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44 protocols using p96 1.5h n

1

Drug Cytotoxicity Screening on Tumor Cells

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Approximately 24 h after seeding, various drug concentrations (500, 100, 50, 10, 1, 0.5, 0.1 and 0 µM) diluted in normal culture media were transferred to G18-T or FWP1 cells plated in 384-well plates by utilizing the OT-2 liquid handler robot and associated software (Opentrons, Brooklin, NY, USA). Custom labware templates for 96-well plate (cat#P96- 1.5H-N, Cellvis, Mountain View, CA, USA), 384-well plate and reservoir were created using the measurements provided by the manufacturer for each item using the Opentrons labware creator. Moreover, a protocol script was created in Python that enable transfer of the drugs to tumor cells cultured in 384-well plates, incorporating the GEN1 single channel p300 pipette and a temperature module to maintain cells at 37 °C, while drugs were transferred to each plate. Before running the protocol, 0.5 mM (500 µM) of 67 drugs were individually diluted in StemPro NSC medium in the wells of row A of seven 96-well plates from the 10 or 2 mM stock concentration of each drugs. Then, the protocol was run through the steps as detailed in Figure S2, and, after drug addition, multiwell plates were incubated in a humidified environment at 37 °C and 5% CO2 for 72 h before viability measurements.
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2

Cell Labeling and Imaging Protocol

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These procedures followed the commonly used cell labeling method19 (link),53 (link), similar to our previous work25 (link). The HeLa cells were cultured in 96-well glass-bottom plates (thickness 170 ± 5 μm, P96-1.5H-N, Cellvis) with 15,000 cells in each unit, with the temperature set at 37 °C, the humidity at 95%, and the CO2 concentration at 5% overnight (>12 h). The cells were rinsed three times using 200-μL pre-warmed PBS buffer (37 °C, 5 min each) to remove the residual culture media and then fixed using PFA for 15 min at room temperature. Subsequently, the cells were rinsed three times using PBS buffer to remove the residual PFA. Next, the cells were permeabilized in 200-μL 0.2% Triton X-100 for 30 min at room temperature and rinsed three times using HEPES buffer. 200 μL Quick Block blocking buffer was added to block the fixed cells for 20 min at room temperature. When the procedure of blocking was completed, 150 μL of freshly prepared phalloidin-bioconjugated lanthanide-doped nanoparticles (with 1% bovine serum albumin in buffer (200 μg mL−1) were added. The cells were kept at room temperature for 4 h and then rinsed twice with pre-warmed (37 °C) HEPES buffer. Finally, the HEPES buffer was removed and a small drop of embedding medium was dropped into the well. The sample was kept at room temperature and in the dark for 24 h to ensure complete dryness before measurement.
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3

Differential Interference Contrast Microscopy of Nucleosomes

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Differential interference contrast (DIC) microscopy was carried out on select NCP samples following 30 min acquisition of turbidity data. For H3(1–44) or H4(1–25)L22Y with 601 DNA or NCP, DIC microscopy was carried out immediately following sample preparation and mixing rather than following turbidity assay due to the timescale of turbidity loss. Imaging was carried out at room temperature in volumes of 75 μL per well. Samples were in black polystyrene with #1.5 cover glass 96-well plates (P96–1.5H-N, Cellvis, Mountain View, CA) that were pre-treated as described above in “Turbidity assay” and sealed with MicroAmp Optical Adhesive Film (ThermoFisher Scientific, Waltham, MA).
Microscopy was performed on a Nikon Eclipse Ti2-E microscope equipped with a Yokogawa confocal scanner unit (CSU-W1) with 20x (Plan Apo; 0.75 NA), 40x (CFI Super Fluor; 0.9 NA), and 100x (Plan Apo; 1.45 NA oil) objectives, as noted in the associated figure legends. The system has a Hamamatsu ORCA-Flash4.0 V3 sCMOS Camera with an 82% quantum efficiency chip and runs the NIS-Elements Advanced Research package software. The field of view for the camera is 2048 × 2044 pixels, with resolution of 326.07, 162.02, and 65.24 nm/pixel for 20x, 40x, and 100x objectives, respectively. Images were processed using Fiji and ImageJ version 2.1.0/1.53c [61 (link),62 (link)] with the BioFormats plugin [63 (link)].
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4

Micropatterned PDMS for High-Density Cell Culture

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Polydimethylsiloxane (Sylgard Silicone Elastomer Kit 184) was prepared as previously described (Thery and Piel, 2009 (link)). Briefly, the elastomer base and curing agent were mixed at a 10:1 ratio, degassed, and cured at 65°C for 3 hours. PDMS was cut into rings with an outer diameter ~4 mm, inner diameter ~2 mm, and height ~3mm using a commercial leather belt hole punch. Glass-bottom 96-well plates (Cellvis P96-1.5H-N) were coated with 100 μg/mL bovine plasma fibronectin (Sigma-Aldrich F1141), washed with sterile water, and dried. PDMS rings were sterilized with UV irradiation and placed inside wells of 96-well plates, firmly adhering to the bottom. Cells were plated inside the PDMS ring at 6,000 cells per well (~1.9 × 105 cm−2), in a mixture of non-fluorescent and fluorescent cells (5:1 ratio) to facilitate tracking at high density. Cells were maintained for two days in growth media, and PDMS barriers were removed with forceps on the day of the experiment.
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5

