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Sample GSM2470514 Query DataSets for GSM2470514
Status Public on May 25, 2017
Title bladder_cancer_turbt_sample_289
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: 55.55342466
cstage: T2
cnode: 0
bca_subtype: Basal
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.NAC289
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 0.171326329655172
7SK 0.700836652272727
A1BG -0.0439422397916667
A1BG-AS1 0.000227303809523815
A1CF -0.0971555578571429
A2M 0.782315300070422
A2M-AS1 -0.239834899
A2ML1 0.0893310389256198
A2ML1-AS2 -0.3800410275
A2MP1 -0.148459795038168
A3GALT2 -0.066507743125
A4GALT 0.132704586086957
A4GNT 0.040270046
AA06 -0.12239972
AAAS 0.272090065
AACS 0.0794267750526316
AACSP1 -0.00942712041666667
AADAC -0.164571219615385
AADACL2 -0.083061031875
AADACL2-AS1 -0.171064316923077

Total number of rows: 46050

Table truncated, full table size 1124 Kbytes.




Supplementary file Size Download File type/resource
GSM2470514_GNDX.NAC289.CEL.gz 19.5 Mb (ftp)(http) CEL
Processed data included within Sample table

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