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9 protocols using mouse anti ha 6e2

1

Schizont Development and Protein Analysis in Synchronized Malaria Parasites

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Parasites were synchronized, washed, and split into two cultures with and without aTc, as previously described. Synchronous parasites were then allowed to develop into mature schizonts to be then incubated with E64 for 4 hours at 37 °C. After treatment, culture pellets were treated with ice-cold 0.04% saponin in 1x PBS to isolate parasites from host cells. The parasite pellets were subsequently solubilized in protein loading dye with Beta-mercaptoethanol (LI-COR Biosciences) and used for SDS-PAGE.
Primary antibodies used in this study included mouse-anti-HA (6E2; Cell Signaling Technology; 1:2000), rabbit-anti-PfEF1α (from Daniel Goldberg, 1:2000), mouse-anti-RAP1 (2.29; from Jana McBride via the European Malaria Reagent Repository; 1:500) (Hall et al. 1983), mouse-anti-RON4 (10H11; from Alan Cowman; 1:500) (Richard et al. 2010), mouse-anti-MSP1 (12.4; from Jana McBride via the European Malaria Reagent Repository; 1:500) (McBride, Newbold, and Anand 1985). Secondary antibodies used were IRDye 680 CW goat-anti-rabbit IgG and IRDye 800CW goat-anti-mouse IgG (Li-COR Biosciences; 1:20 000). Membranes were imaged using the Odyssey Clx Li-COR infrared imaging system (Li-COR Biosciences). Images were processed and analyzed using ImageStudio (Li-COR Biosciences).
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2

Immunofluorescence Assay Protocol for Malaria

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Cells were fixed using a mixture of 4% paraformaldehyde and 0.015% glutaraldehyde and permeabilized with 0.1% Triton-X100 as described previously62 (link). Primary antibodies used for IFAs in this study were the following: mouse anti-MSP1 antibody (European Malaria Reagent Repository, 1:500), rat anti-PfBiP MRA-1247 (BEI Resources, NIAID, NIH, 1:100) and mouse anti‐HA(6E2) (Cell Signaling Technology Inc., 1:100). Anti-mouse and anti-rat antibody conjugated to Alexa Fluor 488 or Alexa Fluor 546 (1:100, Life Technologies, Thermo Fisher Scientific, Waltham, MA, USA) were used as secondary antibodies. Cells were mounted on ProLong Gold with 4′,6′-diamidino-2-phenylindole (DAPI) (Thermo Fisher Scientific, Waltham, MA, USA) and imaged using a Delta-Vision II microscope system with an Olympus IX-71 inverted microscope using a 100 × objective A. Image processing, analysis and display were preformed using DeltaVision softWoRx software version 7.0.0 (GE Healthcare Life Sciences) and Adobe Photoshop 21.2.0 (https://www.adobe.com/products/photoshop.html). Adjustments to brightness and contrast were made for display purposes.
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3

Immunoblotting Antibodies for Protein Detection

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The primary antibodies used in this study were affinity-purified rabbit polyclonal anti-InlC (R134) (16 (link)), mouse antiubiquitin (catalog number 3936; Cell Signaling Technology), rabbit anti-SUMO1 (catalog number 4930; Cell Signaling Technology), mouse anti-ISG15 (F-9, catalog number sc166755; Santa Cruz Biotechnology), mouse anti-HA (6E2, catalog number 2367; Cell Signaling Technology), rabbit anti-HA (C29F4; Cell Signaling Technology), mouse antiactin (AC-15; Sigma-Aldrich), rabbit anti-S100A9 (catalog number pab0423-P; Covalab), and mouse anti-NF-κB-p65 (F6; Santa Cruz).
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4

