Agilent bioanalyzer

Manufactured by Agilent Technologies

Sourced in United States, Germany, United Kingdom, Canada, Singapore, France, Ireland, Spain, Denmark, Japan

The Agilent Bioanalyzer is a lab equipment that performs automated electrophoresis and provides quantitative and qualitative analysis of DNA, RNA, and proteins. It uses microfluidic technology to separate and detect biomolecules in a rapid and sensitive manner.

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Lab products found in correlation

1 652 protocols using agilent bioanalyzer

RNA Disruption in Colon Cancer Cells

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Example 26

Colon adenocarcinoma cells LS174T were incubated with Sunitinib, a receptor tyrosine kinase inhibitor. RNA was isolated from the cells and analyzed using an Agilent Bioanalyzer. RNA Disruption is evident at 24 hr at 54 mM (see FIG. 34A).

Colon adenocarcinoma cells LS174T were incubated with Mafosfamide, a DNA cross-linking agent. RNA was isolated from the cells and analyzed using an Agilent Bioanalyzer. RNA Disruption is evident at 48 hr at 48.2 mM (see FIG. 34B).

Colon adenocarcinoma cells SW480 were incubated with Epirubicin, a DNA synthesis inhibitor. RNA was isolated from the cells and analyzed using an Agilent Bioanalyzer. RNA Disruption is evident at 72 hr at 0.5 mM (see FIG. 34C).

It should be noted that either method 300 or method 400 can be used in determining the values for the combinations of features or the feature sets used in LDA and QDA analysis.

US10731222B2. RNA disruption assay for predicting survival (2020-08-04). RNA Diagnostics Inc. [CA]. Inventors: Kenneth Pritzker [CA], Laura Pritzker [CA], Amadeo Mark Parissenti [CA], Xiaohui Wang [CA].

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Evaluating RNA Sample Quality for RNA-Seq

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Timing: 1 h

The quality of your RNA samples needs to be evaluated before they are used for any downstream applications such as RNA-Seq. The quality of the data will be affected by degraded RNA samples.

12.

Determine RNA quality and concentration using an Agilent BioAnalyzer and the Agilent RNA 6000 Nano Kit, following the manufacturer’s instructions, 1 μL of RNA sample will be sacrificed.

Note: An RNA Integrity Number (RIN) value is provided by the Agilent BioAnalyzer software based on the electrophoresis patterns it has detected from analyzed RNA samples. The software determines a RIN-value between 1 and 10, where 1 signifies highly degraded RNA and 10 indicates completely intact RNA. Agilent BioAnalyzer establishes this score based on the 16S/23S rRNA peak ratio. When RNA is degraded, these peaks will be less pronounced compared to the other RNA signals. These RNA signals are also generally higher and represent shorter RNA strands generated by the breakdown of RNA molecules. Typically, an RNA sample with a RIN score ≥ 8 is suitable for RNA-Seq.² (link)^,³ (link)^,⁴ (link)^,⁵ (link)

13.

Store RNA samples at −80°C.

Verbeelen T., Van Houdt R., Leys N., Ganigué R, & Mastroleo F. (2023). RNA extraction protocol from low-biomass bacterial Nitrosomonas europaea and Nitrobacter winogradskyi cultures for whole transcriptome studies. STAR Protocols, 4(3), 102358.

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RNA-seq Workflow for IDH3α KO NHAs

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RNA was extracted from control or IDH3α KO NHAs using the RNeasy Kit (Qiagen) according to the manufacturer’s protocol. RNA quality control was performed using an Agilent Bioanalyzer. RNA-seq libraries were generated using Illumina TruSeq mRNA stranded kits following Illumina protocols. Libraries were quantitated using an Agilent Bioanalyzer, and the pooled libraries were sequenced with an Illumina HiSeq 4000 system using Illumina reagents and protocols.

May J.L., Kouri F.M., Hurley L.A., Liu J., Tommasini-Ghelfi S., Ji Y., Gao P., Calvert A.E., Lee A., Chandel N.S., Davuluri R.V., Horbinski C.M., Locasale J.W, & Stegh A.H. (2019). IDH3α regulates one-carbon metabolism in glioblastoma. Science Advances, 5(1), eaat0456.

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Mechanism of BRD9 Inhibition in UFs

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To determine the mechanism underlying the inhibitory effect of BRD9 inhibition on the UFs, the UF HuLM cells were treated with BRD9 inhibitor I-BRD9 (5 µM, n = 4) and DMSO vehicle control (n = 4) for 48 h. RNA was isolated using Trizol. RNA quality and quantity were assessed using the Agilent bio-analyzer. Strand-specific RNA-SEQ libraries were prepared using a TruSEQ total RNA-SEQ library protocol (Illumina provided, San Diego, CA, USA). Library quality and quantity were assessed using the Agilent bio-analyzer, and libraries were sequenced using an Illumina NovaSEQ6000 (illumine provided reagents and protocols).

