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50 protocols using r0010

1

Co-immunoprecipitation of Flag- and Myc-tagged Proteins

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For co-immunoprecipitation assays, HEK293T cells were harvested and lysed with either TNE lysis buffer [10 mM Tris-HCl (pH 7.5), 150 mM NaCl, 2 mM EDTA and 0.5% Nonidet P-40] or RIPA buffer (R0010, Solarbio) containing a protease inhibitor mixture (1697498001, Roche). Lysates were incubated with anti-Flag-agarose beads (A2220, Sigma-Aldrich) or protein A-Sepharose beads (101041, Invitrogen) at 4°C for 4 h. Beads were washed four times with TNE or RIPA buffer, and bound proteins were then separated by SDS-PAGE and visualized using western blots.
For immunoblotting experiments, we used the following affinity-purified antibodies: anti-Flag (1:1000; Cell Signaling Technology, 2368S), anti-Myc (1:3000; M047-3, MBL), anti-HA (1:3000; CW0092A, CW), anti-β-tubulin (1:5000, CW0098M, CWBIO), anti-p-Thr (1:300; ab9337, Abcam) and anti-p-Ser (1:250; ab9332, Abcam).
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2

Western Blot Analysis of Apoptosis Proteins

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The expression of apoptosis-related proteins was evaluated by Western blot analysis. Using RIPA buffer containing protease and phosphatase inhibitors (Solarbio, R0010, Beijing, China), the total proteins were extracted from treated ZR-75-30 and BT474 BC cells. After quantification with the BCA Kit (Thermo, PICPI23223), 25 μg of proteins were separated using 10% SDS-polyacrylamide gels and then transferred to polyvinylidene fluoride (PVDF) membranes (Millipore, HATF00010, USA). Subsequently, the membranes were blocked with 5% skim milk (BD Biosciences, BYL40422) for 1 h, followed by incubation in primary antibodies against IQGAP3 (1: 1000, Abcam, Ab88353), ERK1/2 (1: 1000, Cell Signaling Technology [CST], #9102), p-ERK1/2 (1: 1000, CST, #9101), Bax (1: 1000, Abcam, Ab32503), Bcl2 (1: 1000, Abcam, Ab196495), and GAPDH (1: 2000, CST, #5174) overnight at 4°C. The next day, at room temperature, the second antibodies labeled with HRP (1: 1000, Beyotime, Shanghai) goat anti-rabbit (A0208) and goat anti-mouse (A0216) antibodies were used to incubate the membranes for 2 h. The blots were developed by 5-min incubation with chemiluminescent reagent (Millipore, WBKLS0100), and then visualized on an ECL imaging system (Tanon, Tanon-5200, Shanghai). The protein expression, normalized to GAPDH, was analyzed and calculated by version 1.47v Image J software (Bethesda, MD, USA).
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3

Protein Extraction and Western Blot Analysis

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Proteins were extracted from freshly frozen tissues. Briefly, the tissues were homogenized and lysed with radio immunoprecipitation lysis buffer (Solarbio, R0010, Beijing, China), which has 100 mg/ml of phenylmethanesulfonyl fluoride (ADOOQ, A11901, California, USA) and 1 mg/ml of Aprotinin (ADOOQ, A14263). The lysate was collected and centrifugated for liquid supernatant. A total of 50 μg protein samples were separated with 10% SDS-PAGE (Solarbio, P1040) and transferred onto polyvinylidene fluoride (Millipore, HVLP04700, Arklow, Ireland) membranes. Membranes were blocked at room temperature with 5% skim milk (ACMEC, AC11037, Shanghai, China) powder in TBS (Quartett, 402000192, Berlin, Germany) for 1 h. Membranes were then incubated overnight at 4 °C with primary antibodies against the following proteins: Acyl-CoA synthetase long-chain familymember 4 (ACSL4) (1: 1000, ABclonal, A6826, Wuhan, China), transferrin receptor (TFRC) (1: 1000, ABclonal, A5865, Wuhan, China). Secondary antibodies (1: 1000, ABclonal, AS014, Wuhan, China) were incubated for 1 h at 37 °C and washed three times with PBST (PBS+0.1% Tween 20) (Biomed, PA202, Beijing, China). The protein bands were visualized by Molecular Imager Gel Doc XR System (Bio-Rad, Hertfordshire, UK) and quantified by densitometric analysis using an image analyzer (NIH Image J software, Bethesda, USA).
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4

