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Nanodrop one instrument

Manufactured by Thermo Fisher Scientific
Sourced in United States

The Nanodrop One is a spectrophotometer designed for the quantification and analysis of nucleic acids and proteins. It utilizes a small sample volume to measure the absorbance of a sample at various wavelengths, allowing for accurate concentration and purity measurements.

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7 protocols using nanodrop one instrument

1

Isolation and Sequencing of Plant matK Gene

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Leaf samples were taken using clean tweezers and scalpel, and flash frozen in liquid nitrogen and stored at −80°C until use. Approximately 50 mg of frozen tissue was ground in a 1.5 ml reaction tube using a disposable tube pestle. Genomic DNA from the ground leaves of all species grown was isolated using the E.Z.N.A. Plant DNA Kit (OMEGA Bio-Tek, Norcross, GA) following the manufacturer’s recommendations. The gDNA was eluted using 100 μl nuclease-free water and the concentration was estimated using a NanoDrop™ One instrument (ThermoFisher Scientific, Waltham, MA). The 1:10 diluted DNA was used to amplify a region of the maturase K gene using Q5® High-Fidelity DNA Polymerase (NEB, Ipswich, MA) following the manufacturer’s recommendations with following primer combinations: matK_F1 (5′-ATA CTT TAT TCG ATACAA ACT CCT TTT TTT-3′) and matK_R1 (5′-AGT ATT GCA ATT TGA ATA GTT TCA TTA C-3′) using 53°C as annealing temperature or matK_F2 (5′-ATA CTT TAT TCG ATA CAA ACT CCT TTT TTT GGA AG-3′) and matK_R2 (5′-AGT ATT GCA ATT TGA ATA GTT TCA TTA CTC GAA A-3′) using 56°C as annealing temperature. Both primer pairs amplify the same target while matK_F2 and matK_R2 bind approximately 40 bp upstream of their respective F1/R1 counterparts. PCR products were directly sequenced using Sanger sequencing at the Cornell Institute of Biotechnology using the above primers.
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2

Spectrophotometric analysis of enzymes and polymers

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Molar absorption coefficient determinations and kinetic measurements in bulk solution were carried out with a JASCO V-670 or a SPECORD S600 spectrophotometer (from Analytik Jena) using quartz cells with path length of either 1.0 cm or 0.1 cm. For the determination of the concentrations of concentrated enzyme or dendronised polymer stock solutions a NanoDrop One instrument was used (from ThermoFisher Scientific). For spectrophotometric quantifications in the flow-through experiments, a Cary 60 spectrophotometer (from Agilent Technologies) was used in addition to the SPECORD S600, using the same cells mentioned above.
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3

SARS-CoV-2 S Protein Production

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Codon-optimized nucleotide fragments encoding a stabilized foldon-trimerized version of the SARS-CoV-2 S ectodomain (aa 1–1208), the S1 monomer (aa 16–681) and the RBD subdomain (aa 331–519) both preceded by a murine IgK leader peptide and followed by an 8xHis Tag were synthetized and cloned into pcDNA3.1/Zeo(+) expression vector (Thermo Fisher Scientific). Proteins were produced by transient co-transfection of exponentially growing Freestyle 293-F suspension cells (Thermo Fisher Scientific) using polyethylenimine (PEI)-precipitation method as previously described (Lorin and Mouquet, 2015 (link)). Recombinant SCoV-2 proteins were purified by affinity chromatography using the Ni Sepharose Excel Resin according to manufacturer’s instructions (Thermo Fisher Scientific). Protein purity was evaluated by in-gel protein silver-staining using Pierce Silver Stain kit (Thermo Fisher Scientific) following SDS-PAGE in reducing and non-reducing conditions using NuPAGE 3%–8% Tris-Acetate gels (Life Technologies). Purified proteins were dialyzed overnight against PBS using Slide-A-Lyzer dialysis cassettes (10 kDa MW cutoff, Thermo Fisher Scientific). Protein concentration was determined using the NanoDrop One instrument (Thermo Fisher Scientific).
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4

