|
Status |
Public on Mar 17, 2016 |
Title |
Sample_AH-10 Glioblastoma |
Sample type |
SRA |
|
|
Source name |
brain
|
Organism |
Homo sapiens |
Characteristics |
tumor type: glioblastoma (Grade IV)
|
Treatment protocol |
PolyA selection
|
Extracted molecule |
total RNA |
Extraction protocol |
Extract RNA using Qiagen Allprep DNA/RNA mini kit. Tru-Seq RNA sample prep kit
|
|
|
Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina HiSeq 3000 |
|
|
Description |
Glioblastoma tissue sample corresponding to Sample_AH-10
|
Data processing |
Reads were aligned with BWA 0.5.7 to both refseq Ensembl64 transcriptome and hg19 genome. Genome Analysis Toolkit (GATK) 2.8.1 was used to do base recalibration. RNA-SeQC v1.1.7 was used to evaluate and report the sequencing quality and produce the fpkm gene expression values per sample. Genome_build: hg19 Supplementary_files_format_and_content: Gene expression profiles (fpkm) for 32 individual samples were assembled into one plain tex file separated by tab in which rows for genes and columns for samples.
|
|
|
Submission date |
Feb 03, 2016 |
Last update date |
May 15, 2019 |
Contact name |
Amy B Heimberger |
E-mail(s) |
aheimber@mdanderson.org
|
Phone |
713-792-2400
|
Organization name |
The University of Texas MD Anderson Cancer Center
|
Department |
Neurosurgery
|
Street address |
1400 Holcombe Blvd., FC7.2000
|
City |
Houston |
State/province |
TX |
ZIP/Postal code |
77030 |
Country |
USA |
|
|
Platform ID |
GPL21290 |
Series (1) |
GSE77530 |
Gene expression in human glioblastoma specimens |
|
Relations |
BioSample |
SAMN04455038 |
SRA |
SRX1558808 |