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Sample GSM3092116 Query DataSets for GSM3092116
Status Public on Apr 12, 2018
Title miRNA [5050.1]
Sample type RNA
 
Source name plasma, pre-treatment
Organism Homo sapiens
Characteristics tumour stage (ajcc 7th edition): 3b
primary site: rectum
gender: female
age: 46
treatment: FOLFOX
ethnicity: asian
Treatment protocol n/a
Growth protocol n/a
Extracted molecule total RNA
Extraction protocol Total RNA was isolated from plasma using the MirVana PARIS microRNA isolation kit (Ambion/Applied Biosystems), according to the manufacturer's instructions.
Label SYBR Green
Label protocol Global profiling of miRNAs in the plasma samples was carried out using the BioTrove OpenArray platform (Applied Biosystems), according to the manufacturer’s instructions. For each sample, two RT reactions were performed using MegaPlex RT primer pools A and B (Applied Biosystems) on a LabNet Multigene Gradient with 40 cycles of 2 minutes at 16°C, 1 minute at 42°C, and 1 second at 50°C, followed by 5 minutes at 85°C. The entire RT reaction was used for preamplification. Preamplification was carried out on a ViiA 7 instrument (Applied Biosystems) using MegaPlex RT preamplification primer Pools A and B and MegaPlex preamp Master Mix (Applied Biosystems) under the following conditions: 10 minutes at 95°C, 2 minutes at 55°C, 2 minutes at 72°C, followed by 16 cycles of 15 seconds at 95°C, and 4 minutes at 60°C. Preamplification reactions were then incubated at 99.9°C for 10 minutes and cooled to 4°C. The resultant cDNA was diluted, and this frozen at -20°C until further use. The diluted cDNA was thawed, combined with the OpenArray real-time PCR Master Mix and loaded onto the OpenArray miRNA panel plates (Applied Biosystems) using the AccuFill autoloader. The loaded plates were run on the BioTrove OpenArray realtime PCR instrument (Flinders Medical Centre, SA) and run according to the default protocol for reaction conditions.
 
Hybridization protocol n/a
Scan protocol n/a
Description test
5050.1
Data processing MiRNAs that are missing in > 50% of samples were excluded to acquire acceptable distribution of non-detects for down-stream analysis. Quantile normalization was used to adjust for technical variability across multiple samples. Missing data was imputed using the nearest-neighbour method (KNNimpute). The pre-processing of miRNA cycle quantification (Cq) values from quantitative RT-qPCR assays were performed using MATLAB 2014b, Bioinformatics Toolbox and Statistics Toolbox.
 
Submission date Apr 11, 2018
Last update date Apr 12, 2018
Contact name Fatemeh Vafaee
E-mail(s) f.vafaee@unsw.edu.au
Phone 0061403012736
Organization name University of New South Wales
Department School of Biotechnology and Biomolecular Sciences
Street address Gate 11 Botany Street, UNSW Sydney, School of BABS
City Sydney
State/province UNSW
ZIP/Postal code 2052
Country Australia
 
Platform ID GPL17837
Series (1)
GSE112955 Circulating microRNA of advanced colorectal cancer patients

Data table header descriptions
ID_REF
VALUE normalized data

Data table
ID_REF VALUE
hsa-let-7a_000377_A 24.53122132
hsa-let-7c_000379_A 26.74724414
hsa-let-7e_002406_A 26.28635835
hsa-let-7f_000382_A 26.57264536
hsa-let-7g_002282_A 26.22111349
hsa-miR-101_002253_A 26.59378964
hsa-miR-105_002167_A 22.21120213
hsa-miR-106a#_002170_B 19.25368531
hsa-miR-106a_002169_A 28.68347905
hsa-miR-106b#_002380_B 23.70327762
hsa-miR-106b_000442_A 30.11444309
hsa-miR-10b#_002315_B 26.8344051
hsa-miR-10b_002218_A 31.79182079
hsa-miR-1180_002847_B 22.62500069
hsa-miR-122_002245_A 24.09302057
hsa-miR-1247_002893_B 21.46731083
hsa-miR-125a-3p_002199_A 26.96779095
hsa-miR-125a-5p_002198_A 25.82305077
hsa-miR-125b_000449_A 26.29563698
hsa-miR-126_002228_A 24.36725058

Total number of rows: 150

Table truncated, full table size 4 Kbytes.




Supplementary data files not provided
Processed data included within Sample table

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