|
| Status |
Public on Jun 09, 2017 |
| Title |
667N_(HTA-2_0) |
| Sample type |
RNA |
| |
|
| Source name |
adjacent-SCC
|
| Organism |
Homo sapiens |
| Characteristics |
tissue type: Adjacent normal lung tissue
Stage: I
technology: Microarray
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from biological samples using miRNeasy Mini Kit (Qiagen, Hilden, Germany) according to the manufacturer's instructions. RNA quantity was determined using the NanoDrop Spectrophotometer. RNA quality was checked using RNA 6000 NanoChips with the Agilent 2100 Bioanalyzer (Agilent, Diegem, Belgium) and only RNAs with a RIN number >7 were taken forward for microarray experiments.
|
| Label |
biotin
|
| Label protocol |
Labeling has been made using standard Affymetrix protocols.
|
| |
|
| Hybridization protocol |
Hybridation has been made using standard Affymetrix protocols.
|
| Scan protocol |
Scanning has been made using standard Affymetrix protocols.
|
| Data processing |
Pre-processing of Affymetrix CEL-files was performed with Partek® Genomics Suite version 6.6 (Partek® GS) using the robust multi-chip analysis (RMA) algorithm, which performs background adjustment, quantile normalisation and probe summarisation {Irizarry, 2003 #2}. GC-content correction was used, as suggested by the default pipeline of Partek® GS. Gene level expression was estimated using mean of probe set log expression. Further analysis was performed in R/Bioconductor {Team, 2005 #3}.
probe group file: HTA-2_0.r1.pgf
meta-probeset file: HTA-2_0.na33.hg19.probeset.csv
|
| |
|
| Submission date |
Jul 25, 2016 |
| Last update date |
Jun 09, 2017 |
| Contact name |
Arnaud Muller |
| E-mail(s) |
arnaud.muller@lih.lu, arnaud.muller@lns.etat.lu
|
| Organization name |
LIH
|
| Department |
DONC
|
| Lab |
GENPRO
|
| Street address |
84 Val Fleuri
|
| City |
Luxembourg |
| ZIP/Postal code |
1526 |
| Country |
Luxembourg |
| |
|
| Platform ID |
GPL17585 |
| Series (2) |
| GSE84784 |
Compared performance of Affymetrix HTA arrays and Illumina RNAseq for the analysis of tumours [Affymetrix] |
| GSE84788 |
Compared performance of Affymetrix HTA arrays and Illumina RNAseq for the analysis of tumours |
|
