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Sample GSM1006797 Query DataSets for GSM1006797
Status Public on Sep 30, 2015
Title primary tumor_stage 4_#5
Sample type RNA
 
Source name colorectal primary tumor, stage 4
Organism Homo sapiens
Characteristics tissue: colorectal primary tumor
histology: G2,Moderately differentiated
age: 50
Sex: Male
Stage: 4
Extracted molecule total RNA
Extraction protocol On average, 100-150mg of flash frozen sample tissue were prepared for the extraction of total RNA. TRIZOL Reagent (Invitrogen ) were used to extract total RNA according to manufacturer's protocol
Label Cy5
Label protocol 1 μg total RNA was labeled using a miRCURY LNA™ microRNA Hy3/Hy5 power labeling kit (Exiqon).
 
Hybridization protocol Chips with labeled samples were hybridized at 56°C for overnight in a heat-shrunk hybridization bag (Phalanx), and then washed using a miRCURY LNA™ washing buffer kit (Exiqon).
Scan protocol Slides were scanned using a Genepix 4000B laser scanner (Axon, New York) and fluorescent intensities were extracted from the generated images by Genepix Pro 6.0 software (Axon).
Data processing The repeatability of the microarray within each class ( normal, stage1,2,3 and 4) were examined by correlation analysis. Only those data with over 50% of intra-class correlation coefficient greater than 0.8 were selected for further analysis(Chen et al., 2007). Data filter: > 50% of the arrays and gene signal > 50 were selected. Normalization was done using per chip median normalization and median array method(Liu et al.,2004) .RVM F-test was applied to screen the dynamic differentially expressed miRNA for the normal and different TNM group(Wright et al., 2003).
 
Submission date Sep 19, 2012
Last update date Sep 30, 2015
Contact name xiayu li
E-mail(s) lixiayu@163.com
Organization name Xiangya third hospital
Department department of gastroenterology
Lab Provincial key lab of non-resolving inflammation and cancer
Street address Yuelu district, Tongzipo road #138
City Changsha
State/province Hunan
ZIP/Postal code 410013
Country China
 
Platform ID GPL7724
Series (2)
GSE41012 Dynamic Transcriptome Analysis Reveal New Prognosis Biomarker in Colorectal Cancer (miRNA)
GSE41015 Dynamic Transcriptome Analysis Reveal New Prognosis Biomarker in Colorectal Cancer

Data table header descriptions
ID_REF
VALUE Normalized signal intensity

Data table
ID_REF VALUE
10586 10.1926012
10618 7.789533615
10919 8.103287697
10928 9.291171074
10934 13.40057945
10935 8.816983223
10936 7.392317295
10938 6.77148962
10940 7.388017178
10946 9.425215721
10947 7.654635906
10952 6.243174076
10954 6.724514008
10964 6.864186287
10967 8.713386536
10972 6.543031693
10977 6.179909229
10978 11.86370277
10982 6.982993603
10983 6.573647022

Total number of rows: 247

Table truncated, full table size 4 Kbytes.




Supplementary data files not provided
Processed data included within Sample table

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