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90 protocols using 96 well plate

1

High-Resolution Mass Spectrometry for Metabolite Profiling

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Extracts (11.7 µL) obtained using hexane-based extraction were loaded in a 96-well plate (Eppendorf, Hamburg, Germany) together with 15 µL 1.33 mM ammonium formate in 2-propanol. Extracts (15 µL) obtained using chloroform-based extraction were loaded in a 96-well plate (Eppendorf, Hamburg, Germany) and added 15 µL 0.01% methylamine. These extracts were analyzed by high-resolution Fourier transform mass spectrometry (FTMS) in negative ion mode using either an LTQ Orbitrap XL or an Orbitrap Fusion Tribrid (Thermo Scientific, San Jose, CA, USA), both equipped with a Triversa NanoMate robotic nanoflow ion source (Advion Biosciences, Ithaca, NY, USA). On the LTQ Orbitrap XL, each sample was analyzed for 5 min, using an FTMS scan range of m/z 150–420, a max injection time of 250 ms, automated gain control for an ion target of 1e5, two microscans, and target resolution setting of 100,000. On the Orbitrap Fusion Tribrid, each sample was analyzed for 5 min, using a FTMS scan range of m/z 150–420, a max injection time of 100 ms, automated gain control for an ion target of 1e5, three microscans, and target resolution setting of 500,000. The sample injection settings of the NanoMate for samples injected with ammonium formate were −0.96 kV and 1.25 psi. The NanoMate settings for samples injected with methylamine were −0.96 kV and 0.6 psi.
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2

Cytotoxicity Evaluation of Chitosan Extracts on hUC-MSCs

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hUC-MSCs were seeded at 4 × 103 cell density into a 96-well plate (Eppendorf, Hamburg, Germany) in 150 μL of DMEM/F12 medium supplemented with 10 % FBS and 1× Pen/Strep and incubated at 37 °C up to complete adhesion (about 6 h). Then, the culture medium was changed to 150 μL of each chitosan extract supplemented with 2% FBS and 1× Pen/Strep. After 24 h of incubation, the Cytotoxicity Detection Kit (Roche, Basel, Switzerland) was used to evaluate the cytotoxicity of liquid extracts of chitosan on hUC-MSCs. According to the manufacturer’s instruction, plate was centrifuged at 300× g for 5 min. Then, the 100 μL of supernatant was transferred to a new 96-well plate (Eppendorf) and the same volume of the LDH-substrate mixture was added to each well. After 30 min of incubation in the dark at the room temperature, the absorbance at 450 and 620 nm was measured by the Multiskan FC microplate photometer (Thermo Scientific, Waltham, MA, USA). hUC-MSCs cultured in DMEM/F12 medium supplemented with 2% FBS medium and 1× Pen/Strep was used as a control. Three independent experiments were performed. Statistical analysis was performed by one-way ANOVA and the Bonferroni test (post-hoc test) using the GraphPad Prism v.5 software.(GraphPad Software, Inc., CA, USA) p values less than 0.05 (p < 0.05) were considered statistically significant and labelled by an asterisk (*).
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3

Assessing L. aureum Extract Cytotoxicity

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The cell viability was measured using the CCK-8 assay according to the manufacturer's instructions and the hydrogen peroxide induced RAW264.7 cells oxidative stress model was established following the method described by Zhou et al. with some modifications (34 (link)). RAW264.7 cells were seeded in 96-well plates (Eppendorf, Germany) at a density of 6 × 104/ml in culture medium for 4 h. Subsequently, the cells were incubated with DMEM containing different concentrations of L. aureum extracts (dissolved in DMSO) or H2O2 for 24 h. The viability of cells stimulated with L. aureum under oxidative stress were determined as follows: cells were plated in 96-well plates (Eppendorf, Germany) with a density of 1 × 105 in culture medium for 4 h, and the cells were incubated with DMEM containing different concentrations of L. aureum extracts (0, 2, 5, 10 μg/ml) for 20 h. The positive control group and the L. aureum–treated groups were then exposed to H2O2 (400 μM) for 4 h. CCK-8 solution (10 μl) was added to each well and incubated in an atmosphere of 5% CO2 at 37°C for 4 h. The absorption values were measured at 450 nm by using a spectrophotometer (Epoch Microplate Spectrophotometer; BioTek Instruments). The results were expressed as the percentage viability according to the following formula:
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4

