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32 protocols using gfp sc 9996

1

Cell Signaling Pathway Reagent Procurement

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Most chemicals, including dexamethasone, 3-isobutyl-1-methylxanthine, insulin, saponin, cycloheximide (CHX), verteporfin, crystal violet, anti-FLAG M2 affinity gels, Dulbecco's modified Eagle medium (DMEM), and antibodies against vinculin (V4505), β-actin (A2228), α-tubulin (T5168), and FLAG-tag (F1804) were purchased from Sigma-Aldrich (St. Louis, MO, USA). Opti-MEM, Lipofectamine 2000, Lipofectamine RNAiMAX, bovine serum albumin, goat serum, 4′,6-diamidino-2-phenylindole (DAPI), and Alexa Fluor-conjugated secondary antibodies were purchased from Thermo Fisher Scientific (Waltham, MA, USA). Antibodies against PIP5Kα (#9693), PIP5Kγ (#3296), phospho-YAP (Ser127; #4911), YAP (#4912), phospho-LATS1 (Ser909; #9157), LATS1(#9153), phospho-TAZ (Ser89; #59971), TAZ (#4883), Merlin (#6995), HA-tag (#3724), Myc-tag (#2278 and #2276), p44/42 mitogen-activated protein kinase (MAPK, #4695), phospho-p44/42 MAPK (Thr202/Tyr204; #8544), p38 MAPK (#9212), phospho-p38 MAPK (Thr180/Tyr182; #9211), c-Jun N-terminal kinase (JNK, #9258), phospho-JNK (Thr183/Tyr185; #4668), Akt (#9272), and phospho-Akt (Ser473; #9271) were obtained from Cell Signaling Technology (Danvers, MA, USA). Antibodies against lamin B1 (sc-374015), GAPDH (sc-47724), and green fluorescent protein (GFP, sc-9996) were obtained from Santa Cruz Biotechnology (Dallas, TX, USA).
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2

Comprehensive Antibody Inventory for DNA Damage Research

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Anti-FLAG (#2368) and γH2AX (#2577) antibodies were purchased from Cell Signaling Technology, whereas antibodies for BRCA1 (#sc-6954), H1.4 (#sc-393358), RNF8 (#sc-2714620), and GFP (#sc-9996) were from Santa Cruz Biotechnology. Antibodies against α-tubulin (GTX628802) were obtained from GeneTex. Anti-RPA (ab2175), H1.0 (ab11079), H1.2 (ab17677), H1.3 (ab183736), and H1.4 (ab18208) were purchased from Abcam, whereas anti-H1.1 was from Insight Biotechnology (GTX117055). Finally, anti-RPA pS4+pS8 (A300-245A) antibodies were purchased from Bethyl, whereas anti-H3 antibodies were obtained from Sigma-Aldrich (05-928). Goat anti-mouse immunoglobulins/HRP (#P044701-2) and swine anti-rabbit immunoglobulins/HRP (P039901-2) were purchased from Dako. Goat anti-mouse IgG (H + L) secondary antibody, Alexa Fluor 488 (#A10680) and goat anti-rabbit IgG (H + L) cross-adsorbed secondary antibody, and Alexa Fluor 568 (#A11011) were purchased from Thermo Fisher Scientific.
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3

Western Blot Antibodies and Reagents

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The following antibodies were used for western blot: HAX1 (BD Transduction Laboratories: 610825, 1:500), cIAP2 (ABCAM: ab32059, 1:1000), cIAP1 (R&D Systems: AF8171, 1:500), FLAG (F1804, 1:5000), His (H1029, 1:3000), and α-tubulin (T6074, 1:5000) (Sigma-Aldrich Co. LLC.), p100/p52 (#3017, 1:1000), NIK (#4994, 1:1000), and cIAP2 (#3130, 1:1000) (Cells Signaling Technology, Inc.), GFP (sc-9996, 1:1000) and HA (sc-805, 1:1000) (Santa Cruz Biotechnology, Inc.), and ubiquitin (BML-PW8810, 1:100, Enzo Life Science). Recombinant human CD40 ligand/TNFSF5 (617-CL) and recombinant human LIGHT/TNFSF14 (664-LI) were obtained from R&D Systems. Pierce anti-HA agarose (26181) was obtained from Thermo Scientific. Anti-FLAG M2 affinity gels (A2220), 3× FLAG peptide (F4799), anti-c-Myc agarose affinity gels (A7470), cycloheximide (C4859), and MG132 (C2211) were purchased from Sigma-Aldrich Co. LLC. Bortezomib (velcade) (MG-341) and protein G plus/protein A agarose suspension (IP05) were purchased from Merck Millipore. Complete protease inhibitor cocktail (13760700) was purchased from Roche.
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4

