Nd one w

Manufactured by Thermo Fisher Scientific

Sourced in United States

The ND-ONE-W is a laboratory instrument designed for nucleic acid detection and analysis. It utilizes real-time PCR technology to accurately quantify and identify specific DNA or RNA sequences. The core function of the ND-ONE-W is to perform sensitive and reliable nucleic acid detection and quantification in a controlled laboratory environment.

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Lab products found in correlation

Fetal bovine serum (fbs), by Merck Group (1 mentions) Dulbecco modified eagle medium (dmem), by Merck Group (1 mentions) Puromycin, by Thermo Fisher Scientific (1 mentions) Hygromycin, by Thermo Fisher Scientific (1 mentions) Minipreps, by Promega (1 mentions) Ncounter sprint profiler machine, by NanoString (1 mentions) Quanti it pico green dsdna assay kit, by Thermo Fisher Scientific (1 mentions) Truseq nano dna kit, by Illumina (1 mentions) Novaseq 6000, by Illumina (1 mentions) Dna extraction kit, by Roche (1 mentions) Eclipse ti u, by Nikon (1 mentions) Crystal clear sealing tape, by Hampton Research (1 mentions) Minisart rc4, by Sartorius (1 mentions) Mir 154 pj, by Panasonic (1 mentions) Nextera xt dna library preparation kit, by Illumina (1 mentions) 2100 bioanalyzer instrument, by Thermo Fisher Scientific (1 mentions) Miniseq high output kit, by Illumina (1 mentions) Dneasy ultraclean 96 microbial kit, by Qiagen (1 mentions) Abi 7700, by Thermo Fisher Scientific (1 mentions) Bacteria total rna isolation kit, by Sangon (1 mentions)

Close spelling variants of this product

Nanodrop One (ND-ONE-W, (2 citations) Nanodrop One/OneC Microvolume UV–VIS Spectrophotometer (ND-ONE-W) (2 citations) ND-ONE-W-A30221 (2 citations)

10 protocols using nd one w

GPCR Plasmid Preparation and Characterization

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HTLA
cells, HEK293 cells stably expressing a tTA-dependent luciferase reporter,
and a β-arrestin-TEV protease fusion gene (kindly provided by
Brian Roth) were maintained in DMEM (Sigma-Aldrich, D6492), supplemented
with 10% FBS (Sigma-Aldrich, F9665), 2 μg mL^–1 puromycin (58-58-2, ≥98%, Invitrogen), and 100 μg mL^–1 hygromycin (31282-04-9, ≥98%, Invitrogen).
Cells were split 1:5 when confluency reached 70% and discarded after
passage 10. All GPCR plasmids originated from a Roth lab PRESTO-Tango
kit (Addgene, Kit #1000000068) as E. coli glycerol stocks. Each stock was individually cultured, and plasmids
were isolated via minipreps (Promega, A1330). Each GPCR plasmid concentration
was quantified (Nanodrop, One/One^c microvolume UV–vis
spectrophotometer, ND-ONE-W, Thermo Scientific) and had a 260/280
ratio of 1.7–1.9, a 260/230 ratio of ≥1.8, and concentrations
of ≥100 ng/μL. Plasmid stocks for each GPCR were then
diluted for a final concentration of 50 ng μL^–1.

McPartland M., Stevens S., Bartosova Z., Vardeberg I.G., Völker J, & Wagner M. (2024). Beyond the Nucleus: Plastic Chemicals Activate G Protein-Coupled Receptors. Environmental Science & Technology, 58(11), 4872-4883.

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Bacterial Suspension Preparation and Plating

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A bacterial suspension in a phosphate-buffered solution (PBS) (product no. 20-012-027, Fisher Scientific, Hampton, NH, USA) was prepared every day from a solid agar plate incubated for 24 h. The concentration of the suspension was measured using a spectrophotometer (model no. ND-ONE-W, Thermo Fisher), and the suspension was then diluted in PBS to a final concentration of 1–200 CFU per 0.1 mL. One hundred microlitres of the diluted suspension was spread on a CHROMagar™ ECC plate using an L-shaped spreader (product no. 14-665-230, Fisher Scientific, Hampton, NH, USA). The plate was covered with its lid, inverted, and incubated at 37 °C in our optical platform (Fig. 2).

Wang H., Ceylan Koydemir H., Qiu Y., Bai B., Zhang Y., Jin Y., Tok S., Yilmaz E.C., Gumustekin E., Rivenson Y, & Ozcan A. (2020). Early detection and classification of live bacteria using time-lapse coherent imaging and deep learning. Light, Science & Applications, 9, 118.

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UV Spectra of PAMK Solution

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The UV spectra of the PAMK (0.5 mg/mL) was recorded in a spectrophotometer (ND-ONE-W, Thermo fisher, Waltham, MA) in the wavelength range of 200–600 nm at room temperature.

Miao Y.F., Gao X.N., Xu D.N., Li M.C., Gao Z.S., Tang Z.H., Mhlambi N.H., Wang W.J., Fan W.T., Shi X.Z., Liu G.L, & Song S.Q. (2020). Protective effect of the new prepared Atractylodes macrocephala Koidz polysaccharide on fatty liver hemorrhagic syndrome in laying hens. Poultry Science, 100(2), 938-948.

