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Sample GSM1365207 Query DataSets for GSM1365207
Status Public on Nov 30, 2014
Title N_HSC
Sample type RNA
 
Source name Human Schwann Cells
Organism Homo sapiens
Characteristics cell type: Human Schwann Cells
tissue type: Control
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
Description Previously analysed Nerve 9
re-analysis of GSM973629
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
Relations
Reanalysis of GSM973629

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 7.366292564
7896741 7.702818807
7896743 9.731800048
7896745 9.335175401
7896747 9.751996069
7896749 9.856910613
7896751 4.40947543
7896753 8.777511872
7896755 6.470036051
7896757 7.126724223
7896758 6.635912596
7896760 7.716302626
7896762 11.49265466
7896763 5.793330144
7896764 5.765614983
7896765 3.750332155
7896766 8.64450111
7896767 6.020801009
7896768 10.61891852
7896769 6.944466894

Total number of rows: 257430

Table truncated, full table size 4999 Kbytes.




Supplementary file Size Download File type/resource
GSM1365207_1-N_HSC.CEL.gz 4.7 Mb (ftp)(http) CEL
Processed data included within Sample table
Processed data are available on Series record

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