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8 protocols using mirna qpcr kit

1

Transcriptomic Analysis of miRNA and mRNA

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After the test of purity and concentration of RNA samples, cDNA samples were synthesized by RT, with GAPDH and U6 as the internal references. DEPC (Beyotime Biotechnology), SYBR Green (Applied Biosystems) premixed solution, forward (F)/reverse (R) primers, and templates were prepared into PCR solution, which was placed on a RT‐PCR instrument for PCR amplification. miRNAs were reversely transcribed into cDNAs by miRNA RT kit [Tiangen Biotech (Shanghai) Co., Ltd.], and PCR and quantitative analysis of miRNAs were carried out according to miRNA qPCR kit instructions [Tiangen Biotech (Shanghai) Co., Ltd.]. Primer sequences are listed below:
miR‐191‐5p (F: 5′ CAACGGAATCCCAAAAGCAGCTG 3′,
R: As provided by the miScript SYBR Green kit;
U6 (F: 5′ CTCGCTTCGGCAGCACA 3′, R: 5′ ACGCTTCACGAATTTGCGT 3′);
GAPDH (F: 5' GAAGGTGAAGGTCGGAGTC′, R: 5′ GAAGATGGTGATGGGATT TC′);
SATB1 (F: 5′ GATCATTTGAACGAGGCAACTCA 3′, R: 5′ TGGACCCTTCGGATC
ACTCA 3′)
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2

miRNA Isolation and Quantification in hASMCs

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For the isolation of RNA from hASMCs, the miRNA extraction isolation kit (DP501) provided by TIANGEN (China) was utilized. To synthesize cDNA, we used miRNA cDNA first-strand synthesis kit (KR211) bought from TIANGEN (China). Then, qRT-PCR was carried out utilizing a miRNA qPCR kit (FP411, TIANGEN, China) in a PCR system (CFX96, Bio-Rad, USA). Gene-specific primers were as follows: miR-155 forward: 5′‐GGCTAAGGAGATTGGTGCTGTA-3′, Reverse: 5′‐ACGAGGGGCTG-AGACATTTAC-3′; U6 forward: 5′‐AGTAAGCCCTTGCTGTCAGTG-3′, Reverse: 5′‐CCTGGGTCTGATAATGCTGGG-3′.
U6 was validated as the normalizer. The 2−ΔΔCt was employed for data evaluation.
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3

Differential miRNA Expression in Chicken Growth

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We re-selected 6 fast- and slow-growing Jinghai yellow chickens (3 slow-growing chickens and 3 fast-growing chickens) to collected leg muscles. Total RNAs were isolated with Trizol (TIANGEN, Beijing, China) and miRNAs were reverse transcribed into cDNA with the miRNA First-Strand cDNA kit (TIANGEN, Beijing, China). The forward primers used for quantification in the study were designed using Primer 5.0 and U6 small nuclear RNA (U6) was used for the housekeeping gene. The qPCR was conducted on QuantStudio 3 with the miRNA qPCR kit (TIANGEN, Beijing, China), and the reverse primers also came from the qPCR kit. The relative expression of miRNAs was calculated using the 2−ΔΔCT method (Rao et al., 2013 (link)).
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4

Quantification of miRNA and mRNA Levels

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After concentration and purity determination of RNA samples, they were subjected to reverse transcription to synthesize cDNA samples, with U6 and GAPDH as internal reference, respectively. SYBR Green (Applied Biosystems, USA) premix, template, forward/reverse primer and DEPC (Beyotime Biotechnology, China) were used to prepare the PCR reaction solution which was subjected to PCR amplification on a real‐time PCR amplifier. miRNA RT Kit from Shanghai TIANGEN was used for miRNA's PCR reaction. After miRNA was reverse transcribed into cDNA, PCR reaction and quantitative analysis of miRNA were performed as per the instructions mentioned in the MiRNA qPCR kit (TIANGEN, Shanghai). The primer sequences are shown below:
miR‐1281 (F: 5′ ACACTCCAGCTGGGTCGCCTCCTCC 3′, R: 5′ CTCAACTGGTGTCGTGGAGTCGGCAATTCAGTTGAGGGGAGAGG 3′); U6 (F: CTCGCTTCGGCAGCAGCACATATA, R: AAATATGGAACGCTTCACGA); GIHCG (F: 5′CTTTCAAGAAGTTTGGCTGTC 3′, R: 5′ GCTCATTCAACGGATAAGTC 3′), GAPDH (F: 5′GAAGAGAGAGACCCTCACGCTG3′, R: 5′ACTGTGAGGAGGGGAGATTCAGT3′); TLE1 (NCBI Gene ID: 7088) (F: 5′GAGTCCCTGGACCGGATTAAA3′, R: 5′ AATACATCACATAGTGCCTCTGC 3′).
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5

