|
| 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).
|
| |
|
| 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.
|
| |
|
| 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 |
