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Sample GSM3781268 Query DataSets for GSM3781268
Status Public on Jun 27, 2020
Title SU_MB002_TGP_POS_A
Sample type SRA
 
Source name pediatric medulloblastoma
Organism Homo sapiens
Characteristics tissue: pediatric medulloblastoma
molecular subgroup: Group 3
Extracted molecule total RNA
Extraction protocol Total RNA was extracted using the Norgen Total RNA isolation kit and quantified using a NanoDrop Spectrophotometer ND-1000.
The RNA was sequenced using single-end 50 bp reads on the Illumina HiSeq platform (Illumina, San Diego CA, USA).
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 1500
 
Description Singh_HISAT_USCS_VOOM_TMM.csv
SU-MB002-TGP-P-A
Data processing Raw sequence data were exported to FASTQ format and were filtered based on quality scores.
Next the reads were mapped to the GRCh38/hg38 reference version using HISAT.
The counts were obtained by using ht-seq count with the “intersection-strict” option.
Counts were transformed with TMM transformation and then normalized with VOOM.
Genome_build: hg38
Supplementary_files_format_and_content: Processed data file contains a matrix containing data from all samples.
 
Submission date May 20, 2019
Last update date Jun 27, 2020
Contact name Sheila Singh
E-mail(s) ssingh@mcmaster.ca
Organization name McMaster University
Department Biochemistry and Biomedical Sciences
Street address 1280 Main Street West
City Hamilton
State/province ON
ZIP/Postal code L8S4K1
Country Canada
 
Platform ID GPL18460
Series (1)
GSE131473 Wnt activation as a therapeutic strategy in medulloblastoma
Relations
BioSample SAMN11784084
SRA SRX5865885

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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