|
Status |
Public on Apr 12, 2024 |
Title |
Subject_1_pre_NeoVax_region_2 |
Sample type |
SRA |
|
|
Source name |
Glioblastoma brain tumor
|
Organism |
Homo sapiens |
Characteristics |
tissue: Glioblastoma brain tumor subject_id: Subject_1 brain tumor region: Region_2 neovax status: Pre_NeoVax age (years): 51 Sex: male overall surviva; (days): 497
|
Extracted molecule |
total RNA |
Extraction protocol |
High Pure isolation kit (Roche Life Science) Paired-end 2 x 151 bp reads, NovaSeq6000 Illuminia NEBNext Ultra II Directional RNA library kit
|
|
|
Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina NovaSeq 6000 |
|
|
Data processing |
bcl to fastq was performed using Illumina bcl2fastq conversion software version 2.20.0.422 paired-end FASTQ files were used as input for salmon version 0.9.1 (https://combine-lab.github.io/salmon/getting_started/) the salmon transcriptome index was prepared using the following command: "salmon index -t GRCh38_latest_rna.fna -i GRCh38_latest_rna.fna_transcripts_index -k 31"; the GRCh38_latest_rna.fna was obtained from NCBI via ftp.ncbi.nlm.nih.gov the following parameters were used with salmon processing: libType: A numBootstraps: 100 index: GRCh38_latest_rna.fna_transcripts_index Assembly: GRCh38 Supplementary files format and content: tab-delimited text files including transcript per million (TPM) values; each sample has a separate file labeled "Sample_name.quant.sf"
|
|
|
Submission date |
Jul 21, 2023 |
Last update date |
Apr 12, 2024 |
Contact name |
Katherine E Miller |
E-mail(s) |
katherine.miller@nationwidechildrens.org
|
Organization name |
Nationwide Children's Hospital
|
Department |
Institute for Genomic Medicine
|
Street address |
700 Children's Dr.
|
City |
Columbus |
State/province |
OH |
ZIP/Postal code |
43215 |
Country |
USA |
|
|
Platform ID |
GPL24676 |
Series (2) |
GSE237936 |
RNA-sequencing of primary human glioblastoma resected tissue before and after a personalized, neoantigen-based vaccine plus poly-ICLC (NeoVax); tissues from a Phase 1 clinical trial |
GSE238012 |
Integrating multisector molecular characterization into personalized peptide vaccine design for patients with newly diagnosed glioblastoma. |
|
Relations |
BioSample |
SAMN36675048 |
SRA |
SRX21123834 |