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24 protocols using nanodrop 1000 instrument

1

Salmonella Genomic DNA Extraction and Sequencing

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Genomic DNA of all 105 selected Salmonella isolates was extracted from cultures incubated in Luria-Bertani (LB) broth overnight using a FastPure bacterial DNA isolation minikit (Vazyme Biotech Co., Ltd., Nanjing, China) according to the manufacturer’s instructions and quantified using a Nanodrop 1000 instrument (Thermo Fisher Scientific, USA). Genomic DNA of eligible quality was sequenced on the Illumina NovaSeq 6000 platform by Novogene (Beijing, China), as described previously (6 (link)).
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2

Bumetanide Transport Assay Protocol

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Bumetanide and all of the other compounds (with the exception of AR-C155858) were purchased from Sigma-Aldrich (St. Louis, MO). AR-C155858 was purchased from Tocris Bioscience (Bristol, U.K.). [3H]Bumetanide (15–30 Ci/mmol) was purchased from American Radiolabeled Chemicals (St. Louis, MO). GIBCO Leibovitz’s L-15 medium with glutamine (Cat. No. 41300-039) and all Western blotting materials were supplied by Thermo Fisher Scientific (Rockford, IL). The pCR2.1-TOPO, TOPO TA cloning kit, TRIzol Reagent, and mMESSAGE mMACHINE T7 transcription kit were purchased from Thermo Fisher Scientific (Rockford, IL). pGH19 vector was kindly provided by Dr. Walter F. Boron (Case Western Reserve University, Department of Physiology and Biophysics, Cleveland, Ohio).24 (link) The FlashGel System was purchased from Lonza (Portsmouth, NH). All enzymes were purchased from New England Biotechnology (Ipswich, MA). The gel extraction and PCR purification kits were purchased from Qiagen (Valencia, CA). DNA purity and concentration were verified using a NanoDrop 1000 instrument (Thermo Fisher Scientific, Rockford, IL). A ZOE fluorescent cell imager made by Bio-Rad (Hercules, CA) was used for fluorescent microscopy. The mouse anti-Egfp antibody (JL-8, Cat. No. 632381) was purchased from Clontech (Mountain View, CA).
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3

Yeast Protein Expression and Membrane Isolation

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Yeast transformants were inoculated in 4 ml of SD medium and grown at 28°C with shaking at 140 rev./min. After 24 h, cells were inoculated into 200 ml of SD medium and grown for 24 h under the same conditions. Cells were harvested and induced for protein expression in 1 litre of YPG medium at 24°C with shaking at 140 rev./min. After 18–19 h of induction, cells were collected by centrifugation at 3000 g for 5 min at 4°C and washed in 25 ml of ice-cold water. After centrifugation, cells were resuspended in 10 ml of lysis buffer [40 mM Hepes/NaOH, pH 7.5, 150 mM NaCl, 26% (v/v) glycerol, 0.1 mM PMSF, 1 μg/ml aprotinin, 1 μg/ml leupeptin, 1 μg/ml pepstatin A, 5 μg/ml antipain and 157 μg/ml benzamidine HCl (Sigma–Aldrich)] and vortex-mixed with glass beads (200 μm; Sigma–Aldrich). The cell lysate was clarified by two consecutive centrifugation steps at 1000 g for 10 min at 4°C and 10000 g for 15 min at 4°C. Membranes were subsequently collected by centrifugation at 125000 g for 1 h at 4°C. Pellets were homogenized in 1.5 ml of S-buffer (same as lysis buffer but containing 20% (v/v) glycerol) and the protein concentration was measured spectrophotometrically using a Nanodrop™ 1000 instrument (Thermo Fisher Scientific). Total yeast membranes were snap-frozen in liquid nitrogen and stored at −80°C.
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4

FFPE DNA Quantification and Amplification

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Genomic DNA was isolated on a Maxwell® 16 Research (Promega Corporation, Madison, USA) as recommended in the manufacturer’s protocol. Nucleic acid quantification was performed using Qubit (Life Technologies, Carlsbad, USA) and Nanodrop 1000 instrument (Thermo Fisher Scientific, Waltham, USA). To assess the exact amplifiable amount of DNA from FFPE samples, we measured intact DNA amounts by using the Applied Biosystems® TaqMan® RNase P Assay. Amplification was performed on the QuantStudio 5 (Thermo Scientific, Waltham, USA).
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5

MIQE-Compliant RNA Extraction and qPCR Analysis

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These procedures followed MIQE recommendations [36 (link)]. Briefly, total RNA was extracted using the TRI-Reagent kit (Euromedex, Souffelweyersheim, France) according to the manufacturer’s instructions. RNA purity and integrity were evaluated by spectrophotometry on a NanoDrop 1000 instrument (Thermo Fisher Scientific, Waltham, MA, USA) and by SYBR Gold-stained agarose gel electrophoresis (Invitrogen, Carlsbad, CA, USA). Primer sequences designed using Primer Express software (Applied Biosystems, Courtaboeuf, France) are listed in Supplementary Table 1 and were tested for specificity, efficiency, reproducibility, and dynamic range. Amplification was performed in a 10-µL reaction volume with Takara SYBR qPCR Premix ExTaq II (Ozyme, Montigny-le-Bretonneux, France) on a StepOne Plus ABI Real-time PCR instrument (PerkinElmer Life and Analytical Sciences, Boston, MA, USA). The expression levels of selected genes were normalized to those of the TATA-binding protein and 36B4 housekeeping genes and quantified using the comparative ΔCt method.
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6

