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Status
Public on Jul 17, 2024
Title
UC3
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
0.317077916
CHR13FS045100011
0.081579276
CHR13FS045100019
-0.345620893
CHR13FS045100027
0.024859084
CHR13FS045100038
-0.199527712
CHR13FS045100047
0.104436383
CHR13FS045100054
0.110815273
CHR13FS045100065
0.037833161
CHR13FS045100074
-0.246632907
CHR13FS045100083
0.749358246
CHR13FS045100091
0.192227652
CHR13FS045100099
0.112840871
CHR13FS045100108
0.47601267
CHR13FS045100117
-0.389137112
CHR13FS045100126
-0.023188111
CHR13FS045100135
-0.035378876
CHR13FS045100145
-0.00295769
CHR13FS045100189
0.548777881
CHR13FS045100198
-0.019262972
CHR13FS045100206
-0.0241733
385012 11051 Kbytes .Supplementary file Size Download File type/resource GSM1192523_10109802.csv.gz
5.3 Mb
(ftp) (http) CSV
GSM1192523_10109802_532.pair.gz
5.8 Mb
(ftp) (http) PAIR
Processed data included within Sample table Processed data provided as supplementary file