Curcumin Modulates Cell Viability Under Oxidative Stress

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Cells were seeded in 96-well plates (Eppendorf, Germany) at a density of 6×104/mL in culture medium for 4 h. The media were replaced with fresh DMEM containing different concentrations of curcumin (dissolved in DMSO, Sigma, USA) or H2O2 (Aladdin, China) and incubation for 24 h. The viability of cells stimulated with curcumin under oxidative stress were treated as following: cells were plated in 96-well plates (Eppendorf, Germany) at 1×105 density in culture medium for 4 h, the media were replaced with fresh DMEM containing different concentrations of curcumin (0, 5, 10, 20 μM) for 20 h or 16 h. The positive control group and the curcumin-treated groups were then exposed to H2O2 (500 μM) for 4 h or 8 h, respectively. 20 μL MTT (2 mg/mL) was added to each well, followed by 4 h of incubation at 37°C. Viability was determined by formazan crystal pellets dissolved in DMSO (Sigma, USA). The absorbance of the plate was determined by using a microplate reader (Bio-Rad, USA) at 570 nm. The results were expressed as the percentage viability according to the following formula: %Viability = 100×(absorbance of treatment/absorbance of control).
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5

Quantitative gene expression analysis

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Tissue RNA extraction and cDNA synthesis were performed as previously described.37 (link) The SsoAdvanced Universal SYBR Green Supermix (BioRad, Hercules, CA, USA) was used and qPCR data were analyzed using the 2−ΔCt method. MICA mRNA expression was normalized to glyceraldehyde 3-phosphate dehydrogenase gene (GAPDH). The following primers were used: GAPDH forward 5’-CGGATTTGGTCGTATTGG-3’ and reverse 5’-GGTGGAATCATATTGGAACA −3’; MICA forward 5’- TCCTGCTTCTGGCTGGCAT-3’ and reverse 5’-GACAGCACCGTGAGGTTA-3’ (Primm, Milan, Italy). The digital droplet PCR (ddPCR) was performed with the ddPCR™ Supermix for probes with the following primers: TBP dHsaCPE5058363, ADAM10 dHsaCPE502553, ADAM17 dHsaCPE5038420 (Bio-Rad). The total mix was placed into the 8 channel cartridge and the droplets were generated with the QX200™ droplet generator (Bio-Rad). Droplets were transferred to an Eppendorf® 96 well plate (Eppendorf, Germany) and placed into the T100™ Thermal Cycler (Bio-Rad) according to the manufacturer’s instructions. The droplets were subsequently read automatically by the QX200™ droplet reader (Bio-Rad) and the data were analyzed with the QuantaSoft™ analysis PRO version1 software (Bio-Rad).
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6

Quantifying HIV-1 RNA Using Droplet Digital PCR

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HIV-1 RNA was quantified using the QX100™ Droplet Digital™ PCR system (Bio-Rad, Pleasanton, CA). The ddPCR mix for the usRNA assay consisted of: 10 µl 2x ddPCR™ super mix for probes (Bio-Rad); 200 nM of GAG1 and GAG2 primers; 400 nM GAG3 probe mix and 4 µl of the cDNA into a final volume of 20 µl. The total mix was placed into the 8 channel cartridge, 50 µl of droplet generating oil was added and droplets were formed in the QX100™ droplet generator (Bio-Rad). Droplet in oil suspensions were transferred to an Eppendorf® 96 well plate (Eppendorf, Germany) and placed into the T100™ Thermal Cycler (Bio-Rad). Cycling conditions were as follows: 95°C for 5 min, followed by 40 cycles of 95°C for 15 sec and 58°C for 60 sec. The ddPCR mix for the msRNA assay consisted of 10 µl 2x ddPCR™ super mix for probes (Bio-Rad); 250 nM of ks1 and mf83 primers, 500 nM of ks2-tq, and 4 µl of the cDNA into a final volume of 20 µl. PCR cycling conditions were the same as for the usRNA assay, except the annealing temperature which was 60°C. The droplets were subsequently read automatically by the QX100™ droplet reader (Bio-Rad) and the data was analyzed with the QuantaSoft™ analysis software 1.3.2.0 (Bio-Rad).
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7

