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Sample GSM1541433 Query DataSets for GSM1541433
Status Public on Oct 22, 2017
Title Oesophageal Adenocarcinoma 4
Sample type RNA
 
Source name peripheral blood serum exosomes
Organism Homo sapiens
Characteristics disease state: Oesophageal Adenocarcinoma
tumour stage: locally advanced oesophageal adenocarcinoma
Treatment protocol Peripheral blood was collected into serum clot activator tubes
Growth protocol n/a
Extracted molecule total RNA
Extraction protocol Exosomes were isolated from the serum samples using ExoquickTm (System Biosciences, EXOQ20A-1). Extraction of miRNA from exosomes was performed using a miRNeasy Serum/Plasma kit (Qiagen, #217184) with a final elution volume of 24 microlitres ultra pure water
Label FAMTM
Label protocol PCR assays were performed by following the protocol for TaqMan@OpenArray Human MicroRNA Panel (4461104, Life technologies). For each sample, 3μl of RNA was reverse transcribed using pre-defined RT-primers (MegaplexTM Primer Human Pool A and Pool B) and the TaqMan® microRNA Reverse Transcription Kit (Life technologies, #4366596). Pre-amplifications were carried out with MegaplexTM PreAmp Pools and TaqMan PreAmp Master Mix on 7.5μl cDNA/ sample for each pool. The pre-amplified products (4μl per sample) were diluted at the recommended 1:40 dilution with 156μl of RNase-free ultra pure water before loading onto the 384-well TaqMan OpenArray loading plate. PCR runs were performed on XXX.
 
Hybridization protocol n/a
Scan protocol n/a
Description serum from patient with Oesophageal Adenocarcinoma
Data processing Expression data were processed using OpenArray® Real-Time qPCR Analysis Software (BioTrove™, version 1.0.4). CSV files were generated by the software with the cycle threshold (Ct) values for each microRNA with a setting of Ct confidence value threshold of 150.
The CSV files were imported into Realtime Statminer® software (Integromics, Philadelphia, Pa., USA) for quality checking. Data in the CSV files was then analysed using R version 3.0.2 and SPSS v19 (IBM Inc) for Mac. Only microRNAs which amplified in every sample were analysed for further analysis.
Data were analysed in R version 3.0.2 and SPSS v19 (IBM Inc.). The relative expression of each miRNA was calculated as 2(40-Ct). All possible permutations of miRNA ratios were generated from the relative expression values using R version 3.0.2. Mann-Whitney U tests (p<0.05), linear regression (regression coefficient p<0.05), and area under the curve (AUC>0.7) of Receiver Operating Characteristic curves (ROC) were used to generate a list of differentially expressed microRNAs for control and Barrett's oesoghagus vs. oesophageal adenocarcinoma.
Stepwise forward regression (SPSS v19; IBM Inc) was used to select a panel of microRNA ratios that differentiated controls and Barrett's oesophagus from oesophageal adenocarcinoma.
Matrix normalized worksheet reports the miRNA ratio expression values generated by R version 3.0.2
Fold Change worksheet reports the fold difference of expression of the microRNA ratios between the indicated study groups
 
Submission date Nov 07, 2014
Last update date Oct 22, 2017
Contact name Damian James Hussey
E-mail(s) damian.hussey@flinders.edu.au
Organization name Flinders University
Street address Flinders Drive
City Bedford Park
ZIP/Postal code 5042
Country Australia
 
Platform ID GPL17485
Series (1)
GSE63108 Circulating serum miRNAs as potential diagnostic biomarkers for oesophageal adenocarcinoma

Data table header descriptions
ID_REF
VALUE (Ct) values

Data table
ID_REF VALUE
000338_ath-miR159a 14.07
000387_hsa-miR-10a 26.81
000390_hsa-miR-15b 26.34
000391_hsa-miR-16 22.19
000395_hsa-miR-19a 24.71
000396_hsa-miR-19b 19.97
000397_hsa-miR-21 22.98
000402_hsa-miR-24 19.66
000403_hsa-miR-25 23.89
000405_hsa-miR-26a 23.8
000407_hsa-miR-26b 23.71
000408_hsa-miR-27a 26.58
000411_hsa-miR-28 25.83
000417_hsa-miR-30a-5p 28.43
000420_hsa-miR-30d 23.19
000431_hsa-miR-92a 18.24
000436_hsa-miR-99b 25.95
000442_hsa-miR-106b 23.55
000449_hsa-miR-125b 27.22
000451_hsa-miR-126# 29.43

Total number of rows: 758

Table truncated, full table size 16 Kbytes.




Supplementary data files not provided
Processed data are available on Series record

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