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5 protocols using nano instrument

1

Quantitative RT-PCR for Gene Expression

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Total RNA was extracted using Trizol Reagent (Invitrogen) according to the manufacturer's instructions. RNA concentrations were quantified with a Nano instrument (NanoDrop Technologies, Wilmington, DE, USA). cDNA was synthesized using PrimeScript RT reagent kit (Takara Biotechnology, Dalian, China). Real-time PCR (SYBR Green) was performed according to manufacturer's instructions with a sequence detection system (ABI Prism 7500; Applied Biosystems, Foster City, CA, USA). The PCR amplification was conducted in a volume of 20 lL using all-in-one quantitative PCR mix (Takara Biotechnology). The cycling protocol consisted of one cycle of 10 minutes at 958C followed by 40 cycles of 958C for 15 seconds and 608C for 1 minute. To determine the mRNA expression, all samples were tested in duplicate and the average cycle threshold values were used for relative quantification. The mRNA expression was normalized to the endogenous reference gene b-actin. The sequences of the primers are shown in the Table.
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2

IPO13 Gene Expression Analysis in PBMCs

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Peripheral blood mononuclear cells (PBMCs) were isolated from heparinized blood samples by Ficoll-Hypaque density-gradient centrifugation. Total RNA was extracted with TRIzol (Invitrogen, Carlsbad, CA) from PBMCs according to the manufacturer’s instructions. RNA concentrations were determined using a Nano instrument (NanoDrop Technologies, Thermo, US). Then cDNA was synthesized with PrimeScript reverse transcriptase (TaKaRa, Dalian, China) and oligo (dT) following the manufacturer’s instructions. Real-time quantitative PCR was performed using SYBR Green Master (Roche). Specific primers for IPO13 (forward primer, 5’-GTATGAAAGCCTAAAGGCACAGC-3’; and reverse primer, 5’-GCCGAGTCAGTACAATCTTGGAG-3’) were used. The relative expression level of IPO13 messenger RNA (mRNA) was normalized to that of internal control ACTIN using the 2−△△Ct cycle threshold method.
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3

Quantifying Inflammatory Markers in Rat ICB

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At 24 h after LPS injection, rats were killed with an overdose of anesthesia, and the eyes were immediately enucleated. The ICB complex was carefully isolated under a surgical microscope. Total ICB RNA was extracted from tissues using TRIzol (Invitrogen, Paisley, UK) following the manufacturer’s instructions. RNA concentrations were tested using a Nano instrument (NanoDrop Technologies, Wilmington, DE). In addition, cDNA was generated using the PrimeScript® RT reagent Kit (Takara Biotechnology, Dalian, China) according to the manufacturer’s instructions [19 (link)]. Real-time quantitative PCR was performed on Applied Biosystems Prism 7500 (Life Technologies Co., CA). Samples underwent 40 cycles of amplification in a volume of 20 µl using the all-in-one qPCR Mix (GeneCopoeia Inc., Rockville, MD). The conditions were 95 °C for 10 min, followed by 40 cycles of 10 s at 95 °C, 20 s at 60 °C and 15 s at 72 °C. Primers used to analyze TNF-α, IL-1β, iNOS, COX-2, NF-κB p65, and GAPDH expressions are summarized in Table 2. The relative amount of target mRNA was calculated from the obtained ΔCt values for the target and endogenous reference gene GAPDH using the 2-ΔΔCt cycle threshold method. All samples were analyzed in triplicate (n = 4 per group).
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4

Quantitative PCR for Gene Expression

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Total RNA was extracted with TRIzol (Invitrogen) following the manufacturer’s instructions. RNA concentrations were determined with a Nano instrument (NanoDrop Technologies, Wilmington, DE). The first-strand cDNA was synthesized for each RNA sample using the Superscript III Reverse Transcriptase system (Invitrogen). Real-time quantitative PCR was performed on the iCycler (Biorad, UK) using the Quanti Tect SYBR Green PCR kit (Applied Biosystems). The forward and reverse primers for β-actin were designed using the Primer Premier software (Premier Biosoft International). The sequences of the PCR primer pairs were as follows: β-actin forward, 5′-GGA TGC AGA AGG AGA TCA CTG-3′ and reverse, 5′-CGA TCC ACA CGG AGT ACT TG-3′; TLR4 forward, 5′-AGT TTC CTG CAA TGG ATC AAGG-3′ and reverse 5′-CTG CTT ATC TGA AGG TGT TGC AC-3′; IL-6 forward, 5′-AGT GAG GAA CAA GCC AGA GC-3′ and reverse, 5′-CAG GGG TGG TTA TTG CAT CT-3′; IL-8 forward, 5′-GAC ATA CTC CAA ACC TTT CCA CCC-3′ and reverse, 5′-CCA GAC AGA GCT CTC TTC CAT CAG-3′. The human β-actin gene was used as an endogenous control for sample normalization. For each sample, the relative abundance of target mRNA was calculated from the obtained CΔt values for both the target and endogenous reference β-actin genes using the 2-ΔΔCt cycle threshold method.
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5

Quantitative RT-PCR Profiling of Tight Junction and Cell Adhesion Markers

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Total RNA was obtained from the TM cells cultured in 10 ng/ml CRYAB with a Total RNA kit (Omega, USA) and was reverse transcribed into cDNA (1 μg of isolated total RNA) using a qPCR RT Kit (TOBOYO, Japan) according to the manufacturer's instructions. The RNA concentrations were quantified with a Nano instrument (NanoDrop Technologies, Wilmington, DE, USA). Rt-qPCR was carried out using a SYBR Green PCR Master Mix (TOYOBO, Japan). The system of each PCR reaction contained 4 μl of cDNA, 0.8 μl of forward and reverse primers (PCR primers were listed), and 10 μl of SYBR Green PCR Master Mix, with a final volume of 20 μl. All the PCR amplification reactions were performed on a MiniOpticon qPCR (Bio-Rad, USA). The specific primers were the following: zo-1 (forward primer (F), 5′-ACCAGTAAGTCGTCCTGATCC-3′ and reverse primer (R), 5′-TCGGCCAA ATCTTCTCACTCC-3′); claudin-1 (F, 5′-CGAGAGCTACAC GTTCACGG-3′ and R, 5′-GGGTGTCGAGG GAAAAA TAGG-3′); cadherin-E (F, 5′-AAAGG CCCATTTCCTAAAAACCT-3′ and R, 5′-TGCGTTCTCTATCCAGAGGCT-3′); cadherin-N (F, 5′-AGCCAACCTTAAC TGAGGAGT-3′ and R, 5′-GGCAAGTT GATTGGAG GGATG-3′); and vimentin (F, 5′-GACGCCATCAACACCGAGTT-3′ and R, 5′-CTTTGTCGTTGGTTAG CTGGT-3′). The mRNA expression was normalized to the endogenous reference gene GAPDH (F, 5′-TGGAGAAAAT CTGGCACCAC-3′ and R, 5′-ACCACCCTGTTGCTGTAGCCA A-3′) and was analyzed using the 2−ΔΔCt comparative threshold method.
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