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Sample GSM2027562 Query DataSets for GSM2027562
Status Public on Aug 01, 2016
Title TW03
Sample type RNA
 
Source name nasopharyngeal carcinoma cell line TW03
Organism Homo sapiens
Characteristics cell line: nasopharyngeal carcinoma cell line TW03
Extracted molecule total RNA
Extraction protocol Total RNA was isolated using TRIzol (Invitrogen) and miRNeasy mini kit (QIAGEN) according to manufacturer’s instructions, which efficiently recovered all RNA species, including miRNAs. RNA quality and quantity was measured by using nanodrop spectrophotometer (ND-1000, Nanodrop Technologies) and RNA Integrity was determined by gel electrophoresis
Label Hy3
Label protocol After RNA isolation from the samples, the miRCURY™ Hy3™/Hy5™ Power labeling kit (Exiqon, Vedbaek, Denmark) was used according to the manufacturer’s guideline for miRNA labelling. One microgram of each sample was 3'-end-labeled with Hy3TM fluorescent label, using T4 RNA ligase by the following procedure: RNA in 2.0 μL of water was combined with 1.0 μL of CIP buffer and CIP (Exiqon). The mixture was incubated for 30 min at 37°C, and was terminated by incubation for 5 min at 95°C. Then 3.0 μL of labeling buffer, 1.5 μL of fluorescent label (Hy3TM), 2.0 μL of DMSO, 2.0 μL of labeling enzyme were added into the mixture. The labeling reaction was incubated for 1 h at 16°C, and terminated by incubation for 15 min at 65°C
 
Hybridization protocol After stopping the labeling procedure, the Hy3™-labeled samples were hybridized on the miRCURYTM LNA Array (v.18.0) (Exiqon) according to array manual. The total 25 μL mixture from Hy3™-labeled samples with 25 μL hybridization buffer were first denatured for 2 min at 95°C, incubated on ice for 2 min and then hybridized to the microarray for 16–20 h at 56°C in a 12-Bay Hybridization Systems (Hybridization System - Nimblegen Systems, Inc., Madison, WI, USA), which provides an active mixing action and constant incubation temperature to improve hybridization uniformity and enhance signal. Following hybridization, the slides were achieved, washed several times using Wash buffer kit (Exiqon), and finally dried by centrifugation for 5 min at 400 rpm.
Scan protocol Slides were scanned using the Agilent Microarray Scanner (part number G2505C).Scanned images were then imported into GenePix Pro 6.0 software (Axon) for grid alignment and data extraction.
Data processing Replicated miRNAs were averaged and miRNAs that intensities>=30 in all samples were chosen for calculating normalization factor. Expressed data were normalized using the Median normalization. After normalization, differentially expressed miRNAs were identified through Fold Change filtering. Hierarchical clustering was performed using MEV software (v4.6, TIGR).
Normalized signal intensity. The corrected value is the signal of the probe after background correction = Foreground-Background Intensity. If the corrected value is a negative number, then the final normalized value is defined as null.
 
Submission date Jan 05, 2016
Last update date Aug 01, 2016
Contact name ping lan
Organization name Sun Yat-sen University Cancer Center
Street address 651 Dongfend East Road
City Guangzhou
ZIP/Postal code 510060
Country China
 
Platform ID GPL16016
Series (1)
GSE76527 microRNA profiles of nasopharyngeal carcinoma cell line and nasopharyngeal epithelial cell line

Data table header descriptions
ID_REF
VALUE Normalized signal intensity

Data table
ID_REF VALUE
13138 0.558363418
42638 0.315282792
42888 1.571600481
17519 0.478941035
17278 0.060168472
46507 0.197352587
17928 0.214199759
42826 0.815884477
17537 1.29723225
42722 null
42645 0.267148014
46636 0.168471721
11134 0.069795427
17295 0.669073406
32825 0.791817088
46276 null
42812 0.156438026
42918 0.182912154
46457 null
42469 0.028880866

Total number of rows: 3526

Table truncated, full table size 59 Kbytes.




Supplementary file Size Download File type/resource
GSM2027562_TW03.gpr.gz 939.0 Kb (ftp)(http) GPR
Processed data included within Sample table

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