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6 protocols using alexa fluor 488 goat α mouse igg

1

Chromatin Regulation Assays Using Antibodies

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The following chemicals were used in this study: flavopiridol (F3055, Sigma-Aldrich), radicicol (R-370, Alomone), sodium salicylate (S3007, Sigma-Aldrich), copper sulphate (102790, Merck).
The following primary antibodies were used in this study: α-mouse RNA polymerase II CTD repeat (Abcam, ab817), α-mouse RNA polymerase II CTD repeat phosphor S5 (Abcam, ab5408), α-rabbit RNA polymerase II CTD repeat phospho S2 (Abcam, ab5095), α-rat RNA polymerase II CTD repeat phosphor S2 (Active Motif, Cat#61083), α-rabbit HSF (gift from John Lis), α-rabbit Polyhomeotic (Paro lab stock), α-rabbit Pleiohomeotic (gift from Judith Kassis), α-rabbit Pleiohomeotic (gift from Jurg Muller), α-mouse FLAG (Sigma, F1804), α-rat HA (Roche, 11 867 423 001).
The following secondary antibodies were used in this study: α-mouse IgG HRP-linked whole antibody (GE Healthcare, NA931), α-rabbit IgG HRP-linked whole antibody (GE Healthcare, NA934V), α-rat IgG HRP-linked whole antibody (GE Healthcare, NA935V), Goat α-mouse IgG Alexa Fluor 488 (Thermo Fisher Scientific, A-11001), Goat α-rabbit IgG Alexa Fluor 568 (Thermo Fisher Scientific, A-11011).
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2

Antibody Characterization for Yeast Protein Analysis

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Polyclonal Smt3 (1:5,000), Slx5 (1:5,000), and Cdc48 (1:5,000) antibodies were raised in rabbits and have been described previously72 (link)–74 (link). Monoclonal antibodies directed against the HA epitope (1:1,000; 3F10) and monoclonal antibody against GFP (1:1,000; B-2) were purchased from Roche and Santa Cruz Biotechnology, respectively. Mouse monoclonal antibodies against Dpm1 (1:2,000; 5C5A7) and Pgk1 (1:5,000; 22C5D8) were obtained from Invitrogen. Mouse monoclonal antibodies against phospho-H2AX (Ser139) (1:1,000, JBW301) were obtained from Merck Millipore. Rabbit polyclonal antibodies against Nucleophosmin (1:100, ab15440) and Rad53 (1:1000, ab104232) or peroxidase antiperoxidase (1:1,000, p1291) were purchased from Abcam and Sigma-Aldrich, respectively. Secondary antibodies goat-α-mouse IgG Alexa fluor 488 (1:5,000; A11001) and donkey-α-rabbit IgG Alexa fluor 568 (1:5,000; A10042) were obtained from Thermo Fisher Scientific.
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3

Antibody Validation for Protein Studies

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Antibodies against the following proteins (for immunostaining, western blotting, or IPs) were used in this study as described previously: SMG674 (link), UPF175 (link), and CTIF68 (link).
The purchased antibodies against the following proteins are listed in the format “protein name (catalog number, supplier)”: FLAG (DYKDDDDK; 14793, Cell Signaling Technology or A8592, Sigma-Aldrich), Myc (9E10; OP10L, Calbiochem or 2272, Cell Signaling Technology), FTO (ab124892, Abcam), GFP (sc-9996, Santa Cruz Biotechnology), DCTN1 (p150glued; 610474, BD Biosciences), eEF1A1 (CBP-KK1; EF1α; 05-235, Merck Millipore), YTHDF1 (17479-1-AP, Proteintech), YTHDF2 (24744-1-AP, Proteintech), YTHDF3 (sc-377119, Santa Cruz Biotechnology), METTL3 (15073-1-AP, Proteintech), METTL14 (HPA038002, Sigma-Aldrich), p-(S/T)Q ATM/ATR substrate (2851, Cell Signaling Technology), m6A (#202003, Synaptic Systems), m1A (D345-3, MBL), puromycin (12D10; MABE343, Merck Millipore), β-actin (A5441, Sigma-Aldrich), GAPDH (LF-PA0212, AbFrontier), α-tubulin (sc-53030, Santa Cruz Biotechnology), γ-tubulin (sc-17788, Santa Cruz Biotechnology), dynein (sc-9115, Santa Cruz Biotechnology), G3BP1 (13057-2-AP, Proteintech), IMPβ (A301-803A-1, Bethyl Laboratories), Alexa Fluor 488 goat α-mouse IgG (A-11017, Invitrogen), and rhodamine-conjugated goat α-rabbit IgG (31670, Invitrogen).
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4