Western Blot Analysis of OPN3 Protein

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Total protein extracts were obtained by tissue lysis in RIPA lysis buffer (R0010; Solarbio) containing 1 mM phenylmethylsulfonyl fluoride (R0010; Solarbio). For WB, 40 μg protein was separated by sodium dodecyl sulfate‐polyacrylamide gel electrophoresis and then transferred onto polyvinylidene difluoride (PVDF) membranes (Immobilon‐P; Millipore). Membranes were blocked with 5% nonfat milk for 2 h at room temperature and then soaked in primary antibodies overnight at 4°C. The OPN3 (1:500; MD4034‐100; MDL) and β‐Tubulin (1:1000; T2003; Affinity Biosciences) were used as primary antibodies. After washing four times with Tris‐buffered saline Tween washing buffer (TBST buffer), the blots were incubated with HRP‐conjugated anti‐mouse (1:1000; MD912524; MDL) or anti‐rabbit IgG (1:2000, BS912565; MDL) for 2 h at room temperature. After the PVDF membrane was washed three times with TBST, expression of the above proteins was detected using ECL WB detection reagent (7sea Biotechnology). The expression levels were measured with FastStone Image Viewer 5.5 software.
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5

Western Blot Protein Analysis Protocol

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Protein samples were extracted using RIPA lysis (R0010, Solarbio) and quantified by a BCA Protein Assay Kit (PC0020, Solarbio). For the determination of protein level, an equal volume of protein samples was loaded on SDS‐PAGE gel, and then transferred onto PVDF membrane (IPVH00010, Millipore). After blocking in fresh skim‐milk, the membranes were incubated with primary antibodies overnight at 4°C and washed in TBST. Then corresponding secondary antibodies were utilized to conjugate the primary protein targets. Finally, the protein blots were visualized with ECL solution (PE0010, Solarbio), and the optical density was analyzed using Gel‐Pro‐Analyzer (Media Cybernetics).
All antibodies used in this study are listed as follows: PHLPP2 antibody (25244‐1‐AP, Proteintech), FOXO1 antibody (18592‐1‐AP, Proteintech), AKT antibody (#4691, CST), p‐AKT antibody (#4060, CST), Ki67 antibody (A11390, ABclonal), p21 antibody (10355‐1‐AP, Proteintech), p27 antibody (25614‐1‐AP, Proteintech), Cyclin D1 antibody (A0310, ABclonal), cleaved caspase‐3 (#9661, CST), cleaved caspase‐9 (#7237, CST), GAPDH antibody (60004‐1‐Ig, Proteintech), HRP‐conjugated goat anti‐rabbit antibody (SE134, Solarbio), and HRP‐conjugated goat anti‐mouse antibody (SE131, Solarbio). GAPDH was used as internal control.
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6

Western Blot Analysis of γ-H2A.X

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After samples were collected, spinal cord tissues were lysed with ice-cold radio-immunoprecipitation assay buffer (Solarbio, R0010, Beijing, China) supplemented with 1 mM of phenylmethanesulfonyl fluoride and centrifuged, and the supernatant was collected. Protein quantification was determined by the bicinchoninic acid assay. After separation on 13% sodium dodecyl sulphate-polyacrylamide gels, proteins were electrophoretically transferred to polyvinylidene fluoride membranes (Millipore, Billerica, MA, USA). The membrane was blocked with 5% bovine serum albumin in Tris-buffered saline containing 0.1% Tween-20 (TBST) at room temperature for 2 hours. Membranes were incubated with the primary antibody, mouse anti-γ-H2A.X (ab26350, Abcam Incorporation, Cambridge, MA, USA), at 1:1000 dilution in TBST + 1% bovine serum albumin overnight at 4°C, and then incubated with the secondary antibody, a goat anti-mouse horseradish peroxidase-conjugated antibody (ZDR-5307, ZSGB-bio, Beijing, China), at 1:2000 dilution at room temperature for 2 hours. Enhanced chemiluminescence (Millipore) was used to visualize the protein signals. The relative optical densities of the bands were measured using ImageJ software (NIH, Bethesda, MD, USA), with β-actin serving as the loading control.
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7

