NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM900845 Query DataSets for GSM900845
Status Public on Mar 23, 2013
Title Cancer cell only rep1
Sample type RNA
 
Source name Capan1 only
Organism Homo sapiens
Characteristics cell line: Capan1
cell type: Well differentiated human pancreatic cancer cells
exposed to: pancreatic stellate cell line (PS1)
Growth protocol Pancreatic stellate cells were embedded within a gel matrix composing collagen type I and Matrigel, and cancer cells were seeded on top. The gel was lifted on to metal grid after 24 hourd and fed from below. Gels were harvested on day 10 and frozen sections obtained. The cancer cell layer on top of the gel was captured by laser microdissection for RNA extraction.
Extracted molecule total RNA
Extraction protocol RNA was extracted from laser captured Capan1 cells by using RNaqeous micro kit according to manufacturer's instruction
Label biotin
Label protocol Biotinylated cRNA were prepared with the Ambion MessageAmp kit for Illumina arrays.
 
Hybridization protocol Standard illumina hybridisation protocol
Scan protocol Standard illumina illumina scanning protocol
Description c1
Replicate 1
Data processing Quality Control and normalization were performed using BeadStudio (Genome Studio expression analysis module, Genome Studio v2011.1, Gene expression module 1.9.0). Statistical analyses were performed using Bioconductor (www.bioconductor.org) packages within the open source R statistical environment (www.r-project.org)
 
Submission date Mar 23, 2012
Last update date Mar 23, 2013
Contact name Hemant Kocher
E-mail(s) h.kocher@qmul.ac.uk
Organization name Barts and the London
Street address Charterhouse Square
City London
ZIP/Postal code EC1M 6BQ
Country United Kingdom
 
Platform ID GPL10558
Series (1)
GSE36775 Genome wide analysis of pancreatic cancer cell gene expresison exposed to stromal pancreatic stellate cells in 3D gel matrix

Data table header descriptions
ID_REF
VALUE quantile normalized
Detection Pval

Data table
ID_REF VALUE Detection Pval
ILMN_1762337 135.6982 0.02857143
ILMN_2055271 128.2497 0.07792208
ILMN_1736007 109.7797 0.5207792
ILMN_2383229 123.8571 0.1480519
ILMN_1806310 134.7325 0.03116883
ILMN_1779670 99.62627 0.8168831
ILMN_1653355 125.7786 0.1090909
ILMN_1717783 89.60328 0.9792208
ILMN_1705025 111.2092 0.4701299
ILMN_1814316 108.3489 0.5701299
ILMN_2359168 99.36925 0.8220779
ILMN_1731507 93.72987 0.9220779
ILMN_1787689 108.9683 0.5402597
ILMN_3241953 233.2246 0
ILMN_1745607 89.84392 0.9779221
ILMN_2136495 96.25848 0.887013
ILMN_1668111 104.6913 0.6805195
ILMN_2295559 112.6809 0.4233766
ILMN_1735045 131.7363 0.04155844
ILMN_1680754 120.2003 0.2207792

Total number of rows: 47230

Table truncated, full table size 1370 Kbytes.




Supplementary data files not provided
Processed data included within Sample table

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap
External link. Please review our privacy policy.