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Sample GSM1365197 Query DataSets for GSM1365197
Status Public on Nov 30, 2014
Title NonV3
Sample type RNA
 
Source name non-vestibular Schwannoma
Organism Homo sapiens
Characteristics cell type: non-vestibular Schwannoma
tissue type: 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
Description Non-vestibular schwannoma 3
Data processing Scanned images (DAT files) were transformed into intensities (CEL files) by GCOS (Affymetrix).
HuGene-1_0-st-v1.r4.pgf
HuGene-1_0-st-v1.r4.mps
 
Submission date Apr 08, 2014
Last update date Nov 30, 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 GPL10739
Series (2)
GSE56597 Wide methylation analysis in vestibular schwannoma [Affymetrix exon level analysis]
GSE56598 Wide methylation analysis in vestibular schwannoma

Data table header descriptions
ID_REF
VALUE Exon level analysis. 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.

Data table
ID_REF VALUE
7896739 4.175008077
7896741 4.102242938
7896743 7.749804877
7896745 5.463323519
7896747 8.537491927
7896749 8.804438559
7896751 4.807310164
7896753 7.26281277
7896755 6.712663536
7896757 6.881883166
7896758 7.034878547
7896760 8.157479965
7896762 10.84904388
7896763 5.324340109
7896764 6.753430589
7896765 4.650122133
7896766 8.229299625
7896767 5.862802391
7896768 10.02359818
7896769 6.797349885

Total number of rows: 257430

Table truncated, full table size 5000 Kbytes.




Supplementary file Size Download File type/resource
GSM1365197_2-NonV3.CEL.gz 4.2 Mb (ftp)(http) CEL
Processed data included within Sample table
Processed data are available on Series record

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