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Sample GSM973652 Query DataSets for GSM973652
Status Public on Mar 01, 2013
Title Vestibular Schwannoma [407]
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 GSM1326739
Reanalyzed by GSM1365230

Data table header descriptions
ID_REF
VALUE RMA signal log2

Data table
ID_REF VALUE
8000869 6.61912752
8049827 11.20715429
8073548 9.328647782
8017039 7.295146192
8071234 7.999740886
8174692 8.264248517
8132292 10.24042823
8114050 9.300129913
8010161 10.30977893
8054467 9.544786895
8095854 10.58146459
7999206 5.242684905
8139727 5.899199108
7917455 10.88779837
8039748 7.752672225
7933640 5.702809922
7972570 7.659821166
7960947 12.41953682
7953775 6.612595872
8076497 7.251960899

Total number of rows: 17587

Table truncated, full table size 341 Kbytes.




Supplementary file Size Download File type/resource
GSM973652_1-407.CEL.gz 4.6 Mb (ftp)(http) CEL
Processed data included within Sample table

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