Agilent 2100 bioanalyzer profile

Manufactured by Agilent Technologies

Sourced in United States

The Agilent 2100 Bioanalyzer is a lab instrument that provides automated electrophoresis analysis of DNA, RNA, and proteins. It uses microfluidic technology to perform separation and detection of these biomolecules.

Automatically generated - may contain errors

Lab products found in correlation

Mirneasy mini kit, by Qiagen (3 mentions) Agilent g2565ba microarray scanner system, by Agilent Technologies (2 mentions) Hs4800 hybridization station, by Tecan (2 mentions) Taqman microrna reverse transcription kit, by Thermo Fisher Scientific (2 mentions) Taqman microrna assay, by Thermo Fisher Scientific (2 mentions) Trizol reagent, by Thermo Fisher Scientific (2 mentions) Taqman universal master mix, by Thermo Fisher Scientific (2 mentions) Abi prism 7500 sequence detection system, by Thermo Fisher Scientific (2 mentions) Nanodrop, by Thermo Fisher Scientific (2 mentions) Mircury lna microrna array 7th gen, by Qiagen (1 mentions) Mircury lna microrna array, by Qiagen (1 mentions) Sureprint g3 mouse gene expression microarray, by Agilent Technologies (1 mentions) Rneasy mini kit, by Qiagen (1 mentions) Rneasy minelute cleanup, by Qiagen (1 mentions) Qiazol lysis reagent, by Qiagen (1 mentions) Imagene 9, by BioDiscovery (1 mentions) Mircury lna mirna array, by Qiagen (1 mentions) Mircury lna mirna array, by Tecan (1 mentions) Purelink mirna isolation kit, by Thermo Fisher Scientific (1 mentions) Lightcycler 480, by Roche (1 mentions)

13 protocols using agilent 2100 bioanalyzer profile

MicroRNA Array Analysis Protocol

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MicroRNA Array analysis was completed by Exiqon Services (Exiqon, Vedbæk, Denmark). The quality of the total RNA was verified by an Agilent 2100 Bioanalyzer profile. Four hundred nanograms of total RNA from both sample and reference was labeled with Hy3TM and Hy5TM fluorescent label, respectively, using the miRCURY LNA microRNA Hi-Power Labeling Kit, Hy3TM/Hy5TM (Exiqon) following the procedure described by the manufacturer. The quantified signals were background corrected (Normexp with offset value 10) and normalized using the global Lowess (LOcally WEighted Scatterplot Smoothing) regression algorithm. Array data have been deposited in the NCBI's Gene Expression Omnibus (GSE81152).

Gururajan A., Naughton M.E., Scott K.A., O'Connor R.M., Moloney G., Clarke G., Dowling J., Walsh A., Ismail F., Shorten G., Scott L., McLoughlin D.M., Cryan J.F, & Dinan T.G. (2016). MicroRNAs as biomarkers for major depression: a role for let-7b and let-7c. Translational Psychiatry, 6(8), e862-.

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Differential miRNA Expression Analysis

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For the microarray analysis, primary tumors and distant metastases were processed to obtain a miRNA enriched solution using a miRNeasy mini kit, according to the manufacturer’s protocol (Qiagen Inc., Hilden, Germany). Differential miR expression analysis was performed by Exiqon using their miRCURY LNA^™ microRNA Array. All experiments were conducted at Exiqon Services, Denmark. The quality of the total RNA was verified by an Agilent 2100 Bioanalyzer profile. 750 ng of total RNA from both sample and reference was labeled with Hy3^™ and Hy5^™, respectively, using the miRCURY LNA^™ microRNA Hi-Power Labeling Kit, Hy3^™/Hy5^™ (Exiqon, Denmark), following the procedure described by the manufacturer. The Hy3^™-labeled samples and a Hy5^™-labeled reference RNA sample were mixed pair-wise and hybridized to the miRCURY LNA^™ microRNA Array 7th Gen (Exiqon, Denmark), which contains capture probes targeting all murine microRNAs in the miRBASE 18.0. The hybridization was performed according to the miRCURY LNA^™ microRNA Array Instruction manual using a Tecan HS4800^™ hybridization station (Tecan, Austria). The miRCURY LNA^™ microRNA Array slides were scanned using the Agilent G2565BA Microarray Scanner System (Agilent Technologies, Inc., USA) and the image analysis was carried out using the Nexus Expression (Nexus Copy Number Discovery Ver.10.0. BioDiscovery Inc., El Segundo, CA).

Yoo B., Meka N., Sheedy P., Billig A.M., Pantazopoulos P, & Medarova Z. (2019). MicroRNA-710 regulates multiple pathways of carcinogenesis in murine metastatic breast cancer. PLoS ONE, 14(12), e0226356.