Quantitative Analysis of Epigenetic Regulators

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Transduced primary cortical neurons (24-well, 7 d after viral delivery) or transduced tissue samples (4 weeks after viral delivery) were lysed in 50 μl of ice-cold RIPA buffer (Cell Signaling) containing 0.1% SDS and proteases inhibitors (Roche, Sigma). Cell lysates were sonicated for 5 min in a Bioruptor sonicater (Diagenode) and protein concentration was determined using the BCA Protein Assay Kit (Pierce Biotechnology, Inc.). Protein lysates were dissolved in SDS-PAGE sample buffer, separated under reducing conditions on 4–15% Tris-HCl gels (Bio-Rad) and analyzed by western blotting using primary antibodies: rabbit anti-Dnmt3a (H-295, Santa Cruz, 1:500), mouse anti-Dnmt1 (60B1220.1, Novus Biologicals, 1:800), rabbit anti-MeCP2 (07-013, Millipore, 1:400), mouse anti-HA (6E2, Cell Signaling, 1:400) rabbit anti-Tubulin (AA2, Sigma, 1:10,000) followed by secondary anti-mouse and anti-rabbit HRP antibodies (Sigma-Aldrich, 1:10,000). GAPDH was directly visualized with rabbit HRP coupled anti-GAPDH antibody (14C10, Cell Signaling, 1:10,000). Tubulin or GAPDH served as loading control. Blots were imaged with ChemiDoc MP system with ImageLab 4.1 software (Bio-Rad), and quantified using ImageJ software 1.48 h.
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5

Immunofluorescence Assay for Protozoan Parasites

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Parasites were fixed for IFA using 4% Paraformaldehyde and 0.03% glutaraldehyde, then permeabilized with 0.1% Triton-X100. Primary antibodies used were rat-anti-HA 3F10 (Roche, 1:100), mouse-anti-HA 6E2 (Cell Signaling Technology, 1:100), mouse-anti-V5 TCM5 (eBioscence, 1:100), rabbit-anti-V5 D3H8Q (Cell Signaling Technology, 1:100), and mouse-anti-PfPMV (from D. Goldberg 1:1). Secondary antibodies used were Alexa Fluor 488 and Alexa Fluor 546 (Life Technologies, 1:100). Cells were mounted to slides using ProLong Diamond with DAPI (Invitrogen). Fixed and stained cells were imaged using a DeltaVision II microscope system with an Olympus IX-71 inverted microscope. Images were collected as a Z-stack and deconvolved using SoftWorx, then displayed as a maximum intensity projection. Images were processed using Adobe Photoshop, with adjustments made to brightness and contrast for display purposes.
For imaging of parasite cultures using light microscopy, aliquots of culture were smeared onto glass slides and field-stained using Hema3 Fixative and Solutions (Fisher Healthcare), which is comparable to Wright-Giemsa staining. Slides were imaged using a Nikon Eclipse E400 microscope with a Nikon DS-L1-5M imaging camera. To measure parasite size, images were taken and parasites measured using ImageJ (NIH).
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6

Western Blot Analysis of Parasite Proteins

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Western blots were performed as previously described [55 (link)]. Briefly, ice-cold 0.04% saponin in 1x PBS was used to isolate parasites from host cells. Parasite pellets were subsequently solubilized in protein loading dye to which Beta-mercaptoethanol had been added (LI-COR Biosciences) and used for SDS-PAGE. Primary antibodies used in this study were rat-anti-HA 3F10 (Roche, 1:3000), mouse-anti-HA 6E2 (Cell Signaling Technology, 1:1000), rabbit-anti-HA 715500 (Thermofisher, 1:100), mouse-anti-V5 TCM5 (eBioscence, 1:1000), rabbit-anti-V5 D3H8Q (Cell Signaling Technology, 1:1000), rabbit anti-PfBiP MRA-1246 (BEI resources, 1:500), rabbit-anti-PfEF1α (from D. Goldberg, 1:2000), and mouse-anti-PfPMV (from D. Goldberg 1:400). Secondary antibodies used were IRDye 680CW goat-anti-rabbit IgG and IRDye 800CW goat-anti-mouse IgG (Li-COR Biosciences, 1:20,000). Membranes were imaged using the Odyssey Clx Li-COR infrared imaging system (Li-COR Biosciences). Images of membranes were processed using ImageStudio, the Odyssey Clx Li-COR infrared imaging system software (Li-COR Biosciences). Densitometry analysis of western blot signal was also performed using ImageStudio (Li-COR Biosciences).
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7

