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Status
Public on Jul 17, 2024
Title
A20
Sample type
RNA
Source name
Homo Sapiens
Organism
Homo sapiens Characteristics
sample type: Adjacent to Tumor
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
0.372190205
CHR13FS045100011
0.265866738
CHR13FS045100019
-0.437013752
CHR13FS045100027
-0.617384562
CHR13FS045100038
-0.205887353
CHR13FS045100047
0.006412913
CHR13FS045100054
-0.170876362
CHR13FS045100065
0.426429613
CHR13FS045100074
0.476340418
CHR13FS045100083
0.588050915
CHR13FS045100091
-0.2396202
CHR13FS045100099
-0.640835293
CHR13FS045100108
0.082310144
CHR13FS045100117
0.074647655
CHR13FS045100126
0.101380655
CHR13FS045100135
-0.423404601
CHR13FS045100145
-0.060247896
CHR13FS045100189
0.311256306
CHR13FS045100198
0.320763752
CHR13FS045100206
-0.099191412
385012 11047 Kbytes .Supplementary file Size Download File type/resource GSM1192533_10121002.csv.gz
5.3 Mb
(ftp) (http) CSV
GSM1192533_10121002_532.pair.gz
5.7 Mb
(ftp) (http) PAIR
Processed data included within Sample table Processed data provided as supplementary file
