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Agilent bravo

Manufactured by Agilent Technologies
Sourced in United States

The Agilent Bravo is a liquid handling platform designed to automate a variety of liquid-based laboratory workflows. It features precise and accurate pipetting capabilities, allowing for efficient sample transfer and processing in a wide range of applications.

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19 protocols using agilent bravo

1

Automated Protein Sample Preparation

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Sample preparation, including protein extraction, digestion and peptide purification was performed according to the in‐StageTip protocol (Kulak et al, 2014 (link), 20) with automation on an Agilent Bravo liquid handling platform according to (Geyer et al, 2016 (link)). In brief, samples were incubated in the PreOmics lysis buffer (P.O. 00001, PreOmics GmbH) for reduction of disulfide bridges, cysteine alkylation and protein denaturation at 95°C for 10 min. Samples were sonicated using a Bioruptor Plus from Diagenode (15 cycles of 30 s). The protein concentration was measured using a tryptophan assay. In total, 200 μg protein of each organism were further processed on the Agilent Bravo liquid handling platform by adding trypsin and LysC (1:100 ratio—μg of enzyme to μg of sample protein). Digestion was performed at 37°C for 4 h.
The peptides were purified in consecutive steps according to the PreOmics iST protocol (www.preomics.com). After elution from the solid phase extraction material, the peptides were completely dried using a SpeedVac centrifuge at 60°C (Eppendorf, Concentrator plus). Peptides were suspended in buffer A* (2% acetonitrile [v/v], 0.1% trifluoroacetic acid [v/v]) and sonicated for 30 min (Branson Ultrasonics, Ultrasonic Cleaner Model 2510).
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2

Focused Compound Library Generation

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To generate a focused compound library, compounds were purchased from Selleck Chemicals, Tocris and Sigma, either dissolved in dimethyl sulfoxide (DMSO, 472301 Sigma) at 10 mM or as dry powder that was dissolved at 10 mM in DMSO. Experimental compounds were excluded from the outer two rows and columns of each 384-well library plate to avoid the potential impact of edge effects. Each compound screen plate contained 24 compounds arrayed across a 10-point dose curve ranging from 20 μM to 3 nM (24 compound plates in total). To generate library plates, 75 μL of compound were pipetted into the wells of column 3 (C3-N3) and 13 (C13-N13) of an AB0781 plate (Thermo Fisher Scientific). Using an Agilent Bravo, 50 μl of DMSO were pipetted into the remaining wells. Three-fold serial dilutions were then created by aspirating 25 μl of compound (starting in columns 3 and 13) and dispensing into 50 μl of DMSO in the adjacent column, pipetting up and down five times and then transferring 25 μL to the next column. The resultant master compound plates contained at least 50 μl of compound at the desired range of concentrations (10 mM to 0.5 μM; corresponding to 20 μM to 3 nM final concentration in cells). Library screening plates were created by aspirating 11 μL of compound from the AB0781 master plates to AB1056 plates (Thermo Fisher Scientific).
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3

Automated High-C Profiling of FFPE Liver

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Example 19

5 um FFPE sections of mouse liver tissue were de-waxed and rehydrated, and then put through a protocol optimized for FFPE samples, as described herein (no tissue dissociation (extracellular matrix protease), treatment with lysis buffer and 40 min of solubilization and decompaction at 74° C.) and subject to HiC using with 2 4-cutter restriction enzymes. However the entire HiC protocol, from lysis through reverse crosslinking and DNA purification was carried out on the Agilent Bravo automated liquid handling platform (Agilent Technologies, Inc., Santa Clara, Calif.). LPs were sheared using the Bioruptor® Pico instrument (Diagenode, Danville, N.J.) and then DNA was returned to the Bravo for automated library prep using KAPA HyperPrep (KAPABIOSYSTEMS, Capetown, South Africa). Library amplification was carried out in a PCR machine, and the post-PCR amplicons were returned to the Bravo automated liquid handling platform for purification. Upon shallow sequencing and analysis, consistently high long-range cis readouts from each of the 8 replicates analyzed in the automated experiment was observed (see FIG. 19).

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4

Custom Exome Capture and Sequencing

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After library construction, hybridization and capture are performed using the relevant components of IDT’s XGen hybridization and wash kit and following the manufacturer’s suggested protocol, with several exceptions. A set of 12-plex pre-hybridization pools are created. These pre-hybridization pools are created by equivolume pooling of the normalized libraries, Human Cot-1 and IDT XGen blocking oligos. The pre-hybridization pools undergo lyophilization using the Biotage SPE-DRY. Post lyophilization, custom exome bait (TWIST Biosciences) along with hybridization mastermix is added to the lyophilized pool prior to resuspension. Samples are incubated overnight. Library normalization and hybridization setup are performed on a Hamilton Starlet liquid handling platform, while target capture is performed on the Agilent Bravo automated platform. Post capture, a PCR is performed to amplify the capture material.
After post-capture enrichment, library pools are quantified using qPCR (automated assay on the Agilent Bravo), using a kit purchased from KAPA Biosystems with probes specific to the ends of the adapters. Based on qPCR quantification, pools are normalized using a Hamilton Starlet to 2 nM and sequenced using Illumina sequencing technology.
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5

