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Sample GSM2109310 Query DataSets for GSM2109310
Status Public on Oct 28, 2016
Title ST_0_1
Sample type SRA
Source name IMR90_MCPyV ST_0
Organism Homo sapiens
Characteristics cell line: IMR90
cell type: lung embryonic fibroblast
time (hrs): 0
vector: MCPyV ST
Treatment protocol Dox-inducible IMR90 lines expressing ST or GFP were seeded in 6 cm dishes 24 hours before initiation of timecourse with dox-containing DMEM. Cells were harvested every 8 hours for 96 hours. IMR90 cells were re-fed after 48 hours with dox-containing media.
Growth protocol IMR90 cells were cultured in Dulbecco’s modified eagle medium (DMEM) (Cellgro) supplemented with 1% Pen Strep (GIBCO), 1% Glutamax (GIBCO), 1% non-essential amino acids (GIBCO) and 15% fetal bovine serum (FBS) (Sigma)
Extracted molecule total RNA
Extraction protocol Total RNA was purified using RNeasy Plus Mini Kit (Qiagen) and mRNA was isolated with NEBNext Poly(A) mRNA Magnetic Isolation Module (New England BioLabs).
Sequencing libraries were prepared with NEBNext mRNA library Prep Master Mix Set for Illumina (New England BioLabs), passed Qubit, Bioanalyzer and qPCR QC analyses and sequenced on HiSeq 2000 system (Illumina).
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2000
Description MP40_ST_0_1_10_17_13_genes.txt
Data processing Reads were mapped to a transcriptome index generated from the hg19 human reference genome and the Merkel cell polyomavirus sequence, using Tophat 2.0.4 and Bowtie1 with all default parameters except for the following: --no-novel-juncs --transcriptome-only -p 6.
Log-transformed FPKM (fragments per kilobase of transcript per million mapped reads) were quantified using Cufflinks 1.3.0 and correcting for biases and multi-mapped reads using the following parameters: -q -p 5 -u
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files including FPKM values for each transcript
Submission date Apr 06, 2016
Last update date May 15, 2019
Contact name Megha Padi
Organization name University of Arizona
Department Molecular and Cellular Biology
Street address 1071 East Lowell St.
City Tucson
State/province AZ
ZIP/Postal code 85701
Country USA
Platform ID GPL11154
Series (1)
GSE79968 Merkel cell polyomavirus small T antigen promotes pro-glycolytic metabolic perturbations required for transformation
BioSample SAMN04620927
SRA SRX1683670

Supplementary file Size Download File type/resource
GSM2109310_MP40_ST_0_1_10_17_13_genes.txt.gz 785.9 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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