|
| Status |
Public on Jun 20, 2017 |
| Title |
MIA CTRL 1 |
| Sample type |
SRA |
| |
|
| Source name |
pancreatic adenocarcinoma cells
|
| Organism |
Homo sapiens |
| Characteristics |
sirna: ambion silencer select CAT 4390844
|
| 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 |
SAMN06112626 |
| SRA |
SRX2398184 |
