Thermo scientific nanodrop 2000c

Manufactured by Thermo Fisher Scientific

Sourced in United States

The Thermo Scientific NanoDrop 2000c is a compact and easy-to-use UV-Vis spectrophotometer designed for quantifying and assessing the purity of small-volume samples. It measures the absorbance of samples directly, without the need for cuvettes or dilutions. The NanoDrop 2000c can measure sample volumes as low as 0.5 μL.

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Lab products found in correlation

Rnaid kit, by MP Biomedicals (2 mentions) Truseq stranded total rna with ribo zero gold kit, by Illumina (1 mentions) Trizol, by Thermo Fisher Scientific (1 mentions) Nebnext ultra directional rna library prep kit for, by Illumina (1 mentions) 2100 bioanalyzer, by Agilent Technologies (1 mentions) Rneasy mini kit, by Qiagen (1 mentions) Rnalater, by Qiagen (1 mentions) Rnase free disposable pellet pestle, by Thermo Fisher Scientific (1 mentions) Qiaamp dna mini kit, by Qiagen (1 mentions) Rneasy plus mini kit, by Qiagen (1 mentions) Sequencing, by Illumina (1 mentions) Trizol reagent, by Transgene (1 mentions) Nebnext ultra rna library prep kit, by Illumina (1 mentions) Rt reagent, by Takara Bio (1 mentions) Trizol reagent, by Thermo Fisher Scientific (1 mentions)

7 protocols using thermo scientific nanodrop 2000c

RNA-seq Library Preparation and Sequencing

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The total RNA was isolated with TRIzol (Invitrogen, Carlsbad, CA, United States) following the manufacturer’s instructions, and the concentration and quality of RNA were assessed by 1.5% agarose gel electrophoresis and Thermo Scientific NanoDrop 2000c (ThermoFisher Scientific Inc., Waltham, MA, United States).
Equal quantities of RNA were pooled from each sample. Then, the TruSeq Stranded Total RNA with Ribo-Zero Gold Kit (Illumina, San Diego, CA, United States) was used for digesting the ribosomal RNA (rRNA) in the DNA-free RNA. According to the manufacturer’s instructions, we performed the construction of library preparation with NEB Next Ultra Directional RNA LibraryPrep Kit for Illumina (NEB, Ipswich, MA, United States). The size and purity of libraries were validated by Agilent Technologies 2100 Bioanalyzer (Agilent, Santa Clara, CA). Finally, the samples were sequenced using Illumina HiSeq 2500 Technology (LC Sciences, Houston, TX, United States) with a 150-bp paired-end run.

Huang C., Ge F., Ma X., Dai R., Dingkao R., Zhaxi Z., Burenchao G., Bao P., Wu X., Guo X., Chu M., Yan P, & Liang C. (2021). Comprehensive Analysis of mRNA, lncRNA, circRNA, and miRNA Expression Profiles and Their ceRNA Networks in the Longissimus Dorsi Muscle of Cattle-Yak and Yak. Frontiers in Genetics, 12, 772557.

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RNA Extraction from Tissue Samples

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RNA samples were collected from several tissue sources: guinea pig sclera (ex vivo sample), liver and lung, as well as cultured scleral fibroblasts (in vitro sample). Harvested tissue samples were stored in Qiagen RNAlater prior to RNA extraction (Qiagen, Redwood City, CA, USA). Prior to RNA extraction, tissue samples were homogenized using a Bead Ruptor Omni 24 (OMNI International Inc., Kennesaw, GA, USA). Total RNA was extracted from all tissue samples using Qiagen RNeasy Mini Kits (Qiagen). The quality and concentration of RNA was then quantified using a Thermo Scientific NanoDrop 2000c (Thermo Scientific, Denver, CO, USA). Conversion of RNA to cDNA was accomplished using Invitrogen SuperScript III First- Strand Synthesis kits for RT-PCR (Life Technologies, Carlsbad, CA, USA).

Wang K.K., Metlapally R, & Wildsoet C.F. (2017). Expression Profile of the Integrin Receptor Subunits in the Guinea Pig Sclera. Current eye research, 42(6), 857-863.

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Mosquito RNA Extraction and Purification

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RNA extractions were conducted in parallel using a guanidinium thiocyanate-phenol-chloroform extraction method. Mosquito tissues were suspended in a 1 mL solution containing 4 M guanidine thiocyanate (CAS: 593-84-0), 0.5% Sarkosyl (CAS: 137-16-6), chloroform (CAS: 67-66-3), and 0.1 M 2-mercapthoethanol (CAS: 60-24-2). Using RNase-free disposable pellet pestles (Catalog #12-141-364, Thermo Fisher Scientific, Waltham, MA, USA) the samples are then manually homogenized until no visible structures remain. After tissue homogenization, the samples were extracted twice with phenol-chloroform. RNA was purified from the recovered aqueous solution using the RNAid Kit supplied by MPBio (catalog #111007200). RNAMATRIX beads were used to bind RNA using 5 μl for 5 whole heads and 10 μl for 120 sensory tissues. The beads were then washed twice using RNA Wash Concentrate to remove any remaining containments before eluting in 20 μl DEPC-treated water. Sample concentration and quality were determined using Thermo Scientific NanoDrop 2000c (Thermo Fisher Scientific, Waltham, MA, USA).

Mappin F., Bellantuono A.J., Ebrahimi B, & DeGennaro M. (2023). Odor-evoked transcriptomics of Aedes aegypti mosquitoes. PLOS ONE, 18(10), e0293018.