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Genome-wide Analysis of LPS-Stimulated BV2 Cells

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The LS Science Agilent SurePrint G3 Mouse Gene Expression Microarray and service to process the samples were used for genome-wide analysis. Briefly, BV2 cells were grown to 80% confluence and exposed to LPS (1 μg/ml) for 4h. Total RNA was isolated with the RNeasy Mini kit (Qiagen) according to the manufacturer’s instruction (Ambion). The quality of isolated RNAs was verified by an Agilent 2100 Bioanalyzer profile.

Hu G., Gong A.Y., Wang Y., Ma S., Chen X., Chen J., Su C.J., Shibata A., Strauss-Soukup J.K., Drescher K.M, & Chen X.M. (2016). LincRNA-Cox2 Promotes Late Inflammatory Gene Transcription in Macrophages through Modulating SWI/SNF-mediated Chromatin Remodeling. Journal of immunology (Baltimore, Md. : 1950), 196(6), 2799-2808.

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Extraction and Analysis of miRNA and Total RNA from Bone Cells

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miRNA-enriched fraction from hOB cultures was extracted using MiRNeasy mini kit and RNeasy MinElute Cleanup (Qiagen) according to manufacturer instructions.
For RNA extraction of total bone, a piece of tissue was cut out and added to QIAzol Lysis Reagent (Qiagen), then homogenized for 5 min using the TissueLyser system. Chloroform was added to each sample, followed by centrifugation for 15 min (12000 g). The upper water phase was collected and the extraction continued according to manufacturer’s instructions. The quality of the total RNA was verified by an Agilent 2100 Bioanalyzer profile. The concentration of the purified RNA was analyzed on a spectrophotometer (Nanodrop, Thermo Fisher Scientific Inc).

De-Ugarte L., Caro-Molina E., Rodríguez-Sanz M., García-Pérez M.A., Olmos J.M., Sosa-Henríquez M., Pérez-Cano R., Gómez-Alonso C., Del Rio L., Mateo-Agudo J., Blázquez-Cabrera J.A., González-Macías J., Pino-Montes J.D., Muñoz-Torres M., Diaz-Curiel M., Malouf J., Cano A., Pérez-Castrillon J.L., Nogues X., Garcia-Giralt N, & Diez-Perez A. (2017). SNPs in bone-related miRNAs are associated with the osteoporotic phenotype. Scientific Reports, 7, 516.

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Quantitative miRNA Expression Analysis

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Total RNA was isolated from liver biopsy samples using Trizol Reagent from Invitrogen Corp. (Carlsbad, CA, USA) per manufacturer’s instructions. The integrity of the RNA was verified by an Agilent 2100 Bioanalyzer profile from Agilent Technologies Inc. (Santa Clara, CA, USA).
For miRNA, first-strand complementary DNA synthesis was performed using TaqMan^® MicroRNA Reverse Transcription Kit primed with miR-specific primers from Applied Biosystems (Grand Island, NY, USA). Real-time quantitative RT-PCR (qRT-PCR) was performed using TaqMan^® MicroRNA Assays (Applied Biosystems), following the manufacturer’s recommendations with an ABI Prism 7500 Sequence Detection System using TaqMan^® Universal Master Mix (Applied Biosystems). Fold change values were calculated by comparative Ct analysis and normalized to SNORD44 concentrations. SNORD44 was used as an invariant control.

Sendi H., Mehrab-Mohseni M., Russo M.W., Steuerwald N., Jacobs C., Clemens M.G, & Bonkovsky H.L. (2019). Baseline Hepatic Levels of miR-29b and Claudin are Respectively Associated with the Stage of Fibrosis and HCV RNA in Hepatitis C. Clinical & experimental gastroenterology & hepatology, 1(1), 105.

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Quantitative miRNA Expression Analysis

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Profiling miRNA Expression Using Microarray

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All experiments were conducted at Exiqon Services. The quality of the total RNA was verified by an Agilent 2100 Bioanalyzer profile. Total RNA (250 ng) from sample and reference was labeled with Hy3 and Hy5 fluorescent label, respectively, using the miRCURY LNA miRNA Hi-Power Labelling Kit, Hy3/Hy5 (Exiqon, Denmark), following the procedure described by the manufacturer. The Hy3- labeled samples and a Hy5- labeled reference RNA sample were mixed pairwise and hybridized to the miRCURY LNA miRNA Array (sixth generation: hsa, mmu, and rno) (Exiqon, Denmark), which contains capture probes targeting all miRNAs for human, mouse, or rat registered in the miRBASE 16.0. The hybridization was performed according to the miRCURY LNA miRNA Array instruction manual using a Tecan HS 4800 hybridization station (Tecan, Austria). After hybridization, the microarray slides were scanned and stored in an ozone-free environment (ozone level below 2.0 parts per billion) to prevent potential bleaching of the fluorescent dyes. The miRCURY LNA array microarray slides were scanned using the Agilent G2565BA Microarray Scanner System (Agilent Technologies Inc.), and the image analysis was carried out using the ImaGene 9.0 software (BioDiscovery Inc.). The quantified signals were background-corrected (Normexp with an offset value of 10) and normalized using the Quantile normalization algorithm.

