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Sample GSM1363963 Query DataSets for GSM1363963
Status Public on Jun 12, 2017
Title PDAC 100 (exon level)
Sample type RNA
 
Source name PDAC
Organism Homo sapiens
Characteristics tissue: pancreatic ductal adenocarcinoma (PDAC)
cellularity: 80.00
Sex: F
age: 73.00
grading: G2
pt: T3
Extracted molecule total RNA
Extraction protocol Total RNA were extracted. Tumour samples from which the RNA was extracted consisted of at least 60% cancer cells with short and long time survival.
Label biotin
Label protocol Biotinylated cDNA were prepared according to the standard Affymetrix protocol.
 
Hybridization protocol Affymetrix Standard Protocol.
Scan protocol Affymetrix GeneChIP Scanner 3000 7G.
Description Gene expression and alternative splicing between PDAC and normal/adjacent pancreatic tissues.
Data processing Exon array raw CEL files were processed using a pipeline based on the aroma.affymetrix R package. Only the "core" probesets were considered. The custom CDF file "HuEx-1_0-st-v2,coreR2,A20070914,EP.cdf" defining "core" units provided by aroma.affymetrix was used as the default annotation. Within the exon array pipeline, the RMA background correction and quantile normalisation were performed, followed by transcript-level and probeset-level intensity estimation and summarisation. FIRMA scores were also calculated for the alternative splicing analysis. The transcript cluster and probeset mapping to the human genome and gene symbol (hg19) was done using the Affymetrix NetAffx annotations (Release 32), e.g., "HuEx-1_0-st-v2.na32.hg19.transcript.csv" for transcript cluster annotation and "HuEx-1_0-st-v2.na32.hg19.probeset.csv" for probeset annotation. This was followed by intensity filtering as recommended by the Affymetrix exon array whitepaper.
 
Submission date Apr 07, 2014
Last update date Jun 12, 2017
Contact name Jun Wang
E-mail(s) j.a.wang@qmul.ac.uk
Organization name Barts Cancer Institute, Queen Mary, London
Street address Charterhouse Square
City London
ZIP/Postal code EC1M 6BQ
Country United Kingdom
 
Platform ID GPL5188
Series (2)
GSE63111 Gene expression and alternative splicing in pancreatic ductal adenocarcinoma (PDAC) [exon level]
GSE63158 Gene expression and alternative splicing in pancreatic ductal adenocarcinoma (PDAC)
Relations
Alternative to GSM1363848 (gene-level analysis)

Data table header descriptions
ID_REF
VALUE Quantile-normalised expression values from aroma.affymetrix, non-log2-transformed

Data table
ID_REF VALUE
2315252 159.067047119141
2315253 11.8439598083496
2315374 86.185188293457
2315375 17.229154586792
2315376 67.5862503051758
2315377 40.5120658874512
2315586 174.866760253906
2315587 433.463073730469
2315588 142.02067565918
2315589 127.414489746094
2315591 157.411560058594
2315594 190.842559814453
2315595 19.5275230407715
2315596 52.2475471496582
2315598 61.2813186645508
2315602 59.5990562438965
2315603 164.746063232422
2315604 89.4844360351562
2315605 635.304626464844
2315606 153.854553222656

Total number of rows: 284258

Table truncated, full table size 6895 Kbytes.




Supplementary file Size Download File type/resource
GSM1363963_PADC100SET2210409.CEL.gz 23.2 Mb (ftp)(http) CEL
Processed data included within Sample table

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