Western Blot Analysis of CSF1 in Spinal Cord

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The spinal cord (L4-L6 segments) was dissected and homogenized in ice-cold lysis buffer (P0013, Beyotime) containing protease inhibitor cocktail (R0010, Solarbio). Tissue lysates were centrifuged at 12,000 × g for 15 minutes at 4 °C, and the supernatants were collected for subsequent analysis. The protein concentration was determined using a bicinchoninic acid (BCA) protein assay kit (Beyotime). Protein samples (30–50 μg per lane) were separated using 8% sodium dodecyl sulfate-polyacrylamide gel electrophoresis and transferred to a polyvinylidene fluoride (PVDF) membrane (IPVH00010; Millipore). Membranes were blocked for 1 hour in Tris-buffered saline containing 0.1% Tween-20 (TBS-T), followed by overnight incubation at 4°C with the primary mouse antibodies against CSF1 (Santa Cruz Biotechnology) and glyceraldehyde-3-phosphate dehydrogenase (GAPDH; Proteintech). After washing with TBS-T, the membranes were incubated with secondary antimouse antibody (Invitrogen) for 1 hour. Immunoreactive proteins were visualized with enhanced chemiluminescence (Biosharp), and images were acquired using a luminescent image analyzer (a ChemiDoc MP Imaging System, Bio-Rad). All images were analyzed by Image J (NIH). The results were normalized to GAPDH.
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8

Western Blot Protein Analysis Protocol

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The total protein was lysed from cells in radio immuno precipitation assay buffer (R0010, Solarbio) with protease and phosphatase inhibitor (P1045, Beyotime, 1:50) for 30 min at 4°C, and then quantified with a BCA kit (PC0020, Solarbio). ColorMixed Protein Marker (PR1920, Solarbio) served as a protein size marker. Then, protein (20 μg) was isolated by 6–10% sodium dodecyl sulphate-polyacrylamide gel electrophoresis gels (P1200, Solarbio) and transferred onto immobilon-P polyvinylidene fluoride membranes (YA1701, Solarbio). Following incubation with 5% bovine serum albumin (SW3015, Solarbio) for 1 h at room temperature, the membranes were treated with primary antibodies (shown in Table 2) at 4℃ overnight, and then corresponding secondary antibody (shown in Table 2) for 2 h at room temperature. Visualization was achieved with ECL Western Blotting Substrate (PE0010, Solarbio). The intensity of protein band was determined by Quantity One Analysis Software (version 4.62; Bio-Rad Laboratories, Inc.).
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9

Protein Extraction and Western Blotting of Primary Chondrocytes

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Total proteins from primary chondrocytes were extracted with RIPA buffer containing protease and phosphatase inhibitors (R0010, Beijing Solarbio Science & Technology Co., Ltd.) on ice. The concentration of proteins was measured by bicinchoninic acid (BCA) protein assay (Beyotime Institute of Biotechnology, Inc.). Equal amounts of protein (50 μg) were separated by 10 or 12.5% SDS-PAGE (PG112/PG113, EpiZyme, inc.) and transferred onto 0.22 μM NC membranes (P-N66485, Beijing Solarbio Science & Technology Co., Ltd.). The membranes were blocked with 5% dried skimmed milk in Tris-buffered saline with 0.05% Tween-20 (TBS-T) for 1 h at room temperature with sustained shaking. The membrane was washed with TBS-T 3 times then probed with primary antibodies (1:1,000) by incubation at 4°C overnight. The following day, membranes were incubated with horseradish peroxidase (HRP)-conjugated secondary anti-bodies (1:5,000) for 2 h at room temperature. Immunoreactivity was visualized using ECL reagent (Wanlei Biotechnology) using ChemiDoc™ MP Imaging System (Tanon Science & Technology Co., Ltd.). The densities of the bands were quantified using a Bio-Rad Chemi EQ densitometer and Quantity One software (Tanon Science & Technology Co., Ltd.).
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10

Western Blot Analysis of Retinal Autophagy

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Retinal tissue was extracted and lysed with RIPA (Solarbio, R0010, Beijing, China) lysis buffer for 30 min on ice. After centrifuging the lysate at 12,000 rpm for 15 min at 4 °C, the supernatant was collected. The protein concentration was determined using the BCA protein assay kit (Solarbio, PC0020, Beijing, China). The same amount of protein was loaded on a 10% sodium dodecyl sulfate–polyacrylamide gel electrophoresis (SDS-PAGE) gel. Then, the proteins were transferred to polyvinylidene fluoride (PVDF) membranes. The membranes were immersed in a blocking solution of 50 g L−1 nonfat dry milk for 2 h. The corresponding primary antibodies (1/1000, LC3B, 18725-1-AP, Proteintech, USA; 1/1000, P62, AF5384, AffinitY, USA) were added to the membrane overnight at 4 °C. Then, the membranes were incubated with the corresponding secondary antibody (1/1000, MDL, MD912565, Hebei, China) for 1 h at 37 °C on a shaker. Finally, immunoreactive bands were visualized using enhanced chemiluminescence (ECL, Solarbio, PE0010, Beijing, China) and detected using an automated image analysis system (170-8280, ChemiDoc MP Chemiluminescence Imaging System; Bio-Rad, CA, USA). Statistical analysis was performed with β-actin as an internal reference.
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