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5 protocols using 70 μm nylon cell strainer

1

Isolation and Cryopreservation of Murine Bone Marrow-Derived Macrophages

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For obtaining bone marrow, male or female mice were euthanized, and femurs, tibias, and fibulas were excised. Bones were sterilized with 70% ethanol and washed with BMDM media (20% FBS (HyClone), 0.1% β-mercaptoethanol, 1% sodium pyruvate, 10% conditioned supernatant from 3T3 fibroblasts, in DMEM (Gibco) with 4.5 g l–1 glucose and 100 μg/ml streptomycin and 100 U/ml penicillin), and ground with a mortar and pestle. Bone homogenate was passed through a 70 μm nylon cell strainer (Thermo Fisher Scientific, 08-771-2) for particulate removal. Filtrates were then centrifuged at 290 g in an Eppendorf 5810 R centrifuge for 8 min, supernatant was aspirated, and the pellet was resuspended in BMDM media. Cells were plated in 30 ml BMDM media in non-TC-treated 15 cm petri dishes at a ratio of 10 dishes per two femurs/tibias and incubated at 37°C. An additional 30 ml of BMDM media was added 3 d later. At 7 d the media was aspirated, 15 ml cold PBS (Gibco, 10010–023) was added, and cells were incubated at 4°C with for 10 min. BMDMs were scraped from the plate, collected in a 50 ml conical tube, and centrifuged at 290 g for 5 min. PBS was aspirated, and cells were resuspended in BMDM media with 30% FBS and 10% DMSO at 107 cells/ml. One milliliter of aliquots was stored at –80°C for 24 hr in Styrofoam boxes and then moved to long-term storage in liquid nitrogen.
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2

Isolation of AG+ hPGCLCs from hiPSC-Derived Aggregates

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We isolated AG+ hPGCLCs from floating aggregates by using FACS. Floating aggregates containing hPGCLCs, which were induced from hiPSCs, were dissociated into single cells through 0.1% trypsin/EDTA treatment for 15 min at 37°C with periodic pipetting. After the reaction was quenched by addition of an equal volume of fetal bovine serum, cells were resuspended in FACS buffer (0.1% BSA in PBS) and strained through a 70 μm nylon cell strainer (Thermo Fisher Scientific) to remove cell clumps. AG+ cells were sorted with a FACSAria Fusion flow cytometer (BD Biosciences) and collected in an microcentrifuge tube containing CELLOTION (Amsbio). All FACS data were collected in FACSDiva v8.0.2 software (BD Biosciences) and analyzed with FlowJo v10.8.1 (BD Biosciences). For flow cytometry analysis, hPGCLCs were dissociated and resuspended in FACS buffer. AG+ cells were analyzed with FACSCanto or FACSFortessa (BD Biosciences).
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3

scRNA-seq Analysis of hiPSC-derived Aggregates

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WGNT SV20-211 hiPSC-derived aggregates were collected for scRNA-seq analyses: aggregates at fl19 (FACS-sorted whole WG+ fraction [n= 1] or NT+ fraction [n=1]), fl22 (NT+ fraction [n=1]), ali21 (whole WG+ fraction [n=1]) and ali28 (NT+ fraction [n =1]). Aggregates were dissociated in 0.1% Trypsin/EDTA for 10–15 min at 37 °C with periodic pipetting. After the reaction was quenched by adding an equal volume of fetal bovine serum, cells were resuspended in FACS buffer (0.1% BSA in PBS). Cell suspensions were strained through a 70-μm nylon cell strainer (Thermo Fisher Scientific) to remove cell clumps before use. All samples were stained with trypan blue and confirmed to be >85% viable. Cells were loaded into a Chromium microfluidic chip B using the Chromium Single Cell 3ʼ Reagent Kit (v3 chemistry) and Chromium Controller (10X Genomics) to generate gel bead emulsions (GEMs). Gelbead emulsion-RT was performed using a C1000 Touch Thermal Cycler equipped with a deep-well head (Bio-Rad). Subsequent cDNA amplification and library construction steps were performed according to the manufacturer’s instruction. Libraries were sequenced using a NextSeq 500/500 high output kit v2 (150 cycles) (FC-404-2002) on an Illumina NextSeq 550 sequencer.
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4

Establishment of Patient-Derived Organoids

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Fresh tissues were transported from the operating room to the laboratory and processed immediately. The tissue was minced and incubated at 37°C in 5 mL of collagenase B (5 mg/mL; Roche, #11088815001) and DNase I (100 μg/mL; Millipore Sigma, #6918230) with gentle shaking for 30 min to 1 h. The suspension was then filtered through a 70-μm nylon cell strainer (Fisher Scientific) and spun at 350 g for 5 min. The pellet was embedded in Matrigel solution (Corning, #354234) and seeded into a 48-multiwell plate (Corning, #351178). After the Matrigel had solidified, 250 μL of culture medium (Table S4) was added into each well. The PDOs were cultured in a humidity incubator at 37°C and 5% CO2, and culture medium was changed twice per week.
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5

Isolation and Preparation of Lymph Node and Spleen Cells

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During necropsy, mesenteric lymph nodes and spleen were isolated and collected in complete RPMI 1640 medium. The tissues were squeezed through a 70 μm nylon cell strainer (Fisher Scientific) manually, and cells were pelleted by centrifugation at 1500 rpm for 5 min. The supernatant was removed, and the pelleted cells were resuspended in 500 μl (MLN) and 1 ml (spleen) of Red Blood Cell Lysing Buffer Hybri-Max™ (Sigma-Aldrich) for 30 s (MLN) to 1 min (spleen) before adding 10 ml 1xPBS. Cells were pelleted by centrifugation at 1500 rpm for 5 min and resuspended in 1 ml of complete RPMI 1640 medium. Cells were counted on a CASY cell counter (Scharfe System) and diluted to a concentration of 1 × 107 cells/ml.
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