|
| Status |
Public on Dec 31, 2021 |
| Title |
Patient_6_post_G207 |
| Sample type |
SRA |
| |
|
| Source name |
glioblastoma
|
| Organism |
Homo sapiens |
| Characteristics |
patient_id: Patient_106
tissue: brain tumor
diagnosis: glioblastoma
glioblastoma subtype: Mesenchymal
brain location: right frontoparietal
g207 treatment: post-G207 inoculation
age (years): 47
Sex: female
survival post g207 (days): 165
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Covaris truXTRAC® FFPE Kit.
Illumina TruSeq stranded mRNA kit.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina Genome Analyzer IIx |
| |
|
| Description |
mRNA
Paired-end 2 x 50bp reads, Illumina GAIIx
|
| 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
Genome_build: GRCh38
Supplementary_files_format_and_content: *.quant.sf: Salmon output; tab-delimited text files including transcript per million (TPM) values; each sample has a separate file labeled "Sample_name.quant.sf".
|
| |
|
| Submission date |
Dec 03, 2020 |
| Last update date |
Dec 31, 2021 |
| 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 |
GPL10999 |
| Series (2) |
| GSE162643 |
RNA-sequencing of human glioblastoma resected tissue before and after inoculation with G207, an oncolytic herpes simplex virus; tissues from a Phase Ib clinical trial |
| GSE164105 |
Gene expression in human recurrent glioblastoma before and after inoculation with the oncolytic herpes simplex virus G207 |
|
| Relations |
| BioSample |
SAMN16990674 |
| SRA |
SRX9629982 |
