|
Status |
Public on Jun 27, 2020 |
Title |
SU_MB002_L807mts_B |
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).
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|
|
Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina HiSeq 1500 |
|
|
Description |
Singh_HISAT_USCS_VOOM_TMM.csv SU-MB002-L807-B
|
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.
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|
|
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 |
SAMN11784087 |
SRA |
SRX5865877 |