Yang Q., Vafaei S., Falahati A., Khosh A., Bariani M.V., Omran M.M., Bai T., Siblini H., Ali M., He C., Boyer T.G, & Al-Hendy A. (2024). Bromodomain-Containing Protein 9 Regulates Signaling Pathways and Reprograms the Epigenome in Immortalized Human Uterine Fibroid Cells. International Journal of Molecular Sciences, 25(2), 905.

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Droplet-based single-cell transcriptomics

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Library preparation steps follow the same steps as in the DropSeq and SeqWell methods. Briefly, the beads were washed with 6×SSC twice after retrieval, and the captured mRNA was reverse-transcribed using Maxima H Minus reverse transcriptase (ThermoFisher) with a custom template switching oligo (AAGCAGTGGTATCAACGCAGAGTGAATrGrGrG). The cDNA coated beads were treated with Exonuclease I (Exo I, NEB) at 37°C for 45 min to chew away any unbound mRNA capture probes. cDNA on coated beads was amplified using a half PCR reaction. The amplified DNA was purified using Ampure XP beads (Beckman Coulter) at 0.6x ratio, and the quality of the amplified DNA was assessed by Agilent BioAnalyzer using high sensitivity chips. Purified cDNA was pooled and input for standard Nextera tagmentation and amplification reactions (Nextera XT, Illumina) using a custom primer instead of the i5 index primer to amplify only those fragments that contain the cell barcodes and UMIs. The PCR product was further purified using Ampure XP beads at 0.6x ratio and library quality-verified on Agilent BioAnalyzer high sensitivity chips. The libraries were sequenced on HiSeq 2500 (Illumina) using a custom primer with 75 cycles on Read 1 and 75 cycles on Read 2. For Read 1, only the first 20 bases were used in analysis. PhiX libraries were used at 20% as spike-in controls.

Gao Y., Vasic R., Song Y., Teng R., Liu C., Gbyli R., Biancon G., Nelakanti R., Lobben K., Kudo E., Liu W., Ardasheva A., Fu X., Wang X., Joshi P., Lee V., Dura B., Viero G., Iwasaki A., Fan R., Xiao A., Flavell R.A., Li H.B., Tebaldi T, & Halene S. (2020). m6A Modification Prevents Formation of Endogenous Double-Stranded RNAs and Deleterious Innate Immune Responses during Hematopoietic Development. Immunity, 52(6), 1007-1021.e8.

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Feather RNA-Seq Library Preparation

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Feather follicles removed from RNAlater were bead‐milled in a Qiagen TissueLyser and messenger RNA was extracted from feathers using a Qiagen RNeasy mini‐kit, following manufacturer's instructions. RNA integrity was confirmed using the RNA Nano Kit on an Agilent Bioanalyzer (Agilent, CA). For RNAseq library preparation, we first isolated mRNA using a PrepX PolyA mRNA Isolation Kit (Wafergen, CA), then prepared stranded mRNA libraries using PrepX RNA‐Seq Kit (Wafergen, CA) on an Apollo 324 (Takara Bio Inc, Japan). We confirmed library integrity on an Agilent Bioanalyzer and calculated library concentration using a KAPA Library Quantification Kit (Roche, CA) with real‐time qPCR on a Bio‐Rad CFX96. We multiplexed cDNA libraries in equimolar ratio and estimated fragment sizes on an Agilent TapeStation, then sequenced paired‐end 75bp reads across two lanes of Illumina NextSeq 500. Preliminary quality assessment was performed using FastQC.

Enbody E.D., Sin S.Y., Boersma J., Edwards S.V., Ketaloya S., Schwabl H., Webster M.S, & Karubian J. (2022). The evolutionary history and mechanistic basis of female ornamentation in a tropical songbird. Evolution; International Journal of Organic Evolution, 76(8), 1720-1736.

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Elucidating Mechanism of BRD9 Inhibition in uLMS

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To determine the mechanism underlying the inhibitory effect of BRD9 inhibition on the uLMS, the SK-UT-1 cells were treated with iBRD9 TP-472 (5 µM) for 48 h. RNA was isolated using Trizol. RNA quality and quantity were assessed using the Agilent bio-analyzer. Strand-specific RNA-SEQ libraries were prepared using a TruSEQ total RNA-SEQ library protocol (Illumina provided). Library quality and quantity were assessed using the Agilent bio-analyzer and libraries were sequenced using an Illumina NovaSEQ6000 (illumine provided reagents and protocols).

