Nanodrop fluorospectrometer

Manufactured by Thermo Fisher Scientific

Sourced in United States

The NanoDrop Fluorospectrometer is a compact, high-performance fluorescence measurement instrument designed for precise and accurate analysis of small sample volumes. It utilizes state-of-the-art optical technology to measure the fluorescence of various biomolecules, including proteins, nucleic acids, and small molecules.

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Lab products found in correlation

High capacity cdna reverse transcription kit, by Thermo Fisher Scientific (2 mentions) Taqman gene expression master mix, by Thermo Fisher Scientific (2 mentions) Ecodry premix protocol at a glance, by Takara Bio (2 mentions) Chromo4 pcr system, by Bio-Rad (2 mentions) Direct zol rna miniprep plus kit, by Zymo Research (1 mentions) Stepone real time pcr system, by Thermo Fisher Scientific (1 mentions) Taqman gene expression assay, by Thermo Fisher Scientific (1 mentions) Trizol method, by Thermo Fisher Scientific (1 mentions) Steponeplus detection system, by Thermo Fisher Scientific (1 mentions) Reliaprep rna cell miniprep system, by Promega (1 mentions) Pcr array data analysis web portal, by Qiagen (1 mentions) Rt2 profiler pcr array, by Qiagen (1 mentions) Qiashredder 50, by Qiagen (1 mentions) Rneasy mini kit 50, by Qiagen (1 mentions) Smart seq v4 ultra low input rna kit, by Takara Bio (1 mentions) Nextera xt kit, by Illumina (1 mentions) 2100 bioanalyzer, by Agilent Technologies (1 mentions) Nucleospin rna 2 kit, by Takara Bio (1 mentions) Novaseq 6000, by Illumina (1 mentions) Topo ta cloning kit, by Thermo Fisher Scientific (1 mentions)

Spelling variants of this product

NanoDrop (8392 citations) NanoDrop 3300 Fluorospectrometer (70 citations) NanoDrop ND-3300 fluorospectrometer (9 citations) NanoDrop 2000 Fluorospectrometer (5 citations)

8 protocols using nanodrop fluorospectrometer

Quantitative Gene Expression Analysis

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Total RNA was isolated using the Direct-zol RNA MiniPrep Plus Kit (Zymo Research) following instructions provided by the manufacturer. The quality of the isolated RNA was measured by determining the A260/280 and A260/230 ratios using a Nanodrop fluorospectrometer (Thermo Fisher Scientific). Integrity of the isolated RNA was further assessed by visualization of the rRNA on agarose gels. Reverse transcription was performed with 1 μg of each RNA sample using the High-Capacity cDNA Reverse Transcription Kit (Thermo Fisher, Cat. No. 4368814) according to the manufacturer’s instructions. The resulting cDNA was used for quantitative analysis of gene expression with a SYBR green system using a StepOne real-time PCR system (Applied Biosystems). Primer sequences are listed in Supplemental Table S1 and each were previously reported or generated using the NCBI Primer-Blast tool. All primers were verified by testing primer efficiency and specificity using the standard curve method and melt curve analysis, respectively. Levels of gene transcripts in samples were measured in technical duplicates or triplicates within 96-well plates and normalized to β-actin. Comparisons were made using the 2^−ΔΔCt method and then expressed as fold-change relative to the WT mice at room temperature.

Levy J.L., Mirek E.T., Rodriguez E.M., Zalma B., Burns J., Jonsson W.O., Sampath H., Staschke K.A., Wek R.C, & Anthony T.G. (2023). GCN2 is required to maintain core body temperature in mice during acute cold. American Journal of Physiology - Endocrinology and Metabolism, 325(5), E624-E637.

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Astrocyte Gene Expression Analysis

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Astrocyte RNA was isolated by the Trizol method (Thermo Fisher Scientific) followed by DNA digestion and precipitation. A Nanodrop fluorospectrometer (Thermo Fisher Scientific) was used to assess RNA purity and to quantify total RNA levels. Transcripts were made into cDNA with the high-capacity cDNA reverse transcription kit (Thermo Fisher Scientific) at 50–100 μg/ml. Expression levels were measured by real-time polymerase chain reaction (PCR) using Taqman^® gene expression assays and the StepOnePlus detection system (Thermo Fisher Scientific). Assay identifiers used in human cells are compiled in Table 1. The 10 μl reactions with 50–100 ng cDNA were carried out at 50°C for 2 min, 95°C for 20 sec, followed by 40 cycles of 95°C for 1 sec and 60°C for 20 sec in 96-well optical, real-time PCR plates. Transcript levels were normalized to GAPDH quantified in a duplex PCR reaction. Astrocyte expression levels are represented as fold changes to respective controls as calculated by the comparative ΔΔCT method (Livak and Schmittgen 2001 (link)).