Immunohistochemical Analysis of Pancreatic Islets

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Pancreata were harvested and fixed in 4% PFA. Paraffin embedding, sectioning, and slide preparations were done in the SBP Histopathology Core Facility. Sections were stained with the following antibodies; α-glucagon (Abcam, K79bB10), α-PDIA1 (Proteintech, 11245–1-AP), α-proinsulin (HyTest Ltd., 2PR8, CCI-17), and DAPI (Fisher Scientific). Guinea pig polyclonal α-insulin antibody was produced in-house. For secondary antibodies, Alexa Fluor 488 goat α-rabbit IgG, Alexa Fluor 488 goat α-mouse IgG, Alexa Fluor 594 goat α-mouse IgG, and Alexa Fluor 594 goat α-guinea pig IgG antibodies were used (Invitrogen). Images were taken by Zeiss LSM 710 confocal microscope with a 40X objective lens. Scale bar, 20 µm.
For ß cell area measurement, pancreata were harvested, fixed in 4% PFA and embedded in paraffin. Three sections were prepared at 200 µm intervals for each pancreas and stained with guinea pig polyclonal insulin antibody and DAPI. Alexa Fluor 594 goat α-guinea pig IgG was used as a secondary antibody. Images were taken by an Aperio FL Scanner (Leica). Insulin stained ß cell area, islet area, and pancreas area were measured by Aperio Imagescope software.
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5

Immunofluorescence Staining of Embryos

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Fixed embryos were rehydrated in 1 × PBS/0.5% Triton X-100 (PBSTx) and blocked with PBSTx/1% BSA/0.1% DMSO for 3 h. The embryos were then incubated with primary antibodies and secondary antibodies diluted in blocking solution for 2 h. Primary antibodies for GFP (IgG2a mouse monoclonal, Life technology), ZsYellow (anti-RCFP rabbit polyclonal antibody, Clontech), Nkx2.5 (Thermo Fisher, US) and Stat4 (Sigma, US) were incubated at a 1:50 dilution. Secondary antibodies (Alexa Fluor 488 goat α-mouse IgG, Alexa Fluor 546 goat-rabbit IgG (Invitrogen) were used at a 1:500 dilution.
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6

TBX1 Transcription Factor Localization

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Jeg3 cells were grown in 10% FBS in DMEM, trypsinized and plated onto 6-well plates. Cells were transfected 24 hours later with 500 ng of Tbx1-pcDNA3.1, F148Y Tbx1-pCDNA3.1, H194Q Tbx1-pcDNA3.1, or G310S Tbx1-pcDNA3.1, and lipofectamine LTX (Invitrogen). Cells were fixed with 4% paraformaldehyde and 4% sucrose 48 hours later, for 15 minutes at room temperature. Cells were permeabilized with 0.3% Triton X-100 and blocked with 10% BSA/PBS for 30 minutes at 37°C. Cells were then incubated with rabbit polyclonal α mouse TBX1 1∶500 (Zymed) for two hours at 37°C and then with Alexa Fluor 488 goat α mouse IgG (Invitrogen) and DAPI stain (1∶500) for one hour at 37°C.
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