|
| Status |
Public on Feb 09, 2017 |
| Title |
48 hours DLX3 |
| Sample type |
SRA |
| |
|
| Source name |
SCC13_cells_48 hours DLX3
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: Epidermal squamous cell carcinoma
cell line: SCC13
|
| Treatment protocol |
SCC13 cells were infected with Adeno-GFP or Adeno-DLX3 (Vector Biolabs- PFU of 10^10) at an MOI of 50. Cells were collected for RNA extraction after 18, 24, 36, and 48 hours post-infection.
|
| Growth protocol |
SCC13 cells cultured in DMEM/F12 + Glutamax Media (Gibco) supplemented with 10% Fetal Bovine Serum and swiched to 1% Fetal Bovine Serum at time of infection
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Trizol extraction of total RNA from skin was performed according to the manufacturer's instructions.
RNA fragmentation and cDNA library preparation was performed according to the NEB Next and Ovation SP Ultralow Library System protocol. 2nM cDNA library were analyzed by Illumina HiSeq 2500.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
Illumina Casava1.8.2 software was used for basecalling.
Reads were mapped to hg19 using tophat/2.0.8/bowtie-2.1.0
RPKM values were calculated with Partek 6.6
Genome_build: hg19
Supplementary_files_format_and_content: Excel file includes RPKM values
|
| |
|
| Submission date |
Apr 09, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Hong-wei Sun |
| Organization name |
NIAMS
|
| Department |
Office of Science & Technology
|
| Lab |
Biodata Mining & Discovery Section
|
| Street address |
9000 Rockville Pile
|
| City |
Bethesda |
| State/province |
MD |
| ZIP/Postal code |
20892 |
| Country |
USA |
| |
|
| Platform ID |
GPL16791 |
| Series (2) |
| GSE67713 |
DLX3 alters transcriptomic profile of adhesion, cell cycle, and cell death in Squamous Cell Carcinoma Cells |
| GSE67714 |
DLX3-dependent p53 signaling network controls keratinocyte cell cycle and squamous tumor growth |
|
| Relations |
| BioSample |
SAMN03468558 |
| SRA |
SRX984758 |
