Illumina Novaseq 6000 platform with SP or S1 chip. Reads aligning to 40 selected genes were isolated post-alignment for this submission. Prefix used in filenames: T - Tumor samples N - Matched-Normal samples

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Data access policy for NKTL 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
EGAS00001003828 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
EGAF00001590038 fastq.gz 59.3 GB Report
EGAF00001590039 fastq.gz 68.1 GB Report
EGAF00001590040 fq.gz 67.4 GB
EGAF00001590041 fq.gz 74.3 GB
EGAF00002015424 fastq.gz 60.6 GB Report
EGAF00002015425 fastq.gz 71.2 GB Report
EGAF00002015426 fastq.gz 30.7 GB Report
EGAF00002015427 fastq.gz 37.5 GB Report
EGAF00002015428 fastq.gz 25.4 GB Report
EGAF00002015429 fastq.gz 31.3 GB Report
EGAF00002015430 fastq.gz 30.0 GB Report
EGAF00002015431 fastq.gz 32.5 GB Report
EGAF00002015432 fastq.gz 29.8 GB Report
EGAF00002015433 fastq.gz 32.5 GB Report
EGAF00002015434 fastq.gz 27.4 GB Report
EGAF00002015435 fastq.gz 30.0 GB Report
EGAF00002015436 fastq.gz 61.1 GB Report
EGAF00002015437 fastq.gz 70.6 GB Report
EGAF00002015438 fastq.gz 68.9 GB Report
EGAF00002015439 fastq.gz 79.2 GB Report
EGAF00002015440 fastq.gz 74.2 GB Report
EGAF00002015441 fastq.gz 85.3 GB Report
EGAF00002015442 fastq.gz 107.9 GB Report
EGAF00002015443 fastq.gz 120.2 GB Report
EGAF00002015444 fastq.gz 106.2 GB Report
EGAF00002015445 fastq.gz 118.7 GB Report
EGAF00002015446 fastq.gz 111.3 GB Report
EGAF00002015447 fastq.gz 125.0 GB Report
EGAF00002036188 fastq.gz 36.6 GB Report
EGAF00002036189 fastq.gz 45.5 GB Report
EGAF00002036190 fastq.gz 102.0 GB Report
EGAF00002036191 fastq.gz 114.6 GB Report
EGAF00002051981 fastq.gz 30.5 GB Report
EGAF00002051982 fastq.gz 35.9 GB Report
EGAF00002051983 fastq.gz 77.7 GB Report
EGAF00002051984 fastq.gz 96.2 GB Report
EGAF00002051985 fastq.gz 27.4 GB Report
EGAF00002051986 fastq.gz 32.2 GB Report
EGAF00002051987 fastq.gz 75.8 GB Report
EGAF00002051988 fastq.gz 93.9 GB Report
EGAF00002051989 fastq.gz 30.4 GB Report
EGAF00002051990 fastq.gz 35.7 GB Report
EGAF00002051991 fastq.gz 71.3 GB Report
EGAF00002051992 fastq.gz 88.4 GB Report
EGAF00002549039 fastq.gz 31.7 GB Report
EGAF00002549040 fastq.gz 33.0 GB Report
EGAF00002549041 fq.gz 66.7 GB Report
EGAF00002549042 fq.gz 68.5 GB Report
EGAF00002549043 fastq.gz 38.5 GB Report
EGAF00002549044 fastq.gz 40.3 GB Report
EGAF00002549045 fq.gz 59.3 GB Report
EGAF00002549046 fq.gz 63.6 GB Report
EGAF00003470720 fq.gz 908.2 MB Report
EGAF00003470721 fq.gz 942.4 MB Report
EGAF00003470722 fq.gz 2.2 GB Report
EGAF00003470723 fq.gz 2.8 GB Report
EGAF00003470724 fq.gz 2.3 GB Report
EGAF00003470725 fq.gz 2.9 GB Report
EGAF00003470726 fq.gz 1.9 GB Report
EGAF00003470727 fq.gz 2.0 GB Report
EGAF00003470728 fq.gz 1.9 GB Report
EGAF00003470729 fq.gz 1.9 GB Report
EGAF00003470730 fq.gz 2.1 GB Report
EGAF00003470731 fq.gz 2.1 GB Report
EGAF00003470732 fq.gz 2.0 GB Report
EGAF00003470733 fq.gz 2.0 GB Report
EGAF00003470734 fq.gz 1.8 GB Report
EGAF00003470735 fq.gz 1.8 GB Report
68 Files (3.3 TB)