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33 protocols using rabbit anti ha

1

Isolating PfArp4 and PfArp6 proteins

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Synchronized parasites at a parasitaemia level of 2–3% were collected and lysed with 0.15% saponin. After washing twice with 1% PBS, the cells were resuspended in 1× SDS loading buffer (Bio-Rad, Hercules, CA, USA). Since the molecular weight of PfArp4 and PfArp6 is approximately 62 kDa and 121 kDa, respectively, an 8% SDS-PAGE gel was used to isolate the proteins. The antibodies used in the experiment were rabbit anti-HA (1:2000; Abcam, Cambridge, UK), mouse anti-Ty1 (1:1000; Sigma-Aldrich), and rabbit anti-PfAldolase (1:1000; Abcam, Cambridge, UK). An ECL western blot kit (GE Healthcare, Atlanta, GA, USA) was used to develop the blots.
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2

Immunofluorescence Staining of Cells

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Cells were fixed in 4% paraformaldehyde (GIBCO) for 12 min and permeabilized with 0.1% Triton X-100 for 5 min. They were then blocked with 5% normal donkey or goat serum (Sigma) for 30 min and incubated with primary antibodies overnight at 4°C. The following primary antibodies were used: Mouse anti-HA 1:400 (Sigma), Rabbit anti-HA (1:800), Chicken anti-NF200 (1:10,000), Rat anti-MBP 1:400 (Abcam), Rabbit anti-Brn3a 1:500 (Millipore), Phalloidin-TRITC conjugate 1:150 (Sigma). Cells were washed 3X with 0.1% PBS-TX before the species appropriate Alexa Fluorophore secondary antibodies were applied (all 1:1000). Coverslips were mounted with VECTASHIELD Antifade Mounting Medium (Vector Laboratories). Immunostaining was visualized using a confocal microscope (Zeiss LSM 700) and images were acquired using the Zen Black software.
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3

Immunoblotting protocol for protein detection

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For immunoblotting, gels were transferred to nitrocellulose membranes, blocked for 1 h at room temperature with 5% BSA in Tris-buffered saline with 0.1% Tween 20 (TBST) for anti-G3BP1PS149 and Streptavidin-HRP or with 5% milk in TBST for anti-CK2α, anti-G3BP1, anti-HA, and anti-GAPDH antibodies. Primary antibodies diluted in appropriate blocking buffer and incubated on membranes overnight incubation at 4°C with rocking. Primary antibodies consisted of: mouse anti-CK2α (1:1,000; Abcam), rabbit anti-G3BP1 (Sigma, 1:2,000), rabbit anti-G3BP1PS149 (Sigma, 1:1,000), rabbit anti-HA (1:5,000; Abcam), and rabbit anti-GAPDH (1:5,000; Cell Signaling Tech). After washing in TBST, blots were incubated HRP-conjugated anti-rabbit IgG antibodies (1:5,000; Jackson ImmunoRes) diluted in blocking buffer for 1 h at room temperature. For Biotinylated proteins Streptavidin-HRP (Abcam, 1:10,000) was used. After liberally washing in TBST, immunocomplexes were detected using ECL PrimeTM (GE Healthcare).
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4

Western Blot Analysis of Viral Proteins

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Cell lysates were prepared in lysis buffer (150 mM NaCl, 50 mM Tris, 0.5% NP-40, 1 mM dithiothreitol [DTT], and protease inhibitor tablets) and quantified by Bradford assay. Equivalent amounts of each sample were resolved by SDS-PAGE and Western blotted with the following antibodies at 1:1,000 in TBST (Tris-buffered saline, 0.1% Tween 20): rabbit anti-ORF20 (Yenzym) rabbit anti-DHX9/RNA helicase A (Abcam), rabbit anti-glyceraldehyde-3-phosphate dehydrogenase (GAPDH) (Abcam), rabbit anti-vinculin (Abcam), and rabbit anti-HA (Abcam) antibodies. The rabbit anti-ORF59 and anti-K8.1 antibodies were used at 1:10,000 and 1:50,000, respectively, and were a gift from the Glaunsinger lab. Primary antibody incubations were followed by horseradish peroxidase (HRP)-conjugated goat anti-mouse or goat anti-rabbit secondary antibodies (Southern Biotechnology, 1:5,000).
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5

Expression Analysis of PfSWIB Fusion System

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To analyze the expression of the PfSWIB fusion system in integrated parasites lines, total parasite extracts were prepared by treatment with 0.15% saponin and re-suspended in SDS-loading buffer (Bio-Rad), then separated on a 12% SDS-PAGE gel (Bio-Rad) and subjected to western blot analysis. Total proteins from the 3D7 clone were used as controls. An antibody to aldolase (1:1000 dilution; Roche, Indianapolis, USA) was used as a positive control. Rabbit anti-HA (1:1000 dilution; Abcam, Cambridge, UK) was used to identify PfSWIB fusion proteins in different parasite lines. An enhanced chemiluminescence (ECL) western blotting kit (GE Healthcare, Uppsala, Sweden) was used to develop western blots. The theoretical molecular weight of endogenous PfSWIB, HA tag and HA-FKBP-LID tag is 92kD, 3.5kD and 22kD, respectively. The gray-level image analysis procedure was implemented with ImageJ software. Statistical significance was determined (*P < 0.05, **P < 0.01).
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6

