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Sample GSM3447009 Query DataSets for GSM3447009
Status Public on Dec 05, 2018
Title Patient 4 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 SAMN10311474
SRA SRX4939031

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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