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52 protocols using nylon mesh

1

Isolation and Culture of Renal Epithelial Cells

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For RECs isolation from kidney tissues, samples were washed with cold wash buffer (F12 medium containing 5% fetal bovine serum [FBS] and 1% P/S) and minced by sterile scalpel into 0.2–0.5 mm3 sizes to a viscous and homogeneous appearance. The minced tissue was then digested with dissociation buffer including DMEM/F12 (Gibco, USA), 2 mg/ml protease XIV (Sigma, USA), 0.01% trypsin (Gibco, USA) and 10 ng/ml DNase I (Sigma, USA) in 37°C incubator 2 h with gentle agitation. Digested cell suspensions were washed with cold‐wash buffer and passed through 70 μm Nylon mesh (Falcon, USA) to remove aggregates. Cell pellets were collected by centrifuge of 200g and then seeded onto a feeder layer of lethally irradiated 3T3‐J2 cells in modified SCM‐6F8 medium. Human SOX9+ RECs were generated from urine samples and expanded as previously described.29For better visualization of colony growth, td‐Tomato+ RECs derived from mT/mG mice were used. For GFP labelling of cultured SOX9+ RECs, medium containing lentivirus was added to the cell culture together with 10 μg/ml polybrene (1:2000)29 and cell identities were analysed by CytoFLEX LX flow cytometry with appropriate markers before use (SOX9+, ATP1A1− and CDH1−). Analysis was gated using forward and side scatters characteristics and corresponding positive/negative control. Data were analysed using the flow cytometry software, FlowJo (TreeStar).
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2

Isolation and Culture of Airway Stem Cells

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The bronchoscopic brush with the trachea or bronchus epithelium sample was cut into 1 cm long pieces. After removing the sputum, the brush pieces were directly immerged into dissociation buffer (DMEM/F12 medium with 2 mg/mL protease XIV, 0.01% trypsin, and 10 ng/mL DNase I) and incubated for 1 hour at 37°C with gentle shaking. After dissociation, cell samples were passed through a 70 μm nylon mesh (Falcon, USA) to remove aggregates and washed three times with ice-cold F12 medium supplemented with 5% FBS and 1% Pen/Strep. Viable cell counts were determined using a hemocytometer. Cell pellets were collected by centrifugation at 200 × g and directly plated onto mitomycin-inactivated 3T3 fibroblast feeder cells and cultured under 7.5% CO2 condition as previously described [9 (link)]. To obtain a single-cell-derived clone, a clone cylinder (Sigma, USA) and high vacuum grease (Dow Corning, USA) were used to pick up a single colony grown up from one cell. Typically, both DASC and TSC are passaged every 4-6 days in a 1 : 7 ratio.
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3

Adipocyte Differentiation Assay Protocol

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3T3-L1 and C3H10T1/2 cells were purchased from the American Type Culture Collection (ATCC, Manassas, VA, USA) and were maintained in DMEM with 10% FBS mixture at 37°C in a 5% CO2 environment. Mice SVF was isolated from the iWAT of male C57BL/6J mice aged 6–8 weeks. SVF isolation was performed previously (24 (link), 25 (link)). Briefly, tissues were sheared, digested with 1 mg/ml collagenase in PBS supplemented with 0.5% bovine serum albumin (BSA), and 10 mM Hepes mixture for 30 min, with 300 rpm shaking at 37°C. The suspension was strained through a 40 μM nylon mesh (Falcon), collected by centrifugation. Finally, the adipocytes were then cultured in DMEM/F12 containing 10% FBS mixture and placed inside an incubator at 37°C with a 5% CO2 environment.
After reaching 100% confluence, 3T3-L1, C3H10T1/2 cells, and mice SVF were stimulated to differentiate a hormone cocktail containing 50 nM insulin, 100 nM T3, 0.125 mM indomethacin, 2 μg/ml dexamethasone, and 0.5 mM IBMX. After 48 h, the adipocytes were moved to the medium containing 50 nM insulin and 1 nM T3. The media was replaced every 2 days before Rb2 treatment. Dimethyl sulfoxide (DMSO) was used as the vehicle treatment. Finally, the mature adipocytes were confirmed by light microscopy and Oil Red O staining, and then used for further analysis.
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4

