|
| Status |
Public on Aug 27, 2015 |
| Title |
UT_SCC118 |
| Sample type |
SRA |
| |
|
| Source name |
Cutaneous squamous cell carcinoma 118
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: Cutaneous SCC
sample type: Derived from cSCC tumors
|
| Treatment protocol |
NHEK and cSCC cell lines were serum starved for 24 hourse and the cell lysates were harvested.
|
| Growth protocol |
NHKEs and cSCC cell lines were cultured and incubated at 37C.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNAs were extracted according to the manufacturer's instruction and eluted in sterile water (miRNAeasy Mini Kit, Qiagen GmbH, Hilden, Germany).
The whole transcriptome libraries were constructed following the Whole Transcriptome Analysis Kit procedure (SOLiD™, Applied Biosystems, Foster City, CA).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
AB SOLiD System 3.0 |
| |
|
| Description |
Primary cSCC cells
|
| Data processing |
RNA sequencing reads obtained from the instrument were aligned against the human reference genome (GRCh37 assembly) using the standard whole transcriptome pipeline and the colorspace alignment tool provided by Applied Biosystems and distributed with the instrument.
Data were filtered using the following specifications: FC=2, LogFC=1, Ptype=FDR, P=0.05.
Genome_build: GRCh37
Supplementary_files_format_and_content: Normalization was performed using limma package (Bioconductor)
|
| |
|
| Submission date |
Mar 02, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Liisa Nissinen |
| E-mail(s) |
liisa.nissinen@utu.fi
|
| Organization name |
University of Turku
|
| Department |
Dermatology
|
| Lab |
Cancer Research Laboratory
|
| Street address |
Medisiina D, 5th floor; Kiinamyllynkatu 10
|
| City |
Turku |
| ZIP/Postal code |
FI-20520 |
| Country |
Finland |
| |
|
| Platform ID |
GPL9442 |
| Series (1) |
| GSE66412 |
RNA-Seq whole transcriptome analysis of normal human epidermal keratinocytes and cutaneous squamous cell carcinoma cell lines. |
|
| Relations |
| BioSample |
SAMN03381388 |
| SRA |
SRX894077 |
