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Bioanalyzer

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The Bioanalyzer is a lab instrument used for the analysis of biomolecules, such as DNA, RNA, and proteins. It provides automated, high-resolution electrophoretic separation and sensitive detection of these biomolecules.

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Lab products found in correlation

Nanodrop, by Thermo Fisher Scientific (9 mentions) Ampure xp bead, by Beckman Coulter (6 mentions) Bioanalyzer, by Agilent Technologies (6 mentions) Mirvana mirna isolation kit, by Thermo Fisher Scientific (6 mentions) Qubit dsdna hs assay kit, by Thermo Fisher Scientific (6 mentions) Hiseq 2500 system, by Illumina (5 mentions) Ribo zero rrna removal kit human mouse rat, by Illumina (5 mentions) Hiseq 4000, by Illumina (5 mentions) Qubit fluorometry, by Thermo Fisher Scientific (4 mentions) Rneasy mini kit, by Qiagen (4 mentions) Truseq stranded total rna library prep kit, by Illumina (4 mentions) Truseq rna sample prep kit v2 protocol, by Illumina (3 mentions) Truseq rna sample prep kit v2, by Illumina (3 mentions) Nanodrop spectrophotometer, by Thermo Fisher Scientific (3 mentions) Hiseq 2500, by Illumina (3 mentions) Nebnext ultra directional rna library prep kit for, by Illumina (3 mentions) Lightcycler 480 real time pcr system, by Roche (3 mentions) Trizol, by Thermo Fisher Scientific (3 mentions) Smarter stranded total rna seq kit v2 pico input mammalian, by Takara Bio (3 mentions) Phix spike in control, by Illumina (3 mentions)

54 protocols using bioanalyzer

1

Sequencing Drug-Resistant Salmonella Mutants

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From each of the biocide exposure experiments, four drug-resistant mutants representing the range of phenotypes were selected for sequencing. Mutants were selected to reflect those that emerged early and late in the selection period. Genomic DNA was extracted from 5 mL overnight cultures grown in drug-free LB media using a Promega Wizard® Genomic DNA Purification Kit. The quantity and quality of the DNA was confirmed by agarose gel electrophoresis and by analysis using a NanoDrop Spectrophotometer (Life Technologies) and Bioanalyzer (Life Technologies). Mutants were sequenced using a 454 GS FLX instrument (Roche) with Titanium chemistry and the resulting sequence reads were mapped against the SL1344 reference genome using the gsMapper alignment module of Newbler, run through the xBASE-NG web site. High-confidence SNPs were identified as previously described.31 (link) Mutations detected consistently in all sequenced isolates were deemed to be differences between our WT laboratory strain and the sequenced SL1344 reference strain and were excluded from further analysis. Mutations and SNPs identified were verified by PCR and Sanger sequencing.
Webber M.A., Whitehead R.N., Mount M., Loman N.J., Pallen M.J, & Piddock L.J. (2015). Parallel evolutionary pathways to antibiotic resistance selected by biocide exposure. Journal of Antimicrobial Chemotherapy, 70(8), 2241-2248.
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2

Whole Genome Sequencing of Vibrio cholerae

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Cells were inoculated in LB medium and grown at 30 °C overnight. Genomic DNA was extracted from one ml of the culture using the DNeasy Tissue Kit (Qiagen, Hilden, Germany). DNA samples were quantified using a Bioanalyzer (Life Technologies, CA) and sequenced by the NCI CCR genomics sequencing core on the Illumina MiSeq platform. 2-5 million reads were obtained per sample, which were trimmed and mapped to the published N16961 reference genome [52 (link)] on the CLC genomics workbench (Qiagen).
Ramachandran R., Ciaccia P.N., Filsuf T.A., Jha J.K, & Chattoraj D.K. (2018). Chromosome 1 licenses chromosome 2 replication in Vibrio cholerae by doubling the crtS gene dosage. PLoS Genetics, 14(5), e1007426.
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3

RNA-seq analysis of miR-155 knockout and Alzheimer's mouse models

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Total RNAs from PFC of 4- and 8-month-old male WT (n=4), miR155+/− (n=4), miR155−/−(n=4), APP/PSEN1 (n=4), APP/PSEN1;miR155+/− (n=4) or APP/PSEN1;miR155−/− (n=4) mice were subjected to RNA sequencing. The sequencing library was prepared with the TruSeq RNA Sample Prep Kit v2 protocol (Illumina, CA, USA). Ribosomal RNAs were removed using the Ribo-Zero rRNA Removal Kit (Human/Mouse/Rat) (Illumina, CA, USA). Remaining RNAs were fragmented, and the cDNAs synthesized using random hexamers, end-repaired, and ligated with appropriate adaptors for sequencing. The library was processed for size selection and purification using AMPure XP beads (Beckman Coulter, CA, USA). The appropriate Illumina-recommended 6bp barcode bases were introduced at one end of the adaptors during the PCR amplification step. The size and concentration of the RNA-seq libraries were measured by Bioanalyzer and Qubit fluorometry (Life Technologies, NY, USA) before loading onto the sequencer. The rRNA-depleted libraries were sequenced on the Illumina HiSeq 2500 System with 100 nucleotide single-end reads (Illumina, CA, USA).
Readhead B., Haure-Mirande J.V., Mastroeni D., Audrain M., Fanutza T., Kim S.H., Blitzer R.D., Gandy S., Dudley J.T, & Ehrlich M.E. (2020). miR155 regulation of behavior, neuropathology, and cortical transcriptomics in Alzheimer’s disease. Acta neuropathologica, 140(3), 295-315.
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4