Isolation and Expansion of Primary Cells

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Patients were recruited for this study under informed consent consistent with institutional review board protocols. All biopsies were derived from patient’s endoscopy.
1mm endoscopic biopsies were collected into RPMI media (Gibco) with 2% fetal bovine serum and subsequently digested in 2mg/ml collagenase A (Roche) at 37°C for 1.5 hour. Cells were washed by centrifugation in RPMI, digested with 0.5% trypsin (Gibco) 10 min, passed through a 40um Nylon mesh (Falcon), and seeded onto a feeder layer of lethally irradiated 3T3-J2 cells in StemECHO expansion medium and StemECHO enhancer (MultiClonal Therapeutics, West Hartford, CT). The culture medium was changed every two days. Cells were digested by 0.25% trypsin and passaged every seven to 10 days.
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5

Isolation and Analysis of CNS-Mononuclear Cells

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Mice were euthanized by isoflurane inhalation, perfused, and their brains were collected in cold PBS. The isolated brains were minced and digested for 1 h at 37 °C in Hanks' Balanced Salt Solution (HBSS) (02–017-1A, Biological Industries Israel Beit Haemek LTD, Israel) containing 50 μg/ml DNase I and 100 μg/ml collagenase (Roche, Rotkreuz, Switzerland). The resulting cell suspension was passed through a 70-μm Nylon mesh (Falcon, BD Biosciences, Bedford, MA), pelleted, resuspended in 30% Percoll (GE Healthcare Bio-Sciences, NJ) in HBSS and centrifuged at 15,500 rpm for 30 min at 4 °C. After eliminating the myelin debris, the mononuclear cell phase was collected. CNS-mononuclear cells were washed in a FACS buffer (HBSS, 2% FCS, 10 mM EDTA). After blocking non-specific binding of immunoglobulins to Fc receptors (anti-mouse CD16/32, TrueStain FcX TM, BioLegend), the cells were stained for 15 min at 4 °C with specific antibodies, washed, and analyzed. Multicolor FACS analyses were performed with a Cytoflex.
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6

Isolation and Transfection of Chicken Myoblasts

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Chicken primary myoblasts were isolated from the leg muscles of E11 chickens. Leg muscle (1 g) was minced into sections of approximately 1 mm with scissors and digested with 0.25% trypsin (Gibco, Grand Island, NY, USA) at 37 °C in a shaking water bath (90 oscillations/min). Digestions were terminated by adding foetal bovine serum (Gibco) after 30 min. The mixture was filtered through a nylon mesh with 70 µm pores (BD Falcon). The filtered cells were centrifuged at 350g for 5 min, and maintained in Dulbecco’s modified Eagle medium (DMEM) (Gibco), supplemented with 20% foetal bovine serum, and 0.2% penicillin/streptomycin (Invitrogen, Carlsbad, CA, USA) at 37 °C in a 5% CO2, humidified atmosphere. Serial plating was performed to enrich myoblasts and remove fibroblasts. DF-1 cells were cultured in DMEM with 10% foetal bovine serum and 0.2% penicillin/streptomycin. QM-7 cells were cultured in high-glucose M199 medium (Gibco) with 10% foetal bovine serum, 10% tryptose phosphate broth solution (Sigma, Louis, MO, USA) and 0.2% penicillin/streptomycin. Cells were transfected with 50 nM of miRNA mimics, 100 nM of miRNA inhibitors, 100 nM of siRNA or plasmid (1 µg/ml) using Lipofectamine 3000 reagent (Invitrogen) according to the manufacturer’s instructions.
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7