Immunolabeling of Adult Fly Brain

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An adult fly brain was prepared and imaged as previously described21 (link). The dissected brain was incubated with primary antibody at 4 °C for two days, and the dilution ratios were 1:10 for mouse 4F3 anti-DLG (Hybridoma Bank, University of Iowa), 1:500 for rabbit anti-HA (Abcam), and 1:500 for rabbit anti-GFP (Invitrogen). The secondary antibody solution with the fly brain was incubated at room temperature overnight, and the dilution ratio was 1:200 for biotin-conjugated goat anti-mouse IgG (Invitrogen) and biotin-conjugated goat anti-rabbit IgG (Invitrogen), and then the fly brain was labeled by 1:200 dilution with Alexa Fluor 635 streptavidin (Invitrogen) at room temperature overnight.
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7

Immunofluorescence Imaging of Transfected Cells

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HepG2 cells (a gift from Pingsheng Liu’s laboratory), COS-7 cells, U2OS cells, and HEK293T cells were maintained in DMEM (Invitrogen) supplemented with 10% FBS at 37°C in 5% CO2. Transfections were performed using Lipofectamine 3000 (Invitrogen) for DNA plasmids, except for transfection of plasmids after delipidation, which was performed using X-tremeGENE HP DNA Transfection Reagent (Roche) and Lipofectamine RNAi MAX (Invitrogen) for siRNAs according to the manufacturer’s instructions. Cell samples were harvested 24 h after plasmid transfection or 48 h after siRNA transfection unless otherwise indicated. Immunofluorescence experiments were performed as described previously. Transfected cells were grown on coverslips and immunostained with primary antibodies and various Alexa Fluor–conjugated secondary antibodies (Invitrogen). Images were captured at RT on a 3D–structured illumination microscopy (3D-SIM) or Zeiss LSM700 confocal microscope as indicated. The primary antibodies used are mouse–anti-HA (ORIGENE; TA180128), rabbit–anti-HA (Abcam), rabbit–anti-Myc (Sigma; C3956), mouse–anti-Flag (Sigma), rabbit–anti-calreticulin (Abcam; ab2907), mouse–anti–Climp-63 (Enzo; ENZ-ABS669-0100), rabbit–anti–septin 2 (Abcam; ab187654), and mouse–anti–α-tubulin (Abcam; ab7291).
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8

Investigating Six1-Eya1 Transcriptional Complex

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HEK293T cells were transfected with Lipofectamine 2000 (Invitrogen) for both co-immunoprecipitation and luciferase assay. Co-IP and immunoblot were performed as previously described 50 (link). The antibodies used include mouse anti-HA (Covance), rabbit anti-HA (Abcam), mouse anti-FLAG (Sigma), and rabbit-anti-GFP (Cell signaling). For luciferase assay, each transfection was triplicated with 400 ng wild type or mutant Gen1, 100 ng pCX-EGFP, 200 ng HA-Six1, 200 ng HA-Eya1, and 200 ng Gdnf-luc2. Luciferase activity was scored 48 hours after transfection and calibrated by the percentage of GFP positive cells (determined by FACS). Each experiment was performed at least twice independently.
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9

Western Blot Protein Quantification Protocol

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Western blot for protein quantification was performed using a modified RIPA lysis buffer as previously described (9 (link)). The following antibodies were used for immunodetection: rabbit anti-CBP (clone C-20; Santa Cruz Biotechnologies, Dallas, TX), mouse anti-mouse AcH3K27 (cat # 17–683, EMD Millipore, Billerica, MA), rabbit anti histone H3 (#Ab1791, Abcam, Cambridge, UK), rabbit anti-Gapdh (#G9545, Sigma-Aldrich, St. Louis, MO), rabbit anti-HA (#Ab9110, Abcam), mouse anti-RAC1 (clone 23A8, #05–389, EMD Millipore). Secondary antibodies were rabbit anti-mouse (#816729, Life technologies, Carlsbad, CA) and goat anti-rabbit (#G21234, Life Technologies) coupled to HRP. Quantification by densitometry was performed using ImageJ software (NIH, Bethesda, MD).
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10

Immunoprecipitation of Kir2.1 Channels

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Cells were transfected with FUGW-Kir2.1-extHA-FLAG-SNAP or FUGW-Kir2.1-K334R-FLAG-SNAP 36–48 hr before lysis. Cell lysates were generated as above. All steps were performed at 4°C. For immunoprecipitation (IP), equal amounts of protein (0.5–1.0 mg) of lysate was precleared with Protein A/G magnetic beads (Thermo) for 1 hr. Beads were removed with a strong magnet. Four µg of rabbit anti-HA (Abcam) were added to the cleared supernatant and rotated overnight. The next day, 25 µL of Protein A/G magnetic beads were added and samples were rotated for 1 hr. Beads were collected, washed once in one volume of RIPA buffer, three times in one volume of RIPA buffer containing 500 mM NaCl (instead of 150 mM NaCl) and one final time in RIPA Buffer. Beads were then lysed in 1X sample buffer. The entire eluted volume of the IP was used for a gel.
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