Borgmann K, & Ghorpade A. (2017). Methamphetamine augments concurrent astrocyte mitochondrial stress, oxidative burden and antioxidant capacity: tipping the balance in HIV-associated neurodegeneration. Neurotoxicity research, 33(2), 433-447.

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Comprehensive Gene Expression Analysis

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For gene expression analysis, ‘Human Adherens Junctions’ and ‘Human Extracellular Matrix and Adhesion Molecules’ RT2 Profiler PCR Arrays (Qiagen) were used. These RT2 Arrays profile simultaneously the expression of 84 genes involved in cell-cell contact and cell adhesion, within one sample. In brief, cells were harvested and mRNA was isolated using the ReliaPrep^TM RNA Cell Miniprep System (Promega). The mRNA concentration was measured with a NanoDrop Fluorospectrometer (Thermo Fisher Scientific, Inc.; Waltham, MA, USA). For cDNA synthesis the RT2 First Strand Kit was used. A total of 0.5 µg RNA was reverse transcribed and the cDNA was amplified by the RT2 SYBR Green Master mix. Data were evaluated using the Qiagen PCR Array Data Analysis Web portal. Gene expression was normalized to the mean expression of the reference genes (GAPDH, ACTB, B2M HPRT and RPLP0) and was calculated using the ∆∆CT method.

Stadler M., Scherzer M., Walter S., Holzner S., Pudelko K., Riedl A., Unger C., Kramer N., Weil B., Neesen J., Hengstschläger M, & Dolznig H. (2018). Exclusion from spheroid formation identifies loss of essential cell-cell adhesion molecules in colon cancer cells. Scientific Reports, 8, 1151.

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Quantifying NF-κB Pathway Gene Expression

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Cells or spheroids were harvested after transfection and RNA was isolated using the RNeasy Mini Kit 50 and QIAshredder 50 (QIAGEN, Hamburg, Germany). The final RNA concentration was measured using a NanoDrop Fluorospectrometer (Thermo Fisher Scientific, Inc., Waltham, MA, USA). An amount of 2 μg of total RNA was reverse transcribed using RNA to cDNA EcoDry Premix Protocol-At-A-Glance (Clontech, 2 Saint-Germain-en-Laye, France), the resulting cDNA was amplified using TaqMan Gene Expression Master Mix (Applied Biosystems, Vienna, Austria). The PCR products were analyzed on the Chromo4 PCR System (Bio-Rad, Hercules, CA, USA). The following TaqMan probes were used: GAPDH (Hs99999905_m1), IKBKG (NEMO; Hs00415849_m1), MAP3K14 (NIK; Hs00177695_m1), RELA (Hs00153294_m1), RELB (Hs00232399_m1), CREL (Hs00968440_m1), NFKB1 (p100; Hs00765730_m1), NFKB2 (p105; Hs00174517_m1), and MMP1(Hs00899658_m1). qPCR was performed in triplicate for each cDNA template. Gene expression normalized to GAPDH expression (glyceralaldehyde 3-phosphate dehydrogenase) and was calculated using the ΔΔC_T method.

Nguyen C.H., Senfter D., Basilio J., Holzner S., Stadler S., Krieger S., Huttary N., Milovanovic D., Viola K., Simonitsch-Klupp I., Jäger W., de Martin R, & Krupitza G. (2015). NF-κB contributes to MMP1 expression in breast cancer spheroids causing paracrine PAR1 activation and disintegrations in the lymph endothelial barrier in vitro. Oncotarget, 6(36), 39262-39275.

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Quantitative Gene Expression Analysis

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Cells were harvested after transfection, and RNA was isolated using the RNeasy Mini Kit 50 and QIAshredder 50 (QUIAGEN, Hamburg, Germany). The final RNA concentration was measured using a NanoDrop Fluorospectrometer (Thermo Fisher Scientific, Inc., Waltham, MA, USA). An amount of 2 µg of total RNA was reverse transcribed using RNA to cDNA EcoDry Premix Protocol-At-A-Glance (Clontech, 2 Saint-Germain-en-Laye, France). The resulting cDNA was amplified using TaqMan Gene Expression Master Mix (Applied Biosystems, Vienna, Austria). The PCR products were analysed on the Chromo4 PCR System (Bio-Rad, Hercules, CA, USA). The following TagMan probes were used: GAPDH (Hs99999905_m1) and MYLK (Hs00364926_ma). qPCR was performed in triplicate for each cDNA template. Gene expression was normalised to GAPDH expression (glyceraldehyde 3-phosphate dehydrogenase) and was calculated using the ∆∆C_T method.