RNA Extraction and qRT-PCR Analysis

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Total RNAs of decidua tissues were extracted using Trizol (Invitrogen) according to manual instructions. Quantitative RT-PCR (qRT-PCR) was performed using the HiScriptII Supermix (Vazyme, Nanjing, China) following the manufacturer’s instructions. Briefly, RNA was quantified using a Nanodrop One instrument (Thermo, MA, USA) and 1 μg was used for reverse transcription using random primers. For qRT-PCR, SYBR Green master mix and primers (final concentration at 200 nM) were used and results were analyzed in CFX Connect PCR detection system (Bio-Rad, CA, USA). Primers were designed according to a previous publication (22 (link)) for CCL8 and GAPDH, or using an open resource (www.ncbi.nlm.nih.gov/tools/primer-blast) for TRDV1, TRDV2, and TRDV3, whose sequences are listed in Supplementary Table S2. Expression levels were normalized to GAPDH and represented as fold change compared to the control (2−ΔΔCt).
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5

Bacterial DNA Extraction from Diverse Isolates

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In our laboratory, P. aeruginosa was isolated from spoiled wood paint lotion. Other pathogenic bacteria obtained from American Type Culture Collection (ATCC) and German Collection of Microorganisms and Cell Cultures included Staphylococcus aureus ATCC 6538P, Escherichia coli ATCC 8739, Vibrio parahaemolyticus ATCC 17802, Salmonella enterica ATCC 9115, Klebsiella pneumoniae ATCC 4352, Lactobacillus paracasei ATCC 334, Bacillus paralicheniformis ATCC 9945, and Bacillus subtilis DSM 23778. The nucleic acids of the above strains were extracted using the HiPure Bacterial DNA Kit (Magen Biotech Co., Ltd.; Guangzhou, China) according to the manufacturer’s instructions. The concentration of DNA was quantified using the Nanodrop One instrument (Thermo Fisher Scientific, Shanghai, China). Until they were used, all DNA samples were stored at-20°C.
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6

Genomic DNA Extraction and Molecular Diagnosis of Malaria

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Genomic DNA from each sample was extracted with the Qiagen blood Mini kit (CAT 51306, Qiagen, Hilden, Germany), and quantified with NanoDrop One Instrument (Thermo Fisher Scientific™, Wilmington, USA) (Desjardins and Conklin, 2010 (link)). Following microscopic examination, infection with P. falciparum for each sample was confirmed with three described molecular diagnostic techniques targeting the 18S srRNA gene in conventional and real-time PCR; the highly sensitive variable Acidic terminal sequence (varATS) and Telomere Associated Repetitive sequence (TARE)-2 by real-time PCR (Hofmann et al., 2015 (link)). For real time assays, samples were negative when cycle time (Ct) was ≥ 40. For the coupled PCR, the 18S primary PCR product was used as template for the real-Time PCR (Rutledge et al., 2017 (link)). Primers were synthesized by Macrogen Inc, Seoul, Korea.
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7

Quantitative Real-Time PCR for Gene Expression

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Total RNA from cell
cultures grown in either the monolayer culture (MC) or collagen scaffolds
(CSs) and human liver samples was isolated utilizing the RNeasy Mini
Kit (Qiagen, Hilden, Germany) followed by DNA removal using the RNase-Free
DNase Set (Qiagen, Hilden, Germany). The integrity and quantity of
isolated RNA were checked by the Nanodrop One instrument (Thermo Fisher
Scientific, Waltham, MA, USA). Subsequently, cDNA was generated using
the Maxima H Minus First Strand cDNA Synthesis Kit (Thermo Fisher
Scientific, USA). We utilized 2 μg of RNA to synthesize cDNA
according to a previously published protocol.41 (link)Further, we performed quantitative real-time PCR on an Applied
Biosystems Viia7 Real Time PCR system (Applied Biosystems, Waltham,
MA, USA) utilizing the Fast Advanced TaqMan Gene Expression Master
Mix (Thermo Fisher Scientific, Waltham, MA, USA) and specific TaqMan
gene expression assays (Table S4). Data
were assessed using the MS Excel and MaxStat Pro 3.6 software (MaxStat,
Cleverns, Germany). The expression of the target gene was normalized
to GAPDH expression utilizing the 2–ΔΔCT methodology previously published in ref (42 (link)).
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