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21 protocols using 35 mm petri dishes

1

PER2 Circadian Rhythm Bioluminescence Assay

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Bioluminescence was recorded from SCN slices prepared from P4 PER2LUC mice housed in a standard 12:12 h LD cycle. For the preparation of slices, brains were quickly removed and chilled in Hanks’ balanced salt solution (HBSS), supplemented with 0.01 M HEPES, 100 U/ml penicillin, 0.1 mg/ml streptomycin, and 4 mM NaHCO3. Vibratome slices (300 μm) were cut and placed on 0.4 mm membrane inserts (Millipore) in 35-mm Petri dishes (BD Biosciences) with 1-ml HEPES-buffered DMEM supplemented with 10% newborn calf serum (Invitrogen) and 0.1 mM beetle luciferin (Biosynth). Immediately after plating, slices were transduced with either the Kv4.1-targeted shRNA- or the nontargeted shRNA-expressing AAV8. Virus-containing media was removed after 3 d. After 2 weeks in culture, Petri dishes were sealed with vacuum grease and placed under photomultiplier tubes (HC135-11MOD; Hamamatsu) at 36°C in the dark. Bioluminescence was recorded in 10-min bins for at least 5 d. The period of PER2LUC expression was determined using Chronostar and compared using a one-way ANOVA followed by a Tukey post hoc test.
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2

Ratiometric pH Measurement of Cellular Compartments

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The pH-sensing ratiometric dyes SNARF-1 and HPTS (Life Technologies) were used simultaneously for pH measurement of both cytoplasmic (C-SNARF-1) and endosomal–lysosomal (HPTS) compartments as described previously30 . Briefly, cells were cultured in 35 mm Petri dishes (BD Biosciences) and used at 50% confluence. For endocytic labelling, cells were incubated overnight with HPTS (1 mM), washed, followed by a 20 min incubation with SNARF-1 (5 μM) to label the cytoplasmic compartment. Living cells were analysed using an Olympus Fluoview FV1000 confocal microscope. Fluorescence emissions of both pH-sensing probes were recorded and subsequently analysed as described30 .
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3

Colony Forming Assay in Methocult

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1,500 cells were plated in MethoCult™ H4034 optimum medium in 35 mm Petri dishes (Falcon, Cockeysville, MD, USA) in duplicate. Plates were incubated at 37 °C with 5% CO2 and 95% humidity for 7 days. Colonies were scored using an inverted microscope. To visualize the colonies MTT reagent (Thermo Fisher Scientific) was added for 1 h at 37 °C with 5% CO2.
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4

Heterologous Expression of CaV1.2 Channels

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Human embryonic kidney tsA-201 cells were grown at 5 % CO2 and 37 °C to 80 % confluence in Dulbecco’s modified Eagle’s/F-12 medium supplemented with 10 % (v/v) foetal calf serum and 100 units/ml penicillin/streptomycin. Cells were split with trypsin/EDTA and plated on 35-mm Petri dishes (Falcon) at 30–50 % confluence ∼16 h before transfection. Subsequently, tsA-201 cells were co-transfected with complementary DNAs (cDNAs) encoding wild-type or mutant CaV1.2 α1 subunits with auxiliary β2a [29 (link)] as well as α21 [11 (link)] subunits and GFP to identify transfected cells.
The transfection of tsA-201 cells was performed using the FuGENE HD Transfection Reagent (Roche) following standard protocols. tsA-201 cells were used until passage number 15. No variation in channel gating related to different cell passage numbers was observed.
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5

Hippocampal Slice Culture Preparation

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Slices of 350 μm thickness were made using McIlwain tissue chopper (Mickle Laboratory Eng. Co., Surrey, United Kingdom), from the hippocampi of Sprague-Dawley rats of post-natal days 7–8. Tissue cultures were then transferred to a poly-D-lysine (PDL) coated substrates. For substrate microwire recordings (s-MW), 6-well plates (Falcon) were used. MEA recordings were collected from micro-electrode arrays (MEA) (60MEA 200/30 IR-TI, Multichannel systems). For optical recordings, 35mm petri-dishes (Falcon) were used as substrates. In the case of single inserted electrode recordings (i-MW), slices were placed on glass coverslips pre-coated with PDL and cultured in 6-well plates. Slices were maintained in a humidified 37 °C incubator with 5% CO2 on a rocking platform. A serum free culture medium consisted of Neurobasal-A/B27, 30 μg/ml gentamicin, and 0.5 mM GlutaMAX (Invitrogen). Culture media was changed twice per week. All animal use protocols were approved by the Institution Animal Care and Use Committee (IACUC) at Lehigh University and were conducted in accordance with the United States Public Health Service Policy on Humane Care and Use of Laboratory Animals.
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6