Isolation and Transfection of Sheep Satellite Cells

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Sheep skeletal muscle satellite cells (SMSCs) were isolated from the leg muscles of F90. Leg muscle (1 g) was minced into sections of approximately 1 mm2 with scissors and digested with 0.25% trypsin (Gibco, Grand Island, NY, USA) at 37 °C in a shaking water bath (90 oscillations/min). Digestions were terminated by adding fetal bovine serum (Gibco) after 30 min. The mixture was filtered through a nylon mesh with 70 mm pores (BD Falcon). The filtered cells were centrifuged at 350× g for 5 min, and the isolated cells were cultured in DMEM/F12 (Ham) (Gibco) with 20% fetal bovine serum and 0.2% penicillin/streptomycin.
The wild-type and mutated sequences of circCHRNG were synthesized and cloned into the pmirGLO dual-luciferase reporter vector (Promega) with the NheI and XhoI restriction sites. Cells were transfected with 50 nM of miRNA mimics and 100 nM of siRNA or plasmid (1 µg/mL) using Lipofectamine 3000 reagent (Invitrogen) according to the manufacturer’s instructions (Table S2).
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8

Isolation and Enrichment of Astrocytes

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Postnatal day 8 Wistar rats were anesthetized with isoflurane and decapitated. Hippocampi were removed rapidly under stereomicroscopic observation using sterile conditions, cut into 1 mm pieces, transferred to a tube with 0.7 mg/ml protease dissolved in PIPES solution (130 mM NaCl, 1 mM CaCl2, 5 mM KCl, 10 mM Pipes, 25 mM Glucose and 1 mM MgCl2, pH was adjusted to 7.4 with NaOH) and incubated at 33°C for 30 min with 100% oxygen bubbling into the solution. After removal of protease, the tissues were washed twice in culture medium (Neurobasal with B27 supplement (Invitrogen), with 2 mM L-glutamine and 10% fetal bovine serum), and gently triturated with ten to fifteen passes through the 0.78 mm opening of a tip of a P-1000 Pipetman. Cell suspensions were gravity-filtered through a 70 mm Nylon mesh (Falcon, Oxnard, CA) to remove large debris. Approximately 1–2 million cells were plated in a T75 flask (Corning, Corning, NY). Cultures were maintained at 36°C in a 5% CO2 incubator. After 24 hours the medium was removed and replaced with 14ml of fresh culture medium. When the cells were 50–70% confluent, cells were passaged repeatedly to remove neurons and enrich the astrocyte population. Typically five passages were required to obtain a pure astrocyte population. Astrocytes were maintained in culture and plated onto 16- or 96-well plates for transport assays.
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9

Cell Cycle and Apoptosis Assay

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For cell cycle assay, cell suspensions of M‐204 sh‐Ctrl and sh‐ILF2 (5 × 105 cells in 0.5 ml complete RPMI medium) were filtered through a nylon mesh (40 μm, BD Falcon) to remove cell clumps. The cells were stained with Vybrant® DyeCycle™ Ruby in 5 μM final concentration (Cat# V10309, Thermo Fisher Scientific) at 37˚C for 30 min in the dark. The cells were analysed using BD FACS Melody (BD Biosciences, Franklin Lakes, NJ) based on the fluorescence emission intensity, which was correlated with the DNA content. Apoptosis was measured using Annexin V‐PE Apoptosis Detection Kit I (Cat# 559763, BD Biosciences). A total of 1 × 105 cells of M‐204 sh‐Ctrl or sh‐ILF2 (in 100 μl binding buffer) were stained with 5 μl Annexin V‐PE and 5 μl 7‐AAD for 15 min at RT in dark. Four hundred microliters of binding buffer was then added to the samples and analysed using BD FACS Melody.
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10

Tumour Sphere Culture Assay for ESCC

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For tumour sphere culture, ESCC cells were seeded as a single cell at a density of 4 × 103 cells per well in ultra-low attachment six-well plates (Corning, NY, USA) under serum-free DMEM/F12 (Gibco) medium supplemented with 4 μg/mL heparin, 20 ng/mL basic fibroblast growth factor, 20 ng/mL epidermal growth factor (PeproTech Inc., Rocky Hill, USA), 5 μg/mL insulin (Sigma-Aldrich) and 1× B-27 (Invitrogen). After incubation for 10 days, small clusters of ESCC cells could be observed under a microscope and harvested with a nylon mesh (BD Falcon). For the sphere-forming assay, the ESCC cells were plated at a density of 2 × 103 cells per well in 6-well plates with triplicate. The number of tumour spheres in each well was counted carefully under the microscope.
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