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8 protocols using anti human igm

1

In vitro T-B Cell Co-culture Assay

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For co-cultures of in vitro polarized T cells (Fig. 4f–h and Extended Data Fig. 5g–i). CD4 T cells were purified using MACS (Miltenyi Biotec) from healthy donor PBMCs and cultured in the presence of plate-bound anti-CD3 (OKT3, 10 μg ml−1) and anti-CD28 (CD28.2, 5 μg ml−1) antibodies in complete RPMI alone (unstimulated control) or with (1) IL-2 (50 ng ml−1), IL-12 (5 ng ml−1) and anti-IL-4 (1 μg ml−1, R&D MAB204-SP) (TH1 conditions); (2) IL-6 (50 ng ml−1) with or without IL-2 (50 ng ml−1); or (3) plasma from HC individuals or individuals with DS (1:2 ratio). After 4 days, T cells were washed and irradiated (5,000 rad) and co-cultured with freshly MACS-sorted naive B cells from the same donor. Cells were co-cultured for 3–6 days in complete RPMI supplemented with IL-21 (50 ng ml−1), IL-2 (50 ng ml−1) and anti-human IgM (5 μg ml−1, Southern Biotech) and collected for flow cytometry. The supernatants were collected for IFNγ ELISA quantification (BioLegend) according to the manufacturer’s instructions.
For T cell–B cell co-cultures from HC donors and donors with DS (Fig. 4i,j), CD4 T cells were MACS-purified and co-incubated with sort-purified CD19+CD38CD27CD11c B cells on the same day. B and T cells were co-cultured for 3 days in complete RPMI supplemented with IL-21, IL-2 and anti-human IgM as above and collected for flow cytometry.
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2

Quantifying Somatic Hypermutation by sIgM Loss

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sIgM loss frequency provides a convenient surrogate assay for SHM (1, 2). To determine fractions of sIgM- cells, 2-5x105 cells were fixed in 3.7% formaldehyde and stained with anti-human IgM (1:500, Southern Biotech), and sIgM- variants quantified by FACS as described [46 (link)]. To establish that selective pressure was not sufficient to affect the frequency of sIgM loss, we assayed loss of mCherry signal posttransduction (S15 Fig). There was modest loss of mCherry expression between days 3 and 7 in the AID-mCherry-CDT1 transductants (decrease from 37.2% to 31.3%), consistent with some selective pressure against AID-mCherry-CDT1 expression, but not sufficient to alter interpretation of the sIgM loss data.
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3

Teriflunomide Impacts EBV Reactivation

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D4 LCLs were treated for 7 days with 6.5 to 70 μg/ml of teriflunomide, added one hour after cells were plated with or without uridine at 3 × 105 cells/ml. Growing D4 LCLs were expanded into fresh medium supplemented with drugs as needed. All D4 LCLs were given fresh teriflunomide on day 3, day 5 (Figure 3C only), and day 6.5. M81-Luc LCLs, Mutu I, and Kem I cells at 2–5 × 105 cells/ml were treated for 3 days with 6.5 to 50 μg/ml teriflunomide, 150 μM uridine, or 0.1% DMSO control, on day 0 only, and were not expanded. The following reagents were added one hour after teriflunomide treatment to induce lytic EBV reactivation: phorbol 12-myristate 13-acetate (TPA; 20 ng/ml; Sigma-Aldrich), sodium butyrate (3 mM; Sigma-Aldrich), anti-human IgG (10 μg/ml; Sigma-Aldrich), anti-human IgM (6.8 μg/ml; Southern Biotech), or TGFβ (5 ng/ml; R&D Systems). HONE-Akata cells were treated with TPA and sodium butyrate as above on day 0 and were collected on day 3.
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4

SARS-CoV-2 RBD-Specific Antibody Assay

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RBD-specific antibodies were measured generally according to the protocol developed in the Krammer Lab18 (link). Briefly, 384-well MaxiSorp plates (Thermo Fisher Scientific) were coated with purified recombinant RBD at concentration of three μg per ml in PBS. The coating volume and reaction volumes were 25 μl per well. Plates were incubated overnight at 4 °C, washed 3 × with PBS-Tween20, and blocked with PBS containing 3% dry milk for one hour at room temperature. Blocking buffer was removed, and samples (one log dilutions in blocking buffer, 5 × 101–5 × 104) were added to the wells. Plates were incubated for two hours at room temperature before washing three times. Horse radish peroxidase conjugated to anti-human IgG FC (Southern Biotech) or anti-human IgM (Southern Biotech) was diluted 1:2000 in PBS containing 1% dry milk, added to the wells, and incubated at room temperature for 1 h. Plates were washed five times and developed with tetramethyl-benzidine (Southern Biotech). After 30 min, development was stopped by adding 25 μl of 2 N H2SO4 to each well. Absorbance was measured at 450 nm. The end point dilution titer is the serum dilution that results in an absorbance of 0.2 absorbance units over background.
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5