RNA-seq of Tyrobp-deficient APP/PSEN1 mouse brains

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Total RNAs from PFC of 8-month-old male WT (n=4), Tyrobp+/− (n=3), Tyrobp−/−(n=4), APP/PSEN1 (n=4), APP/PSEN1;Tyrobp+/− (n=4) or APP/PSEN1;Tyrobp−/− (n=5) mice were subjected to RNA sequencing. The sequencing library was prepared with the TruSeq RNA Sample Prep Kit v2 protocol (Illumina, CA, USA). Ribosomal RNAs were removed using the Ribo-Zero rRNA Removal Kit (Human/Mouse/Rat) (Illumina, CA, USA). Remaining RNAs were fragmented, and the cDNAs synthesized using random hexamers, end-repaired, and ligated with appropriate adaptors for sequencing. The library was processed for size selection and purification using AMPure XP beads (Beckman Coulter, CA, USA). The appropriate Illumina-recommended 6bp barcode bases were introduced at one end of the adaptors during the PCR amplification step. The size and concentration of the RNA-seq libraries were measured by Bioanalyzer and Qubit fluorometry (Life Technologies, NY, USA) before loading onto the sequencer. The rRNA-depleted libraries were sequenced on the Illumina HiSeq 2500 System with 100 nucleotide single-end reads (Illumina, CA, USA).
Haure-Mirande J.V., Wang M., Audrain M., Fanutza T., Kim S.H., Heja S., Readhead B., Dudley J.T., Blitzer R.D., Schadt E.E., Zhang B., Gandy S, & Ehrlich M.E. (2018). Integrative approach to sporadic Alzheimer’s disease: deficiency of TYROBP in cerebral Aβ amyloidosis mouse normalizes clinical phenotype and complement subnetwork molecular pathology without reducing Aβ burden. Molecular Psychiatry, 24(3), 431-446.
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5

Transcriptional Profiles of Sex-1 and Apo-1 Seedlings

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Seventeen to eighteen days old seedlings from Sex-1 and Apo-1 accessions were subjected to mRNA sequencing. Seedlings were snap-frozen and kept at -80°C until RNA extraction; tissue was ground using a tissue lyser (Retsch, Germany). RNA extraction was performed using QIAGEN RNeasy Mini Kit and DNase–treated according to manufacturer’s instructions (Qiagen, USA). The RNA quality was further validated in a Bioanalyzer (Life Technologies, USA). mRNA transcripts purification, cDNA synthesis, library preparation and NGS sequencing were performed as per the routine pipeline established at the facility of Fasteris, Geneva, Switzerland. Illumina HiSeq2000 was used to carry out paired-end sequencing generating a minimum of 100 bp per read.
Shah J.N., Kirioukhova O., Pawar P., Tayyab M., Mateo J.L, & Johnston A.J. (2016). Depletion of Key Meiotic Genes and Transcriptome-Wide Abiotic Stress Reprogramming Mark Early Preparatory Events Ahead of Apomeiotic Transition. Frontiers in Plant Science, 7, 1539.
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6

Total RNA Extraction and Sequencing

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Total RNA extraction was performed with miRvana kit (Ambion). RNA quantity and quality were verified by Nanodrop (Thermo Scientific) and capillary electrophoresis (Bioanalyzer, Agilent) respectively. RNAs (3.5 μg) were rRNA depleted using either Ribominus (Life Techologies) or Ribozero kits (Epicentre). Barcoded libraries were prepared for each sample using SOLiD total RNA-Seq kit (Life Techologies) and following the manufacturer's instructions. Library profiles and concentration were verified with Bioanalyzer and Qubit (Life Technologies) before equimolar pooling of the libraries.
Esposti D.D., Hernandez-Vargas H., Voegele C., Fernandez-Jimenez N., Forey N., Bancel B., Calvez-Kelm F.L., McKay J., Merle P, & Herceg Z. (2016). Identification of novel long non-coding RNAs deregulated in hepatocellular carcinoma using RNA-sequencing. Oncotarget, 7(22), 31862-31877.
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7

