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7 protocols using cd24 pacific blue

1

Isolation and Flow Cytometry of Intestinal Stem Cells

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Following crypt isolation, the crypt suspensions were pelleted (100 g, 5 min, 4°C) and supernatant was discarded. Crypts were resuspended in TrypLE (GIBCO, no phenol red, 12604039) and dissociated into individual cells by warming crypts in water bath at 32°C for 60 s. Dissociated single cells were treated with the following antibody cocktail for flow cytometry analysis: CD45-PE (eBioscience, 12-0451-83), CD31-PE (Biolegend, 102514), Ter-119PE (Biolegend, 116208), CD24-Pacific Blue (Biolegend, 101820), CD117-APC/Cy7 (Biolegend, 105826), and EpCAM-APC (eBioscience, 17-5791-82). 7AAD (Invitrogen, A1310) was used a viability dye to exclude dead cells from the analysis. ISCs were isolated as Lrg5-eGFPhiEpCAM+CD24low/−CD31Ter119CD457AAD. eGFPlow progenitors were isolated as Lrg5-eGFPlowEpCAM+CD24low/−CD31Ter119CD457AAD. Cells were sorted using a BD FACS II SORP cell sorter.
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2

Immunofluorescence and Western Blot Protocols

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Primary antibodies for western blot were against LC3 (Novus Biologicals, NB600), SQSTM1 (Abcam, ab56416), ATG13 (Sigma Aldrich, SAB4200100) and ACTIN (EMD Millipore, MAB1501). Primary antibodies used for immunofluorescence and immunocytochemistry were against LC3 (MBL, PM036), SQSTM1 (Progen, GP62-C), ATG16L1 (Abgent, AP1817b), AQP5 (Alomone labs, AQP5-005) and BrdU (Bio-Rad, MCA2483GA). Fluorescently-labeled antibodies for FACS sorting were against PECAM1/CD31 (PECAM1/CD31-PE; eBioscience, 12–0311-82), PTPRC/CD45 (PTPRC/CD45-PE, Biolegend, 103106), LY76/TER119 (LY76/TER119-PE/Cy7; Biolegend, 116222), CD24 (CD24-Pacific Blue, Biolegend, 101820) and ITGB1/CD29 (ITGB1/CD29-FITC, BD Biosciences, 555005). The following secondary antibodies from ThermoFisher Scientific were used for the visualization of the primary antibodies: Alexa Fluor 488-conjugated goat anti-mouse (A-11001), Alexa Fluor 568-conjugated goat anti-mouse (A-11031) or goat anti-rabbit (A-11011), Alexa Fluor 647-conjugated goat anti-mouse (A-21235), and Alexa Fluor 568 conjugated goat anti-Guinea pig (A-11075).
Hoechst 33342 was from Sigma Aldrich (B2261), Chloroquine (C6628) was from Sigma Aldrich and bafilomycin A1 was from BioAustralis (BIA-B1012). Tat-beclin 1 was from Selleck Chemicals (S8595), while propidium iodide was from Sigma Aldrich (P4170).
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3

Flow Cytometric Immunophenotyping of Immune Cells

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For flow cytometry, cells were stained with mAbs in PBS with 1% BSA for 20 minutes in the dark at 4°C. Cells were subsequently washed and fixed with a 1% paraformaldehyde/PBS solution before analysis on BD FACSCalibur flow cytometer (BD Immunocytometry Systems, [BDIS] San Jose, CA) or MACSQuant® Analyzer (Miltenyi Biotec). The anti-human antibodies used were CD19 Pacific Blue, CD24 PE-Cy7, CD38 APC, CD27 APC-Cy7, CD21 FITC, CD1c PE (all from Biolegend, San Diego, CA), CD10 PE, CD5 PE, CD23 PE, IgD PE, IgM PE-Cy5 (all from BD Bioscience), BAFF-R PE (eBioscience Inc., San Diego, CA). The following anti-mouse antibodies were used: CD24 Pacific Blue, CD21 FITC, CD23 PE, BAFF-R PE, CD21 APC, SA-APC-Cy7 (secondary antibody for IgD biotin staining), IgM PE-Cy7 (all from Biolegend), and IgD Biotin (eBioscience). Living cells were identified by forward scatter and side scatter gating and/or exclusion of 7-aminoactinomycin-D (eBioscience) added immediately prior to data acquisition or fixation. Flow cytometry data analysis was performed using Flowjo data analysis software (TreeStar, Ashland, OR).
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4

