|
| Status |
Public on Oct 28, 2016 |
| Title |
GFP_40_2 |
| Sample type |
SRA |
| |
|
| Source name |
IMR90_GFP_40
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: IMR90
cell type: lung embryonic fibroblast
time (hrs): 40
vector: GFP
|
| 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 |
MP17_GFP_40_2_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 |
| E-mail(s) |
mpadi@email.arizona.edu
|
| 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 |
|
| Relations |
| BioSample |
SAMN04620899 |
| SRA |
SRX1683647 |
