hum0035 Release Note
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|Research ID||Release Date||Type of Data|
|hum0035.v2||2017/12/26||NGS (Exome, Target amplicon deep sequencing, RNA-seq), SNP-chip, Methylation array|
Analyses data about 522 neuroblastoma (NB) patients, 39 neuroblastoma cell lines (JGAS00000000046), and 10 pancreatoblastoma (PBL) patients (JGAS00000000088) were added.
• SNP-chip: 39 neuroblastoma cell lines and tumor tissues and peropheral blood cells (non-tumor tissues) from 522 NBs and 10 PBLs
GeneChip Human Mapping 250k Nspl (Affymetrix) was used for genotyping.
• Target amplicon deep sequencing: tumor tissues from 522 NBs
HiSeq 2000, MiSeq (Illumina) was used for genotyping.
• Exome: tumor tissues and peripheral blood cells (as non-tumor tissues) from 10 PBLs
Exons were narrowed down by using of SureSelect Human ALL Exon kit (50Mb kit, v4/v5) and read by Illumina HiSeq 2000/2500 (paired-end: 75-108 bp).
• RNA-seq: tumor tissues from 10 PBLs
RNA liberally was builded using BioLabs NEBNext Ultra RNA Library Prep Kit for Illumina or Illumina TruSeq RNA Sample Preparation Kit v2, and read by Illumina HiSeq 2500 (paired-end: 108 bp).
• Methylation array: tumor tissues from 10 PBLs
Infinium MethylationEPIC (Illumina) was used for methylation analysis.
DNAs extracted from fresh tumors and corresponding normal blood samples of 16 rhabdomyosarocoma and 7 pleuropulmonary blastoma patients were used for the whole exome sequencing (bam files) (JGAS00000000036). DNA fragments containing whole coding exons were concentrated using SureSelect Human ALL Exon kit (50Mb kit, v4) followed by 75-108 bp paired-end sequencing by Hiseq 2000/2500 (Illumina).