|
| Status |
Public on Mar 18, 2016 |
| Title |
Pt4 |
| Sample type |
SRA |
| |
|
| Source name |
tumor biopsy_Partial Response
|
| Organism |
Homo sapiens |
| Characteristics |
patient id: Pt4
anti-pd-1 response: Partial Response
study site: UCLA
gender: M
age (yrs): 62
disease status: M1c
overall survival (days): 948
vital status: Alive
previous mapki: Y
anatomical location: Adrenal
braf: L331F
nf1: S2597*
treatment: Pembrolizumab
biopsy time: pre-treatment
tissue: Melanoma biopsies
stranded/unstranded rnaseq: unstranded
|
| 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 4 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 |
SAMN04510535 |
| SRA |
SRX1597729 |
