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Status
Public on Jul 17, 2024
Title
T20
Sample type
RNA
Source name
Homo Sapiens
Organism
Homo sapiens Characteristics
sample type: High Grade Bladder Cancer
Extracted molecule
total RNA
Extraction protocol
Total RNA was extracted using the RNeasy Mini kit (Qiagen Inc., Valencia, CA, USA) and the RNAprotect reagent (Qiagen) and DNA was removed by on-column DNase digestion with the RNase-Free DNase set (Qiagen). RNA quality and concentration was determined by analysis with an Agilent 2100 bioanalyzer at the Harvard-Partners Center for Genetics and Genomics (Harvard Medical School, Cambridge, MA USA).
Label
Cy3
Label protocol
Cy3 9mer Wobble TriLink, Biotechnologies, 50 O.D., N46-0001-50
Hybridization protocol
MAUI Hybridization System, BioMicro Systems, 02-A002-03
Scan protocol
DNA Microarray Scanner, Agilent, G2565B
Data processing
Raw values were trimmed to exclude 4295 random probes. Raw values were log2-transformed, and samples were median centered. The median-centered log2 values were then quantile-normalized in R (normalize.quantiles).
Submission date
Jul 18, 2013
Last update date
Jul 17, 2024
Contact name
Bogdan Czerniak
E-mail(s)
bczernia@mdanderson.org Organization name
UT MD Anderson Cancer Center
Department
Pathology
Street address
1515 Holcombe
City
Houston
State/province
TX
ZIP/Postal code
77030
Country
USA
Platform ID
GPL17471 Series (1)
GSE49024 Expression analysis of RB1 region in bladder cancer cases
Data table header descriptions ID_REF VALUE quantile-normalized, median-centered, log2 transformed raw intensity values.
Data table ID_REF VALUE CHR13FS045100002
-0.392481436
CHR13FS045100011
-0.122077984
CHR13FS045100019
-0.306998719
CHR13FS045100027
-0.275710865
CHR13FS045100038
-0.408053271
CHR13FS045100047
0.274057618
CHR13FS045100054
0.178790225
CHR13FS045100065
0.137550219
CHR13FS045100074
-0.318013404
CHR13FS045100083
0.042687758
CHR13FS045100091
-0.324891984
CHR13FS045100099
-0.436627514
CHR13FS045100108
0.054865047
CHR13FS045100117
-0.201841398
CHR13FS045100126
-0.109900296
CHR13FS045100135
0.073429702
CHR13FS045100145
-0.001329666
CHR13FS045100189
-0.320294115
CHR13FS045100198
-0.591367038
CHR13FS045100206
-0.602938722
385012 11050 Kbytes .Supplementary file Size Download File type/resource GSM1192532_10120702.csv.gz
5.3 Mb
(ftp) (http) CSV
GSM1192532_10120702_532.pair.gz
5.8 Mb
(ftp) (http) PAIR
Processed data included within Sample table Processed data provided as supplementary file
