|
| Status |
Public on Nov 13, 2019 |
| Title |
meningioma [18-38] |
| Sample type |
SRA |
| |
|
| Source name |
meningioma, WHO II, Validation
|
| Organism |
Homo sapiens |
| Characteristics |
cohort: Validation
tissue: Meningioma
pathology: WHO II
gender: Male
age: 57
wes: Y
|
| Treatment protocol |
na
|
| Growth protocol |
na
|
| Extracted molecule |
total RNA |
| Extraction protocol |
AllPrep DNA/RNA/Protein Mini Kit (Qiagen).
Illumina, using SOP from BCM-HGSC (https://www.hgsc.bcm.edu).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Description |
18-38
Primary tumor
|
| Data processing |
Individual libraries within the samples were demultiplexed using CASAVA 1.8.2 (CASAVA, RRID:SCR_001802).
TopHat2 (RRID:SCR_013035) was used for read alignment.
FastQC (RRID:SCR_014583) and RSeQC (RRID:SCR_005275) were used for read and alignment quality assessment.
HTSeq (RRID:SCR_005514) was used for expression count.
The reads were aligned to GRCh37 Human reference genome and mapping to the human transcriptome according to UCSC gene annotations.
Genome_build: GRCh37
Supplementary_files_format_and_content: *_htseq.counts.txt: Tab-delimited text files include expression count values for each Sample.
|
| |
|
| Submission date |
Aug 30, 2019 |
| Last update date |
Nov 27, 2021 |
| Contact name |
Tiemo J Klisch |
| E-mail(s) |
klisch@bcm.edu
|
| Phone |
8328248885
|
| Organization name |
Baylor College of Medicine
|
| Department |
Department of Molecular and Human Genetics
|
| Lab |
Klisch
|
| Street address |
1250 Moursund Street, N1370.08
|
| City |
Houston |
| State/province |
Texas |
| ZIP/Postal code |
77030 |
| Country |
USA |
| |
|
| Platform ID |
GPL20301 |
| Series (1) |
| GSE136661 |
Molecular profiling predicts meningioma recurrence and reveals loss of DREAM complex repression in aggressive tumors |
|
| Relations |
| Reanalyzed by |
GSM5705842 |
| BioSample |
SAMN12661738 |
| SRA |
SRX6777570 |