Aging Drosophila Melanogaster Maintenance

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Flies were raised on standard cornmeal-yeast-molasses diet at 25C under a 12 h light/12 h dark (LD) regimen (where Zeitgeber time (ZT) 0 is time of lights on and ZT12 is time of lights off). Light intensity was kept at ∼1500 lux. Mated males were separated 1–2 days after emergence. Aging males were kept in inverted 8 oz round bottom polypropylene bottles (Genesee Scientific, San Diego, CA, USA) on 35 mm petri dishes (BD Falcon, San Jose, CA, USA) containing 15 ml of diet. Fresh diet was provided three times a week. All experiments were completed using the w1118 strain.
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7

HEK293 Cell Transfection for Cav1.2 Channels

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Human embryonic kidney (HEK293) tsA-201 cells were grown at 5% CO2 and 37 °C to 80% confluence in Dulbecco’s modified Eagle’s/F-12 medium supplemented with 10% (v/v) fetal calf serum and 100 units/ml penicillin/streptomycin. Cells were split with accutase solution and plated on 35-mm Petri dishes (Falcon) at 60–80% confluence ~24 h before transfection. Subsequently, tsA-201 cells were co-transfected with cDNAs encoding WT or mutant Cav1.2 α1 subunits with auxiliary β3a as well as α2-δ1 [16 (link)] subunits and GFP to identify transfected cells.
The transfection of tsA-201 cells was performed using the TurboFect transfection reagent (Thermo Fisher Scientific) following standard protocols. HEK293 cells were used until passage number 26. No variation in channel gating related to different cell passage numbers was observed.
In order to avoid calcium-dependent inactivation, barium ions (20 mM) were used as a charge carrier.
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8

Embryo Culture and Zona Removal

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Pre-implantation embryos were flushed from oviducts (morulae) or uterine horns (blastocyst stages) using M2 or FHM medium (Millipore) as described in [51 ]. For in vitro culture, embryos were placed in groups of 3–10 embryos and held within 10–15 μl microdrops of amino acid-supplemented Potassium Simplex Optimized Medium (KSOM-AA, Millipore), covered with mineral oil (Sigma), on 35 mm Petri dishes (Falcon) and allowed to develop at 37°C in a humidified 5% CO2 atmosphere. KSOM-AA was placed within the incubator at least 15 minutes prior to embryo culture to allow for pH equilibration. Morula-stage embryos were cultured within the Zona Pellucida until the time of cavitation (~24 hours into the culture), at which point the Zona was removed before continuing culture. All blastocyst-stage embryos were denuded before in vitro culture. Zona Pellucidae were removed by brief incubation in Acid Tyrode’s solution (Millipore) followed by washes in M2 or FHM.
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9

Lentiviral Transduction of Hematopoietic Stem Cells

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Cre Recombinase Gesicles (Takara) were added to cultures according to the manufacturer’s protocol. Briefly, purified LT-HSCs or LSK cells were plated in 35 mm petri dishes (2 × 105/dish, FALCON, Durham, NC) containing 1 ml of infection medium [serum-free RPMI-1640 medium plus 6 µg Polybrene (Sigma) and 10 µl Cre Recombinase Gesicles]. After 4 h incubation at 37 °C, medium was changed and cells further cultured in RPMI-1640 supplemented with 1% FBS, 100 ng/ml Thpo, 50 ng/ml SCF, and 0.3 ng/ml IL-3 at 37 °C in a humidified atmosphere containing 5% CO2 in air for 20 h.
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10

Hematopoietic Stem Cell Assay

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Purified LSK cells from BM or fetal liver (1 × 103/dish) were plated in triplicate in 35-mm petri dishes (FALCON) containing 1 ml MethoCult GF M3434 medium (StemCell Technologies Vancouver, BC). After 10 days incubation at 37 °C in 5% CO2 in air, CFU-GM, G, M, GEMM, and BFU-E were counted.
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