|
Status |
Public on Jun 20, 2017 |
Title |
PANC1 siL1 LC 1 |
Sample type |
SRA |
|
|
Source name |
pancreatic adenocarcinoma cells
|
Organism |
Homo sapiens |
Characteristics |
sirna: ambion silencer select s37905
|
Treatment protocol |
Cells are transfected with 20 nM siRNA in Opti-MEM for 6 hours. Cells are collected 48 hours post transfection
|
Growth protocol |
cells are grown in DMEM with 10% FBS + 1X pen strep.
|
Extracted molecule |
total RNA |
Extraction protocol |
RNA was extracted from cell pellets using Zymo Quick-RNA MiniPrep Kit Catalog: 11-327 Constructed using the KAPA stranded mRNA kit
|
|
|
Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina HiSeq 3000 |
|
|
Data processing |
Raw reads were aligned to the UCSC Human Genome hg19 using Bowtie2 aligner (version 2.29) with the following parameters: -sensitive, -dpad 0, -gbar 99999999, -mp 1,1, -np 1, -score min L,0, -0.1 Read count was performbed by RSEM (version 1.2.25) Differential expression analysis was performed with the edgeR Bioconductor package Genome_build: UCSC Genome hg19 Supplementary_files_format_and_content: tab-delimited text files include TPM and FPKM, generated using RSEM
|
|
|
Submission date |
Dec 06, 2016 |
Last update date |
May 15, 2019 |
Contact name |
David Dawson |
Organization name |
UCLA
|
Department |
Pathology
|
Lab |
Dawson
|
Street address |
650 Charles E Young Dr South
|
City |
Los Angeles |
State/province |
California |
ZIP/Postal code |
90095 |
Country |
USA |
|
|
Platform ID |
GPL21290 |
Series (1) |
GSE90926 |
TCF7L1 knockdown in pancreatic cancer |
|
Relations |
BioSample |
SAMN06112629 |
SRA |
SRX2398193 |