|
| Status |
Public on May 17, 2012 |
| Title |
tumor 58 [EXPID7188] |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
lung adenocarcinoma tumor RNA
|
| Organism |
Homo sapiens |
| Characteristics |
subtype: magnoid
age (90=greater than or equal to 90): 74
Sex: M
smoking_status(0=nonsmoker,1=smoker): Smoker
pack_years: 50
Stage: IB
grade: 2
tumor_percent: 60
marked_lymphocytes: 0
adenosquamous_content (0='no', 1='yes'): 0
bronchioloalveolar_content (0='no', 1='yes'): 0
survival_months: 61.6016427104723
survival_status(0='alive',1='dead'): 1
egfr (0='wt',1='mutated'): 0
kras (0='wt',1='mutated'): 1
tp53 (0='wt',1='mutated'): 1
stk11 (0='wt',1='mutated'): 0
|
| Treatment protocol |
Not applicable
|
| Growth protocol |
Not applicable
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using RNeasy kit from Qiagen following manufacturer's instructions. These total RNA samples were run on an Agilent Bioanalyzer 2100 (Agilent Technologies, Inc) to ensure RNA quality.
|
| Label |
Cy5
|
| Label protocol |
The total RNA labeling and hybridization protocol used is described in the Agilent low RNA input linear amplification kit (http://www.chem.agilent.com/Scripts/PDS.asp?lPage=10003 ), with the following two changes: 1) a Qiagen PCR purification kit was used to clean up the cRNA instead of the LiCl precipitation, and 2) all regents volumes were reduced by one half.
|
| |
|
| Channel 2 |
| Source name |
Stratagene Human Universal Reference
|
| Organism |
Homo sapiens |
| Characteristics |
reference: Stratagene Human Universal Reference that contained 1/10 added MCF7 and ME16C RNAs
|
| Treatment protocol |
Not applicable
|
| Growth protocol |
Not applicable
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using RNeasy kit from Qiagen following manufacturer's instructions. These total RNA samples were run on an Agilent Bioanalyzer 2100 (Agilent Technologies, Inc) to ensure RNA quality.
|
| Label |
Cy3
|
| Label protocol |
The total RNA labeling and hybridization protocol used is described in the Agilent low RNA input linear amplification kit (http://www.chem.agilent.com/Scripts/PDS.asp?lPage=10003 ), with the following two changes: 1) a Qiagen PCR purification kit was used to clean up the cRNA instead of the LiCl precipitation, and 2) all regents volumes were reduced by one half.
|
| |
|
| |
| Hybridization protocol |
Microarrays were hybridized in an Robbins Scientific hybridization oven with 850ng of labeled Cy3 Reference and 850ng of Cy5 experimental samples using the Agilent hybridization kit as described by the manufacturer. The arrays were incubated overnight and then washed once for 10 minutes in 2X SSC and 0.0005% triton X-102, twice for 5 minutes in 0.1XSSC, and then immersed into Agilent Stabilization and Drying solution for 20 seconds.
|
| Scan protocol |
Microarrays were scanned with Agilent Scanner and intensity was recorded using Agilent Feature Extraction Software.
|
| Description |
tumor 58
|
| Data processing |
Agilent feature extraction output was processed by normexp background correction and loess normalization using Bioconductor library limma.
|
| |
|
| Submission date |
Jan 28, 2011 |
| Last update date |
May 17, 2012 |
| Contact name |
Matthew D Wilkerson |
| E-mail(s) |
mwilkers@med.unc.edu
|
| Phone |
919-966-3864
|
| Fax |
919-966-8212
|
| URL |
http://cancer.unc.edu/nhayes
|
| Organization name |
University of North Carolina at Chapel Hill
|
| Department |
Lineberger Comprehensive Cancer Center
|
| Lab |
D. Neil Hayes
|
| Street address |
450 West Drive
|
| City |
Chapel Hill |
| State/province |
NC |
| ZIP/Postal code |
27599-7295 |
| Country |
USA |
| |
|
| Platform ID |
GPL9053 |
| Series (2) |
| GSE26939 |
Human lung adenocarcinoma mRNA expression and gene mutations. |
| GSE36471 |
Human lung adenocarcinoma |
|
