|
| Status |
Public on May 23, 2017 |
| Title |
P_GSKJ4_rep2 |
| Sample type |
SRA |
| |
|
| Source name |
NCI-H1299 cell line
|
| Organism |
Homo sapiens |
| Characteristics |
histology: NSCLC, Large cell carcinoma
age: 43
gender: M
race: Caucasian
smoking status: Smoker
pack-years: 50
treatment: Parental cells treated with GSKJ4
|
| Treatment protocol |
H1299 Parental and H1299 T18 cells were treated for 24 h with either DMSO control or 1 µM GSK-J4.
|
| Growth protocol |
NSCLC cell lines were maintained in RPMI-1640 (Life Technologies Inc.) with 5% FBS.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using RNeasy Plus Mini kit (Qiagen).
RNA libraries were prepared for sequencing using standard Illumina protocols.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
Basecalls were performed using CASAVA (v. 1.8.2)
Reads were aligned to hg19 geneome assembly and transcript assembly was performed using tophat (v.2.0.13)
RPKM calculation and differential expression analysis was performed using cufflinks (v.2.2.1)
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample ...
|
| |
|
| Submission date |
May 20, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Ralf Kittler |
| E-mail(s) |
Ralf.Kittler@UTSouthwestern.edu
|
| Organization name |
University of Texas Southwestern Medical Center
|
| Street address |
5323 Harry Hines Blvd
|
| City |
Dallas |
| State/province |
Texas |
| ZIP/Postal code |
75390 |
| Country |
USA |
| |
|
| Platform ID |
GPL11154 |
| Series (2) |
| GSE81687 |
Targeting Taxane-Platin Resistant Lung Cancers with JumonjiC Lysine Demethylase Inhibitors (RNA-Seq) |
| GSE81689 |
Targeting Taxane-Platin Resistant Lung Cancers with JumonjiC Lysine Demethylase Inhibitors |
|
| Relations |
| BioSample |
SAMN05151712 |
| SRA |
SRX1782923 |
