|EGAD00001004140||HiSeq X Ten,Illumina HiSeq 2000,Illumina NovaSeq 6000||34|
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
Who controls access to this dataset
For each dataset that requires controlled access, there is a corresponding Data Access Committee (DAC) who determine access permissions. Access to actual data files is not managed by the EGA. If you need to request access to this data set, please contact:
DAC for NKTL study. National Cancer Centre Singapore.
Contact person: Lim Jing Quan
Email: lim [dot] jing [dot] quan [at] nccs [dot] com [dot] sg
More details: EGAC00001000640