|
| Status |
Public on Dec 31, 2014 |
| Title |
lung adenocarcinoma 6 rep1 |
| Sample type |
RNA |
| |
|
| Source name |
resected cancer tissue with >70% tumor content
|
| Organism |
Homo sapiens |
| Characteristics |
tissue type: lung adenocarcinoma
pathologic stage: I
microarray experiment: 1
|
| Extracted molecule |
total RNA |
| Extraction protocol |
The affinity spin column–based Roche® High Pure™ FFPE RNA kit was used to extract total RNA from eight resected stage I lung adenocarcinoma FFPE tumor specimens (~3 mm3) with >70% tumor content. RNA was quantified by RiboGreen fluorescence assay.
|
| Label |
cyanine 3-cytidine bisphosphate (pCp)
|
| Label protocol |
RNA (120 ng) was labeled with cyanine 3-cytidine bisphosphate (pCp) using reagents and methods provided with the Agilent® miRNA Complete Labeling and Hybridization Kit.
|
| |
|
| Hybridization protocol |
Labeled RNA in 45 ul volume was hybdridized for 20 h at 45 ºC under rotation at 20 r.p.m. to Agilent® SurePrint™ G3 Human miRNA 8x60k (release 16.0) microarrays using reagents and methods provided with the Agilent® miRNA Complete Labeling and Hybridization Kit.
|
| Scan protocol |
Microarray slides were scanned on an Agilent® G2505C microarray scanner and data from images was extracted using Agilent® Feature Extraction software (version 9.5.3).
|
| Data processing |
AgiMicroRna Bioconductor package (version 2.10.1) was used in R 3.0.1. Data from all 16 microarrays was processed together. The RMA method was used for summarization. Background correction was not applied. Quantile method was used for inter-array normalization.
|
| |
|
| Submission date |
May 20, 2014 |
| Last update date |
Dec 31, 2014 |
| Contact name |
Santosh Kumar Patnaik |
| Phone |
716-8458364
|
| Organization name |
Roswell Park Comprehensive Cancer Center
|
| Department |
Thoracic Surgery
|
| Street address |
Elm and Carlton Streets
|
| City |
Buffalo |
| State/province |
NY |
| ZIP/Postal code |
14263 |
| Country |
USA |
| |
|
| Platform ID |
GPL15019 |
| Series (1) |
| GSE57835 |
Comparison of microarray and RNA sequencing platforms for profiling microRNAs in formalin-fixed, paraffin-embedded human lung adenocarcinoma specimens |
|
