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9 protocols using anti c kit

1

Bone Marrow Transplantation and Progenitor Assay

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WT mice were lethally irradiated with 900 cGy TBI and transplanted with 5 × 105 BM cells from donor mice. The survival rates of the mice were monitored for 3 months. Ten weeks after transplantation, bone marrow cells of the recipients were stained with anti-c-kit, anti-Sca-1, and anti-lineage cocktail antibodies (BioLegend, San Diego, CA, USA) to measure c-Kit+Sca-1+Lin (KSL) progenitor cells by a FACSCalibur cytometer (BD Biosciences, San Jose, CA, USA).
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2

Comprehensive Bone Marrow Cell Analysis

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Total BM cells were collected from two femurs and two tibias and flushed gently to analyze the hematopoietic cells. Dissociated BM cells were then washed with 1% fetal bovine serum (FBS) in PBS. Cells were stained with any of the following antibodies for 20 min on ice: anti-CD16/32 (Invitrogen), lineage antibody cocktail-v450 (BD), anti-Sca-1 (Invitrogen, D7), anti-CD45 (BD, 30-F11), anti-CD45.1 (BD, A20 or Invitrogen, A20), anti-CD45.2 (Invitrogen, 104), anti-CD48 (Invitrogen, HM48-1), anti-CD150 (Invitrogen, 9D1 or BioLegend, TC15-12F12.2), anti-c-Kit (BioLegend, ACK2 or Invitrogen, ACK2), anti-CD34 (Invitrogen, RAM34), anti-CD41 (BioLegend, MWReg30), and anti-CD105 (BioLegend, MJ7/18). Goat anti-LepR-biotin polyclonal antibody (R&D Systems), Live/Dead dye (Invitrogen), anti-CD45 (BD, 30-F11), anti-Ter119 (Invitrogen, Ter119), anti-CD31 (BioLegend, MEC 13.3), and streptavidin (BD) were used to analyze the MSCs. Cells were then fixed and permeabilized using Cytofix/Cytoperm (BD) for 20 min during intracellular staining. Next, the cells were washed with Perm/Wash buffer (BD), incubated with rabbit anti-SCF polyclonal antibody (LSbio), and stained with Alexa Fluor 488-conjugated donkey anti-rabbit IgG (Invitrogen). Flow cytometry data were collected using LSR II (BD Biosciences), and the files were analyzed using FlowJo software (Tree Star).
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3

Detailed Antibody Characterization for Immunoblotting and Flow Cytometry

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Primary antibodies used for immunoblotting were: anti-Snrnp40 (HPA026527) from Atlas; anti-FLAG M2 (F1804) from Sigma-Aldrich; anti-Themis (06–1328) and anti-GAPDH (MAB374) from Millipore; anti-Snrnp200 (A303–453A-T) from Bethyl; anti-Eftud2 (10208–1-AP) from Proteintech; anti-Cd2bp2 (PA5–18286) from Invitrogen; anti-Ikzf3 (Aiolos, 15103), anti-IL-17A (13838), anti-IL-17F (13186), anti-α-tubulin (3873), anti-β-actin (3700), anti-Hsp90 (4874) and anti-GFP (2956) from Cell Signaling. Antibodies used for flow cytometry were: anti-CD3ε (145–2C11), anti-CD4 (RM4–5), anti-CD8α (53–6.7), anti-B220 (RA3–6B2), anti-NK-1.1 (PK136), anti-CD25 (PC61.5), anti-CD44 (IM7), anti-CD62L (MEL-14), anti-CD11c (HL3), anti-CD11b (M1/70), anti-F4/80 (BM8), anti-mouse Lineage Cocktail (CD3/Ly-6G/CD11b/B220/Ter-119), anti-c-Kit (CD117, 2B8), anti-Sca-1 (Ly-6A/E, D7), anti-IL-7Rα (CD127, SB/199), anti-CD16/32 (93), anti-Flk-2 (CD135, A2F10), anti-CD45.1 (A20), anti-CD45.2 (104), anti-CD107a (Lamp-1, 1D4B), anti-TNF (MP6-XT22) from BioLegend or BD Biosciences, and anti-CD34 (RAM34), anti-granzyme B (NGZB), anti-IFN-γ (XMG1.2) from eBioscience.
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4

Antibody Immunoblotting for Stem Cell Markers

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The following antibodies were used were used for immunoblotting. Anti-SOX9 (Merck Millipore, AB5535), anti-HSD3b (TransGenic, KO607), anti-TRA98 (Abcam, ab82527), anti-FLAG (clone M2, Sigma, A8592), anti-VASA (Abcam, ab13840), anti-EPCAM (clone G8.8, eBioscience, no. 14-5791-85), anti-FOXO1 (CST, no. 2880), anti-PLZF (Santa Cruz, H300), anti-c-KIT (BioLegend, no. 105803), anti-JMJD1B (Abvnova, PAB15833), anti-H3K9me1 (Abcam, ab9045), Anti-H3K9me2 (clone 6D11) (Kimura et al., 2008 (link)), anti-H3K9me3 (clone 2F3) (Kimura et al., 2008 (link)), anti-JMJD1A (clone F0618) (Abe et al., 2015 (link)), and anti-JMJD1B (Abvnova, PAB15833). Anti-H3K9me2 (Abcam, Ab1220) was used for ChIP analysis.
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5

