|
| Status |
Public on Sep 24, 2009 |
| Title |
S395T [exon level] |
| Sample type |
RNA |
| |
|
| Source name |
S395T,surgically resected from patient of gastric cancer
|
| Organism |
Homo sapiens |
| Characteristics |
Sample_ID:S395T
Sex:Female
Age:84
Histopathology:Adenocarcinoma
Stage:T2
Lymph Nodes:N3
Metastasis:M0
Differentiation:Poor differentiation
Hp:+
CEA(ng/L):1.19
|
| Biomaterial provider |
department of surgery, Changhai Hospital,Shanghai,China
|
| Treatment protocol |
Sample was frozen in liquid nitrogen after surgically resected. 8 um cryostat sections was made and pathologically re-inspected by another pathologist with H&E staining. Pure tumor cells were obtained by LCM before RNA extraction.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA were isolated by RNAqueous-Micro kit (Ambion) according to the manufacturer’s instructions.
|
| Label |
biotin
|
| Label protocol |
Biotinylated cDNA were prepared according to the standard Affymetrix protocol from 100ng total RNA(GENECHIP WHOLE TRANSCRIPT (WT) SENSE TARGET LABELING ASSAY MANUAL,Affymetrix).
|
| |
|
| Hybridization protocol |
5 ug of cDNA were hybridized for 17 hr at 45C and 60 rpm on GeneChip Human Exon 1.0 ST Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
|
| Scan protocol |
Genechips were scanned using the Genechip scanner 3000.
|
| Description |
Gene expression and alternative splicing between cancer and normal mucosa.
|
| Data processing |
The Expression Console software version 1.0 integrated RMA algorithm was selected to derive the signal intensities for both gene-level and probeset (exon level), and “Detection Above Background” (DABG) p-value for each probeset from the .CEL files of the 25 sample pairs. Core exons and transcripts were selected in later analysis.
|
| |
|
| Submission date |
Oct 14, 2008 |
| Last update date |
Jan 16, 2014 |
| Contact name |
Zhang Qinghua |
| E-mail(s) |
qinghua_zhang@shbiochip.com
|
| Organization name |
Shanghai shbiochip co
|
| Street address |
151# libing road
|
| City |
shanghai |
| ZIP/Postal code |
201203 |
| Country |
China |
| |
|
| Platform ID |
GPL5188 |
| Series (1) |
| GSE13195 |
Gene expression and alternative splicing in human gastric cancer |
|
