GEO help: Mouse over screen elements for information.
Status
Public on Jul 17, 2024
Title
UC6
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
-0.505258165
CHR13FS045100011
0.397313997
CHR13FS045100019
-0.367106228
CHR13FS045100027
-0.291206809
CHR13FS045100038
-0.179164334
CHR13FS045100047
0.216972355
CHR13FS045100054
0.158436823
CHR13FS045100065
0.286626516
CHR13FS045100074
0.085529248
CHR13FS045100083
0.084471153
CHR13FS045100091
0.095669972
CHR13FS045100099
-0.202288739
CHR13FS045100108
0.399235534
CHR13FS045100117
0.045845994
CHR13FS045100126
0.111796626
CHR13FS045100135
-0.369993762
CHR13FS045100145
0.339116658
CHR13FS045100189
0.072958846
CHR13FS045100198
0.148775961
CHR13FS045100206
-0.18870822
385012 11048 Kbytes .Supplementary file Size Download File type/resource GSM1192524_10111902.csv.gz
5.3 Mb
(ftp) (http) CSV
GSM1192524_10111902_532.pair.gz
5.7 Mb
(ftp) (http) PAIR
Processed data included within Sample table Processed data provided as supplementary file
