Qubit r 2.0 fluorometer

Manufactured by Thermo Fisher Scientific

Sourced in United States

The Qubit R 2.0 Fluorometer is a compact and precise instrument designed for the quantitation of nucleic acids and proteins. It utilizes fluorescence-based detection technology to provide accurate and sensitive measurements. The Qubit R 2.0 Fluorometer is capable of analyzing small sample volumes and offers a user-friendly interface for straightforward operation.

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Lab products found in correlation

Nanodrop 2000 spectrophotometer, by Thermo Fisher Scientific (2 mentions) Nanodrop 2000, by Thermo Fisher Scientific (1 mentions) Dna extraction kit, by Omega Bio-Tek (1 mentions) Nanophotometer r spectrophotometer, by Implen (1 mentions) Nebnext r ultra rna library prep kit for r, by Illumina (1 mentions) Hiseq 2000, by Illumina (1 mentions) Bioanalyzer 2100 system, by Agilent Technologies (1 mentions) Qubit 1x dsdna hs high sensitivity assay kit, by Thermo Fisher Scientific (1 mentions) Qubit protein assay kit, by Thermo Fisher Scientific (1 mentions) Qiaamp viral rna kit, by Qiagen (1 mentions) Dneasy plant mini kit, by Qiagen (1 mentions) Ab65321, by Abcam (1 mentions) Pe150, by Illumina (1 mentions) Agilent 2100 bioanalyzer, by Agilent Technologies (1 mentions)

6 protocols using qubit r 2.0 fluorometer

Quantifying Biofilm Proteins and DNA

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For the quantification of unbound proteins, 3 mL of the biofilm suspension was subjected to centrifugation (10,000×g for 10 min). The resulting supernatant fluid was collected to measure the concentration of unbound proteins. The pellet obtained from centrifugation was resuspended in 1 mL of phosphate buffer solution. A10 μL aliquot of the suspension was used to quantify the total bound and intracellular proteins. The quantification of total proteins in each sample fraction was performed using Qubit™ Protein Assay Kit (Invitrogen, USA) and a Qubit ^R 2.0 Fluorometer without protein isolation.
To extract the total DNA concentration from biofilm samples, the QIAamp Viral RNA Kit (Qiagen, USA) was used. The QIAamp Viral RNA Mini Kit can extract small quantities of viral RNA and cellular DNA if both are present in the sample. The biofilm suspension (900 μL) was concentrated by centrifugation at 10,000×g for 10 min. Supernatant fluid was decanted. Phosphate buffer solution was added to the pellet to a final volume of 140 μL. The subsequent extraction by the QIAamp Viral RNA Kit was done according to the manufacturers protocol. Quantification of DNA was conducted using Qubit™ 1X dsDNA HS (High Sensitivity) Assay Kit (Invitrogen, USA) and Qubit R 2.0 Fluorometer.

Alidokht L., Fitzpatrick K., Butler C., Hunsucker K.Z., Braga C., Maza W.A., Fears K.P., Arekhi M, & Lanzarini-Lopes M. (2024). UV emitting glass: A promising strategy for biofilm inhibition on transparent surfaces. Biofilm, 7, 100186.

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Morphological and Genetic Identification of Catfish Species

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Single specimens of C.aeneus and C.paleatus were collected from the temple of Confucius flower and wood fish market, Nanjing city, Jiangsu province, China (

32°0'27.1"N, 118°50'11.5"E

) in June 2020 and identified based on their morphological characteristics, according to the latest taxonomic classification of fish (Popazoglo and Boeger 2000 (link); Huysentruyt and Adriaens 2005a , b (link)). Their geographic data and specific origins were unknown. All fresh tissues were immediately stored at -80 °C in 95% ethanol until DNA extraction. Total DNA was extracted from the muscle tissue using a TIANamp Marine Animals DNA Kit DP324 (Tiangen Biotech Co., Ltd., Beijing, China) according to the manufacturer’s instructions. DNA integrity and purity were evaluated by 1% agarose gel electrophoresis, and DNA purity was determined with a NanoDrop 2000 (NanoDrop Technologies, Wilmington, DE, USA). DNA concentrations were quantified using a Qubit^R 2.0 Fluorometer (Life Technologies, Carlsbad, CA, USA). To ensure the accuracy of morphological identification, COI primers were designed based on the latest DNA barcoding database (NCBI and FishBase) and were amplified, sequenced, and compared. The COI sequences are provided in the Suppl. material 1. The results of the sequence alignment verify the accuracy of the morphological identification.

Sun C.H., Huang Q., Zeng X.S., Li S., Zhang X.L., Zhang Y.N., Liao J., Lu C.H., Han B.P, & Zhang Q. (2022). Comparative analysis of the mitogenomes of two Corydoras (Siluriformes, Loricarioidei) with nine known Corydoras, and a phylogenetic analysis of Loricarioidei. ZooKeys, 1083, 89-107.

