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Sample GSM1520749 Query DataSets for GSM1520749
Status Public on Aug 17, 2016
Title 8
Sample type RNA
 
Source name body/tail of pancreas
Organism Homo sapiens
Characteristics tissue: pancreatic tumor
Stage: 1b
grouped stage: Early
Biomaterial provider Baki Topal (Department of Abdominal Surgical Oncology, University Hospitals Leuven, KU Leuven)
Treatment protocol NA
Growth protocol Snap-frozen tissue samples were stored in liquid nitrogen and/or at -80C in RNALater (Qiagen) until further use.
Extracted molecule total RNA
Extraction protocol total RNA was extracted using the RNeasy Mini kit (Qiagen) according the manufacturer's instructions. Only samples with an RNA integrity number (RIN) of >7.0 were used.
Label biotin
Label protocol RNA concentration and purity were determined spectrophotometrically using the NanoDrop ND-1000 (NanoDrop Technologies), and RNA integrity was assessed using a Bioanalyser 2100 (Agilent). Using the NuGEN Ovation Pico WTA System, an amount of 2 ng of total RNA was amplified and converted to cDNA. An amount of 5 ug of cDNA was fragmented and labeled with biotin using the NuGEN Encore Biotin Module.
 
Hybridization protocol A mixture of fragmented biotinylated cDNA and hybridisation controls (Affymetrix) was hybridised on Affymetrix HG U219 arrays, followed by staining and washing in a GeneChip Fluidics Station 450 (Affymetrix) according to the manufacturer's procedures.
Scan protocol To assess the raw probe signal intensities, chips were scanned using a GeneChip Scanner 3000 (Affymetrix).
Description PDAC
Data processing Data were normalized using RMA as implemented in the xps package of Bioconductor. Expression values are represented on a log2-scale.
 
Submission date Oct 08, 2014
Last update date Aug 17, 2016
Contact name Rekin's Janky
E-mail(s) Nucleomics.Bioinformatics@vib.be
Organization name VIB
Department Nucleomics Core
Street address Herestraat 49 Box 816
City Leuven
ZIP/Postal code B-3000
Country Belgium
 
Platform ID GPL13667
Series (1)
GSE62165 Prognostic relevance of molecular subtypes and master regulators in pancreatic ductal adenocarcinoma

Data table header descriptions
ID_REF
VALUE RMA

Data table
ID_REF VALUE
11715100_at 3.38000083812206
11715101_s_at 3.78294990402981
11715102_x_at 2.92839112454491
11715103_x_at 4.16688787288745
11715104_s_at 2.99077102253336
11715105_at 2.94030084455075
11715106_x_at 3.45753098053616
11715107_s_at 3.21644671935559
11715108_x_at 2.58207702070087
11715109_at 3.04129143916189
11715110_at 3.10041228580648
11715111_s_at 5.32209653888845
11715112_at 3.08693380548518
11715113_x_at 4.70893838425142
11715114_x_at 4.60600112727958
11715115_s_at 2.68883004361276
11715116_s_at 2.91601663469382
11715117_x_at 2.69816298648975
11715118_s_at 3.26787414901257
11715119_s_at 11.0264980220696

Total number of rows: 49386

Table truncated, full table size 1467 Kbytes.




Supplementary file Size Download File type/resource
GSM1520749_hyb10958.CEL.gz 2.2 Mb (ftp)(http) CEL
Processed data included within Sample table

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