Schmolka N., Papotto P.H., Romero P.V., Amado T., Enguita F.J., Amorim A., Rodrigues A.F., Gordon K.E., Coroadinha A.S., Boldin M., Serre K., Buck A.H., Gomes A.Q, & Silva-Santos B. (2018). MicroRNA-146a controls functional plasticity in γδ T cells by targeting NOD1. Science immunology, 3(23), eaao1392.

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Identification of miRNA Profiles

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Small RNA was isolated per the PureLink miRNA isolation kit (Invitrogen). The quality of total RNA was verified by an Agilent 2100 bioanalyzer profile. The miRNA identification was performed by Exiqon (Exiqon, Woburn, MA, USA). Briefly, all microRNAs were polyadenylated and reverse transcribed into cDNA in a single reaction step. cDNA and SYBR Green Mastermix was transferred to qPCR panels preloaded with primers. Amplification was performed in a Roche Lightcycler480.

Jiang N., Xiang L., He L., Yang G., Zheng J., Wang C., Zhang Y., Wang S., Zhou Y., Sheu T.J., Wu J., Chen K., Coelho P.G., Tovar N.M., Kim S.H., Chen M., Zhou Y.H, & Mao J.J. (2017). Exosomes Mediate Epithelium–Mesenchyme Crosstalk in Organ Development. ACS nano, 11(8), 7736-7746.

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Microrna Profiling of Fracture Repair

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For miRNA microarray analysis, tissues were harvested on post-fracture day 14 and stored in RNAlater (Ambion, Austin, TX, USA). Total RNA, including miRNA, was extracted from the tissue specimens of five different animals in each group using a miRCURY RNA Isolation Kit-Tissue (Exiqon, Vedbaek, Denmark). The quality of the total RNA was verified using an Agilent 2100 Bioanalyzer profile (Agilent Technologies, Santa Clara, CA, USA). One microgram of total RNA from sample and reference RNAs was labeled with Hy3 and Hy5 fluorescent labels, respectively, using a miRCURY LNA microRNA Hi-Power Labeling Kit (Exiqon). The Hy3-labeled samples and a Hy5-labeled reference RNA sample were mixed pair-wise and hybridized to a miRCURY LNA Array, version 6^th Generation (Exiqon), which contains capture probes targeting all human, mouse, and rat miRNAs registered in miRBASE version 16.0. Labeling, hybridization, washing, and scanning were performed following the instructions of the manufacturers. Data analysis was carried out using Feature Extraction 10.7.3.1 (Agilent Technologies).

Waki T., Lee S.Y., Niikura T., Iwakura T., Dogaki Y., Okumachi E., Oe K., Kuroda R, & Kurosaka M. (2016). Profiling microRNA expression during fracture healing. BMC Musculoskeletal Disorders, 17, 83.

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Hippocampal miRNA Expression Profiling

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Total RNA of hippocampus was extracted with TRIzol (Invitrogen) and an Rnase mini kit (QIAGEN) in accordance with the manufacturer’s instruction. The quality of the total RNA was verified by an Agilent 2100 Bioanalyzer profile. Then total RNA was labeled using a miRCURY Hy3/Hy5 power labeling kit (Exiqon, Denmark).The miRNA expression profiling of hippocampus from 4 rats in each group was performed using miRCURY LNA Array (v.14.0) system. The array sequence contents were sourced from the Sange miRBASE database (Release 14.0). Scanning was performed with an Axon GrenePix 4000B microarray scanner. The raw intensity of the image was read by the GenePix pro V6.0. Normalized log2-transformation were applied. System-related variations was eliminated by a filter on low miRNAs expression. Differentially expressed miRNAs were identified as having a more than 1.5-fold expression difference among groups, with a statistically significant p value < 0.05 calculated by ANOVA statistic.

Luo T., Yin S., Shi R., Xu C., Wang Y., Cai J., Yue Y, & Wu A. (2015). miRNA Expression Profile and Involvement of Let-7d-APP in Aged Rats with Isoflurane-Induced Learning and Memory Impairment. PLoS ONE, 10(3), e0119336.

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