|
| Status |
Public on Mar 01, 2013 |
| Title |
Vestibular Schwannoma [450] |
| Sample type |
RNA |
| |
|
| Source name |
Vestibular Schwannoma
|
| Organism |
Homo sapiens |
| Characteristics |
group: Tumor
batch: 2
|
| Treatment protocol |
Samples were frozen in liquid Nitrogen immediately after surgical resection, and then conserved at -80ºC until extraction
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was isolated using RNeasy® Mini Kit (QIAGEN) following instructions. Rnase-Free Dnase Set (QIAGEN) was used to eliminate DNA contamitations.
|
| Label |
biotin
|
| Label protocol |
library preparation and amplification were performed following the distributor’s (Sigma-Aldrich) recommendations for whole transcriptome amplification (WTA2). Amplification was performed for 17 cycles, and amplified cDNA was purified and quantified on a NanoDrop ND-1000 spectrophotometer (Thermo-Fischer). Some 8 µg cDNA was subsequently fragmented by DNAseI and biotinylated by terminal transferase obtained from a GeneChip Mapping 10Kv2 Assay Kit (Affymetrix).
|
| |
|
| Hybridization protocol |
Hybridization, washing, staining and scanning of Affymetrix Human Gene ST 1.0 arrays were performed following the manufacturer's recommendations
|
| Scan protocol |
GeneChip® Scanner 3000 7G
|
| Data processing |
Scanned images (DAT files) were transformed into intensities (CEL files) by GCOS (Affymetrix).
probe group file: HuGene-1_0-st-v1.r4.pgf
meta-probeset file: HuGene-1_0-st-v1.r4.mps
RMA signal log2 converted from Expression Console Software 1.1.2800.29167. As samples were processes in two batches, ComBat method was used to remove batch effect. Only NM_ probes from RefSeq annotation were selected for analysis, since the amplification and labeling method is not intended for use with other types of RNAs such as miRNAs, tRNAs, etc. Olfactory receptor were removed to avoid the cross hybridization issues with these genes.
|
| |
|
| Submission date |
Jul 25, 2012 |
| Last update date |
Apr 08, 2014 |
| Contact name |
Miguel Torres-Martin |
| E-mail(s) |
migtorres.martin@gmail.com
|
| Organization name |
Hospital Universitari Germans Trias i Pujol
|
| Department |
Clinical Genomics Unit
|
| Street address |
Carretera de Canyet, s/n
|
| City |
Badalona |
| State/province |
Barcelona |
| ZIP/Postal code |
08916 |
| Country |
Spain |
| |
|
| Platform ID |
GPL6244 |
| Series (1) |
| GSE39645 |
Microarray Analysis in Vestibular Schwannomas |
|
| Relations |
| Reanalyzed by |
GSM1326725 |
| Reanalyzed by |
GSM1365223 |
