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6 protocols using anti rps6

1

Western Blot Antibodies for OXPHOS

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Antibodies used for Western blot included the Total OXPHOS Human WB Antibody Cocktail (#ab1104a1; Abcam), anti-Aco2 (#ab110321; Abcam), anti-4E-BP1 (#9644; Cell Signaling) and anti-phospho-4E-BP1 (#2855; Cell Signaling), anti-EF-1α1/2 (#sc-377439; Santa Cruz), anti-Hsp60 (#ab59457; Abcam), anti-Hsp70 (#ab47455; Abcam), anti-Hsp90 (#16F1; Enzo), anti-Mdh2 (#sc-293474; Santa Cruz), anti-Mia40 (#sc-365137; Santa Cruz), anti-rpS6 (#ab40820, Abcam); anti-phospho-rpS6 (#ab65748; Abcam), anti-SMAC (#ab8114; Abcam), anti-Tim22 (#14927-1-AP; Proteintech), anti-ubiquitin (#701339; Thermo Scientific), and anti-VDAC (#sc-390996; Santa Cruz). Total proteins were stained with REVERT Total Protein Stain (#926-11011; LI-COR).
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2

Comprehensive Antibody Catalog for Research

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In this work, the following antibodies were used: primary antibodies: anti-hnRNP UL1 (Abcam #ab68480 or Santa Cruz Biotechnology #sc-393434), anti-FLAG (Sigma #A8592), anti-Actin (MP #691001), anti-Fibrillarin (Santa Cruz Biotechnology #sc-25397), anti-Nucleolin (Abcam #ab22758), anti-FUS (Santa Cruz Biotechnology #sc-47711), anti-γH2A.X (Santa Cruz Biotechnology #sc-517348), anti-RPS6 (Abcam #ab70227), anti-RPS15 (Antikoerper #ABIN2786563), anti-RPA32 (Bethyl Laboratories #A300-245A), anti-pChk1 (Cell Signaling Technology #2341), anti-XRCC1 (Invitrogen #MA5-13412), anti-53BP1 (Abcam #ab175933), anti-Rad50 (Abcam #ab124682), anti-RPA194 (Santa Cruz Biotechnology #sc-46699), normal mouse IgG (Santa Cruz Biotechnology #sc-2025), and anti-digoxygenin-AP Fab fragments (Roche #11093274910); secondary antibodies: goat anti-mouse IgG-horseradish peroxidase (HRP) (Santa Cruz Biotechnology #sc-516102), goat anti-rabbit IgG-HRP (Santa Cruz Biotechnology #sc-2004), anti-mouse Alexa Fluor 555 (Thermo Fisher Scientific #A21422), anti-mouse Alexa Fluor 488 (Thermo Fisher Scientific #A32723), anti-rabbit Alexa Fluor 555 (Thermo Fisher Scientific #A32732) or anti-rabbit Alexa Fluor 488 (Thermo Fisher Scientific #A32731).
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3

Comprehensive Protein Immunoblotting Protocol

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Proteins were separated by standard 10% SDS-PAGE, with samples loaded in Laemmli buffer, transferred for 2h to a PVDF membrane, and immunoblotted using the following antibodies: anti-K63 ubiquitin (1:4,000; EMD Millipore, cat. No. 05–1308, clone apu3); anti-GAPDH (1:4,000; Abcam, cat. No. ab9485); anti-Rps10 (1:6,000, Sigma, cat no. WH0004736M1); anti-Rps6 (1:4,000; Abcam cat no. ab40820), anti-puromycin (1,2:500, EMD Millipore MABE343, clone 12D10), anti HA (1:2,500; Invitrogen, cat no. 71–5500), anti-K48 ubiquitin (1:8,000; Cell Signaling, cat. No 8081).
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4

Whole-Cell Lysate Preparation and Immunoblotting

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Whole-cell lysates were prepared from cells collected in lysis buffer (50 mM Tris pH7.5, 150 mM NaCl, 1 mM EDTA, 1% NP40, 0.5% sodium deoxycholate, 1.0% SDS, 2 mM NaF, 2 mM Na3VO4, and protease inhibitors (Roche) followed by sonication and centrifugation at 13,000g for 10 minutes. Tumor lysates were prepared by homogenizing tumor tissue in lysis buffer and centrifuging at 13,000g for 10 minutes at 4°C. Proteins were quantified using a BCA assay kit, separated by electrophoresis on SDS PAGE gels, and transferred to PVDF membranes. After one hour in blocking buffer (SuperBlock), membranes were incubated overnight with primary antibodies. The following antibodies were used: anti-p-Akt (Cell Signaling), anti-Akt (Cell Signaling), anti-rpS6 (Abcam), anti-p-rpS6 (Abcam), anti-mTOR (Sigma-Aldrich), anti-p-mTOR (Sigma-Aldrich), anti-ERK (Abcam), anti-p-ERK (Abcam), anti-LC3B-II (Abcam), anti-Atg7 (Santa Cruz Biotechnology), anti-Atg12 (Santa Cruz Biotechnology), anti-Beclin-1 (Abcam), anti-C/EBPα (Abcam), anti-PPARγ (Abcam), anti-FABP4 (Abcam), anti-FAS (Abcam), anti-Tubulin (Abcam), and anti-β-Actin (Santa Cruz Biotechnology). The anti-Tubulin and anti-β-Actin were used as controls. Specific protein bands were imaged using secondary antibody conjugated with horseradish peroxidase and chemiluminescent ECL reagents. Image J was used for quantification.
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5

Western Blot Analysis of mTOR Pathway

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Cells were lysed with SDS sample buffer (62.5 mM Tris-HCl, 2% SDS, 2% glycerol). Protein content was determined using the Pierce bicinchoninic acid (BCA) protein assay kit (Thermo Fisher). Whole-cell lysates were subject to immunoblot analysis using anti-MLST8 (GβL) (CST), anti-phospho-4EBP1(T37/46) (CST), anti-4EBP1 (CST), anti-phospho RPS6 (S240/244) (Merck), anti-RPS6 (Abcam), anti-phospho-p70-S6K (T389) (CST), anti-p70-S6K (CST), anti-phospho mTOR (S2448) (CST), anti-mTOR (CST), and anti-tubulin (Sigma) antibodies.
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6

HDA714 Interacts with Ribosomal Proteins in Vivo

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To confirm the interaction between HDA714 and ribosomal proteins in vivo, the proteins were extracted from Nicotiana benthamiana leaves expressing 35Spro:HDA714-GFP/ 35Spro:RPS3-FLAG, 35Spro:HDA714-GFP/35Spro:RPS6-FLAG or 35Spro:HDA714-GFP/35Spro:RPL7a-FLAG constructs using lysis buffer (10 mM Tris/Cl pH 7.5, 150 mM NaCl, 0.5 mM EDTA, 0.5% Nonidet™ P40 Substitute) and then incubated with anti-GFP agarose beads (ChromoTek) for 5 h at 4°C. After three washes with washing/dilution buffer (10 mM Tris/Cl pH 7.5, 150 mM NaCl, 0.5 mM EDTA), the co-immunoprecipitated proteins were separated by SDS-PAGE and detected with anti-GFP (Abmart, 1:1000 dilution) and anti-FLAG (Sigma, 1:1000 dilution) antibodies, respectively. For co-immunoprecipitation, ten-day wild type rice seedlings were ground into power by liquid nitrogen and extracted by lysis buffer (10 mM Tris–HCl pH 7.5, 150 mM NaCl, 0.5 mM EDTA, 0.5% Nonidet™ P40 Substitute) and then incubated with anti-HDA714 (the full length HDA714 protein was used as antigen to produce polyclonal antibodies in rabbit) coated with protein-A magnetic beads (Thermo Fisher Scientific) for 5 h at 4°C. After four washes with PBST buffer, the co-immunoprecipitated proteins were separated by SDS-PAGE and detected with anti-RPS6 (Abcam, 1:1000 dilution) and anti-RPS3 (Abcam, 1:1000 dilution) antibodies.
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