Protein Phosphatase and Protease Inhibitor Cocktails

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Protein phosphatase inhibitor and protease inhibitor cocktails were purchased from Sigma-Aldrich. Antibodies for ClpX (ab168338, 1:2000), ClpP (ab124822, 1:1000), VDAC (ab34726, 1:1000), α-Synuclein (ab27766, 1:1000), α-Synuclein (ab138501, 1:3000) and α-Synuclein phosphor S129 (ab168381, 1:1000) were from Abcam. GFP (sc-9996, 1:1000), c-Myc (sc-40, 1:1000), α-Synuclein (sc-12767, 1:1000), Enolase (sc-15343, 1:1000) and HSP60 (sc-13115, 1:2000) were from Santa Cruz Biotechnology. β-Actin (A1978, 1:10000) was from Sigma-Aldrich. TH (MAB318, 1:1000) was from Millipore. ClpP (GTX115070, 1:200) was from Genetex. ClpP (NBP1–89557, 1:200) was from Novus. LonP (15440–1-AP, 1:2000), ERAL1 (11478–1-AP, 1:2000), CHCHD3 (25624–1-AP, 1:1000) and WFS1 (11558–1-AP, 1:1000) were from Proteintech. SOD2 (611580, 1:1000) was from BD bioscience. MFN1 (H00055669-M04, 1:1000) was from Abnova. Sirt3 (5490S, 1:1000) was from cell signaling technology.
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5

Arsenite and Ambroxol Cytotoxicity Assay

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Ammonium chloride (NH4Cl), arsenic trioxide (As2O3) and oleic acid (OA) were purchased from Sigma-Aldrich (Milwaukee, WI, USA); Ambroxol hydrochloride (Amb) and cyclohexylamine were from Santa Cruz Biotechnology (Santa Cruz, CA, USA). An arsenite solution was prepared by dissolving As2O3 in minimal volumes of 1 N sodium hydroxide (NaOH). The arsenite solution (referred to in the manuscript as As III) was then diluted with phosphate buffered saline to a concentration of 10 mM as a stock solution.
For Amb and OA, the desired concentrations were obtained by dissolving Amb in DMSO and OA in ethanol. Other compound solutions were prepared as per the manufacturer's recommendations. The AR (N-20, used at a 1:1000 dilution) and GFP (sc-9996; also used at a 1:1000 dilution) antibodies were purchased from Santa Cruz Biotechnology. The β-catenin antibody (#4270; 1:1000) was purchased from Cell Signaling Technology (Danvers, MA, USA) and the anti-α-tubulin antibody (1:3000) from Sigma-Aldrich; the anti-BCL2 antibody (clone 124; 1:500) was from Dako (Santa Clara, CA, USA).
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6

Immunoprecipitation and Western Blot Analysis

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Cells were lysed and intracellular protein samples were prepared as described [31 (link)]. For immunoprecipitation, concentrated cell culture medium were precipitated with specific antibodies in Co-IP buffer. Cell lysate and precipitated samples were separated by 8–15% SDS-PAGE and transferred to polyvinylidene difluoride membranes. Membranes were incubated with specific primary antibodies and followed by HRP conjugated anti-IgG secondary antibodies. Membranes were developed and visualized by ECL (Advansta, K12045) substrate and MyECL Imager (Thermo Scientific). Flotillin-1 antibody was obtained from BD Bioscience (610821); RIP140 antibody was purchased from Abcam (AB42126); CD9 (SC-13118), β-actin (SC-47778) and GFP (SC-9996) antibodies were obtained from Santa Cruz.
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7

Western blot analysis of skin fibroblasts

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Western blots were performed as previously described (Ramos et al. 2019 (link)). Briefly, cellular extracts and purified protein samples were fractionated on NuPAGE Bis-Tris polyacrylamide gels (Thermo Scientific) followed by transfer to Immobilon FL PVDF membrane (Millipore) for immunoblotting. For analysis of skin fibroblasts, 1 × 106 cells were harvested and proteins were extracted using radioisotope immunoprecipitation assay (RIPA) buffer (50 mM TrisHCl, pH 7.5, 1% NP-40, 0.5% sodium deoxycholate, 0.1% SDS, 150 mM NaCl, 2 mM EDTA). Antibodies were against the following proteins : 6xHis tag (MA1-21315, Thermo Fisher), GFP (sc-9996, Santa Cruz Biotechnology), Strep-tag II-tag (NC9261069, Thermo Fisher), ADAT3 (Abcam, ab192987), ADAT3 (H00113179-B01P, Abnova), ADAT2 (ab135429, Abcam), and actin (CST). Primary antibodies were detected using IRDye 800CW Goat anti-Mouse IgG (SA5-35521, Thermofisher) or Rabbit (SA5-35571, Thermofisher) or Rat (925-32219, LI-COR Biosciences), or IRDye 680RD Goat anti-Mouse IgG (926-68070, LI-COR Biosciences) or Rabbit (925-68071). Immunoblots were scanned using direct infrared fluorescence via the Odyssey System (LI-COR Biosciences).
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8

Antibody panel for mitochondrial proteome

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Protein phosphatase inhibitor and protease inhibitor cocktails were purchased from Sigma–Aldrich. Antibodies for ClpX (ab168338, 1:2000), ClpP (ab124822, 1:1000), VDAC (ab34726, 1:1000), α-Synuclein (ab27766, 1:1000), α-Synuclein (ab138501, 1:3000) and α-Synuclein phosphor S129 (ab168381, 1:1000) were from Abcam. GFP (sc-9996, 1:1000), c-Myc (sc-40, 1:1000), α-Synuclein (sc-12767, 1:1000), Enolase (sc-15343, 1:1000) and HSP60 (sc-13115, 1:2000) were from Santa Cruz Biotechnology. β-Actin (A1978, 1:10000) was from Sigma–Aldrich. TH (MAB318, 1:1000) was from Millipore. ClpP (GTX115070, 1:200) was from Genetex. ClpP (NBP1-89557, 1:200) was from Novus. LonP (15440-1-AP, 1:2000), ERAL1 (11478-1-AP, 1:2000), CHCHD3 (25624-1-AP, 1:1000) and WFS1 (11558-1-AP, 1:1000) were from Proteintech. SOD2 (611580, 1:1000) was from BD bioscience. MFN1 (H00055669-M04, 1:1000) was from Abnova. Sirt3 (5490S, 1:1000) was from cell signaling technology.
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9

Immunoprecipitation of mCherry-SidJ and GFP-SdeA

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HEK293 cells were co-transfected transiently with mCherry-SidJ (pmCherry-C1 vector) and either GFP (pEGFP-C1 vector) or GFP-SdeA (pEGFP-C1) using polyethylenimine. Cells were harvested at 18 h post-transfection, washed with PBS (phosphate-buffered saline), and lysed in immunoprecipitation buffer (50 mM Tris-HCl pH 7.5, 150 mM NaCl, 1% Triton X-100, and protease inhibitor cocktail (cOmplete Mini EDTA-free from Roche) and mixed with GFP-Trap Agarose beads (ChromoTek) and incubated for 2 h at 4 °C while being subjected to end-to-end rotation. The beads were washed three times with the immunoprecipitation buffer. Finally, proteins were eluted by boiling with 4x Laemmli buffer for 10 min, then separated through SDS-PAGE, and visualized following western blot. The Antibody used for mCherry detection was DSRed2 sc-101256 with a dilution of 1:1000 (Santa Cruz Biotechnology), and GFP was detected with GFP sc-9996 and a dilution of 1:2000 (Santa Cruz Biotechnology). The raw western blot image is available in the supplementary information file.
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10

Mitochondrial Fractionation and Analysis

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Mitochondria-enriched fractionation was performed using the Mitochondria Isolation Kit (Thermo Scientific, Pittsburgh, PA, USA) according to the manufacturer’s instructions. The fractions were examined by Western blot analysis using anti-green fluorescent protein (GFP) (SC-9996, Santa Cruz Biotechnology, Santa Cruz, CA, USA), cytochrome c oxidase (COX) IV (#4850, Cell Signaling Technology, Beverly, MA, USA) and glyceraldehyde-3-phosphate dehydrogenase (GAPDH, KC-5G4, Kangchen Biotechnology, Shanghai, China) antibodies.
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