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5 protocols using 24 or 96 well plates

1

Immunoblotting Protein Detection Protocol

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For immunoblotting, cells were seeded in 24 or 96 well plates (Corning) then later harvested by trypsinisation, centrifuged, washed and lysed in SDS buffer (0.35 M Tris pH 6.8, 0.1 g/ml sodium dodecyl sulfate, 93 mg/ml dithiothreitol, 30% glycerol, 50 μg/ml bromophenol blue). Proteins were resolved by SDS-PAGE then electro-blotted onto Immobilion-P membranes (Millipore). Membranes were blocked in 5% dried milk in TBST (50 mM Tris, pH 7.6, 150 mM NaCl, 0.1% Tween-20) then incubated overnight at 4°C with the following primary antibodies diluted in milk: rabbit anti-Mcl-1 (Santa-Cruz), sheep anti-Tao1 [60 (link)], mouse anti-Cyclin B1 (Millipore), rabbit anti-Bcl-xL (Cell Signalling), sheep anti-Bub3 (Holland and Taylor, unpublished), rabbit anti-FBW7 (Bethyl), mouse anti-Bak (Calbiochem), rabbit anti-Bax (Santa-Cruz), mouse anti-myc tag (4A6, Millipore), rabbit anti-GFP (Cell Signalling). Following TBST washes, blots were incubated with appropriate horseradish-peroxidase-conjugated secondary antibodies (Zymed). Bound secondaries were then detected by addition of EZ-ECL Chemiluminescence Reagent (Biological Industries) or Luminata™ Forte Western HRP Substrate (Millipore) and imaged using a Biospectrum 500 imaging system (UVP).
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2

Cultivation of Colorectal Adenocarcinoma Cells

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Colorectal adenocarcinoma cells (Caco-2) were cultured in eagle medium (Ludwik Hirszfeld Institute of Immunology and Experimental Therapy) supplemented with 10% fetal bovine serum (FBS, Gibco, Thermo Fisher Scientific, Waltham, MA, USA) and 2 mM L-glutamine (Sigma–Aldrich, Saint Louis, MO, USA). Cells were cultured on Petri dishes (Sarstedt AG and Co. KG, Nümbrecht, Germany), flasks, and 24- or 96-well plates (Corning Life Sciences, Kennebunk, ME, USA) at 37 °C in a humidified atmosphere of 5% CO2.
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3

CRISPR-Cpf1 Transfection in HEK293T and Neuro2a Cells

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Human embryonic kidney 293 and Neuro2a cell lines were maintained in Dulbecco’s modified Eagle’s medium supplemented with 10% FBS (Gibco) at 37°C with 5% CO2 incubation. Cells were seeded one day prior to transfection in 24- or 96-well plates (Corning) at a density of approximately 1.2 × 105 cells per 24-well or 2.4 × 104 cells per 96-well and transfected at 50–80% confluency using Lipofectamine 2000 (Life Technologies), according to the manufacturer’s recommended protocol. For cell lysates, 500 ng of Cpf1 plasmid was delivered per 24-well. For indel analysis in HEK293T cells, a total of 400ng of Cpf1 plasmid plus 100ng crRNA plasmid was delivered per 24-well, or 100ng Cpf1 plus 50ng crRNA plasmid per 96-well. For BLISS and for indel analysis in Neuro2a cells, 500 ng of a plasmid with both Cpf1 and crRNA were delivered per 24-well. All indel and BLISS experiments used a guide length of 23 nucleotides.
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4

CRISPR-Cpf1 Transfection in HEK293T and Neuro2a Cells

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Human embryonic kidney 293 and Neuro2a cell lines were maintained in Dulbecco’s modified Eagle’s medium supplemented with 10% FBS (Gibco) at 37°C with 5% CO2 incubation. Cells were seeded one day prior to transfection in 24- or 96-well plates (Corning) at a density of approximately 1.2 × 105 cells per 24-well or 2.4 × 104 cells per 96-well and transfected at 50–80% confluency using Lipofectamine 2000 (Life Technologies), according to the manufacturer’s recommended protocol. For cell lysates, 500 ng of Cpf1 plasmid was delivered per 24-well. For indel analysis in HEK293T cells, a total of 400ng of Cpf1 plasmid plus 100ng crRNA plasmid was delivered per 24-well, or 100ng Cpf1 plus 50ng crRNA plasmid per 96-well. For BLISS and for indel analysis in Neuro2a cells, 500 ng of a plasmid with both Cpf1 and crRNA were delivered per 24-well. All indel and BLISS experiments used a guide length of 23 nucleotides.
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5

Peritoneal Macrophage Isolation from Mice

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Male B6 mice (6-8 weeks old) were purchased from Zhejiang Province Experimental Animal Center (Zhejiang, China). CD209a knockout mice on B6 background (6-8 weeks old) were purchased from the Mutant Mouse Resource Regional Center. The total number of wild type mice used for cell culture was 196, and the number of CD209a knockout mice used was 8. For peritoneal macrophage isolation, mice were injected intraperitoneally with 2 mL thioglycollate broth to elicit peritoneal macrophages. Four days later, cells were collected by lavaging the peritoneal cavity with ice-cold RPMI-1640 medium. The isolated cells were then washed and resuspended in RPMI-1640 supplemented with 10% (v/v) heat-inactivated fetal bovine serum (FBS; Invitrogen, Shanghai, China), 2 mM glutamine, 100 U/mL penicillin, and 100 mg/mL streptomycin. Cells were seeded (in triplicates) at a density of 1 x 10 6 /mL on 24-or 96-well plates (Corning, Acton, MA, USA), and allowed to adhere for 2 h at 37°C under 5% CO 2 . Cells were then washed twice to remove non-adherent cells, supplied with fresh medium as described above, and allowed to rest for 18-24 h. Recombinant mouse LECT2 proteins were generated from Chinese hamster ovary cells, as previously described (Lu et al., 2013) (link). In all experiments, 5 mg/mL LECT2 was used for treatment.
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