|
| Status |
Public on Dec 05, 2018 |
| Title |
Patient 16 tumor |
| Sample type |
SRA |
| |
|
| Source name |
Recurrent glioblastoma
|
| Organism |
Homo sapiens |
| Characteristics |
therapy: neoadjuvant pembrolizumab
|
| Extracted molecule |
total RNA |
| Extraction protocol |
QIAGEN Rneasy Mini Kit without Dnase
NUGEN mRNA PLUS kit (stranded)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 3000 |
| |
|
| Description |
mRNA from fresh surgical samples
|
| Data processing |
The reads are first mapped to Grch38 using HISAT2
Gene level raw read counts are quantified using htseq-count
Ensemble ID to HUGO gene mapping using biomaRt R package
Gene set enrichment analysis using GSVA R package
Genome_build: GRCh38
Supplementary_files_format_and_content: Gene level raw count matrix
|
| |
|
| Submission date |
Oct 25, 2018 |
| Last update date |
Dec 05, 2018 |
| Contact name |
Willy Hugo |
| E-mail(s) |
hwilly@mednet.ucla.edu
|
| Organization name |
UCLA
|
| Department |
Medicine
|
| Street address |
10833 Le Conte Ave, 52-121 CHS, Division of Dermatology
|
| City |
Los Angeles |
| State/province |
California |
| ZIP/Postal code |
90095 |
| Country |
USA |
| |
|
| Platform ID |
GPL21290 |
| Series (1) |
| GSE121810 |
Neoadjuvant anti-PD-1 immunotherapy promotes a survival benefit with intratumoral and systemic immune responses in recurrent glioblastoma |
|
| Relations |
| BioSample |
SAMN10311469 |
| SRA |
SRX4939036 |
