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580 protocols using moflo xdp

1

Hepatoma Cell Surface Marker Profiling

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Hepatoma cells were incubated with the primary anti‐CD133 (Cat. no. 18470‐1‐AP; Proteintech, Hubei, China) or anti‐EpCAM (Cat. no. ab8666; Abcam, Shanghai, China) for 30 min at room temperature. The cells were then subjected to flow cytometry using a MoFlo XDP cell sorter from Beckman Coulter (Indianapolis, IN) according to the manufacturer's instructions.
SMMC7721 or HCCLM3 miR‐365 and their control cells were incubated with the primary anti‐CD133 or anti‐EpCAM for 30 min at room temperature. Flow‐cytometric analysis was performed using a MoFlo XDP from Beckman Coulter according to the manufacturer's instructions.
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Cell Sorting and Molecular Analysis of HCC

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For CD133+ and EpCAM+ cell sorting, primary HCC patients’ cells and hepatoma cells were incubated with the primary anti-CD133 (cat. no. 372806; BioLegend, San Diego, CA, USA) or anti-EpCAM (cat. no. ab8666; Abcam, USA) for 30 min at room temperature. The cells were then subjected to flow cytometry using a MoFlo XDP cell sorter from Beckman Coulter (Indianapolis, IN, USA), according to the manufacturer’s instructions. The sorted cells from three independent experiments were subjected to real-time PCR assay.
miR-552 mimic or miR-552 sponge and control hepatoma cells were incubated with the primary anti-EpCAM for 30 min at room temperature. The flow cytometry analysis was performed using a MoFlo XDP from Beckman Coulter, according to the manufacturer’s instructions.
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Flow Cytometry Immunophenotyping

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Antibodies to the following were purchased from Biolegend, eBioscience and Bioss and were used at 1:100-1:400 dilutions: B220-FITC, CD11b-FITC, CD4-FITC, CD8-FITC, TER-119-FITC, Gr-1-FITC, SCAL-1-APC-CY7, SCAL-1-percpcy5.5, C-KIT-PE-CY7, C-KIT-APC, CD16/32-PRE-CY5, CD16/32-PE, CD150-PE, CD34-Alexa Fluor®700, CD11b-PE-CY5, CD45-PE-CY7, CD115-PE, LY6G-FITC, rabbit anti-mouse AQP1, and goat anti-rabbit 488. For flow cytometric analysis of surface markers, cells were stained with antibodies in PBS containing 0.1% (w/v) BSA and 0.1% NaN3. For the myeloid progenitors isolated method, lineage cells were isolated by the negative selection procedure of magnetic-activated cell sorting using MS Lineage Panel Biotin (Biolegend) and BD beads (#559971). MoFlo™ XDP (Beckman) was used to sort HSC (LinSca-1+c-Kit+CD150+), CMP (LinSca-1c-Kit+CD150CD34+FcγRlow), and GMP (LinSca-1c-Kit+CD150CD34+FcγRhigh) cells. Biotin-CD3e antibody, biotin-TER119 antibody, biotin-CD45R antibody, and biotin-Ly6G antibody were used with magnetic-activated cell sorting to remove T cells, B cells, and granular cells, followed by MoFlo™ XDP (Beckman) to sort monocytes (CD11b+CD45highCD115+Ly6G-).
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Generation of Knockout and Knock-in Cell Lines Using CRISPR/Cas9

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All of the KO cell lines were generated using a CRISPR/Cas9 approach (Ran et al., 2013 (link)). The target oligonucleotides (5′-CCA​GGA​CTG​GAG​GAC​ACC​AC-3′ and 5′-GCA​GAA​GGA​TCG​AGC​AAA​CC-3′ for USP19, 5′-CTT​AAG​CAC​TTT​GTC​ACT​GC-3′ for MFN2, 5′-GTA​GCT​ACC​CAG​ATT​GTA​AT-3′ for FUNDC1, and 5′-GCT​AGA​AAG​CCT​GGT​GGG​GA-3′ for Drp1) were synthesized and ligated into the gRNA vectors. HeLa cells were then transfected with gRNA plasmids, together with the Cas9 and pEGFP-C2 plasmids. Four days later, GFP-positive cells were selected and monocloned by flow cytometry (MoFlo XDP; Beckman Coulter). The expanded clones were screened by Western blotting and genome sequencing.
To generate 3×Flag-mNeonGreen-USP19 knock-in HeLa cell lines, HeLa cells were transfected with two independent target oligos (5′-ACC​AAG​CGG​CTC​AAG​ATG​TC-3′ and 5′-AAG​CGG​CTC​AAG​ATG​TCT​GG-3′), ligated into the gRNA vector, and an arm sequence (3×Flag-mNeonGreen flanked by 1 kb homologous sequence of the USP19 genome) was constructed into the pcDNA3.1 vector. Seven days after transfection, cells were monocloned by flow cytometry (MoFlo XDP; Beckman Coulter) and seeded onto 96-well plates. Successful knock-in cells were confirmed by Western blotting.
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5

