Rq1 rnase free dnase

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The RQ1 RNase-Free DNase is a laboratory product designed to degrade DNA without affecting RNA. It is a recombinant DNase I enzyme that is specifically treated to remove RNase activity, ensuring the preservation of RNA samples during DNA removal.

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1 091 protocols using rq1 rnase free dnase

Virus-Infected Plant RNA and Aphid Extraction

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A. thaliana infected leaves were stored at -80 °C before RNA extraction. Total plant RNA was extracted according to a modified Edwards protocol (Edwards et al., 1991) including an additional washing step with 70% ethanol, followed by a DNAse treatment (RQ1 RNase-free DNase, Promega).
Total RNA was extracted from whole M. persicae (15 aphids were pooled per sample) that had fed on TuYV-infected WW or WD plants for 24 h. Aphids were then transferred to healthy plants for 2 days to clear the gut content from non-internalized virus particles. Aphids were stored at -80 °C before RNA extraction. Aphids were first ground with a pestle in the RLT lysis buffer in Eppendorf tubes (Eppendorf, Hamburg, Germany) and RNA was extracted using the RNeasy Mini Kit (QIAGEN) following the procedure for animal tissue. Finally, RNA was eluted in 35 μl of RNase-free water prior to an additional DNAse treatment using RQ1 RNase-free DNase (Promega).
Quality and quantity of nucleic acid extraction was assessed by spectroscopic measurements at 230, 260 and 280 nm (NanoDrop 2000; Thermo Fisher Scientific), and by agarose gel electrophoresis. RNA extracts were stored at -80 °C before used.

Yvon M., Vile D., Brault V., Blanc S, & van Munster M. (2017). Drought reduces transmission of Turnip yellows virus, an insect-vectored circulative virus. Virus research, 241.

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DNase Treatment for RNA Purification

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Contaminating DNA was removed from each RNA extract by means of DNase treatment, according to the manufacturer’s recommendations.
DNase digestion of the EM RNA extracts (35 μl) (Fig 1D1) was carried out by adding 7 μl of RQ1 RNase-free DNase 10X reaction buffer, 7 μl of RQ1 RNase-free DNase (1 U/μg RNA) (Promega Benelux, Leiden, the Netherlands) and 21 μl of nuclease-free water (total volume of 70 μl) and incubation for 30 min at 37 °C. The reaction was stopped by adding 7 μl of RQ1 DNase Stop Solution and incubation for 10 min at 65 °C (Fig 1D1). The final volume after DNase treatment and inactivation was therefore 77 μl.
The RE RNA extraction procedure comprises an on-column DNase treatment using RNase-free DNase (Qiagen), as described by the manufacturer.
DNase digestion of the RP RNA extracts (Fig 1D2) was carried out by adding 5.5 μl of 20x DNase buffer and 1 μl of 8 U DNase I/μl (RiboPure) to the 100 μl of RNA eluates, mixing gently but thoroughly and incubation for 30 min at 37 °C. The DNase reaction was inactivated by adding 20 μl of DNase inactivation reagent and incubation for 2 min at room temperature. The DNase inactivation reagent was pelleted by centrifugation for 1 min at 20,800 g, and the supernatant was transferred to a new RNase-free tube. The final volume after DNase treatment and inactivation was 126.5 μl.

Rodríguez A., Duyvejonck H., Van Belleghem J.D., Gryp T., Van Simaey L., Vermeulen S., Van Mechelen E, & Vaneechoutte M. (2020). Comparison of procedures for RNA-extraction from peripheral blood mononuclear cells. PLoS ONE, 15(2), e0229423.

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Transcriptional Analysis of TMPyP4-Treated HEK 293T Cells

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HEK 293T cells treated with 100 μM TMPyP4 for
48 h before being harvested were compared to untreated HEK 293T cells.
RNA was isolated using a RNeasy kit (Qiagen). RNA was quantified using
a NanoDrop 2000C instrument (Thermo Scientific). DNase digestion was
performed on 1 μg of isolated RNA with 1 unit of RQ1 RNase-free
DNase (Promega) in 1× RQ1 RNase-free DNase reaction buffer at
37 °C for 30 min. cDNA was synthesized with an iScript cDNA Synthesis
Kit (BioRad) following the manufacturer’s recommended protocol
in a 20 μL reaction mixture with synthesis for 5 min at 25 °C,
20 min at 46 °C, and 1 min at 95 °C. cDNA was amplified
using Sso Advanced Universal SYBR Green Supermix (Bio-Rad) with 300
nM forward and reverse primers (Table S2) in a Bio-Rad CFX96 Real Time PCR Machine. Each reaction mixture
(20 μL) contained 2 μL of template. The PCR cycle was
one cycle of 98 °C for 3 min and 40 cycles of 98 °C for
15 s and 53 °C for 30 s, followed by a melt curve from 65 to
90 °C to determine specificity. Information about the amplicons
is available in Table S3. Experiments were
performed in biological and technical triplicates. The fold change
in expression was calculated using the ΔC_t method^{35 (link)} with ΔC_t = C_{t_target} – C_{t_ref}. The 2^–ΔC_t values were averaged and normalized to β-actin,
and significance was determined using GraphPad Prism 8.2 to perform
a two-tailed t test.

