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Sample GSM1841107 Query DataSets for GSM1841107
Status Public on Sep 28, 2016
Title miRNA expression data from Non-arthritic synovium pooled from 3 mice 1
Sample type RNA
 
Source name Nonarthritic Synovium
Organism Mus musculus
Characteristics host strain: C57BL/6J
serum source strain: K/BxN
mouse model: serum transfer arthritis (STA) model
time point: day 0 (Non Arthritic)
tissue: synovium
Extracted molecule total RNA
Extraction protocol Synovial samples were isolated from the region of the tibiotalar joint and processed for RNA. Extraction of total RNA was performed according to the manufacturer's instructions for mirVaNa miRNA isolation kit (Ambion, AM1560)
Label Rox
Label protocol 500ng of RNA samples were converted to cDNA using TaqMan MicroRNA Reverse Transcription Kit (Life Technologies, Foster City, CA). The RNA was converted to cDNA using the following conditions: 16°C for 20 min, 42°C for 1 min, and 50°C for 1 second total 40 cycles. Then, 85°C for 5 min and 4°C hold until further processing or storage.
 
Hybridization protocol Prior to PCR, cDNA samples were pre-amplified using Megaplex Primer Pools, Rodent Pools Set v3.0 and TaqMan PreAmp Master Mix (Life Technologies, Foster City, CA). PreAmp Master Mix and 0.2x Primers were added to the cDNA samples and pre-amplified as follows: 95°C for 10 min once, 95°C for 15 sec, 60°C for 4 min, (final two steps repeated for 14 cycles). Quantitative Real-Time PCR reactions (qRT-PCR) were performed using the high-throughput BioMark Real-Time PCR system (Fluidigm, South San Francisco, CA). Pre-amplified cDNA samples were diluted with 0.1 mM EDTA in TE Buffer (1:5) and mixed with TaqMan Gene Expression Master Mix (Life Technologies, Foster City, CA), and Sample Loading Reagent (Fluidigm), then pipetted into sample inlets of Dynamic Array 96.96 chips (Fluidigm). Assay Loading Reagent (Fluidigm) and TaqMan miRNA Assays (Fluidigm, South San Francisco, CA) were mixed and pipetted into assay inlets of Dynamic Array 96.96 chips. This platform allows PCR reactions for 96 samples and 96 primers simultaneously. The IFC Controller HX (Fluidigm) was used to distribute primers and samples into chip reaction wells for qRT-PCR by microfluidic delivery. Real-Time PCR reactions are performed in BioMark System and PCR protocols was 95°C for 10 min denaturation 95°C for 15 seconds and 60°C for 1 min for 30 cycles.
Scan protocol n/a
Description Non-Art pool1
Data processing The raw data was normalized by global normalization method (Mestdagh et al., 2009).
Prior to normalization, those miRNA assays with poor or no amplification across all samples were removed. The mean Ct values across all detectable miRNAs for each sample were subtracted from individual miRNA assay Ct values to generate normalized ΔCt values.
The quality of the data was assessed using Principal component Analysis and Pearson correlation to determine replicate efficacy (Spotfire DecisionSite).
 
Submission date Jul 31, 2015
Last update date Sep 28, 2016
Contact name yukiko maeda
E-mail(s) yukiko.maeda@umassmed.edu
Phone 508 856 6357
Organization name Umass Medical School
Department Medicine
Lab Gravallese
Street address 364 Plantation Street
City worcester
State/province massachusetts
ZIP/Postal code 01605
Country USA
 
Platform ID GPL20759
Series (2)
GSE71600 miRNA Expression data from synovium in mouse serum transfer arthritis model (STA) model
GSE71601 Gene and miRNA Expression data from synovium in mouse serum transfer arthritis model (STA) model

Data table header descriptions
ID_REF
VALUE Matrix normalized worksheet reports normalized signal

Data table
ID_REF VALUE
mmu-miR-107 0.726197365
mmu-miR-467c 0
mmu-miR-674* 0.80412565
rno-miR-351 0
mmu-miR-350 0.707058785
rno-miR-339-3p 3.146357755
mmu-miR-133b 3.648732875
mmu-miR-331-5p 2.789785735
hsa-miR-423-3p 2.6506891
mmu-miR-1930 4.30829127
mmu-miR-467a 0.77156871
mmu-miR-329 1.722792155
mmu-miR-340-3p 3.56631378
mmu-miR-17* 3.057118785
mmu-miR-485-3p 2.591855375
mmu-miR-10a 2.71387135
mmu-miR-301a 4.381358305
mmu-miR-20b 5.23657267
mmu-let-7c-1* 4.628596955
hsa-miR-27b* 4.537148275

Total number of rows: 174

Table truncated, full table size 4 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
Processed data are available on Series record

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