Isolation and Characterization of CD133+ and EpCAM+ Cells from HCC

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For CD133+ and EpCAM+ cells sorting, primary HCC patients' cells and hepatoma cells were incubated with the primary anti-CD133 (Cat. no. 372806, Biolegend, Inc., San Diego, CA) or anti-EpCAM (Cat. no. ab8666; Abcam, USA) for 30 minutes at room temperature. The cells were then subjected to flow cytometry using a MoFlo XDP cell sorter from Beckman Coulter (Indianapolis, IN, USA) according to the manufacturer's instructions. The sorted cells from three independent experiments were subjected to Real-time PCR assay.
miR-96 mimic or miR-96 sponge and control hepatoma cells were incubated with the primary anti-EpCAM for 30 minutes at room temperature. The flow-cytometry analysis was performed using a MoFlo XDP from Beckman Coulter according to the manufacturer's instructions.
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6

Sorting SSEA-1+ Cells by FACS

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At the 3rd passages, FACS were performed using MoFlo XDP (Beckman, USA). Briefly, the 3rd -passage-EpCAM+ cells were digested with 0.25% trypsin/1 mM EDTA and washed with Stain Buffer (BD Biosciences, USA). The detached cells were incubated with the APC-conjugated anti-human CD15 antibody (BioLegend, USA) in Stain Buffer containing 3% antibiotic–antimycotic mixture at a 1:20 dilution. The sorted SSEA-1+ cells were collected in TEM containing 3% antibiotic–antimycotic mixture.
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7

Annexin V/PI Apoptosis Assay

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At least 104-106 cells were analyzed by flow cytometry with the Annexin V/PI kit (BD Biosciences) using a Beckman Coulter MoFlo XDP. Briefly, the medium was removed and cells were treated with serum-reduced medium (0.5% FBS) with GYY4137 (100 μM) or NAC (5 μM) for 24 h. Cells were suspended in 300 μl binding buffer, and then stained with Annexin-FITC and propidium Iodide (PI). Positive controls for cell apoptosis or necrosis were indicated by staining with only Annexin-FITC or PI (Beckman Coulter, Inc.). Cell apoptosis was counted using summit V5.2.0.7477 software.
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8

Isolation and Activation of T Cells

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Peripheral blood of healthy donors was drawn through routine venipuncture. Peripheral blood lymphocytes (PBLs) were isolated using human lymphocyte separation medium (Dakewe Biotech Co, Ltd) through differential density gradient centrifugation. Cells were plated in U-shaped bottom 96-well cell culture plates (2 × 105 cells/well) using the Roswell Park Memorial Institute 1640 medium containing 10% fetal bovine serum (Invitrogen, Carlsbad, CA, USA) at 37℃. Antibodies against CD3 (16-0037-85, eBioscience) and CD28 (16-0289-85, eBioscience) were added into the media at a concentration of 2 μg/mL. After 72 hours, PBLs were dyed with fluorescently conjugated antibodies against CD3 (300 308, BioLegend), CD8 (300 906, BioLegend), and CD25 (302 610, BioLegend) and then sorted by flow cytometer (MoFlo XDP, Beckman Coulter, Inc). Activated T cells (CD3+CD8+CD25+) were collected.
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9

Flow Cytometry Analysis of C. glutamicum

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Samples for flow cytometry were prepared and analyzed as described previously in ref. 49 (link). Briefly, the C. glutamicum strains for sRNA knockdown were inoculated to 50 mL falcon tubes containing 5 mL BHIS media containing Km (25 μg mL−1) and Spc (200 μg mL−1) and cultivated at 30 °C for 25 h with agitation at 200 rpm. Cells were harvested by centrifugation at 13,200 rpm, washed with phosphate-buffered saline (PBS) and resuspended with the same buffer for flow cytometry analysis using fluorescence-activated cell sorting (FACS; MoFlo XDP, Beckman Coulter, Inc., Miami, FL, USA) based on high fluorescence intensity detection through a 530/40 band-pass filter for the GFP emission spectrum (Fig. 1d, Supplementary Fig. 1b–d). BD FACS LSRFortessa cell analyzer (BD Biosciences, NJ, USA) installed at the KAIST Bio Core Center was also used through a 530/30 band-pass filter for the GFP emission spectrum (Fig. 1d, Supplementary Fig. 2a; Supplementary Fig. 8).
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10

Isolation and Characterization of Adipose Cell Populations

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Primary SVF from EAT, SAT, BAT was resuspended in PBS with 2% FBS, and incubated with FACS antibodies for 30 min on ice. Cells were initially selected by size on the basis of forward scatter (FSC) and side scatter (SSC), following separated on the basis of cell-surface markers using a flow cytometer MoFlo XDP (Beckman Coulter, Brea, CA). To detect beige progenitors in SVF, primary SVF was separated on the basis of cell-surface markers including anti-PDGFRα (CD140a)-APC (1:50, BioLegend, San Diego, CA) and anti-CD34-FITC (1:100, eBioscience, San Diego, CA). To quantify MCs in adipose tissues, to isolate MCs from SVF, and to remove MCs from SVF, we stained and sorted MCs with anti-CD34-FITC (1:100, eBioscience), anti-CD45-PE (1:500, eBioscience) and MC markers anti-CD117-APC (1:200, eBioscience) and anti-FCεR1-PE-CY7 (1:200, eBioscience). The MC-removed SVF and MCs (1×105) were collected for TPH1 mRNA expressional analysis.
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