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7 protocols using ab109290

1

Immunofluorescence Analysis of Stem Cell Markers

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To assess the protein expression levels, cells were fixed with 4% paraformaldehyde for 20 min at room temperature. Fixed cells were then washed twice with PBS and permeabilised in PBS with 0.2% Triton X-100 for 20 min (Amresco, OH, USA). Cells were blocked for 30 min in PBS with 5% normal goat serum (Millipore, CA, USA) and with 0.2% Triton-x-100, followed by overnight incubation at 4°C with the primary antibodies: anti-Nestin antibody (abcam, ab22035) and anti-sox1 antibody (abcam, ab109290). After the incubation, the cells were rinsed with PBS and incubated with secondary antibodies Alexa Fluor 488-conjugated goat anti mouse and Alexa Fluor 488-conjugated goat anti rabbit on a shaker for 30 min at room temperature. Subsequently, cells were rinsed in PBS and 0.5 μg /ml Hoechst (sigma) was added and incubated for 5 min to stain the nuclei. An inverse fluorescence microscope was used for cell imaging.
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2

Pluripotent Stem Cell Characterization

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The cells were digested by 0.25% trypsin, collected, and resuspended with 1 mL of 4% paraformaldehyde for 3 min. The cells were resuspended in PBS containing 0.1% Triton X-100 and permeabilized for 30 min. The collected cells were then sealed with 5% sheep serum at 37°C for 30 min, and the supernatant was discarded after centrifugation. The cells were resuspended with primary antibodies against sex determining region Y-box 1 (SOX1; ab109290, Abcam), paired box gene 6 (Pax6; ab5790, Abcam), and octamer-binding protein (Oct4; ab181557, Abcam) at a 1 : 500 dilution with 3% goat serum at 37°C for 1 h. The cells were then treated with secondary antibodies diluted to 1 : 1000 using 3% goat serum for 30 min, after which the fluorescence of the PBS-resuspended cells was measured by flow cytometry.
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3

Protein Expression Analysis by Western Blot

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Total proteins were isolated from cells in RIPA lysis buffer. Following detecting the protein concentration using a BCA kit (Pierce, USA), 30 μg proteins were separated by 10% sodium dodecyl sulfate – polyacrylamide gels (SDS-PAGE). Then, the proteins were transferred onto PVDF membranes. The membranes were incubated with specific primary antibodies at 4°C overnight followed by incubating with the secondary antibody. Protein bands were visualized with ECL western blot substrate (Pierce). The antibodies were listed as follows: anti-NANOG (ab109250, 1/3000, Abcam, USA), anti-CD133 (ab222782, 1/2000, Abcam), anti-GAPDH (ab181602, 1/10000, Abcam), anti-SOX1 (ab109290, 1/1000, Abcam), anti-SOX2 (ab97959, 1/1000, Abcam), anti-SOX3 (ab183606, 1/2000, Abcam), anti-SOX9 (ab185230, 1/5000, Abcam), anti-SOX12 (23939–1-AP, 1/500; Proteintech, USA). The secondary antibody was goat anti-rabbit IgG conjugated HRP (ab6721, 1/3000, Abcam). Anti-Pan-Histone lysine lactylation (Kla; PTM1401, 1/1000, PTM Biolabs, China) was used to detect total lactylation protein levels.
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4

Immunoprecipitation of SOX Transcription Factors

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A549 and H838 cells were lysed using the pre-cold IP lysis buffer. After centrifugation, the supernatant was collected to incubate with anti-SOX1 (ab109290, 1/50, Abcam), anti-SOX2 (ab133337, 1/10, Abcam), anti-SOX3 (ab183606, 1/100, Abcam), anti-SOX9 (ab185230, 1/60, Abcam), anti-SOX12 (23939–1-AP, 1/20, Proteintech) at 4°C overnight. Meanwhile, the protein A/G-agarose beads were suspended with lysis buffer containing protease inhibitor. These suspensions were added to the samples in the next day to incubate for 4 h at 4°C.
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5