Immunofluorescence and TEM Imaging Protocols

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All procedures (TEM and Immunofluoresence) were performed as previously described [14 (link), 15 (link)]. The primary antibodies used in this study were: mouse anti-elav (9F8A9, 1:200, Developmental Studies Hybridoma Bank); mouse anti-Crumbs (Cq4, 1:100, Developmental Studies Hybridoma Bank), rabbit anti-aPKC ζ (zeta) (1:200, SAB4502380 Sigma), mouse anti-HA (6E2, 1:500, Cell Signaling), mouse anti-myc (9B11, 1:500 Cell Signaling), rat anti-Crumbs (1:500) [73 (link)], mouse anti-armadillo (N2 7A1, 1:100, Developmental Studies Hybridoma Bank). The C-terminal peptide KVNKLISRFEGGRPRLC (produced in the laboratory of Dr. Charles Zuker) was used as the antigen in rabbits, and the resulting antibody was used at a concentration of 1:200. Fluorescent conjugated secondary antibodies were obtained from either Jackson ImmunoResearch Laboratories or Life Technologies. Rhodamine or Alexa Fluor 647 conjugated phalloidin (1:200, Life Technologies) were utilized for the detection of F-Actin. Confocal images were captured on a Leica TCS SP5. TEM imaging was conducted with a JOEL 1010 and JOEL 1400. All images were processed in Adobe Photoshop.
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8

Detection of Protein Markers in Cells

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Primary antibodies were mouse anti-Myc (9B11) (Cell Signaling Technology), rabbit anti-FLAG (F7425) (Merck), mouse anti-HA (6E2) (Cell Signaling Technology), rabbit anti-human GPVI cytoplasmic tail [46 (link)], mouse anti-human GPVI (11A7) [47 (link)], mouse anti-human GPVI (336A9) (Bernhard Nieswandt, unpublished), mouse anti-human ADAM10 (11G2) (a gift from Eric Rubinstein, Paris, France) [47 (link)] and control mouse IgG1 (MOPC-21) (MP Biomedicals).
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9

Protein Extraction and Western Blotting

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Cells were collected by centrifugation, washed once with water and disrupted by bead beating with a FastPrep 24 (MP Biomedicals) in 50 mM Tris-HCl pH 7.5 containing 0.5 mM EDTA, 1 mM PMSF and complete protease inhibitors (Roche). Proteins were solubilized by addition of 1.5% SDS and incubation at 65 C for 5 min. Lysates were cleared at 16,000 g at 4 C for 2 min and protein concentrations were determined with the BCA assay kit (Thermo Scientific Pierce). Equal amounts of protein were resolved by SDS-PAGE and transferred onto nitrocellulose membranes. Membranes were probed with primary and HRP-coupled secondary antibodies and incubated with homemade ECL. Chemiluminescence was detected with an ImageQuant LAS 4000 imaging system (GE Healthcare). Images were quantified with ImageJ and processed with Adobe Photoshop. Antibodies were mouse-anti GFP 7.1/13.1 (Roche), mouse anti-mCherry 1C51 (Abcam) for detection of Luciferase-mCherry, rabbit anti-mCherry (Biovision) for detection of R-mCherry-sfGFP, rabbit anti-Sec61 (Peter Walter, UCSF), mouse anti-Pgk1 22C5 (Abcam), mouse anti-Pho8 1D3A10 (Abcam), mouse anti-FLAG M2 (Sigma), mouse anti-HA 6E2 (Cell Signaling) for detection of CFTR-HA, and rat anti-HA 3F10 (Roche) for detection of HA-tagged Roq1.
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