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Guanidine Thiocyanate RNA Extraction

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RNA extractions were conducted in parallel using a guanidinate thiocyanate-phenol-chloroform extraction method. Mosquito tissues were suspended in a 1 mL solution containing 4 M guanidine thiocyanate (CAS: 593-84-0), 0.5% Sarkosyl (CAS: 137-16-6), chloroform (CAS 67-66-3), and 0.1 M 2-mercapthoethanol (CAS: 60-24-2). Using RNase-free disposable pellet pestles (Catalog #12-141-364, Thermo Fisher Scientific) the samples are then manually homogenized until no visible structures remain. After tissue homogenization, the samples were extracted twice with phenol-chloroform. RNA was purified from the recovered aqueous solution using the RNAid Kit supplied by MPBio (catalog #111007200). RNAMATRIX beads were used to bind RNA using 5 μl for 5 whole heads and 10 μl for 120 sensory tissues. The beads were then washed twice using RNA Wash Concentrate to remove any remaining containments before eluting in 20 μl DEPC-treated water. Sample concentration and quality were determined using Thermo Scientific NanoDrop 2000c (Thermo Fisher Scientific).

Mappin F., Bellantuono A.J., Ebrahimi B, & DeGennaro M. (2023). Odor-evoked transcriptomics of Aedes aegypti mosquitoes. bioRxiv.

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Extraction and Storage of Tumor and Normal Tissue DNA and RNA

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Matched pairs of tumor and normal tissues were collected from each patient following surgery, immediately stored at −80 °C and then transferred to liquid nitrogen. Genomic DNA from 102 tissue pairs and messenger RNA from 43 tissue pairs were extracted using the QIAamp DNA Mini Kit (Qiagen, Bonn, Germany, Cat. No. 51306) and the RNeasy Plus Mini Kit (Qiagen, Bonn, Germany, Cat. No. 74134), respectively. The RNA and DNA were quantified, and the purity was verified by measuring the A260/A280 ratio (which ranged from 1.8 to 2.0) [25 (link)] using a Thermo Scientific™ NanoDrop 2000c (Thermo Fisher Scientific, Waltham, MA, USA.) For further experimentation, genomic DNA was then stored at −20 °C, while mRNA was stored at −80 °C.
Blood samples were collected using Streck BCT or PAXgene cfDNA tubes, and a double centrifugation process was used to isolate plasma. Circulating cell-free DNA (cfDNA) was extracted from 63 of the plasma samples using the iCatcher Circulating cfDNA 1000 kit (CatchGene, New Taipei City, Taiwan) according to the manufacturer’s recommended protocol.

Shen H.T., Hung C.S., Davis C., Su C.M., Liao L.M., Shih H.M., Lee K.D., Ansar M, & Lin R.K. (2024). Hypermethylation of the Gene Body in SRCIN1 Is Involved in Breast Cancer Cell Proliferation and Is a Potential Blood-Based Biomarker for Early Detection and a Poor Prognosis. Biomolecules, 14(5), 571.

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RNA Extraction and RNA-seq Library Preparation

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Total RNA was extracted using a Trizol reagent (Transgen Biotech, Beijing, China). Thermo Scientific NanoDrop 2000c (ThermoFisher Scientific Inc., Waltham, MA, USA) was used to determine the concentration and purity of the extracted RNA. The integrity of the RNA was detected by 1% agarose gel electrophoresis. The total amount of RNA should be ≥1 μg, the concentration ≥ 50 ng/μL, and the value of OD 260/OD 280 should be between 1.8 and 2.2 [20 (link)]. An oligomer magnetic bead (dT) approach was used to enrich Poly A mRNA from total RNA (6 samples) [21 (link),22 (link)]. A cDNA library was constructed by synthesizing cDNA from random hexamers, purifying cDNA, and amplifying it by PCR. A NEBNext^® Ultra RNA Library Prep Kit for Illumina was used to perform RNA-seq library preparation and, after library inspection, qualified. Finally, paired-end sequencing of different libraries was accomplished using Illumina sequencing.

Zhang M., Zha X., Ma X., La Y., Guo X., Chu M., Bao P., Yan P., Wu X, & Liang C. (2024). Genome-Wide Transcriptome Profiling Reveals the Mechanisms Underlying Hepatic Metabolism under Different Raising Systems in Yak. Animals : an Open Access Journal from MDPI, 14(5), 695.

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Single Cell RNA Extraction and Amplification

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The total RNA of single cell suspension were extracted using TRIzol Reagent (Invitrogen, Carlsbad, CA, USA), and the complementary DNA (cDNA) was synthesized using reverse transcription (RT) reagent (Takara, Dalian, Liaoning, China), following the kit instructions. The RNA was then amplified using PCR as follows: 95 °C for 8 min, then 30 cycles of 95 °C for 20 s, 65 °C for 35 s, and 70 °C for 30 s, after which the RNA was denatured at 90 °C for 20 s, 55 °C for 1 min, then stored at 4 °C. A 1.5% agarose gel electrophoresis was used to detect the integrity of 28S and 18S bands, as well as their ratio; the concentration was determined using a ThermoScientific NanoDrop 2000c (ThermoFisher Scientific Inc., Waltham, MA, USA). Only samples with 1.8 < OD 260/280 nm < 2.0, OD 260/230 nm ≥ 2.0, RNA Integrity Number: RIN ≥ 6.5, and 28S/18S ≥ 1.0 were used for subsequent analyses, and the PCR primers are listed in Supplementary Table S1.

Wu Y., Guo T., Li J., Niu C., Sun W., Zhu S., Zhao H., Qiao G., Han M., He X., Lu Z., Yuan C., Han J., Liu J., Yang B, & Yue Y. (2022). The Transcriptional Cell Atlas of Testis Development in Sheep at Pre-Sexual Maturity. Current Issues in Molecular Biology, 44(2), 483-497.

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