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Sample GSM1520757 Query DataSets for GSM1520757
Status Public on Aug 17, 2016
Title 13
Sample type RNA
 
Source name body/tail of pancreas
Organism Homo sapiens
Characteristics tissue: pancreatic tumor
Stage: 2b
grouped stage: LNM
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 2.99361780220331
11715101_s_at 4.0305979631973
11715102_x_at 2.8016856397442
11715103_x_at 4.17370237323544
11715104_s_at 3.11588746666257
11715105_at 3.23819855605938
11715106_x_at 3.19175129593062
11715107_s_at 3.05090575326341
11715108_x_at 2.58404729745826
11715109_at 3.22129546631635
11715110_at 3.3772050129393
11715111_s_at 4.83166567802444
11715112_at 3.57977881223639
11715113_x_at 4.54842207856143
11715114_x_at 4.40300837140208
11715115_s_at 2.75048171591644
11715116_s_at 2.95896088703794
11715117_x_at 2.72303652335192
11715118_s_at 3.28898264690712
11715119_s_at 9.3054843097315

Total number of rows: 49386

Table truncated, full table size 1467 Kbytes.




Supplementary file Size Download File type/resource
GSM1520757_hyb10966.CEL.gz 2.2 Mb (ftp)(http) CEL
Processed data included within Sample table

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