Protein Expression Analysis in Cell Lysates

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Cells were lysed in RIPA lysis buffer (50 mM Tris–HCl, 150 mM NaCl, 1 mM EDTA-Na2, 1% Triton X-100, 1% sodium deoxycholate, 0.1% SDS) supplemented with protease inhibitors and phosphatase inhibitor on ice for 15 min. The cell lysates were cleared by centrifugation at 12,000×g for 10 min, then heat-denatured with 5 ×  Laemmli buffer (G2013, Servicebio). The prepared samples with equal amount of total protein (20 μg) were subjected to SDS-PAGE and immunoblotting, as per the standard procedure. The following antibodies were used: anti-SOX1 (ab109290, Abcam), anti-β-catenin (ab32572, Abcam), anti-HES1 (#11988, Cell Signaling Technology [CST]), anti-PROX1 (11067-2-AP, Proteintech), anti-p38 (#8690, CST), anti-phospho-p38 (#9215, CST), anti-ERK (#4695, CST), anti-phospho-ERK (#4370, CST), anti-AKT (#4691, CST), anti-phospho-AKT (#4060, CST), anti-JNK (#9252, CST), anti-phospho-JNK (#700031, Invitrogen), anti-RAF (#9422, CST), anti-phospho-RAF (#9427, CST), anti-MEK (51080-1-AP, Proteintech), anti-phospho-MEK (#9154, CST), anti-α-Tubulin (11224-1-AP, Proteintech), anti-GAPDH (BM1623, Boster), anti-BCL2 (Proteintech, 12789-1-AP), anti-PCNA (BM0104, Boster). All antibodies were diluted by antibody dilutions (G2025, Servicebio) with a ratio of 1:1,000. All quantitative analyses were performed using the software image J.
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6

Western Blot Analysis of SOX1 Protein

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RIPA (Beyotime, Shanghai, China) was applied to isolate total protein. BCA (Thermo Fisher Scientific) was used to quantify the total protein. SDS-PAGE (10%) was used to separate proteins (40 μg per lane), and then proteins were transferred onto PVDF membranes (Thermo Fisher Scientific). The membranes were incubated with primary antibodies against SOX1 (1:1000, #ab109290, ABCAm, Cambridge, UK) and β-actin (1:5000, #ab8226, ABCAm, Cambridge, UK) at 4 °C overnight after being blocked with 5% skimmed milk for 1 h. After that, the membranes were incubated with secondary antibodies HRP-conjugated (1:5000, #ab20272, ABCAm, Cambridge, UK) for 1 h at room temperature. Protein bands were visualized using the enhanced chemiluminescent (ECL) kit (Thermo Fisher Scientific). β-actin was used for normalization. Image-Pro Plus 6.0 was applied for densitometric analysis.
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7

Optimizing Cell Proliferation and Protein Expression Analysis

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Doxycycline (HY-N0565B) and CFSE (HY-D0938) were purchased from Medchem Express (MCE). Bovine serum albumin (BSA, FC0077) and propidium iodide (PI, 219545810) were purchased from MP Biomedicals. RNase A (10406ES03) was purchased from Yeasen Biotechnology. 5-Bromo-2′-deoxyuridine (BrdU, B5002), Hoechst 33342 (B2261), Triton X-100 (T8787), Pyronin Y (213519), and 4′,6-Diamidino-2-phenylindole dihydrochloride (DAPI, D9542) were purchased from Sigma-Aldrich. Paclitaxel was purchased from Beijing SL Pharmaceutical Co., Ltd. (China). Cisplatin was purchased from Jiangsu Hansoh Pharmaceutical Co., Ltd. (China).
Antibodies against SOX1 (ab109290) and RPS3 (ab128995) were purchased from Abcam. Antibody against RPL7A (DF9137) was purchased from Affinity Biosciences. Antibodies against β-actin (60008-1-Ig), Ki-67 (27309-1-AP), and c-MYC (10828-1-AP) were purchased from Proteintech. Antibody against p27 Kip1 (sc-528) was purchased from Santa Cruz Biotechnology. Alexa Fluor 488 cross-adsorbed goat anti-rabbit IgG secondary antibody (A11008) was purchased from Invitrogen.
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