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Abioanalyzer

Manufactured by Agilent Technologies
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Sourced in United States

The Agilent Bioanalyzer is a lab instrument that performs automated electrophoresis and microfluidic analysis of biological samples, such as DNA, RNA, and proteins. It provides rapid and sensitive separation, detection, and sizing of these biomolecules.

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Lab products found in correlation

Trizol, by Thermo Fisher Scientific (2 mentions) Nanodrop 1000, by Thermo Fisher Scientific (2 mentions) Smart library construction kit, by Takara Bio (1 mentions) Topo ta cloning kit, by Thermo Fisher Scientific (1 mentions) Qubit 4.0 fluorimeter, by Thermo Fisher Scientific (1 mentions) Ahiseq4000 system, by Illumina (1 mentions) Agilent rna 6000 pico kit, by Agilent Technologies (1 mentions) Nebnext ultra dna library prep kit, by New England Biolabs (1 mentions) Hiseq 1500 sequencer, by Illumina (1 mentions) Truseq capture kit, by Illumina (1 mentions) Allprep dna rna mini kit, by Qiagen (1 mentions)

7 protocols using abioanalyzer

1

Comprehensive RNA Sequencing Protocol

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The concentration and quality of each sample was assessed on a
Bioanalyzer (Agilent), with all samples having a minimum RNA Quality Number
of 8.0 and 28S/18S ratio of 1.0. 4μg of each sample of RNA was
shipped to BGI for library preparation and sequencing. Polyadenylated RNAs
were selected using oligo dT beads and then fragmented. N6 random primers
were then used to reverse transcribe the library into double-stranded cDNA.
A minimum of 20 million single-end 50bp reads were then generated with the
BGISEQ-500 platform.
Stanney W I.I.I., Ladam F., Donaldson I.J., Parsons T.J., Maehr R., Bobola N, & Sagerström C.G. (2019). Combinatorial action of NF-Y and TALE at embryonic enhancers defines distinct gene expression programs during zygotic genome activation in zebrafish. Developmental biology, 459(2), 161-180.
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2

High-Quality RNA Extraction for FANTOM5

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A Bioanalyzer (Agilent, Santa Clara, CA) was used to examine RNA quality. All RNA samples used for the time series achieved high RNA Integrity (RIN) scores above 9.0. The samples were sent to RIKEN Omics Center at Yokohama, Japan, as part of Functional Annotation of the Mammalian Genome 5 (FANTOM5) collaboration for CAGE analysis.
Zhang P., Dimont E., Ha T., Swanson D.J., Hide W, & Goldowitz D. (2017). Relatively frequent switching of transcription start sites during cerebellar development. BMC Genomics, 18, 461.
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3

Salivary Gland Transcriptome Analysis

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Total RNA was isolated from 300 pairs of salivary glands using TRI reagent following the
protocol provided by the manufacturer. RNA quality and integrity were assessed using a
Bioanalyzer (Agilent Technologies, Santa Clara, CA). cDNA libraries were constructed using
a “SMART” library construction kit from Clontech (Palo Alto, CA) as described by Chen et al. (2004) (link). Briefly, cDNA inserts were
ligated into the pPCRXL-TOPO plasmid contained in a TOPO TA cloning kit (Invitrogen,
Carlsbad, CA) instead of a phage vector. Individual clones were picked up for plasmid DNA
isolation, which were sequenced with the M13 forward and reverse primers following the
Sanger DNA sequencing method via a commercial contract (GENEWIZ, South Plainfield,
NJ).
Al-jbory Z., Anderson K.M., Harris M.O., Mittapalli O., Whitworth R.J, & Chen M.S. (2018). Transcriptomic Analyses of Secreted Proteins From the Salivary Glands of Wheat Midge Larvae. Journal of Insect Science, 18(1), 17.
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4

Total RNA Extraction and Quality Assessment

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Total RNA was isolated by hot phenol extraction (Lyne et al, 2003 ). The residual DNA was digested with Qiagen's DNase via
in column digestion using Qiagen's RNAeasy mini kit protocol. RNA quality was assessed on a
Bioanalyzer instrument from Agilent. All RNAs used in this assay had a RIN (RNA Integrity Number)
above 9.
Clément-Ziza M., Marsellach F.X., Codlin S., Papadakis M.A., Reinhardt S., Rodríguez-López M., Martin S., Marguerat S., Schmidt A., Lee E., Workman C.T., Bähler J, & Beyer A. (2014). Natural genetic variation impacts expression levels of coding, non-coding, and antisense transcripts in fission yeast. Molecular Systems Biology, 10(11), 764.
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5

