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Status
Public on Jul 17, 2024
Title
UC16
Sample type
RNA
Source name
Homo Sapiens
Organism
Homo sapiens Characteristics
sample type: Bladder Cancer Cell Line
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
0.184275334
CHR13FS045100011
0.122723994
CHR13FS045100019
0.146618599
CHR13FS045100027
-0.039573647
CHR13FS045100038
-0.032615292
CHR13FS045100047
0.350164984
CHR13FS045100054
-0.039380094
CHR13FS045100065
0.284728251
CHR13FS045100074
0.333454323
CHR13FS045100083
0.105445389
CHR13FS045100091
0.286200667
CHR13FS045100099
0.005262707
CHR13FS045100108
-0.043980262
CHR13FS045100117
0.02649733
CHR13FS045100126
0.104756387
CHR13FS045100135
-0.434635927
CHR13FS045100145
-0.032426622
CHR13FS045100189
-0.107608559
CHR13FS045100198
0.057071492
CHR13FS045100206
-0.509198822
385012 11051 Kbytes .Supplementary file Size Download File type/resource GSM1192529_10119702.csv.gz
5.4 Mb
(ftp) (http) CSV
GSM1192529_10119702_532.pair.gz
5.8 Mb
(ftp) (http) PAIR
Processed data included within Sample table Processed data provided as supplementary file