Comprehensive RNA Extraction and Quantification

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Total RNA was extracted from cells and tissues using TRIzol reagent (Invitrogen), according to the manufacturer's instructions. miRNA was extracted from the serum using the miRcute serum/plasma miRNA isolation kit (TIANGEN), according to the manufacturer's protocol. U6 and GAPDH were used as endogenous controls to normalize miRNA and mRNA, respectively. mRNA and miRNA were then reverse transcribed to complementary DNA (cDNA) using the Revert Aid First‐Strand cDNA kit (Thermo Scientific) and miRNA First‐Strand cDNA kit (TIANGEN), respectively, according to the manufacturer's protocols. qRT‐PCR was performed in triplicate on the Rotor‐Gene Q MDx detection system (QIAGEN) using the SYBR Green PCR kit (QIAGEN) and miRNA qPCR kit (TIANGEN) to detect mRNA and miRNA, respectively. Relative changes in the expression levels of the mRNA and miRNA were quantified using the 2−ΔΔCT method. All primers used in our study were as follows: MOB1B forward, 5′‐TTCGGATGGCT GTCATGCTTCC‐3′, reverse, 5′‐GCTGACA TCACTGGACAACTCTC‐3′; CCND1 forward, 5′‐TCTACACCGACAACTCCATCCG‐3′, reverse, 5′‐TCTGGCATTTTGG AGAGGAAGTG‐3′; XIAP forward, 5′‐TGGCAGATTATGAAGCACGGATC‐3′, reverse, 5′‐AGTTAGCCCTCCTCCACAGTGA‐3′; GAPDH forward, 5′‐GGTGGTC TCCTCTGACTTCAA‐3′, reverse, 5′‐TCTTCC TCTTGTGCTCTTGCT‐3′.
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6

Quantitative Real-Time PCR Analysis

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After the concentration and purity of RNA samples were tested, cDNA samples were synthesized by reverse transcription with U6 and GAPDH as the internal reference, respectively. SYBR Green (Applied Biosystems, USA) premixed solution, templates, forward (F)/reverse (R) primers, and DEPC (Beyotime Biotechnology, China) were prepared into PCR solution, which was placed on a RT‐PCR instrument for PCR amplification. MiRNAs were reversely transcribed into cDNAs by miRNA RT Kit [Tiangen Biotech (Shanghai) Co., Ltd.], and PCR and quantitative analysis of miRNAs were carried out according to miRNA qPCR kit instructions [Tiangen Biotech (Shanghai) Co., Ltd.]. 2‐△△ct method was applied to calculate the relative expression levels and the control genes were U6 and GAPDH. Primer sequences are listed below:
miR‐656‐3p (F: 5'ACACTCCAGCTGGGAATATTATACAGTCA 3',.
R: 5'CTCAACTGGTGTCGTGGAGTCGGCAATTCAGTTGAGAGAGGUUG 3');
U6 (F: CTCGCTTCGGCAGCAGCACATATA,R: AAATATGGAACGCTTCACGA);
NORAD (F: 5'TGATAGGATACATCTTGGACATGGA3'),
R: 5'AACCTAATGAACAAGTCCTGACATACA3');
GAPDH (F: 5'GAAGAGAGAGACCCTCACGCTG3', R: 5'ACTGTGAGGAGGGGAGATTCAGT3');
AKT1 (F: 5'AGCGACGTGGCTATTGTGAAG3', R: 5'GCCATCATTCTTGAGGAGGAAGT3').
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7

Zebrafish Embryo Microrna Analysis

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On the night before spawning, the paired adult zebrafish are placed separately on both sides of the breeding tank, and the divider is opened at 8:30 a.m. on the spawning day to start mating. One-cell stage embryos were placed on a fluted agarose plate containing a small amount of EM solution. Approximately 1 nL of the mix solution or mRNA was injected per embryo.
Total miRNA was isolated from the 4 dpf (day post fertilization) larvae which expressed red fluorescence using the miRNA Isolation Kit (Tiangen, DP501, China), according to the manufacturer’s protocols. RNA concentration was measured by Nanodrop (Thermo Scientific, Waltham, USA). 1 μg miRNA was reversely transcribed into cDNA with miRNA First-Strand cDNA Kit (Tiangen, KR211, China) and cDNA was quantified by qPCR system (Light-Cycler 96, Roche) with miRNA qPCR Kit (Tiangen, FP411, China).To detect RNA levels, 4 dpf larvae with red fluorescence were selected to isolate total RNA using TRIzol (TARAKA, China), and the RNA was reverse-transcribed into cDNA with HiScript II qRT SuperMix II (Vazyme, China). The mRNA expression levels were quantified by the qPCR system using AceQ qPCR SYBR Master Mix (Vazyme, China). Twenty-five larvae were collected for each experimental condition. Each experiment was repeated three times in biology and technology. The qPCR primers used are listed in the Supplementary Table S1.
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8

Quantitative Analysis of lnc-NEAT1 and miR-638

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TRIzol® reagent obtained from Invitrogen; Thermo Fisher Scientific, Inc. was employed for total RNA extraction in accordance with the manufacturer's guidelines. Following the measurement of the concentration and purity of RNA specimens, RT was performed to synthesize cDNA specimens with U6 and GAPDH as the internal reference. A PCR solution was prepared with a premixed solution containing forward (F)/reverse (R) primers, DEPC from Beyotime Institute of Biotechnology, SYBR Green from Applied Biosystems; Thermo Fisher Scientific, Inc., and templates. Subsequently, the prepared solution was placed on an RT-PCR instrument for PCR amplification. miRNAs underwent RT into cDNAs with the use of a miRNA RT Kit from Tiangen Biotech Co., Ltd. and then subjected to PCR and quantitative analysis on the basis of the instructions of the miRNA qPCR kit from the same company. The primer sequences were as follows: lnc-NEAT1 F, TGTCCCTCGGCTATGTCAGA and R, GAGGGGACGTGTTTCCTGAG; GAPDH F, TGACCACAGTCCATGCCATCAC and R, GCCTGCTTCACCACCTTCTTGA; miR-638 F, AAGGGATCGCGGGCGGGT and R, CAGTGCAGGGTCCGAGGT; and U6 F, CTCGCTTCGGCAGCACATATACTA and R, ACGAATTTGCGTGTCATCCTTGC.
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