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Sample GSM991934 Query DataSets for GSM991934
Status Public on Aug 24, 2013
Title Bladder_LG4 [mRNA]
Sample type RNA
 
Source name Bladder
Organism Homo sapiens
Characteristics tissue: low-grade papillary urothelial carcinoma
tumor stage: pTaG2
gender: male
age: 76y
Extracted molecule total RNA
Extraction protocol Total RNA including mRNA and miRNA were extracted using the miRNAeasy Mini Kit (Qiagen, Hilden, Germany) following manufacturer`s instructions. An additional DNA digestion step on the RNA binding silica gel membrane of the spin column was performed with DNase I. RNA concentration and the absorbance ratio of 260 nm to 280 nm were measured on the NanoDrop 1000 spectrophotometer (NanoDrop Technologies, Wilmington, DE, USA). The quality of isolated RNA was determined by the RNA integrity number (RIN) with an Bioanalyzer 2100 (Agilent Technologies, Santa Clara, CA, USA).
Label Cy3
Label protocol Samples were labeled using the miRNA Complete Labelling and Hyb Kit from Agilent Technologies. In brief, 100 ng total RNA was dephosphorylated with Calf Intestine Alkaline Phosphatase, denaturated with DMSO and used as RNA acceptor in a T4 RNA ligase mediated reaction with the RNA donor 3’, 5’-cytidine bisphosphate (Cy3-pCp). The labeling reaction was column purified, dried down using a speed-vac at 45°C and resuspended in blocking and hybridization buffer.
 
Hybridization protocol Labeled samples were hybridized on human catalog 8-plex 15K miRNA microarrays (Agilent Technologies) according to the supplier’s protocol.
Scan protocol Microarrays were washed and subsequently scanned at 5 µm resolution with DNA microarray laser scanner (Agilent Technologies) and processed according to the supplier’s protocol.
Description mRNA Gene expression corresponds to miRNA Data archived under: GSM881450
Data processing Expression files were generated using Agilent's Genespring GX software
 
Submission date Aug 24, 2012
Last update date Aug 24, 2013
Contact name Hellmuth-A Meyer
Organization name Charite
Department Department of Urology
Street address Charitéplatz 1
City Berlin
ZIP/Postal code 10117
Country Germany
 
Platform ID GPL13497
Series (1)
GSE40355 Bladder cancer: analysis of miRNA-mRNA interactions

Data table header descriptions
ID_REF
VALUE Normalized signal intensity (persentile 75 shift, median baseline transformation of all samples) log2 values

Data table
ID_REF VALUE
GE_BrightCorner 1.5126
DarkCorner 0.5098
A_23_P146146 2.8490
A_23_P42935 1.0500
A_23_P117082 -0.8777
A_23_P2683 -0.2029
A_24_P358131 1.3057
A_33_P3367647 1.0185
A_23_P157316 -0.6460
A_32_P14850 2.2412
A_23_P158596 -1.5172
A_23_P350107 -0.0834
A_23_P388190 -1.2062
A_23_P106544 -0.0605
A_33_P3219745 1.9576
A_32_P85539 -0.6881
A_23_P94998 -1.1092
A_33_P3235677 -1.3264
A_23_P417014 -0.2036
A_23_P103905 -0.9237

Total number of rows: 34183

Table truncated, full table size 694 Kbytes.




Supplementary file Size Download File type/resource
GSM991934_US22502595_252665210968_S01_GE1_105_Jan09_1_3_LG4.txt.gz 9.2 Mb (ftp)(http) TXT
Processed data included within Sample table

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