|
| Status |
Public on Apr 12, 2024 |
| Title |
Subject_3_pre_NeoVax_region_3 |
| Sample type |
SRA |
| |
|
| Source name |
Glioblastoma brain tumor
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: Glioblastoma brain tumor
subject_id: Subject_3
brain tumor region: Region_3
neovax status: Pre_NeoVax
age (years): 62
Sex: female
overall surviva; (days): 486
|
| 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 |
SAMN36675041 |
| SRA |
SRX21123841 |