Zafar M.K., Hazeslip L., Chauhan M.Z, & Byrd A.K. (2020). The Expression of Human DNA Helicase B Is Affected by G-Quadruplexes in the Promoter. Biochemistry, 59(26), 2401-2409.

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RNA Extraction and RT-qPCR Analysis Protocol

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Total RNA was extracted from immature inflorescences (stages 1–12) or aerial parts of three-week-old seedlings using guanidine hydrochloride (8 M guanidine hydrochloride, 20 mM MES (2-morpholinoethanesulfonic acid), 20 mM EDTA and 50 mM β-mercaptoethanol at pH 7.0). For gel-based RT–PCR analyses, 0.05 μg of DNase-treated (RQ1 RNase-free DNase; Promega) total RNA was reverse transcribed and PCR-amplified using the One-Step RT-PCR kit (Qiagen) in a final volume of 10 μl. For RT-qPCR analyses, 0.2 μg of DNase-treated (RQ1 RNase-free DNase; Promega) total RNA was reverse transcribed using the PrimeScript RT reagent kit (Perfect real time) (TaKaRa) in a final volume of 10 μl, using a mix of oligo-dT and random hexanucleotides. One microlitre of cDNA was used for subsequent amplification using SYBR Premix Ex Taq II (Tli RnaseH Plus) (TaKaRa) and the Eco Real-Time system (Illumina) in a final reaction volume of 15 μl. Amplification of ACTIN2 was used as a reference. Relative quantities were determined using the ‘delta-delta method' formula 2^{−((Ct target sample−Ct actin2 sample)−(Ct target calibrator−Ct actin2 calibrator))}. At least two biological replicates were analysed for each genotype. Original images of gels are shown in Supplementary Fig. 19.

Ikeda Y., Pélissier T., Bourguet P., Becker C., Pouch-Pélissier M.N., Pogorelcnik R., Weingartner M., Weigel D., Deragon J.M, & Mathieu O. (2017). Arabidopsis proteins with a transposon-related domain act in gene silencing. Nature Communications, 8, 15122.

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Hepatic Cytochrome P450 Gene Expression

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Hepatic tissue from 6 rats were pooled for each group in order to extract total RNA
using Trizol^® (Invitrogen, USA), according to the manufacturer's
instructions. Samples were then treated with DNase RQ1 RNase Free (Promega, USA),
according to manufacturer's instructions, to avoid any contaminating DNA. The RNA was
quantified by spectrophotometry and the integrity checked by electrophoresis on a
formaldehyde agarose gel. RNA reverse transcription and PCR reactions were performed
as previously described (18 (link)). PCR conditions
were optimized to demonstrate that the amplification of GAPDH, CYP1A1,
CYP1A2, CYP2B1, CYP2B2, and CYP2E1 was in the linear
range, in order to allow a semi-quantitative comparison of each gene expression
between C- and MPR-group samples. The PCR products were run on a 6% polyacrylamide
gel, stained with silver and analyzed using the LabImage software (USA). The
semi-quantitative comparison of CYP1A1, CYP1A2, CYP2B1, CYP2B2, and
CYP2E1 expression between C- and MPR-group samples was performed
normalizing the expression of these genes by GAPDH expression.

Da Costa N.M., Visoni S.B., Dos Santos I.L., Barja-Fidalgo T.C, & Ribeiro-Pinto L.F. (2016). Maternal protein restriction during lactation modulated the expression and activity of rat offspring hepatic CYP1A1, CYP1A2, CYP2B1, CYP2B2, and CYP2E1 during development. Brazilian Journal of Medical and Biological Research, 49(11), e5238.

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Plant Total RNA Extraction using Trizol

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Total RNA was extracted from plant leaves using Trizol reagent (Thermo Fisher Scientific, Waltham, MA, USA) according to the instructions of the manufacturer. To eliminate genomic DNA contamination, RNA was treated with DNase RQ1 RNase-Free (Promega, Madison, WI, USA) and stored at minus 70 °C.

Efremova L.N., Strelnikova S.R., Gazizova G.R., Minkina E.A, & Komakhin R.A. (2020). A Synthetic Strong and Constitutive Promoter Derived from the Stellaria media pro-SmAMP1 and pro-SmAMP2 Promoters for Effective Transgene Expression in Plants. Genes, 11(12), 1407.