Cell Viability Assay of GH and Phen Treatment

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T98G cells (3000 cells/well) were seeded in 384-well tissue culture treated black-walled, clear-bottom microplates (Corning Life Sciences, Tewksbury, MA, USA). After 24 h, cells were treated with either solvents (PBS or DMSO) control, GH, Phen, or the combination of GH and Phen using an Agilent Bravo automated liquid handling system (Agilent Technologies, Santa Clara, CA, USA). CellTiter-Fluor™ Cell Viability Assay (Promega, Madison, WI, USA, Cat.# G6080) was performed following manufacturer protocol to measure live-cell protease activity in cells treated from day 0 to day 3. Briefly, cells were treated with drugs in 25 µL and, at indicated time points, an equal volume of GF-AFC substrate was added. The cleaved compound generates a fluorescence signal proportional to the number of living cells. After 30 min of incubation at 37 °C, the signal was measured using a Spectramax M2e microplate reader (380–400 nm Ex/505 nm Em) (Molecular Devices, San Jose, CA, USA).
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6

High-throughput COVID-19 Diagnostic Protocol

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Pools that tested positive were deconvoluted and each of the five component specimens were repeated using the TaqPath™ COVID-19 Combo Kit currently employed at the LSTC. As previously described [8 (link)], RNA extraction was performed using the MVPII kit with 5 μL of Proteinase K, 200 μL sample, 275 μL lysis buffer with RNA binding beads, and 5 μL MS2 phage extraction control. Purification procedure was performed using an Agilent Bravo liquid handler (Agilent Technologies, Santa Clara, CA) whereby, after initial shaking 2 minutes at 3 x g and 5 minutes incubation at 65°C, the beads underwent three cycles of resuspension/aspiration in 165 μL wash buffer, 165 μL 80% ethanol, and 50 μL elution buffer, respectively. RT-qPCR was performed using 10 μL of eluate added to 15 μL of reaction mix that contained 6.25 μL TaqPath™ 1-Step Multiplex Master Mix (cat: A28523; No ROX™, Thermo Fisher, Waltham, MA), 1.25 μL COVID-19 Real Time PCR Assay Multiplex (cat: A47814; Thermo Fisher, Waltham, MA), and 7.5 μL Nuclease-free water (cat: 4387936; Ambion™, Thermo Fisher, Waltham, MA).
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7

Whole Exome Sequencing Library Preparation

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After post-capture enrichment, library pools were quantified using qPCR (KAPA Biosystems) using an automated assay on the Agilent Bravo with probes specific to the ends of the adapters. Based on qPCR quantification, libraries were normalized to 2nM. Cluster amplification of DNA libraries was performed following manufacturer’s protocol (Illumina) using exclusion amplification chemistry and flowcells. Flow cells were sequenced utilizing sequencing-by-synthesis chemistry. The flow cells were then analyzed using RTA v.2.7.3 or later. Each pool of whole exome libraries was sequenced on paired 76-cycle runs with two 8-cycle index reads across the number of lanes needed to meet coverage for all libraries in the pool. Pooled libraries were run on HiSeq4000 paired-end runs to achieve a minimum of 150x on-target coverage per library. The raw Illumina sequence data were demultiplexed and converted to FASTQ files; adapter and low-quality sequences were trimmed. The raw reads were mapped to the GRCh38/hg38 human reference genome and the validated BAMs were used for downstream analysis and variant calling.
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8

Luminescent Cell Viability Assay

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Compound toxicities in replicon-transfected cells were determined via the CellTiter-Glo (CTG) luminescent assay (Promega), where the number of viable cells is determined based on the quantitation of ATP. After the compound plates were scanned in the Acumen eX3, they were equilibrated to room temperature for 30 min. The CTG assay was carried out according to manufacturer’s protocol. Briefly, 30 µL of the premixed CTG reagents was added into each well using the Agilent Bravo. After gently mixing, the reaction was incubated at room temperature for 10 min, and luminescent signals were measured using the EnVision (Perkin-Elmer).
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9

Pan-Cancer Targeted Exome Sequencing

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After library construction, hybridization and capture were performed using the relevant components of IDT’s XGen hybridization and wash kit and following the manufacturer’s suggested protocol, with several exceptions. A set of 12-plex pre-hybridization pools were created. Custom exome bait (TWIST Biosciences) along with hybridization mastermix was added to the lyophilized pre-hybridization pool prior to resuspension. Library normalization and hybridization setup were performed on a Hamilton Starlet liquid handling platform, while target capture was performed on the Agilent Bravo automated platform. Post capture, a PCR was performed to amplify the capture material. After post-capture enrichment, library pools were quantified using qPCR (automated assay on Agilent Bravo), using a kit purchased from KAPA Biosystems with probes specific to the ends of the adapters. Based on qPCR quantification, pools were normalized using a Hamilton Starlet to 2nM and sequenced using Illumina sequencing technology. The targeted panel bait set used in this study was designed at the Broad Institute to maximize pan-cancer utility and contains regions from 396 driver genes previously annotated in cancer literature.
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10

Quantification and Normalization of NGS Libraries

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After post-capture enrichment, library pools were quantified using qPCR (automated assay on the Agilent Bravo), using a kit purchased from KAPA Biosystems with probes specific to the ends of the adapters. Based on qPCR quantification, libraries were normalized to 2nM, then denatured using 0.1 N NaOH on the Hamilton Starlet. After denaturation, libraries were diluted to 20pM using hybridization buffer purchased from Illumina.
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