Quantitative Gene Expression Analysis

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Specific timeless and cry1, period and beta- actin (housekeeping) primers and probe were planned and sequenced by Agentek (www.agentek.co.il; Table S5). The primers were first verified with rt-PCR and agarose gel. Subsequently gradient PCR was used to establish the optimal annealing temperature. cDNA was quantified using the QX100TM Droplet DigitalTM PCR system (Bio-Rad, Pleasanton, CA). The ddPCR mix consisted of: 10 ml 2× ddPCRTM super mix for probes (Bio-Rad); 200 nM of forward and reverse primers; 400 nM probe mix and 4 ml of the cDNA into a final volume of 20 ml. The total mix was placed into an 8 channel cartridge, 50 ml of droplet generating oil was added and droplets were formed in the QX100TM droplet generator (Bio-Rad). Droplets in oil suspensions were transferred to an Eppendorf 96 well plate (Eppendorf, Germany) and placed into the T100TM Thermal Cycler (Bio-Rad). Cycling conditions were as follows: 95 °C for 5 min, followed by 40 cycles of 95 °C for 15 sec and 58 °C for 60 sec. The droplets were subsequently read automatically by the QX100TM droplet reader (Bio-Rad) and the data was analyzed with the QuantaSoftTM analysis software 1.3.2.0 (Bio-Rad), and then exported to Excel (Microsoft) for further analysis.
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8

Comprehensive Proteomics Sample Preparation

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Chemicals were purchased from Sigma-Aldrich (St. Louis, MO) unless
specified otherwise. The Eppendorf 96-well plate, matrix D.A.R.T.s tips
(20–300 μL), and automation reservoirs were
obtained from Thermo Fisher Scientific (Hudson, NH). The C18 SepPak columns and
Oasis Mix Mode Anion eXchange (MAX) column were purchased from Waters
Corporation (Milford, MA). MS-grade trypsin and Lys-C were from Promega
Corporation (Madison, WI). C4 reverse phase resin and C18 analytical LC column
(NanoViper, 75 μm, 150 mm, 2 μm
particle size) were purchased from Separation Method Technologies (Newark, DE)
and Fisher ScientiFB01c (Waltham, MA), respectively. The polyethylene sheet has
a median pore size of 15–45 μm (thickness = 1.57
mm or 0.062 in.; Interstate Specialty Products; Sutton, MA).
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9

Mass Spectrometry Sample Preparation

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Chemicals were purchased from
Sigma-Aldrich (St. Louis, MO) unless specified otherwise. An Eppendorf
96-well plate, matrix D.A.R.T.s tips (20–300 μL), and
automation reservoirs were obtained from Thermo Fisher Scientific
(Hudson, NH). Oasis Mix Mode Anion eXchange (MAX) columns were purchased
from Waters Corporation (Milford, MA). MS-grade trypsin was from Promega
Corporation (Madison, WI). MS-grade LysC was from FUJIFILM Wako Chemicals.
C4 reverse phase resin was purchased from Separation Method Technologies
(Newark, DE) and Fisher Scientific (Waltham, MA). The polyethylene
sheet has a median pore size of 15–45 μm (thickness =
1.57 mm or 0.062 in.; Interstate Specialty Products; Sutton, MA).
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10

Negative Ion Mode FTMS Analysis of Fatty Acids

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The total FA extracts were dissolved in 500 µL chloroform/methanol/2-propanol (1:2:4, v/v/v) containing 0.75 mM ammonium formate and loaded in a 96-well plate (Eppendorf, Hamburg, Germany). Ten µL of each fatty acid extract was infused using the robotic nanoflow ion source TriVersa NanoMate (Advion Biosciences, Ithaca, NY, USA) and analyzed in negative ion mode using an Orbitrap Fusion Tribrid mass spectrometer (Thermo Fisher Scientific, San Jose, CA, USA). Ionization voltage was −0.96 kV and back pressure was 1.25 psi. The temperature of the ion transfer tube was 275 °C. S-lens radio frequency level was set to 60%. Negative ion mode FTMS analysis was performed in m/z range 150–420. Each sample was analyzed for 1 min. All full scan FTMS data were acquired in profile mode, using a max injection time of 100 ms, automated gain control for an ion target of 105, three microscans (to reduce file size), and a target resolution setting of 500,000.
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