Comprehensive Immune Cell Phenotyping

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Cells were pre-incubated with 1 µg/ml of FcR blocker [Miltenyi-Biotech]. For intracellular cytokine staining, cells were first stimulated with PMA [0.1 µg/ml] and ionomycin [1 µg/ml] in the presence of Brefeldin A [3 µg/ml] for 4 h at 37°C before being surface-stained, fixed, and permeabilised [eBioscience kit]. The following antibodies were used for flow cytometry staining: intracellular staining panel including anti-CD45, anti-CD3, anti-CD8, anti-IL-17A, anti-IL-22, anti-TNF-α [all from Biolegend], and anti-IFN-γ [eBioscience] antibodies; CCR panel including anti-CXCR3 and anti-CCR4 [BD Biosciences], anti-CCR6 and anti-β7 [Biolegend], anti-CCR9 [eBioscience] and anti-CCR10 [R&D Systems] antibodies; ILC panel including anti-lineage [CD34, TCRαβ, TCRγδ, BDCA-2, FCεR1a, CD123, CD1a, CD11c, CD14, CD3, CD19, CD16], anti-CD45, anti-c-Kit, anti-CRTH2, anti-CD127 [all from Biolegend], anti-CD56 and anti-CD94 [BD Pharmingen]. All antibody cocktails contained a fluorescent dye [Invitrogen/Life technologies] to discriminate dead cells during analysis. Stained cells were acquired on an LSRII flow cytometer and analysis was performed using FlowJo software [Tree Star]. For critical discrimination, cell populations were gated against corresponding isotype or fluorescence minus one [FMO] control antibody panels.
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6

Flow Cytometry Antibody Staining

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The following antibodies were used for the flow cytometry analysis: FITC-, PE-, PECy7-, APC- and PerCP5.5-conjugated anti-mouse antibodies: anti-CD45, anti-CD11b, anti-Sca-1, anti-CD44, anti-CD3, anti-CD8, anti-CD29, and anti-c-kit (BioLegend). The cells were incubated with fluorochrome-conjugated mouse Abs directed against the cell surface at 4 °C for 30 min. The cells were washed with 1X PBS and resuspended in a 10% formalin solution (Sigma). The labeled cells were analyzed on a FACS Canto II cytometer equipped with FACS Diva software (BD Biosciences), and the flow cytometry data were analyzed using FlowJo software (Tree Star).
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7

Comprehensive Immune Cell Profiling

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For phenotypic analysis, immune cells in the epidermis, dermis, peripheral blood, spleen, draining lymph nodes and bone marrow were surface-stained with different antibodies, including anti-CD45 (Cat#103116,Biolegend), anti-CD11b(Cat#612800, Biolegend), anti-F4/80 (Cat#, 123120, Biolegend), anti-Gr-1 (Cat# 108442, Biolegend), anti-Ly6G (Cat# 127639, Biolegend), anti-CD3 (Cat# 612771, Biolegend), anti-γδ T (Cat# 118124, Biolegend), anti-CD4 (Cat#100449, Biolegend), anti-CD8 (Cat# 100742, Biolegend), anti-B220 (Cat#, 103232, Biolegend), anti-NK1.1 (Cat#108710, Biolegend), anti-cKit (Cat#105805, Biolegend), anti-FcεRIα (Cat# 134307, Biolegend), anti-CD11c (Cat# 117310, Biolegend), anti-CD207 (Cat# 144204, Biolegend), for 30 mins at 4°C in PBS containing 1% FBS. Cells were washed with 1× PBS once, and acquired using BD FACS Fortessa and BD FACS Aria II Cell Sorter. Dead cells were excluded using the Zombie UV™ Fixable Viability Kit (Cat# 423108, Biolegend). All the data were analyzed with FlowJo 10.1 software.
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8

Multiparametric Flow Cytometry Analysis

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Human or mouse cells were harvested and Fc receptors of cells were blocked with anti-CD16/32 (BioLegend) or human IgG (Sigma-Aldrich) for 10 min followed by staining of cells for 15 min at room temperature. For intracellular staining, cells were fixed in 2% formaldehyde and then permeabilized using the Perm/Wash buffer kit (BD Biosciences) followed by antibody incubation. Monoclonal antibodies used for flow cytometry include the following: anti–c-Kit, anti-Sca1, anti-CD48, anti-CD150, anti-Flt3 ligand, anti-CD3, anti-TER119, anti–Gr-1, and anti-B220 (BioLegend) for mouse studies and anti-CD68 (BioLegend), anti-CD163 (Biolegend), and anti-206 (eBioscience) for human studies. Rabbit antitrimethylated H3K4 (Abcam) and antitrimethylated H3K27 (Millipore) were used to detect histone marks, followed by secondary stain with FITC-AffiniPure goat anti-rabbit IgG (Jackson ImmunoResearch). All populations were routinely back gated to verify purity and gating. Samples were analyzed on an LSR II (BD Biosciences). One million viable cells were analyzed. Data were analyzed using FlowJo software version 9.0 (Tree Star, Inc.) and compiled using Prism (GraphPad Software).
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9

Murine Hematopoietic Stem Cell Isolation

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Bone marrow cells from the femur and tibia were flushed with PBS. After hemolysis of blood or bone marrow samples, the cells were counted using an Abbott Cell Dyn 3700 machine. The cells were then labeled using the following antibodies: anti-Lin + (MACS), anti-c-Kit (BioLegend), anti-Sca1 (Thermo Fisher), anti-IL7R (BD Bioscience), anti-CD3 (BioLegend), anti-B220 (Thermo Fisher), anti-Gr1 (BioLegend), and anti-FLK2 (Thermo Fisher). Data acquisition was performed on a FACSCanto II (BD Biosciences), and the data were analyzed with FlowJo software.
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