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Status |
Public on Sep 24, 2009 |
Title |
S800N [exon level] |
Sample type |
RNA |
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|
Source name |
S800N,surgically resected from patient of gastric cancer
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Organism |
Homo sapiens |
Characteristics |
Sample_ID:S800N Sex:Female Age:80 Histopathology:Normal Stage:NA Lymph Nodes:NA Metastasis:NA Hp:NA CEA(ng/L):NA
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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 normal gastric mucosa cells were obtained by LCM before RNA extraction.
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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).
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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.
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Scan protocol |
Genechips were scanned using the Genechip scanner 3000.
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Description |
Gene expression and alternative splicing between cancer and normal mucosa.
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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.
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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 |
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