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Sample GSM1520821 Query DataSets for GSM1520821
Status Public on Aug 17, 2016
Title 68
Sample type RNA
 
Source name head 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 3.38639498557866
11715101_s_at 4.37535889365179
11715102_x_at 3.04431384471049
11715103_x_at 4.31196026490143
11715104_s_at 3.31678492427424
11715105_at 3.31278484514482
11715106_x_at 2.85822891264674
11715107_s_at 3.25010319575602
11715108_x_at 3.13530324271175
11715109_at 3.225882765522
11715110_at 2.98270616408997
11715111_s_at 4.37244202090953
11715112_at 3.09622843397376
11715113_x_at 4.84732175591115
11715114_x_at 4.60405513047648
11715115_s_at 2.72878380914188
11715116_s_at 2.80977762923565
11715117_x_at 2.88663850058093
11715118_s_at 3.20186248960104
11715119_s_at 5.29842848895094

Total number of rows: 49386

Table truncated, full table size 1467 Kbytes.




Supplementary file Size Download File type/resource
GSM1520821_hyb11035.CEL.gz 2.2 Mb (ftp)(http) CEL
Processed data included within Sample table

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