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Nanostring-based Immune Profiling

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Total RNA was extracted as described above. RNA concentrations were quantified and evaluated for purity using a nanodrop spectrophotometer (Thermofisher, # ND-ONE-W). For immune profiling we utilized Nanostring’s 770-gene Mouse nCounter® PanCancer Immune Profiling Panel. Reporter codesets were thawed at room temperature and subsequently mixed with 70 μL of hybridization buffer to form a master mix. From this master mix, 8 μL was aliquoted into PCR tubes. RNA samples were normalized to 10 ng/uL and 5 μL from each sample was added into the PCR tubes. Next, 2uL of Capture probeset was added to each tube. The reaction mixture was then gently mixed, spun down, and loaded into a prewarmed 65°C thermocycler with a heated lid set to 70°C. Samples were allowed to hybridize for 16–20 hours, after which they were immediately placed on ice. At this time, a SPRINT cartridge was thawed and allowed to equilibrate to RT. Samples were then individually loaded into the cartridge and inserted into the NanoString nCounter SPRINT Profiler machine (NanoString nCounter Analysis System, RRID:SCR_021712). Raw data was analyzed using NanoString nSolver 4.0. mRNA counts were processed to account for hybridization efficiency, background noise, and sample content, and were normalized using the geometric mean of housekeeping genes.

Wu M.J., Shi L., Dubrot J., Merritt J., Vijay V., Wei T.Y., Kessler E., Olander K.E., Adil R., Pankaj A., Tummala K.S., Weeresekara V., Zhen Y., Wu Q., Luo M., Shen W., García-Beccaria M., Fernández-Vaquero M., Hudson C., Ronseaux S., Sun Y., Saad-Berreta R., Jenkins R.W., Wang T., Heikenwälder M., Ferrone C.R., Goyal L., Nicolay B., Deshpande V., Kohli R.M., Zheng H., Manguso R.T, & Bardeesy N. (2022). Mutant-IDH inhibits Interferon-TET2 signaling to promote immunoevasion and tumor maintenance in cholangiocarcinoma. Cancer discovery, 12(3), 812-835.

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Whole Genome Sequencing of NCOR1/2 DKO Mice

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To perform whole genome sequencing, we harvested bone marrow from two wildtype and three NCOR1/2 DKO mice (both males and females that ranged between 7–9 weeks). We flow sorted 300,000 CD19⁺B220⁺ B cells from each sample; CD19⁺B220⁺ B cells were subject to DNA isolation using a DNA extraction kit (11796828001, Roche). Nucleic acid quantification was performed using both a nanodrop (ND-ONE-W, ThermoFisher) and Quanti-iT PicoGreen dsDNA assay kit (P11496, ThermoFisher). Library preparation for whole genome sequencing was performed using the TruSeq Nano DNA kit (20015964, Illumina). Sequencing was performed on a NovaSeq 6000 with 2×150 bp paired-end reads (Illumina).

Lee R.D., Knutson T.P., Munro S.A., Miller J.T., Heltemes-Harris L.M., Mullighan C.G., Jepsen K, & Farrar M.A. (2022). Nuclear corepressors NCOR1/NCOR2 regulate B cell development, maintain genomic integrity, and prevent transformation. Nature immunology, 23(12), 1763-1776.

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Microfluidic Lysozyme Crystallization

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Lysozyme solution was prepared
by dissolving an appropriate amount of lysozyme into 100 mM acetate
buffer at pH 4.5. The protein concentration was measured using a NanoDrop
instrument (ND-ONE-W, Thermo Scientific, Tokyo, Japan) and adjusted
to 80 mg/mL. A precipitant solution of 1.4 M sodium chloride in 100
mM acetate buffer (pH 4.5) was prepared. Lysozyme and precipitant
solutions were filtered through 0.2 μm syringe filters (Minisart
RC4 or RC25, Sartorius Stedim Biotech, Gottingen, Germany). Equal
volumes of both solutions were mixed to prepare the crystallization
solution, which was then pipetted onto the inlet of the microfluidic
device (Figure 1d).
The crystallization solution was introduced into the microfluidic
device using a vacuum pump; after loading into the microwells, inlets
of the fluidic and control channels were sealed with a Crystal Clear
sealing tape (HR-3-511, Hampton Research, Aliso Viejo, CA, USA). Microfluidic
devices were incubated at 20 °C in an incubator (MIR-154-PJ,
Panasonic, Osaka, Japan). Any protein crystals that formed in the
microwells were observed on an optical microscope (ECLIPSE Ti-U, Nikon,
Tokyo, Japan).

Maeki M., Yamazaki S., Takeda R., Ishida A., Tani H, & Tokeshi M. (2020). Real-Time Measurement of Protein Crystal Growth Rates within the Microfluidic Device to Understand the Microspace Effect. ACS Omega, 5(28), 17199-17206.