Cotl1 Expression in Mouse Cortex

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A bioanalyzer (Agilent Technologies, USA) was used to test Cotl1 expression in mouse cerebral cortex at different embryonic stages. Total RNA was extracted on ice by lysing cortical tissue in Trizol (Thermo Fisher Scientific, USA). Then, the cell lysate was centrifuged at 4℃, the supernatant removed, and isopropyl alcohol added. The solution was allowed to stand at room temperature for 10 min and then centrifuged at 4℃, discarded the supernatant. Then 75% alcohol was added to the solution and centrifuged at 4℃ to discard the supernatant. Diethylpyrocarbonate H2O was added to dissolve the precipitate. Finally, total RNA was transcribed to cDNA by using reverse transcripition kit (Thermo Fisher Scientific). We examined the cDNA sequences to determine the expression of Cotl1 in mouse cerebral cortex. Glyceraldehyde 3-phosphate dehydrogenase (GAPDH) was used as the internal reference. Forward 5′-AGCGAGACCCCACTAACA-3′ and reverse 5′-ATGAGCCCTTCCACAATG-3′ primers were used.
Li G., Yin Y., Chen J., Fan Y., Ma J., Huang Y., Chen C., Dai P., Chen S, & Zhao S. (2018). Coactosin-like protein 1 inhibits neuronal migration during mouse corticogenesis. Journal of Veterinary Science, 19(1), 21-26.
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6

Single-Cell RNA Sequencing of Sorted Populations

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RNA was extracted from sorted cell populations using a Direct-zol
RNA Kit. RNA quality and concentration were determined with a Qubit 4.0
fluorimeter (Thermo Fisher Scientific) with the RNA IQ Assay and a
Bioanalyzer (Agilent) with Agilent RNA 6000 Pico Kit. Only samples with RIN
> 8 were proceed to reverse transcription. cDNA was synthesized with
the SMART-Seq® v4 Ultra Low Input RNA Kit following
manufacturer’s recommendations. Adapters were used as priming sites
for cDNA synthesis and downstream PCR to amplify the cDNA. Amplified cDNA
was purified using KAPA Pure Beads, and the yield and quality were
determined with a Qubit 4.0 fluorimeter using the dsDNA HS Assay Kit. The
DNA library was constructed using a KAPA HyperPlus Kit, following the
manufacturer’s recommendations. Sequencing was performed using a
HiSeq 4000 system (Illumina) at the Duke University Center for Genomic and
Computational Biology.
Yeh C.H., Finney J., Okada T., Kurosaki T, & Kelsoe G. (2022). Primary germinal center-resident T follicular helper cells are a physiologically distinct subset of CXCR5hiPD-1hi T follicular helper cells. Immunity, 55(2), 272-289.e7.
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7

Genomic DNA Extraction and Sequencing

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Genomic DNAs were extracted from tumors and non-neoplastic mucosae at proximal surgical resection margins using the AllPrep DNA/RNA Mini kit (Qiagen). The extracted DNA was analyzed on 0.7% agarose gels and the quality and quantity were examined by Nanodrop 1000 (Thermo Scientific), Qubit (Life Technologies) and a bioanalyzer (Agilent), respectively. The library preparation, capture, and sequencing were performed by the Centre for Genomic Sciences at the University of Hong Kong. In brief, 250 ng genomic DNA were fragmented by an ultrasonicator (Covaris). These fragments were amplified using NEBNext Ultra TM DNA library Prep Kit (NEB) and then hybridized to the Illumina TruSeq capture kit for enrichment. Paired end, 100 bp read-length sequencing was performed using the HiSeq 1500 sequencer (Illumina).
Dai W., Ko J.M.Y., Choi S.S.A., Yu Z., Ning L., Zheng H., Gopalan V., Chan K.T., Lee N.P., Chan K.W., Law S.Y., Lam A.K, & Lung M.L. (2017). Whole-exome sequencing reveals critical genes underlying metastasis in oesophageal squamous cell carcinoma. The Journal of pathology, 242(4).
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