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Sample GSM2470457 Query DataSets for GSM2470457
Status Public on May 25, 2017
Title bladder_cancer_turbt_sample_232
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: 72.2
cstage: T4
cnode: 0
bca_subtype: 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.NAC232
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 0.36102240862069
7SK 0.580918641818182
A1BG -0.134364541875
A1BG-AS1 0.0468443814285714
A1CF -0.0352024888095238
A2M 1.196338895
A2M-AS1 0.037017788
A2ML1 -0.167126632561983
A2ML1-AS2 -0.396026885
A2MP1 -0.104099801068702
A3GALT2 -0.386453609375
A4GALT 0.0817195852173913
A4GNT 0.0114305588
AA06 -0.34297691
AAAS 0.27495189375
AACS 0.01287151
AACSP1 0.00665941125
AADAC -0.0863899203846154
AADACL2 -0.0701752078125
AADACL2-AS1 -0.21458044

Total number of rows: 46050

Table truncated, full table size 1124 Kbytes.




Supplementary file Size Download File type/resource
GSM2470457_GNDX.NAC232.CEL.gz 20.0 Mb (ftp)(http) CEL
Processed data included within Sample table

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