|
| Status |
Public on Sep 24, 2024 |
| Title |
Patient 41, extension |
| Sample type |
SRA |
| |
|
| Source name |
glioblastoma
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: glioblastoma
treatment: neoadjuvant pembrolizumab
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA were extracted from resected tumor specimens preserved in AllProtect tissue reagent (Qiagen) at the time of surgery. For the initial cohort, we simultaneously isolated RNA and DNA using Qiagen AllPrep DNA/RNA kits (#80204). In the expanded cohort, we divided the tumor tissue in half and employed the Qiagen RNeasy Mini Kit (#74104) for RNA isolation.
TruSeq RNA exome kit is used to construct the RNA sequencing libraries
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 3000 |
| |
|
| Description |
mRNA from fresh surgical samples
|
| Data processing |
Paired-end, 2 × 100 base pair (bp) transcriptome reads generated using Illumina NovaSeq S4 were mapped to the Genome Reference Consortium Human Build 38 (GRCh38) reference genome using HISAT2 (version 2.0.6).
The gene level counts were generated by the HTSeq-count program (version 0.5.4p5)
We utilized the edgeR (version 3.38.1 ) R package's cpm() function to compute the normalized gene expression values from the raw gene expression counts. These normalized expression values were log2 transformed after adding a pseudo count of 1. We used the limma (version 3.52.4) R package's removeBatchEffect() to remove batch effects of the log2 transformed normalized expression data.
Assembly: GRCh38
Supplementary files format and content: Gene level raw counts of each sample as computed by htseq-count (tab delimited)
|
| |
|
| Submission date |
Apr 23, 2024 |
| Last update date |
Sep 24, 2024 |
| Contact name |
Lu Sun |
| Organization name |
University of California, LA
|
| Street address |
10833 Le Conte Avenue
|
| City |
Los Angeles |
| State/province |
California |
| ZIP/Postal code |
90095 |
| Country |
USA |
| |
|
| Platform ID |
GPL21290 |
| Series (1) |
| GSE264695 |
Neoadjuvant anti-PD1 immunotherapy for surgically accessible recurrent glioblastoma: clinical and molecular outcomes of a stage 2 single-arm expansion cohort |
|
| Relations |
| BioSample |
SAMN41063239 |
| SRA |
SRX24349130 |