RNA Extraction and Sequencing Library Preparation

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RNA was extracted from pooled technical triplicate sucrose gradient fractions by ethanol precipitation followed by acid phenol:chloroform extraction. Direct phenol:chloroform extraction was precluded by phase inversion in high sucrose fractions. RNA was then DNase treated, acid phenol:chloroform extracted, and ethanol precipitated. Cytoplasmic RNA was TRIzol extracted (Life Technologies, Grand Island, NY) and ethanol precipitated. Total RNA integrity was verified using a BioAnalyzer (Agilent, Santa Clara, CA). Ribosomal RNA was then depleted using Ribo-Zero (Illumina, San Diego, CA) and biological duplicate sequencing libraries were generated using the TruSeq RNA Sample Prep v2 kit (Illumina) without the poly-A selection steps. An equal mass (100 ng) of rRNA-depleted RNA was used as input to each individual library preparation. Libraries were verified using a BioAnalyzer and quantified using a Qubit (Life Technologies) prior to pooling for sequencing. Library insert sizes were typically ~150 ± ~25 bp. Pooled libraries were 75-bp paired-end sequenced on an Illumina HiSeq 2500 and runs of the same library in different lanes or flowcells were merged.
Floor S.N, & Doudna J.A. (2016). Tunable protein synthesis by transcript isoforms in human cells. eLife, 5, e10921.
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8

Illumina RNA-seq Library Preparation

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The sequencing library was prepared with the standard TruSeq RNA Sample Prep Kit v2 protocol (Illumina, CA, USA). Briefly, ribosomal RNA was removed using the Ribo-Zero rRNA Removal Kit (Human/Mouse/Rat) (Illumina, CA, USA). The remaining RNA was then fragmented, and the cDNA was synthesized using random hexamers, end-repaired, and ligated with appropriate adaptors for sequencing. The library then underwent size selection and purification using AMPure XP beads (Beckman Coulter, CA, USA). The appropriate Illumina-recommended 6 bp barcode bases were introduced at one end of the adaptors during the PCR amplification step. The size and concentration of the RNAseq libraries was measured by Bioanalyzer and Qubit fluorometry (Life Technologies, NY, USA) before loading onto the sequencer. The rRNA-depleted libraries were sequenced on the Illumina HiSeq 2500 System with 100 nucleotide single-end reads, according to the standard manufacturer’s instructions (Illumina, CA, USA).
Readhead B., Haure-Mirande J.V., Zhang B., Haroutunian V., Gandy S., Schadt E.E., Dudley J.T, & Ehrlich M.E. (2015). Molecular systems evaluation of oligomerogenic APPE693Q and fibrillogenic APPKM670/671NL/PSEN1Δexon9 mouse models identifies shared features with human Alzheimer's brain molecular pathology. Molecular Psychiatry, 21(8), 1099-1111.
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9

RNA-seq Library Preparation and Sequencing

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The sequencing library was prepared with the standard TruSeq RNA Sample Prep Kit v2 protocol (Illumina, San Diego, CA, USA). Briefly, ribosomal RNA was removed using the Ribo-Zero rRNA Removal Kit (Human/Mouse/Rat) (Illumina). The remaining RNA was then fragmented, and the cDNA was synthesized using random hexamers, end-repaired and ligated with appropriate adaptors for sequencing. The library then underwent size selection and purification using AMPure XP beads (Beckman Coulter, CA, USA). The appropriate Illumina-recommended 6 bp barcode bases were introduced at one end of the adaptors during the PCR amplification step. The size and concentration of the RNAseq libraries was measured by Bioanalyzer and Qubit fluorometry (Life Technologies, Grand Island, NY, USA) before loading onto the sequencer. The rRNA-depleted libraries were sequenced on the Illumina HiSeq 2500 System with 100 nucleotide single-end reads, according to the standard manufacturer's instructions (Illumina).
Readhead B., Haure-Mirande J.V., Zhang B., Haroutunian V., Gandy S., Schadt E.E., Dudley J.T, & Ehrlich M.E. (2015). Molecular systems evaluation of oligomerogenic APPE693Q and fibrillogenic APPKM670/671NL/PSEN1Δexon9 mouse models identifies shared features with human Alzheimer's brain molecular pathology. Molecular Psychiatry, 21(8), 1099-1111.
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10

Titrating MNase for Mint-ChIP

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MNase (New England BioLabs M0247S) was stored as frozen aliquots at −80°C. To titrate MNase for specific cell types, we lysed and digested 10,000–100,000 cells in the same conditions as for Mint-ChIP, using 4 to 600 MNase units. MNase was inactivated with 30 mM EGTA and we performed a 2× SPRI bead cleanup to isolate DNA (Agencourt AMPure XP beads). DNA was eluted in 40 μl H2O with 0.4 μl RNase (Roche 11119915001) and 1 μl Proteinase K (Life Technologies 25530-031) and incubated for 15 minutes at 37°C and for 1 hour at 62°C. Another 2× SPRI bead cleanup was performed, and eluted DNA was run on a 2% E-gel (Life Technologies G402002) or BioAnalyzer. MNase concentrations that yielded most fragments of 1–5 nucleosomes (150–800 bp) were selected for Mint-ChIP.
van Galen P., Viny A.D., Ram O., Ryan R.J., Cotton M.J., Donohue L., Sievers C., Drier Y., Liau B.B., Gillespie S.M., Carroll K.M., Cross M.B., Levine R.L, & Bernstein B.E. (2015). A multiplexed system for quantitative comparisons of chromatin landscapes. Molecular cell, 61(1), 170-180.
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