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Sample GSM2470330 Query DataSets for GSM2470330
Status Public on May 25, 2017
Title bladder_cancer_turbt_sample_105
Sample type RNA
 
Source name FFPE bladder cancer
Organism Homo sapiens
Characteristics disease state: muscle-invasive bladder cancer (MIBC)
treatment: pre-NAC
sample_type: transurethral resection of bladder tumor (TURBT)
age: 62.26849315
cstage: T2
cnode: 0
bca_subtype: Infiltrated Luminal
Treatment protocol Not Applicable.
Growth protocol Not Applicable.
Extracted molecule total RNA
Extraction protocol After pathologic review, tissue was harvested from formalin-fixed, paraffin-embedded tumor blocks by 1mm punch under RNase-free conditions. Total RNA was extracted and purified using RNeasy FFPE kit (Qiagen, Valencia, CA).
Label biotin
Label protocol RNA was amplified, fragmented and biotinylated using the WT-Ovation FFPE system (NuGen, San Carlos, CA) according to the manufacturer’s recommendations with minor modifications.
 
Hybridization protocol Samples were hybridized using Affymetrix hybridization kit materials and protocols.
Scan protocol Affymetrix GeneChip Scanner 3000 7G.
Description GNDX.NAC105
bca_subtype=bladder cancer subtype
Data processing Data was normalized using SCAN (SCAN.UPC package from Bioconductor).
 
Submission date Jan 26, 2017
Last update date Feb 10, 2019
Contact name Elai Davicioni
E-mail(s) [email protected]
Organization name GenomeDx
Street address 1152 Mainland St #430
City Vancouver
State/province BC
ZIP/Postal code V6B 4X2
Country Canada
 
Platform ID GPL22995
Series (1)
GSE87304 Impact of molecular subtypes in muscle-invasive bladder cancer on predicting response and survival outcome to neoadjuvant chemotherapy: results from a multi-institutional validation study

Data table header descriptions
ID_REF
VALUE SCAN.UPC value

Data table
ID_REF VALUE
5S_rRNA 0.22768361
7SK 0.98929967
A1BG -0.0535043125
A1BG-AS1 0.0438510671428571
A1CF -0.0665148926190476
A2M 0.980869148028169
A2M-AS1 -0.307026065
A2ML1 0.0325529310743802
A2ML1-AS2 -0.3230949275
A2MP1 -0.153794668320611
A3GALT2 -0.148298871875
A4GALT 0.528927157826087
A4GNT -0.062194212
AA06 -0.22999502
AAAS 0.459053978611111
AACS 0.160554767473684
AACSP1 -0.0666526308333333
AADAC -0.115201932307692
AADACL2 -0.164976879375
AADACL2-AS1 -0.222662902307692

Total number of rows: 46050

Table truncated, full table size 1122 Kbytes.




Supplementary file Size Download File type/resource
GSM2470330_GNDX.NAC105.CEL.gz 20.4 Mb (ftp)(http) CEL
Processed data included within Sample table

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