Light-Induced YAP Translocation Assay

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To establish the light titration curve, LEXY-YAP transfected cells were differentiated in spontaneous differentiation media at 15 000 cells/well for 1.5d on 96-well glass bottom plates (Cellvis, P96-1.5H-N) and illuminated with different light intensities for 20 min. Cells were PFA fixed under continuous illumination and stained for YAP by IF to quantify YAP export in reference to a dark control.
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6

Confocal Imaging of Transfected HEK293T Cells

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HEK293T was maintained in DMEM supplemented with 10% fetal bovine serum (FBS). Every 3 to 4 days, cells were trypsinized, diluted (1 to 5), and plated onto new dish to avoid high confluency. For confocal imaging, cells were plated on a 96-well glass bottom plate (P96-1.5H-N, Cellvis), which was precoated with poly-l-lysine (Sigma), and 150 ng per well of total plasmids were transfected with Lipofectamine 2000 (Life Technologies, 11668027) following manufacturer’s recommended protocol. Actinomycin D (2 to 5 μg/ml, A1410, Sigma), PF9366 (5 to 20 μM, HY-107778, MedChemExpress), and/or ADOX (40 μM, S8608, Selleckchem) were pretreated for 4 hours before imaging. DMSO was used as vehicle control. SAM (S-Adenosyl-L-methionine p-toluenesulfonate, NA04017, Carbosynth) were supplied to PF9366-pretreated cells 1 hour before imaging (3 hours after PF9366 treatment), together with PF9366. p-Toluenesulfonic acid monohydrate (Sigma) was used as vehicle control for SAM.
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7

Live-Cell Imaging of DNA Damage Response

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To perform live-cell imaging, cells were seeded in 96-well glass-bottom plates (Cellvis, P96–1.5H-N). DLD-1 cells expressing H2B-mCherry, the dCas9-SunTag system, and 53BP1-Halo were treated with DOX/IAA for 72 hours, and 200 nM JF646 ligand (Promega) was added 15 min prior to imaging. Images were captured every 20 minutes for 48 hours using an ImageXpress Confocal HT.ai High-Content Imaging System (Molecular Devices) equipped with a 40x objective in CO2-independent medium (Thermo Fisher) at 37°C. Images were acquired at 7 × 1.5 μm z-sections under low power exposure. Maximum intensity projections were generated using MetaXpress and movies were analyzed using Fiji (v.2.1.0/1.53c).
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8

Cell Viability Assay with Imaging

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Cells were plated at 5 × 104 cells per well in various media to assess viability. Imaging plates (Cellvis P96-1.5H-N) were used, and outer wells were filled with PBS to buffer evaporation. Plates were incubated at 37 °C with 5% CO2 in a humidified atmosphere. Monocyte medium (s. below) was run on all plates as reference. NucGreen (Thermo Fischer) and NucBlue (Thermo Fischer) with final concentrations of 1:250 and 1:45 respectively, were added directly into the medium and incubated for 1 h at 37 °C before imaging. 16 fields of view were imaged and analyzed per well, while a total of 4 wells was analyzed per condition.
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9

Microscopic Imaging of Cell Dynamics

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MCF-10A cells were either plated on plastic (Corning 3904) or glass-bottom 96 well plates (Cellvis P96-1.5H-N), coated with 20 µg/mL bovine plasma fibronectin (Sigma-Aldrich F1141). Images were acquired on an ImageXpress Micro and Micro Confocal microscope (Molecular Devices) or an ECLIPSE Ti2 inverted microscope (Nikon) in a 37 °C humidified chamber with 5% CO2. A 10x objective (0.3 N.A.) with no binning was used for most fixed-cell immunofluorescence and for live-cell imaging of H2B, cyclin E/A-CDK activity reporter, and APC/CCdh1 degron reporter. For fixed-cell puncta immunofluorescence, a 20x objective (0.75 N.A.) with 2-by-2-pixel binning was used. The MetaXpress software (Molecular Devices) and an Andor Zyla sCMOS camera were used for image acquisition. During live-cell imaging, cells were imaged in growth media and images were taken every 12 min or 15 min, with the total light exposure being under 300 ms for each multi-color image. Fixed cells were imaged in PBS.
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10

Mitochondrial Dynamics in Macrophage Activation

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hMDMs were differentiated at 30,000 cells per well in glass-bottom 96-well plates (Cellvis, P96-1.5H-N). Parallel plates were prepared for live-cell imaging and LDH + CellTiter Glo analysis. hMDMs were either left untreated or pre-treated with glycine (50 mM) and primed with 1 μg/mL LPS (E. coli serotype 0111:B4) in RPMI complemented with 1% fetal calf serum for 3 hr before stimulation with 20.7 μM of nigericin (Invivogen). Tetramethylrhodamine ethyl ester perchlorate (TMRE, 200 or 10 nM, Sigma-Aldrich) was added to cells before the plates were placed in a heated incubator (37°C, 5% CO2), and images were taken every 30 min over 18 or 22 hr (two independent experiments). In the second experiment, at the end of LPS priming, cells were labeled with CellTracker Deep Red (0.5 μM Invitrogen) for 15 min and washed before addition of fresh medium with TMRE (10 nM) with or without LPS, nigericin, and glycine. In parallel plates treated identically, supernatants were harvested and assayed for LDH, and cellular ATP was measured using CellTiterGlo (Promega) at 0, 2, 6, and 18/22 hr.
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