Isolation and Flow Cytometry of Intestinal Stem Cells

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Following crypt isolation, the crypt suspensions were pelleted (100 g, 5 min, 4°C) and supernatant was discarded. Crypts were resuspended in TrypLE (GIBCO, no phenol red, 12604039) and dissociated into individual cells by warming crypts in water bath at 32°C for 60 s. Dissociated single cells were treated with the following antibody cocktail for flow cytometry analysis: CD45-PE (eBioscience, 12-0451-83), CD31-PE (Biolegend, 102514), Ter-119PE (Biolegend, 116208), CD24-Pacific Blue (Biolegend, 101820), CD117-APC/Cy7 (Biolegend, 105826), and EpCAM-APC (eBioscience, 17-5791-82). 7AAD (Invitrogen, A1310) was used a viability dye to exclude dead cells from the analysis. ISCs were isolated as Lrg5-eGFPhiEpCAM+CD24low/−CD31Ter119CD457AAD. eGFPlow progenitors were isolated as Lrg5-eGFPlowEpCAM+CD24low/−CD31Ter119CD457AAD. Cells were sorted using a BD FACS II SORP cell sorter.
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5

Isolation of Splenic CD8α+ and pre-cDC1 Cells

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Splenic pan DCs were isolated from nine age-matched, female, littermate BALB/c mice and pooled per three mice for a total of three biological replicates. Pooled DCs were washed in flow buffer (PBS with 0.5% FBS), incubated with anti-mouse Fc Block (Thermo Fisher Scientific), and then stained with CD8α PE-Cy7 (Thermo Fisher; clone: 53–6.7), and CD24 Pacific Blue (Biolegend; clone: M1/69). CD8α+ and pre-cDC1 (CD24high CD8α-) were sorted using FACSAria III (BD).
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6

Isolation of Intestinal Stem Cells and Paneth Cells

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Intestinal stem cells and Paneth cell isolation was performed as described previously (Igarashi & Guarente, 2016; Roth et al., 2012: Yilmaz et al., 2012). Briefly, the crypt suspensions were centrifuged for 5 min at 250 g at 4°C. The pellets were gently resuspended in 1.0 ml of undiluted TrypLE Express (Life Technologies) +120 μl of DNase I (10 U/μl, Roche). The suspended crypts were incubated in a 32°C water bath for 1.5 min were then placed on ice. 12 ml of cold MEM was added, and crypts were gently triturated twice. After centrifugation, the pellets were resuspended and incubated for 15 min on ice in 1 ml MEM containing CD45‐PE (1/500 eBioscience), CD31‐PE (1/500 Biolegend), Ter119‐PE (1/500 Biolegend), and CD24‐Pacific Blue (1/500 Biolegend). After centrifugation, the pellets were resuspended with MEM containing 1.5 μM propidium iodide (PI) (Thermo Scientific). The samples were filtered through a 40‐μm mesh (Corning) and immediately sorted on a FACS Aria (Becton Dickinson).
Intestinal stem cells were isolated as Lgr5‐EGFPhiCD24low/−CD31Ter119CD45PI,and Paneth cells were isolated as CD24hiSideScatterhiLgR5‐EGFPCD31Ter119CD45PI (Igarashi & Guarente, 2016).
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7

Intestinal Epithelial Cell Isolation

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After 6 h of recovery from surger, alive mice were sacrificed via cervical dislocation, and PCs were harvested from crypts of the ileum, as previously described [18] . In brief, crypts from the ileum were mainly collected from mixed intestinal fragments through a 70-μm mesh filter. Next, the crypt suspensions were marked with an antibody cocktail consisting of CD45-PE, EPCAM-APC (eBioscience, CA, USA), CD31-PE, Ter119-PE, CD31-PE, Ter119-PE and CD24-Pacific Blue (BioLegend, CA, USA), and resuspended with SEME/7-aminoactinomycin D (7-AAD) solution (1:500 dilution), followed by flow cytometry selection and analysis using a forward and side scatter gating strategy (BD Biosciences, San Jose, CA, USA). PCs were isolated as CD24 hi Epcam + CD31 -Ter119 -CD45 -7-AAD - cells, with the percentage in the crypt suspensions recorded. Dead cells were abandoned for subsequent studies, using the viability dye 7-AAD.
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