Stadler S., Nguyen C.H., Schachner H., Milovanovic D., Holzner S., Brenner S., Eichsteininger J., Stadler M., Senfter D., Krenn L., Schmidt W.M., Huttary N., Krieger S., Koperek O., Bago-Horvath Z., Brendel K.A., Marian B., de Wever O., Mader R.M., Giessrigl B., Jäger W., Dolznig H, & Krupitza G. (2016). Colon cancer cell-derived 12(S)-HETE induces the retraction of cancer-associated fibroblast via MLC2, RHO/ROCK and Ca2+ signalling. Cellular and Molecular Life Sciences, 74(10), 1907-1921.

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RNA-seq from Blood Neutrophils

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RNA was isolated from blood neutrophils using the Nucleospin RNA II Kit (Takara, Mountain View, Calif) with on-column genomic DNA digestion according to the manufacturer’s protocol as described previously.¹⁹ RNA was quantified using the NanoDrop Fluorospectrometer (ThermoFisher Scientific). RNA was quality-assessed using the 2100 Bioanalyzer (Agilent, Santa Clara, Calif) in the Emory Integrated Genomics Core. cDNA was generated using the SMART-Seq v4 Ultra Low Input RNA Kit (Takara), and the final RNA-seq library was generated using the Nextera XT Kit (Illumina, San Diego, Calif). RNA-seq libraries were sequenced on the NovaSeq 6000 (Illumina) with a sequencing depth of 30M PE100 reads per sample.

Fitzpatrick A.M., Huang M., Mohammad A.F., Stephenson S.T., Kamaleswaran R, & Grunwell J.R. (2024). Dysfunctional neutrophil type 1 interferon responses in preschool children with recurrent wheezing and IL-4–mediated aeroallergen sensitization. The Journal of Allergy and Clinical Immunology: Global, 3(2), 100229.

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Quantification of Influenza B Lineage-Specific Genes

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Plasmids containing the Influenza B Victoria or Yamagata lineage-specific sequences targeted by the genotypic assay were prepared for the quantification of gene copy number. In brief, cDNAs of one Victoria lineage sample and one Yamagata lineage sample were generated from viral RNA from the corresponding lineages. The two viral hemagglutinin (HA) genes were amplified by PCR using HA primers MDV-B5′ BsmBI-HA (5-TATTCGTCTCAGGGAGCAGAAGCAGAGCATTTTCTAATATC-3′) and MDV-B3′ BsmBI-HA (5′-ATATCGTCTCGTATTAGTAGTAACAAGAGCATTTTTC-3′) (Hoffmann et al., 2002 (link)). The amplicons were purified using a QIAquick gel purification kit followed by cloning into pCR2.1-TOPO Vector using the TOPO TA Cloning Kit (Life Technologies) according to manufacturer instructions. The plasmids were transformed into chemically competent E. coli DH5α cells and the sequence identities were confirmed by standard Sanger sequencing. The plasmids were quantified by NanoDrop fluorospectrometer (Thermo Fisher Scientific).

Wong C.K., Tsang G.C., Chan K.H., Li O.T., Peiris M, & Poon L.L. (2014). A novel molecular test for influenza B virus detection and lineage differentiation. Journal of medical virology, 86(12), 2171-2176.

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Nanoscale Fluorescent Polystyrene Characterization

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Fluorescently labeled carboxylated polystyrene nanoparticles of different sizes (30 nm, 50 nm, 100 nm) were purchased from Magsphere (Pasadena, CA). These nanoparticles have an excitation peak of 538 nm and an emission peak at 584 nm. Solution-based characterizations of nanoparticle size and charge distributions were measured using Zeta-Sizer Nano instrument (Malvern, MA). Gel electrophoresis of nanoparticles after conjugation were performed with 0.5–1% Agarose gel, running at 100 V for 45 min and imaged with gel imager (Typhoon, GE healthcare, US). Fluorescence intensity measurements of the nanoparticles were performed using the Nanodrop Fluorospectrometer (Thermo Scientific).

Qie Y., Yuan H., von Roemeling C.A., Chen Y., Liu X., Shih K.D., Knight J.A., Tun H.W., Wharen R.E., Jiang W, & Kim B.Y. (2016). Surface modification of nanoparticles enables selective evasion of phagocytic clearance by distinct macrophage phenotypes. Scientific Reports, 6, 26269.

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