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Microbial DNA Extraction and Sequencing

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L5-L6 DNA was extracted again, using DNeasy UltraClean 96 Microbial Kit [Qiagen, Hilden, Germany]. A Nanodrop device [ND-ONE-W] was used to control purity and concentration for each sample [Thermofisher, Waltham, USA]. The Qiagen kit allows to obtain good quality purified DNA as assessed by a 280/260 and 260/230 ratio close to 2 and the concentration of the DNA was sufficient to perform library preparation on some samples [concentration 100 ng/μl].Samples were prepared for further sequencing. Library was produced using the Nextera XT DNA Library Preparation kit [Illumina, San Diego, USA]- with a control of the fragment size on a 2100 Bioanalyzer Instrument [Thermofisher, Waltham, USA]. Sequencing was performed using the Miniseq High Output Kit [Illumina, San Diego, USA] generating paired-end reads of 150 bp. Quality of reads was then analyzed by fastqc and a combination of web-based analysis (TB-Profiler) (available at https://tbdr.lshtm.ac.uk) or through a proprietary pipeline (TB-Annotator)[16 ].

Sahal M.R., Senelle G., La K., Panda T.W., Taura D.W., Guyeux C., Cambau E, & Sola C. (2023). Mycobacterium tuberculosis complex drug-resistance, phylogenetics, and evolution in Nigeria: Comparison with Ghana and Cameroon. PLOS Neglected Tropical Diseases, 17(10), e0011619.

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MRSA Transcriptional Analysis via RT-PCR

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In this assay, the Bacteria Total RNA Isolation Kit (B518625) was obtained from Sangon Biotech (Shanghai, China) and applied to isolate a total RNA sample from treated MRSA N315 bacteria, and then the concentration of RNA sample was detected using the spectrophotometer (ND-ONE-W, ThermoFisher Scientific, Waltham, Massachusetts, USA). For the RT-PCR analysis of hlaA, the RT-PCR reaction mix solution (including Abstract Taq, one-step RT-PCR buffer, solution I, hlaA primer, RNA, and RNase-free H₂O) was prepared with the help of one-Step RT-PCR Mix (B110025, Sangon Biotech, Shanghai, China), and then was performed on the RT-PCR system (ABI7700, Applied Biosystems, Carlsbad, California, USA). Ultimately, the hlaA gene expression was analyzed using the 2^−ΔΔct method, and 16S rRNA gene (16S) was used as an endogenous control [24 (link)]. The sequence of primers of hlaA and 16S is itemized in Table 1.

Sun Y., Sun F., Feng W., Wang Q., Liu F., Xia P, & Qiu X. (2022). Luteolin Inhibits the Biofilm Formation and Cytotoxicity of Methicillin-Resistant Staphylococcus aureus via Decreasing Bacterial Toxin Synthesis. Evidence-based Complementary and Alternative Medicine : eCAM, 2022, 4476339.

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Bacterial Suspension Preparation Protocol

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We used E. coli (ATCC 25922) to prepare bacterial suspensions in phosphate buffered saline (Product No. 20-012-027, Fisher Scientific, Hampton, NH, USA). Plates containing tryptic soy agar plates were inoculated with the bacteria and incubated at 37 °C for 24 h. The bacteria were then collected from the culture agar plates using a disposable loop and suspended at different concentrations in the buffer solution. The concentration of each suspension was measured using a spectrophotometer (ND-ONE-W, ThermoFisher Scientific, Waltham, MA, USA).

Ceylan Koydemir H., Rajpal S., Gumustekin E., Karinca D., Liang K., Göröcs Z., Tseng D, & Ozcan A. (2019). Smartphone-based turbidity reader. Scientific Reports, 9, 19901.

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Quantifying Viral RNA in Bee Samples

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To estimate reaction efficiency, DNA templates were in vitro transcribed with the HiScribe T7 Quick High Yield RNA synthesis kit (NEB, E2040S) according to the manufacturer’s instruction. 100 ng of RNA was used as template for cDNA synthesis using the Superscript IV VILO kit (ThermoFisher #11756050) and 10x serial dilutions were performed and ran alongside samples being tested to establish standard curves. The equation of the slope for each standard curve was used to establish the correlation between Ct values and viral copy number per µL. A Ct of 38 was used as the standard cut-off for all positive reactions.
Extracted RNAs (whole bees or viral aliquots) were quantified using a nanodrop (ThermoFisher, #ND-ONE-W), diluted in RNase-free water and 100 ng RNA input was used for cDNA synthesis. For RT-qPCR setup, PowerUP SYBR green master mix (ThermoFisher #25742) and appropriate primer sets (Supplementary Data 1) were prepared for 10 µL total reactions in a 384-well plate format, with 2 µL of cDNA input, or controls, added to each well. Real-time PCR was performed on a Bio-Rad CFX-384 system with standard cycling and melt curve analysis. Ct of 38 was used as the standard cutoff.

Karlikow M., Amalfitano E., Yang X., Doucet J., Chapman A., Mousavi P.S., Homme P., Sutyrina P., Chan W., Lemak S., Yakunin A.F., Dolezal A.G., Kelley S., Foster L.J., Harpur B.A, & Pardee K. (2023). CRISPR-induced DNA reorganization for multiplexed nucleic acid detection. Nature Communications, 14, 1505.

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