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Sample GSM973643 Query DataSets for GSM973643
Status Public on Mar 01, 2013
Title Vestibular Schwannoma [467]
Sample type RNA
 
Source name Vestibular Schwannoma
Organism Homo sapiens
Characteristics group: Tumor
batch: 1
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 GSM1326721
Reanalyzed by GSM1365221

Data table header descriptions
ID_REF
VALUE RMA signal log2

Data table
ID_REF VALUE
8000869 7.307710406
8049827 11.15773477
8073548 9.948221747
8017039 7.43004878
8071234 8.290037825
8174692 7.454405291
8132292 10.44159207
8114050 10.02667708
8010161 10.69202349
8054467 9.843750116
8095854 10.46265303
7999206 5.390287121
8139727 5.690370963
7917455 10.83666346
8039748 7.615279083
7933640 5.587979005
7972570 7.5532633
7960947 11.75009926
7953775 6.184806833
8076497 7.454212637

Total number of rows: 17587

Table truncated, full table size 341 Kbytes.




Supplementary file Size Download File type/resource
GSM973643_1-467.CEL.gz 4.5 Mb (ftp)(http) CEL
Processed data included within Sample table

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