|
| Status |
Public on Nov 10, 2014 |
| Title |
PDAC 100 (gene 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 |
Sep 08, 2015 |
| 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 |
GPL5175 |
| Series (2) |
| GSE56560 |
Gene expression and alternative splicing in pancreatic ductal adenocarcinoma (PDAC) [gene level] |
| GSE63158 |
Gene expression and alternative splicing in pancreatic ductal adenocarcinoma (PDAC) |
|
| Relations |
| Alternative to |
GSM1363963 (exon-level analysis) |
