|
| Status |
Public on Feb 04, 2014 |
| Title |
PCI35-GM |
| Sample type |
SRA |
| |
|
| Source name |
PCI35_pcDNA3.1-GNAS/R201H-V5/His
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: PCI35
cell type: human pancreatic cancer cell line
transfected with: pcDNA3.1-GNAS/R201H-V5/His
|
| Treatment protocol |
Cells of pancreatic cancer cell lines, PK-8, PCI-35,and MIA PaCa-2, were seeded at 4 × 105 cells/well in 6-well plates and incubated for 24 hours at 37°C in 5% CO2 with humid atmosphere. Then the cells were transfected with either pcDNA 3.1/V5-His vector or pcDNA3.1-GNAS(R201H)-V5-His vector using Lipofectamine 2000 reagent (Life Technologies) according to the manufacturer’s recommendations. The cells were incubated for 24 hours and collected by dissociation using trypsin.
|
| Growth protocol |
PCI35 and PK8 were cultured with RPMI1640 medium supplemented with 10% fetal bovine serum. MIA PaCa-2 was cultures with Dulbecco's modified Eagles medium supplemented with 10% fetal bovine serum.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNAs were isolated using the RNeasy Mini kit (Qiagen, Hilden, Germany).
Serial analysis of gene expression (SAGE) library was constructed using a SOLiD SAGE Kit (Life Technologies) according to the manufacture’s instruction.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
AB 5500xl Genetic Analyzer |
| |
|
| Data processing |
library strategy: SAGE-seq
XSQ files generated from 5500xl SOLiD sequencer were converted into CSFASTA and QUAL files using XSQ Tools.
Sequenced reads were aligned to the NCBI RefSeq reference sequence and SAGE tags were counted using SOLiD SAGE Analysis Software v1.10.
SAGE tag counts were normalized to reads per million (RPM) using R.
Values of RPM were expressed as binary logarithm values (log2 RPM).
Genome_build: NCBI RefSeq
Supplementary_files_format_and_content: log2 RPM
|
| |
|
| Submission date |
Dec 16, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Toru Furukawa |
| E-mail(s) |
toru.furukawa@med.tohoku.ac.jp
|
| Organization name |
Tohoku University Graduate School of Medicine
|
| Department |
Department of Histopathology
|
| Street address |
2-1 Seiryomachi, Aobaku
|
| City |
Sendai |
| ZIP/Postal code |
980-8575 |
| Country |
Japan |
| |
|
| Platform ID |
GPL16288 |
| Series (1) |
| GSE53350 |
A GNAS mutation found in pancreatic intraductal papillary mucinous neoplasms induces drastic alterations of gene expression profiles with upregulation of mucin genes. |
|
| Relations |
| BioSample |
SAMN02444755 |
| SRA |
SRX392672 |
