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6 protocols using janus automated liquid handling workstation

1

Proteomic Analysis of IL-1β Stimulated RTS-11 Cells

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Supernatant (20 μL) from RTS-11 cells stimulated with 25 ng/mL IL-1β for 36 h was size separated in a 4–12% Bis-tris SDS-PAGE gel as described above. Supernatant sample equivalent to ~11 kDa to ~14 kDa was cut out from the gel and stored in double-distilled water at 4 °C. Proteins were digested in gel using a JANUS automated liquid-handling workstation (PerkinElmer, Beaconsfield, UK) with a customised method adapted from that of Shevchenko and colleagues [29 (link)]. Tryptic peptides were dried by vacuum centrifugation and dissolved in 0.1% TFA for liquid chromatographic–tandem mass spectrometric (LC-MS/MS) analysis using a Q Exactive Plus/UltiMate 3000 RSLCnano system (Thermo Fisher Scientific, Hemel Hempstead, UK) equipped with an EASY-Spray source and configured for pre-concentration onto a 25-cm long PepMap RSLC C18 analytical column (Thermo Fisher Scientific). Tandem mass spectra were acquired using a data-dependent “Top 10” method as described before [30 (link)]. Peptides were identified by comparison with the O. mykiss proteome (UniProt proteome UP000193380, downloaded 17 January 2019) using Proteome Discoverer (version 2.2, Thermo Scientific) and a workflow incorporating the Mascot search engine (version 2.6, Matrix Science, London, UK) and decoy database validation with a strict target false discovery rate (FDR) of 0.01.
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2

Automated Serum Antibody Quantification

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Serial 3.16 fold dilutions of serum were prepared with assay diluent [1% ECL Blocking Agent (GE Healthcare Biosciences, Piscataway, NJ) in 1X PBST (PBS—0.1% Tween 20)], starting with 1:10 dilution or 1:100 dilution and higher. For each sample, a minimum of 3 dilutions were tested. Serial dilution was performed by Janus® automated liquid handling workstation (PerkinElmer, Waltham, MA). All other steps were performed manually. Plates were blocked for 1 h with 5% ECL Blocking Agent in 1X PBST at room temperature (24 °C ± 2), 150 μl per well, on a lab rotator set at 650 rpm. All incubations for subsequent steps were at 37 °C for 1 h with shaking at 650 rpm. After removal of the blocking agent, 25 μl of sample per well was added and the plate incubated. After each incubation plates were washed 4 times with 150 μl per well of 1X PBST using an automated plate washer (ELx405VRS, Biotek, Winooski, VT). 25 μl of biotin-labeled mouse anti-human IgG (Fc specific) (Biotrend Chemicals LLC, Destin, FL) at 1 μg/ml in assay diluent, followed by 25 μl of Streptavidin-Sulfo Tag(MSD) (1:500 dilution in assay diluent) was added to each well in subsequent steps. 150 μl of 1X Read Buffer T (MSD) was added to each well and the plate was immediately read on the Sector Imager 6000 (MSD) (read time: 70 s/plate). RLU for each spot was exported to Microsoft Excel.
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3

High-throughput chemical screening protocol

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Chemical screen using C2-KMT1A-4RE reporter cells was standardized in a 96 well format plating 5 × 103 cells per well. Cells were exposed to the Spectrum Collection compound library (MicroSource Discovery System) of pharmacological compounds at 10 μM in DMSO for 36 hours in DM using JANUS Automated Liquid Handling Workstation and PlateStak Automated Microplate System (PerkinElmer). Luciferase activity was determined using Envision 2103 Multilabel Reader (PerkinElmer). CPT was purchased from Sigma and stocks were dissolved in DMSO. CPT-11 was purchased from LC Laboratories (I-4122), and SN38 was received as a gift from the laboratory of Katerina Gurova (Roswell Park) where it was purchased from Tocris (#2684). CPT-11 was consistently used at higher concentrations relative to CPT and SN38, as it is a pro-drug and requires higher doses for cytotoxic effects [45 (link)]. LMP400 and LMP776 were obtained from the NCI Developmental Therapeutics Program Open Chemicals Repository and dissolved in DMSO. All compounds used were stored at −20°C.
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4

High-Content 3D Spheroid Imaging Assay

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A549 cells were trypsinized, and 1 × 103 cells per well were plated in 40 μl fully supplemented medium in 384-well spheroid plates (Corning) using a PerkinElmer JANUS automated liquid handling workstation (PerkinElmer). After 4 d of cultivation, spheroids were stained with 1 μM calcein AM cell-permeant dye and 1 μg/ml Hoechst for 3 h at 37°C. Spheroids were washed with PBS and spun down at 79g for 1 min. A time point zero image was made of the spheroids, PBS was aspirated, therapy was added to each well, and spheroids were briefly spun down at 79g. Wells were imaged directly afterwards every 3 min for 30 consecutive minutes using the PerkinElmer Opera Phenix high-content imaging microscope (PerkinElmer). For each time point, images were taken of each spheroid on five different planes in the z-axis (i.e., 0, 5, 10, 15, and 20 μM). Images were analysed using the image analysis algorithms of Harmony software. The amount of total calcein AM per cell per spheroid was calculated by dividing the amount of calcein AM expression per image by the amount of Hoechst-positive nuclei over all five z-axis planes. The spheroid was subsequently divided over an inner region (30% of spheroid) and an outer region (70% of spheroid) to calculate the out/in ratio and approximate speed of diffusion and toxicity.
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5

High-throughput Screening Platform Protocol

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Plate and liquid handling was performed using a high-throughput screening platform composed of an EL406 washer dispenser (Biotek, Winooski, VT) and a JANUS automated liquid-handling workstation (PerkinElmer, Billerica, MA). Cell seeding and assays were performed in black 96-well imaging plates (Greiner Bio-One). Image acquisition and quantification were performed with an ImageXpress Micro High-Content Analysis System (Molecular Devices, Sunnyvale, CA; Suppl. Fig. S1B).
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6

Goat Protein Identification by LC-MS

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The protein samples were digested in-gel (SDS-PAGE) with trypsin according to the method of Shevchenko et al. (2007) , adapted for use with a JANUS automated liquid handling workstation (Perkin Elmer, Beaconsfield, UK). The extracted peptide digestion products were dried in a vacuum centrifuge (SpeedVac) and dissolved in 10 µL LC-MS loading solvent. One-fifth (2 µL) was sampled for LC-MS analysis as described previously by Ni et al. ( 2018) using a Q Exactive Plus LC-MS system (Thermo Scientific, Hemel Hempstead, UK) and a 'Top 10' data-dependent MS2 method. All parameters were as previously described by Ni et al. (2018) . Database searches were carried out against the Capra hircus (Goat) protein sequences, downloaded from www.uniprot.org/uniprot in fasta format. A Mascot significance value of 0.05 was used to filter unreliable peptide matches.
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