NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM1365200 Query DataSets for GSM1365200
Status Public on Nov 30, 2014
Title N_511
Sample type RNA
 
Source name Auricular Nerve
Organism Homo sapiens
Characteristics cell type: Auricular Nerve
tissue type: Control
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 Previously analysed Nerve 2
re-analysis of GSM973622
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 GSM973622

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 5.997173801
7896741 7.420749247
7896743 8.849534568
7896745 8.411436647
7896747 8.982459089
7896749 8.465678581
7896751 4.020943552
7896753 7.445410061
7896755 6.818453604
7896757 7.469912992
7896758 6.806037177
7896760 8.286399906
7896762 11.95942147
7896763 6.893394517
7896764 7.012974975
7896765 4.479555453
7896766 7.972873632
7896767 6.207899509
7896768 10.78812418
7896769 6.033308683

Total number of rows: 257430

Table truncated, full table size 5000 Kbytes.




Supplementary file Size Download File type/resource
GSM1365200_2-N_511.CEL.gz 3.6 Mb (ftp)(http) CEL
Processed data included within Sample table
Processed data are available on Series record

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap