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Sample GSM1006765 Query DataSets for GSM1006765
Status Public on Sep 30, 2015
Title distant normal_stage 1_#4
Sample type RNA
Source name colorectal distant normal mucosa, stage 1
Organism Homo sapiens
Characteristics tissue: colorectal distant normal mucosa
histology: Normal mucosa
age: 60
Sex: Female
paired_tumor_stage: 1
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).
Description matched distant normal mucosa come from the same patient marked with identical sample name(I,II,III and IV stands for TNM stage 1,2,3 and 4,respectively, ca stands for tumor, n stands for normal mucosa);sample name with identical stage and number represent the same patient(for example, I-n-2 and I-ca-2 represent the normal mucosa and tumor from patient #2 of stage I,respectively).
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
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
VALUE Normalized signal intensity

Data table
10586 10.55602741
10618 8.596189499
10919 7.820178986
10928 9.698270798
10934 11.41098118
10935 9.380460739
10936 8.449148178
10938 6.285402298
10940 5.643856049
10946 11.0054493
10947 6.511752605
10952 5.643856049
10954 5.924812317
10964 6.417852402
10967 8.091435432
10972 6.027905941
10977 6.632995129
10978 11.47510052
10982 7.631176949
10983 5.888743401

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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