|
Status |
Public on Mar 18, 2016 |
Title |
Pt31 |
Sample type |
SRA |
|
|
Source name |
tumor biopsy_Progressive Disease
|
Organism |
Homo sapiens |
Characteristics |
patient id: Pt31 anti-pd-1 response: Progressive Disease study site: VIC gender: M age (yrs): 47 disease status: M1c overall survival (days): 704 vital status: Alive previous mapki: N anatomical location: Sigmoid colon braf: V600E treatment: Pembrolizumab biopsy time: pre-treatment tissue: Melanoma biopsies stranded/unstranded rnaseq: stranded
|
Extracted molecule |
polyA RNA |
Extraction protocol |
mirVana RNA extraction kit TruSeq RNA Sample Preparation Kit v2 (unstranded) and KAPA stranded RNA kit (stranded) Poly A transcript enrichment, paired end RNAseq
|
|
|
Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina HiSeq 2000 |
|
|
Description |
Patient 31 melanoma, pre anti-PD-1 treatment, 1st biopsy
|
Data processing |
FASTQ files were mapped by Tophat2 Tophat BAMs were quantified and normalized using Cuffnorm (for gene analysis) and by htseq-count followed by edgeR's log CPM (for gene-set analysis) Genome_build: hg19 Supplementary_files_format_and_content: The normalized expression levels by cuffnorm
|
|
|
Submission date |
Feb 23, 2016 |
Last update date |
Dec 08, 2021 |
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 |
GPL11154 |
Series (1) |
GSE78220 |
mRNA expressions in pre-treatment melanomas undergoing anti-PD-1 checkpoint inhibition therapy |
|
Relations |
BioSample |
SAMN04510520 |
SRA |
SRX1597750 |