Yang Q., Bariani M.V., Falahati A., Khosh A., Lastra R.R., Siblini H., Boyer T.G, & Al-Hendy A. (2022). The Functional Role and Regulatory Mechanism of Bromodomain-Containing Protein 9 in Human Uterine Leiomyosarcoma. Cells, 11(14), 2160.

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RNA Sequencing of Liver Tissue

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Liver tissues were disrupted with disposable probes using the Qiagen TissueRuptor, and total RNA was extracted using Qiagen AllPrep DNA/RNA Kit (Qiagen, Germantown, MD, USA). The quality of RNA samples was evaluated with Agilent BioAnalyzer (Agilent, Santa Clara, CA, USA) using the Nano RNA Kit. Five hundred ng of total RNA was used for mRNA isolation with the NEBNext^® Poly(A) mRNA Magnetic Isolation Module (New England Biolabs, Ipswich, MA, USA). Libraries for Next Generation Sequencing were prepared using NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (New England Biolabs) following the manufacturer instructions. The quality of the libraries was evaluated with the Agilent BioAnalyzer using High Sensitivity DNA chips. To ensure optimal cluster density, the libraries were quantified with qPCR using KAPA/Roche Library Quantification Kit. Libraries were normalized, pooled, denatured and loaded on the flow cell at the 1.8 pM concentration. Sequencing was conducted with Illumina NextSeq 500 platform High Output/300 cycle kits (Illumina, San Diego, CA, USA).

Seale L.A., Khadka V.S., Menor M., Xie G., Watanabe L.M., Sasuclark A., Guirguis K., Ha H.Y., Hashimoto A.C., Peplowska K., Tiirikainen M., Jia W., Berry M.J, & Deng Y. (2019). Combined Omics Reveals That Disruption of the Selenocysteine Lyase Gene Affects Amino Acid Pathways in Mice. Nutrients, 11(11), 2584.

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Microarray Analysis of hESCs Treated with JC011

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hESCS used for the microarray experiment were grown feeder-free and were >95% positive for the Tra-1-60 marker. Cell viability analysis with Resazurin prior to treatment with JC011 showed all cells to be >98.5% viable. RNA was extracted using standard Trizol™ protocol and subjected to spectrophotometric measurement (BioSPEC-Mini, Shimadzu) and quality determined using an Agilent Bioanalyzer. All samples show OD260/OD280 ratios of between 1.78–2.02 with concentrations ranging from ∼600 ng/µL to ∼980 ng/µL. Results from an Agilent Bioanalyzer analysis showed that all the samples had the RIN (RNA integrity Number) of 7.5 to 9.5. The Agilent™ two-colour microarrays were used for comparative microarray analysis. cRNA was prepared according to the manufacturer's recommended protocol (Agilent™ Two-Color Microarray-Based Gene Expression Analysis, Quick Amp Labeling v5.7). Normalization and data analysis was done using GeneSpring GX version 10.0 and Microsoft Excel. All experiments were performed in triplicate (N = 3). A gene was considered differentially expressed if fold-difference relative to controls was ≥3.

Richards M., Phoon C.W., Goh G.T., Seng E.K., Guo X.M., Tan C.M., Chan W.K, & Lee J.M. (2014). A New Class of Pluripotent Stem Cell Cytotoxic Small Molecules. PLoS ONE, 9(3), e85039.

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RNA Isolation from Mouse Liver Samples

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We used a total of 4 animals per treatment group. The total RNA from the liver samples of mice treated with PCN/LPS was isolated using the RNeasy kit according to the manufacturer’s standard protocols (Qiagen, Valencia, CA). Following the total RNA isolation, the sample concentration was assayed using a NanoDrop-8000 (Thermo Scientific, Wilmington, DE, USA), and quality checks were performed using the NanoDrop spectrophotometer and the Agilent Bioanalyzer. RNA quality parameters were as follows: the 260/280 and 260/230 ratios needed to be greater than 1.8. Further, the RNA Integrity Number (RIN) was analyzed using the Agilent Bioanalyzer. The samples needed to have RIN values of 7–10 and with a range of 1–1.5.

Taneja G., Maity S., Jiang W., Moorthy B., Coarfa C, & Ghose R. (2019). Transcriptomic profiling identifies novel mechanisms of transcriptional regulation of the cytochrome P450 (Cyp)3a11 gene. Scientific Reports, 9, 6663.

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