Nanodrop and bioanalyzer

Manufactured by Agilent Technologies

Sourced in United States

The NanoDrop is a UV-Vis spectrophotometer designed for the analysis of small sample volumes. It measures the concentration and purity of nucleic acid and protein samples. The Bioanalyzer is a microfluidic electrophoresis system that analyzes the size, quantity, and quality of DNA, RNA, and proteins.

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Lab products found in correlation

Allprep dna rna mini kit, by Qiagen (4 mentions) 2200 tapestation instrument, by Agilent Technologies (2 mentions) Nanodrop 8000 uv vis spectrometer, by Thermo Fisher Scientific (2 mentions) Qubit 2.0 fluorometer, by Thermo Fisher Scientific (2 mentions) Rna access library prep kit, by Illumina (2 mentions) Qiaamp dna blood mini kit, by Qiagen (1 mentions)

Spelling variants of this product

Bioanalyzer (3289 citations) Nanodrop (270 citations) Nanodrop and 2100 Bioanalyzer (2 citations)

4 protocols using nanodrop and bioanalyzer

Nucleic Acid Extraction and Quantification

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Genomic DNA and RNA in tissues were purified using ALLPrep DNA/RNA Mini Kit (Qiagen). Genomic DNA concentration and purity were measured by a Nanodrop 8000 UV-Vis spectrometer (Thermo Scientific Inc.) and Qubit 2.0 Fluorometer (Life Technologies Inc.), respectively. To estimate DNA degradation, DNA median size was measured with a 2200 TapeStation Instrument (Agilent Technologies). For RNA, the concentration and purity was measured by Nanodrop and Bioanalyzer (Agilent Technologies).

Lee H., Joung J.G., Shin H.T., Kim D.H., Kim Y., Kim H., Kwon O.J., Shim Y.M., Lee H.Y., Lee K.S., Choi Y.L., Park W.Y., Hayes D.N, & Um S.W. (2018). Genomic alterations of ground-glass nodular lung adenocarcinoma. Scientific Reports, 8, 7691.

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RNA Extraction and Sequencing of FFPE Tumor Samples

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RNA was purified from formalin-fixed paraffin-embedded (FFPE) or fresh tumor samples using the AllPrep DNA/RNA Mini Kit (Qiagen, USA). The RNA concentration and purity were measured using the NanoDrop and Bioanalyzer (Agilent, USA). The library was prepared following the manufacturer’s instructions using the RNA Access Library Prep Kit (Illumina, USA). Tumor response was assessed by physicians using the Response Evaluation Criteria in Solid Tumors (RECIST) version 1. 1 criteria. All 22 patients were treated with pembrolizumab, and all biopsy samples were obtained prior to the treatment.

Lee J.S., Nair N.U., Dinstag G., Chapman L., Chung Y., Wang K., Sinha S., Cha H., Kim D., Schperberg A.V., Srinivasan A., Lazar V., Rubin E., Hwang S., Berger R., Beker T., Ronai Z., Hannenhalli S., Gilbert M.R., Kurzrock R., Lee S.H., Aldape K, & Ruppin E. (2021). Synthetic lethality-mediated precision oncology via the tumor transcriptome. Cell, 184(9), 2487-2502.e13.

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Transcriptomic Analysis of Advanced NSCLC

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An unpublished cohort of patients with advanced NSCLC treated with pembrolizumab alone was identified (n=59). The median age of patients was 61.4 years. Patients were included if they were ≥18, had pathologically confirmed advanced NSCLC, and received ≥1 dose of pembrolizumab. All the patients in this cohort had lung adenocarcinoma. Prior to treatment initiation, tumor biopsy samples were obtained. RNA was purified from formalin-fixed paraffin-embedded or fresh tumor samples using the AllPrep DNA/RNA Mini Kit (QIAGEN, USA). The RNA concentration and purity were measured using the NanoDrop and Bioanalyzer (Agilent, USA). The library was prepared following the manufacturer’s instructions using the RNA Access Library Prep Kit (Illumina, USA).

Naqash A.R., McCallen J.D., Mi E., Iivanainen S., Marie M.A., Gramenitskaya D., Clark J., Koivunen J.P., Macherla S., Jonnalagadda S., Polsani S., Jiwani R.A., Hafiz M., Muzaffar M., Brunetti L., Stroud C.R., Walker P.R., Wang K., Chung Y., Ruppin E., Lee S.H., Yang L.V., Pinato D.J., Lee J.S, & Cortellini A. (2023). Increased interleukin-6/C-reactive protein levels are associated with the upregulation of the adenosine pathway and serve as potential markers of therapeutic resistance to immune checkpoint inhibitor-based therapies in non-small cell lung cancer. Journal for Immunotherapy of Cancer, 11(10), e007310.

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Comprehensive DNA and RNA Extraction Protocol

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Genomic DNA and RNA in tissues were purified using the AllPrep DNA/RNA Mini Kit (Qiagen, Valencia, CA). Genomic DNA from peripheral blood was extracted using the QIAamp DNA Blood Mini Kit (Qiagen). Genomic DNA concentration and purity were measured using a NanoDrop 8000 UV-Vis Spectrometer (Thermo Scientific Inc., Wilmington, DE) and a Qubit 2.0 Fluorometer (Life Technologies Inc., Grand Island, NY). To estimate DNA degradation, median DNA size and ΔCt values were measured using a 2200 TapeStation Instrument (Agilent Technologies, Santa Clara, CA) and real-time PCR (Agilent Technologies), respectively. For RNA, concentration and purity were measured using the NanoDrop and Bioanalyzer (Agilent Technologies).Table 1

Patient Characteristics of Five SRCCs

Table 1

Characteristics	SRCC1	SRCC2	SRCC3	SRCC4	SRCC5
Age	46	40	38	60	29
Gender	M	M	M	M	F
Tumor location	Descending colon	Rectum	Ascending colon	Rectum	Rectosigmoid junctions
MSI status	MSS	MSS	MSS	MSS	MSS
TNM stage	IVB	IVA	IVB	IVB	IVA
Metastasis	Yes	Yes	Yes	Yes	Yes
Lymphatic invasion	Positive	Positive	Negative	Positive	Positive
Perineural invasion	Negative	Negative	Positive	Negative	Negative
Vascular invasion	Negative	Negative	Positive	Positive	Positive

Nam J.Y., Oh B.Y., Hong H.K., Bae J.S., Kim T.W., Ha S.Y., Park D., Lee W.Y., Kim H.C., Yun S.H., Park Y.A., Joung J.G., Park W.Y, & Cho Y.B. (2018). Molecular Characterization of Colorectal Signet-Ring Cell Carcinoma Using Whole-Exome and RNA Sequencing. Translational Oncology, 11(4), 836-844.

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