|
| Status |
Public on Jun 27, 2017 |
| Title |
AS_F3_1-15-0549-3 |
| Sample type |
RNA |
| |
|
| Source name |
NEC specimen
|
| Organism |
Homo sapiens |
| Characteristics |
lung cancer status: No Lung Cancer
smoking status: Current Smoker
time since quit: <15y
mass size: <3cm
age: 50.1589041096
gender: Female
rin: 3.7000000477
batch: 4.5
pack years: 51
|
| Treatment protocol |
not applicable
|
| Growth protocol |
not applicable
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA isolated using miRNeasy kit from Qiagen, quantified using Nanodrop and quality determined using Bioanalyzer 2100 (Life Technologies). RNA was amplified using Ambion WT expression kit (Life Technologies).
|
| Label |
biotin
|
| Label protocol |
Biotin labeling was performed using the Ambion WT Expression Kit (Life Technologies, Grand Island, NY) according to the manufacturer's protocol, followed by the GeneChip WT Terminal Labeling and Controls Kit (Affymetrix, Santa Clara, CA).
|
| |
|
| Hybridization protocol |
The labeled, fragmented DNA was hybridized to the GeneChip Human Gene 1.0 ST Array for 18 hours in a GeneChip Hybridization oven 640 at 45oC with rotation (60 rpm). The hybridized samples were washed and stained using an Affymetrix fluidics station 450.
|
| Scan protocol |
After staining, microarrays were immediately scanned using an Affymetrix GeneArray Scanner 3000 7G Plus.
|
| Description |
Gene expression data from NEC specimen
|
| Data processing |
All 505 microarray CEL files were normalized together using the RMA algorithm implemented in the affy Bioconductor R package and the corresponding default Gene 1.0 ST CDF. ComBat (sva Bioconductor package) was used to correct for microarray batch effects. No covariates other than batch were included in the ComBat model.
|
| |
|
| Submission date |
Apr 28, 2016 |
| Last update date |
Jun 27, 2017 |
| Contact name |
Joseph Perez-Rogers |
| E-mail(s) |
[email protected]
|
| Organization name |
Boston University
|
| Department |
Bioinformatics
|
| Lab |
Spira/Lenburg
|
| Street address |
72 East Concord St
|
| City |
Boston |
| State/province |
MA |
| ZIP/Postal code |
02218 |
| Country |
USA |
| |
|
| Platform ID |
GPL6244 |
| Series (1) |
| GSE80796 |
Gene expression profiling of nasal epithelial cells in current and former smokers with and without lung cancer |
|