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Fecal Microbiome DNA Extraction

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Fresh fecal samples were collected from control, 500 and 1500 mg/kg (fecal samples from random six animals in each group) DEHP‐exposed groups, placed in sterile tubes in an ice bath, and immediately transferred to the laboratory. All fecal samples were stored at −80°C. Microbial genomic DNA was isolated and purified from each fecal sample using a DNA Extraction Kit (Omega Bio‐tek, Norcross) according to the manufacturer's instruction. The DNA integrity and concentrations were determined using a Nanodrop2000 spectrophotometer (Thermo Fisher Scientific) and Qubit R 2.0 Fluorometer (Life Technologies, CA).

Fu X., Han H., Li Y., Xu B., Dai W., Zhang Y., Zhou F., Ma H, & Pei X. (2021). Di‐(2‐ethylhexyl) phthalate exposure induces female reproductive toxicity and alters the intestinal microbiota community structure and fecal metabolite profile in mice. Environmental Toxicology, 36(6), 1226-1242.

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RNA-Seq Transcriptome Assembly and Annotation

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First, we assessed the quality and quantity of RNA samples by using agarose gels, the NanoPhotometer R Spectrophotometer (IMPLEN, CA, United States), the Qubit R 2.0 Fluorometer (Life Technologies, CA, United States), and the Bioanalyzer 2100 System (Agilent Technologies, CA, United States), respectively. Next, 1 µg of total RNA for each tissue evenly mixed by three biological pools was used to constructed a cDNA library using the NEBNext R Ultra TM RNA Library Prep Kit for Illumina R (NEB Inc., United States). Lastly, the prepared libraries were sequenced with 150-bp paired-end reads on an Illumina HiSeq TM 2000 instrument.
After cDNA libraries were sequenced, redundant sequences were discarded from the resulting raw reads, including adapter, low quality and containing poly-N sequences. The qualityfiltered reads (clean reads) were assembled into transcripts by Trinity v2.5.1 (Grabherr et al., 2011) (link) as the transcript transcriptome. Further, the assembled transcripts were clustered by Corset v1.05 (Davidson and Oshlack, 2014) (link), and the longest transcript for each cluster was selected as one unigene. All the unigenes were pooled into the unigene transcriptome.

Wang Z., Wu C., Li G., Nuo S., Yin N., & Liu N. (2021). Transcriptome Analysis and Characterization of Chemosensory Genes in the Forest Pest, Dioryctria abietella (Lepidoptera: Pyralidae). Frontiers in Ecology and Evolution, 9.

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Exome Sequencing of Bulked Segregant Analysis for Salt Tolerance

Cited 1 time

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Twenty lines with high RRP under salt conditions (high fertility group: HF) and 20 lines with low RRP under salt conditions (low fertility group: LF) were selected. Genomic DNA was isolated from fresh leaves from each F₆ RIL using a DNeasy Plant Mini Kit (Qiagen, Hilden, Germany), and DNA concentration was measured using a Qubit R 2.0 fluorometer (Thermo Fisher Scientific, Waltham, MA, USA). DNA from each RIL was adjusted to a concentration of 20 ng/μL and mixed in an equal ratio to produce two bulked DNA pools per trait from the HF and LF groups, which are referred to hereafter as the HF bulk and LF bulk, respectively. Exome-captured (EC) libraries were prepared from these DNA pools as described previously (Hisano et al. 2017 (link)). The EC libraries were sequenced via two runs of MiSeq (Illumina, San Diego, CA, USA) with an MiSeq v2 Reagent Kit, 300 Cycles (Illumina) following the manufacturer’s protocol.

Kodama A., Narita R., Yamaguchi M., Hisano H., Adachi S., Takagi H., Ookawa T., Sato K, & Hirasawa T. (2018). QTLs maintaining grain fertility under salt stress detected by exome QTL-seq and interval mapping in barley. Breeding Science, 68(5), 561-570.

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Mitochondrial DNA Sequencing Protocol

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Oocytes were collected and used for mtDNA isolation following manufacturer's guidelines (ab65321; Abcam). Harvested mtDNA were detected by the agarose gel electrophoresis and quantified by QubitR 2.0 fluorometer (Thermo Fisher). Sequencing libraries were generated using a NEBNextR Ultra DNA library Pre Kit from Illumina (NEB, USA) following manufacture's protocol, and index codes were added to each sample. Libraries were analyzed for size distribution by Agilent2100 Bioanalyzer and quantified by qPCR. The libraries were sequenced using Illumina PE150. Trimmomatic‐0.38 was used for data filter and data cleaning. Bwa‐0.7.12 was employed for data mapping to the reference sequence (accession NC_0 05089.1), and GATK‐3.8‐0, Samtools‐1.9 and Varscan‐v2.4.3 were used for SNP/Indel detection.^[³⁸ (link)
^] The mutations were not included if their minimal heteroplasmic fraction was less than 1% per strand.

Chen Y., Ma G., Gai Y., Yang Q., Liu X., de Avila J.M., Mao S., Zhu M, & Du M. (2024). AMPK Suppression Due to Obesity Drives Oocyte mtDNA Heteroplasmy via ATF5‐POLG Axis. Advanced Science, 11(20), 2307480.

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