Quantification of Isotype-specific Antibodies

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Biotinylated Goat F(ab)2 anti-human isotype antibodies (anti-human IgM, SouthernBiotech, Cat # 2022-01; anti-human IgA, SouthernBiotech, Cat # 2052-01, and anti-human IgG, SouthernBiotech, Cat # 2042-01) were conjugated on to selected peaks of Streptavidin coated 4um polystyrene capture beads, respectively, and incubated with 0.75x serial dilutions of purified polyclonal human antibodies (IgG, SouthernBiotech, Cat # 0150-01; IgM, SouthernBiotech, Cat # 0158L-01; IgA, SouthernBiotech, Cat # 0155K-01) at known concentrations. Standard curves were obtained based on MFI detected by secondary antibodies bound using CytoFLEX cytometer. Flow cytometry standard (FCS) files of both samples and the standard curve were applied to a set of MATLAB programs (https://github.com/UAB-Immunology-Institute/cba-toolbox) generated by Dr. Rosenberg at UAB for the quantification of peptide-specific antibodies in the corresponding isotype(66 ).
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6

Immune Cell Signaling Pathway Study

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Pacritinib was provided by CTI BioPharma Corp. (Seattle, WA, USA). Ruxolitinib, fedratinib, and momelotinib were obtained from Selleckchem (Houston, TX, USA). Primary human endothelial cells (HuVEC), neonatal foreskin fibroblasts (HDFn), bronchial epithelial cells (BE), coronary arterial smooth muscle cells (CASMC), and keratinocytes (HEK) were obtained from Lonza, Lifeline Cell Technologies and Cell Applications. Peripheral blood mononuclear cells (PBMCs) and positively selected primary normal human CD19+ B cells, CD4+ T cells, and CD14+ monocytes were purchased (AllCells, Emeryville, CA) or were isolated in-house (LeukoPak [StemCell and Physicians Plasma Alliance]). All primary cells were obtained under protocols that were reviewed by Institutional Review Board(s) that operate in accordance with the requirement of EPA Regulation 40 CFR 26 and HHS Regulation 45 CFR 46 of the US Department of Health and Human Resources for the protection of human research subjects. Stimuli include recombinant human IFNγ, TNFα, and IL-1β, IL-4, PDGF, FGF, EGF, and TGFβ (Peprotech, SEB, and TSST [Toxin Technologies]) Histamine, LPS, (Sigma), anti-human IgM (Southern Biotechnology), and Zymosan (Invivogen). Mouse detection antibodies against human biomarkers were obtained from commercial sources, including BD BioSciences, Sigma, and R&D Systems.
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7

Quantifying Plasma IgM and Circulating Interleukins

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For determination of IgM titers in plasma, 96-well plates were coated with 100 μl/well of purified anti-human IgM (Southern Biotech), diluted 1:8000 in 0.05 M carbonate buffer. Detection was performed after washes with PBST and 2 h of incubation with HRP-conjugated anti-human IgM (Southern Biotech) diluted 1:8,000 in blocking solution.
For the determination of circulating interleukins, enzyme-linked immunosorbent assay (ELISA) was performed using Human IL-4 ELISA Set, Human IL-6 ELISA Set and Human IL-10 ELISA Set (BD OptEIATM - BD Pharmingen-U.S.A.), according to manufacturer’s instructions.
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8

Phospho-signaling in Activated B Cells

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Human B cells were isolated as described above and plated at 1× 106 cells/mL in complete RPMI. LY3541860 or isotype control antibody was added at 1 μg/mL, and cells were incubated in the presence of the antibody overnight at 37°C and 5% CO2, after which cells were stimulated with 2 μg/mL anti–human IgM (Southern Biotech, 9022-01) plus 12 μg/mL rabbit anti–mouse IgG (Thermo Fisher Scientific, 31190) for 10 minutes, followed by addition of 1× Lyse/Fix buffer (BD Bioscience) for 5 minutes. Cells were washed, fixed in ice-cold methanol (MilliporeSigma) on ice for 20 minutes, washed in FACS buffer, and stained with anti–pERK1/2-PE (clone MILANBR, Invitrogen) and anti–pAKT (S473)-APC (clone SDRNA, Invitrogen) antibodies for 1 hour at room temperature. Next, cells were washed twice in FACS buffer, acquired on a BD Fortessa X-20, and results were analyzed using FlowJo software.
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