Yeast DNA Extraction Protocol

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Initially, yeast cells were disrupted by heating and freezing steps, under denaturing conditions. Briefly, after growing on SDA at 28°C for 48 hr, 50–100 mg of biomass of each sample were suspended in 500 μl of extraction buffer (250 mmol/L Tris‐HCl; 25 mmol/L EDTA; 0.5% (w/v) SDS; 250 mmol/L NaCl; pH 8.0), then vortexed for 1 min, and heated at 80°C for 20 min followed by freezing at −20°C for the same period. Then, the samples were centrifuged at 1,077g for harvesting the supernatant. DNA isolation from the upper aqueous phase was carried out by using a chloroform–isoamyl alcohol mixture (24:1) (14,475 g; 25°C for 10 min), followed by the DNA precipitation with 0.7 vol of isopropanol (14,475 g; 4°C for 30 min), and a washing step with 70% (v/v) ethanol (14,475 g; 4°C for 10 min). At last, DNA was suspended in 40 μl of sterile ultrapure water, and after measuring its concentration by using Nanodrop 1,000 instrument (Thermo Fisher Scientific), it was stored at −20°C.
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7

Producing Active DENV NS2B-NS3pro Complex

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NS2B and NS3pro were co-refolded by one-step dialysis overnight at 4 °C in a 2:1 molar NS2B:NS3pro ratio to maximize formation of the active complex. The refolding buffer was 25 mM Tris pH 8.5 (pH set at 4 °C), 5% glycerol, 100 mM NaCl. Thrombin (GE Healthcare) and/or TEV protease was added to a dialysis cassette (3,500 or 7,000 MWCO Slide-A-Lyzer, Thermo Fisher Scientific) to cleave off the His tag from NS2B and/or NS3pro. After refolding the solution was centrifuged at 50,000 × g to remove any precipitate or particles. Refolding yield was determined by measuring protein concentration of the two IMAC pools (NS2B: ε 5,500, MW 7.7 kDa; NS3pro: ε 36,400, MW 21.0 kDa) before refolding and comparing that to the protein concentration after refolding and centrifugation (complex: ε 41,940, MW 28.7 kDa), using a Nanodrop 1000 instrument (Thermo Scientific). The complex was then purified on an ÄKTA Explorer (GE Healthcare) by size exclusion on a HiLoad Superdex 200 column (GE Healthcare) in SEC buffer: 50 mM Tris pH 8.5 (4 °C), 5% glycerol, 50 mM NaCl.
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8

Intestinal Microbiome DNA Extraction

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The same physical samples were used for all sequencing experiments across platforms and bioinformatics pipelines. Total genomic DNA was extracted using E.Z.N.A. Stool DNA Kit (Omega Bio-Tek, Norcross, GA) according to manufacturer’s instructions with minor modifications. Briefly, 200 mg of intestinal content were added to a tube containing 540 μl of SLB buffer and 200 mg of glass beads. Samples were homogenized using a TissueLyser (Qiagen, Germantown, MD) for 5 min at 30 Hz in 1 min intervals between bead beating and ice incubation cycles. DS buffer and proteinase K were added according to the manufacturer’s instruction. The mix was incubated at 70 °C for 10 min, followed by another incubation at 95 °C for 5 min. Quality of the isolated DNA was assessed by agarose gel electrophoresis and purity verified using 260/280 and 260/230 ratios measured by NanoDrop 1000 instrument (Thermo Fisher Scientific, Waltham, MA). DNA concentration was quantified using Quant-iT™ PicoGreen dsDNA Reagent (Molecular Probes, Thermo Fisher Scientific division, Eugene, OR).
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9

CTAB-based DNA Extraction from Plant and Animal

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A cetyltrimethylammonium bromide (CTAB) extraction method [20 (link)] was assessed for its ability to efficiently extract DNA from a range of plant and animal materials (SOP). In brief, the CTAB method consists of an initial step to separate polysaccharides and organic soluble molecules using a CTAB extraction buffer (1X CTAB, 1.4 M NaCl, 0.1 M Tris-HCl [pH 8.0], and 20 mM NA2EDTA) and chloroform. Next, the DNA was precipitated with 96% ethanol and purified with 70% ethanol, and the obtained DNA was stored at 4°C until further use. DNA was extracted from 100-mg reference materials (plant and animal), artificially made complex mixtures, and real-life samples (TMs), along with an extraction control. The concentration and purity (OD260/280 and OD260/230 ratios) of the obtained DNA was determined by spectrophotometer (NanoDrop 1000 instrument, Thermo Fisher Scientific Inc.). OD260/280 ratios between 1.7 and 2.0 were considered to indicate purity of the obtained DNA. In cases where the extraction control contained DNA, the DNA isolation procedure was repeated.
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10

Salmonella Genomic DNA Extraction and Sequencing

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Genomic DNA of all 105 selected Salmonella isolates was extracted from cultures incubated in Luria-Bertani (LB) broth overnight using a FastPure bacterial DNA isolation minikit (Vazyme Biotech Co., Ltd., Nanjing, China) according to the manufacturer’s instructions and quantified using a Nanodrop 1000 instrument (Thermo Fisher Scientific, USA). Genomic DNA of eligible quality was sequenced on the Illumina NovaSeq 6000 platform by Novogene (Beijing, China), as described previously (6 (link)).
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