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Sample GSM2417575 Query DataSets for GSM2417575
Status Public on Jun 20, 2017
Title MIA CTRL 2
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
BioSample SAMN06112637
SRA SRX2398185

Supplementary file Size Download File type/resource
GSM2417575_MIA-CTRL-041116-2.genes.results.txt.gz 531.7 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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