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RNA Extraction and cDNA Synthesis

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Total RNA was purified using Trizol (Invitrogen, Waltham, MA, USA), according to the manufacturer’s instructions, from MC3T3-E1 cells cultured on different supports including Petri dishes, and all the different types of PLA scaffolds above defined at days 1, 7, 14, and 21. RNA concentrations and quality were verified by measuring the optical density at Abs260 nm and Abs260/280 nm. The RNA integrity was evaluated by denaturing 1.5% agarose gel. To remove any residual trace of DNA contamination, 500 ng of extracted RNA was digested with DNase RQ1 RNase-Free (Promega, Madison, WI, USA) for 30 min at 37 °C, while DNase was inactivated by adding 25 mM EDTA. First-strand cDNA was synthesized from 250 ng DNase-treated RNA as a template in the presence of random primers and using the SuperScript III First-Strand Synthesis System (Life Technologies Corporation, Carlsbad, CA, USA) according to the manufacturer’s instructions. The cDNA mixtures were then stored at −20 °C until used.

Lopresti F., Campora S., Rigogliuso S., Nicosia A., Lo Cicero A., Di Marco C., Tornabene S., Ghersi G, & La Carrubba V. (2024). Improvement of Osteogenic Differentiation of Mouse Pre-Osteoblastic MC3T3-E1 Cells on Core–Shell Polylactic Acid/Chitosan Electrospun Scaffolds for Bone Defect Repair. International Journal of Molecular Sciences, 25(5), 2507.

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Total RNA Extraction from Plant Leaves

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Total RNA was extracted from plant leaves using Trizol reagent (Thermo Fisher Scientific, Waltham, MA, USA) according to the instructions of the manufacturer. To eliminate genomic DNA contamination, the RNA was treated with DNase RQ1 RNase-Free (Promega, Madison, WI, USA) and stored at −70 °C.

Strelnikova S.R., Krinitsina A.A, & Komakhin R.A. (2021). Effective RNAi-Mediated Silencing of the Mismatch Repair MSH2 Gene Induces Sterility of Tomato Plants but Not an Increase in Meiotic Recombination. Genes, 12(8), 1167.

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RNA Extraction and cDNA Synthesis

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Total RNA was purified using Trizol (Invitrogen, Waltham, MA, USA) according to the manufacturer’s instructions from newly isolated ad-MVFs and ad-MVFs cultured on 3D collagen type-I hydrogel at day 1 and day 8.
RNA concentrations and quality were verified by measuring the optical density at Abs260 nm and Abs260/280 nm. The RNA integrity was evaluated on denaturing 1.5% agarose gel. To remove DNA contamination, 500 ng of extracted RNA was treated with DNase RQ1 RNase-Free (Promega, Madison, WI, USA) for 30 min at 37 °C. DNase was then inactivated by adding 25 mM EDTA.
First-strand cDNA was synthesized from 250 ng DNase-treated RNA using a High-Capacity cDNA Reverse Transcription Kit (Life Technologies Corporation, Carlsbad, CA, USA) according to the manufacturer’s instructions. The cDNA mixtures were stored at −20 °C.

Salamone M., Rigogliuso S., Nicosia A., Campora S., Bruno C.M, & Ghersi G. (2021). 3D Collagen Hydrogel Promotes In Vitro Langerhans Islets Vascularization through ad-MVFs Angiogenic Activity. Biomedicines, 9(7), 739.

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Total RNA Extraction and cDNA Synthesis

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Total RNA was extracted from plant leaves (100 mg) using Trizol reagent (Invitrogen, USA) according to the instructions of the manufacturer. To eliminate genomic DNA contamination, RNA was treated with DNase RQ1 RNase-Free (Promega, USA) and stored at minus 70 °C.
The first chain cDNA was obtained by reverse transcription using the oligonucleotide oligo-dT (Syntol, Russia) as a primer and RNA-dependent DNA polymerase of Malone mice leukemia virus (M-MLV). The final incubation mixture contained 50 mM Tris–HCl (pH 8.2), 8 mM MgSO₄, 10 mM DTT, 50 mM KСl, 0.4 mM each of dNTPs, 100 pmol oligo-dT primer, 5 units of RNase inhibitor, 25 units of reverse transcriptase and 1 μg of total RNA. The reaction was carried out for 1 h at 37 °C.

Komakhin R.A., Vysotskii D.A., Shukurov R.R., Voblikova V.D., Komakhina V.V., Strelnikova S.R., Vetchinkina E.M, & Babakov A.V. (2016). Novel strong promoter of antimicrobial peptides gene pro-SmAMP2 from chickweed (Stellaria media). BMC Biotechnology, 16, 43.

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