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7 protocols using ab70598

1

Investigating SOX4 in Cell Cycle Regulation

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All-trans retinoic acid (ATRA) was from Sigma (R2625, Ronkonkoma, NY, USA). Fetal bovine serum was from Gibco (Brisbane, Australia). RPMI-1640 medium, glutamine, antibiotics (penicillin 100 units/mL, streptomycin 100 μg/mL), and PBS were from Bioind (Beit-Haemek, Israel). Trizol was from Solarbio (R1100, China), the GoScriptTM Reverse Transcription system was from Promega (A5001, Madison, WI, USA), and TB Green was from TAKARA (RR820A, Beijing, China). Antibody against SOX4 (ab70598) and Goat polyclonal Secondary Antibody to Rabbit IgG-H&L (Alexa Fluor 488, ab150077) were from Abcam, and the antibody against GAPDH and α-Tubulin was from Proteintech (Wuhan, China). Cell counting kit-8 (CCK8) was from Bimake (B34304, Shanghai, China). The cell cycle analysis kit was from Beyotime (C1052, Shanghai, China).
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2

Evaluating circRNA-mediated regulation in anti-PD-1 therapy

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Mice xenograft anti-PD-1 therapy study, western blot, circRNA immunoprecipitation (circRIP), RNA pull-down, and dual luciferase reporter assays were evaluated with SPSS software (19.0, SPSS, Inc., Chicago, IL) as described in our previously studies[8 (link),10 (link),14 (link)]. Experimentation on C57BL/6 mice were approved by the Animal Experimentation Ethics Committee of Zhongshan Hospital, Fudan University. And the antibody used in western blot and circRIP assays were listed as follows: Tubulin (Abcam, ab52623), AGO2 (Abcam, ab186733), and SOX4 (Abcam, ab70598).
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3

Chromatin Immunoprecipitation of Osteogenic Markers

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Chromatin immunoprecipitation (ChIP) was performed according to the previous protocol (ref). Briefly, MC3T3 at different timepoint post osteogenic differentiation were washed and chemically cross-linked by formaldehyde at the concentration of 1% and incubated for 10 min at 37 °C followed by stop of the reaction by 125mM glycine for 5 min at 37 °C. Cells were then collected and suspended in lysis buffer, and sonicated on ice using Sonicator 3000 (Misonix, Farmingdale, NY) to generate a library of DNA sized from 200 to 1000 bp. Specific DNA was pulled down by Dynabeads (Life Technologies) pretreated by RUNX2 antibody (Santa Cruz, M-70, 5µg per 100µL Dynbeads), SOX4 antibody (Abcam, ab70598, 5µg per 100µl Dynabeads) or IgG Dynabeads (Life Technologies) as control overnight. The next day, beads were washed sequentially with different washing buffer, and cross-linked DNA bound to the beads was eluted using SDS solution, and reversed by overnight incubation with 5M NaCl. ChIPed DNA was subjected to qPCR.
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4

Western Blot Analysis of Apoptosis Markers

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Cells were lysed using RIPA lysis buffer (Beyotime) on ice and centrifuged (20 min, 14, 000g, 4°C) to extract total protein. Thereafter, the protein samples were denatured by heating at 100°C for 3–5 min. After measuring protein concentration with BCA protein assay kit (Abcam, Cambridge, UK), extracted protein samples (about 30 μg/lane) were separated using sulfate-polyacrylamide gel electrophoresis (SDS-PAGE; Sangon Biotech), and protein was then transferred to nitrocellulose membranes (Invitrogen). After blocking with 5% skim milk (Beyotime), the membranes were then incubated with the primary antibodies at 4°C for 12–16 h: B-cell lymphoma-2 (Bcl-2; ab194583, 1:500, Abcam), BCL2-associated X protein (Bax; ab77566, 1:1000, Abcam), SOX4 (ab70598, 1:500, Abcam), β-actin (ab227387, 1:5000, Abcam). Afterwards, these membranes were probed with corresponding secondary antibody (ab205718/ab205719, 1:4000, Abcam). Finally, the combined signals were detected by enhanced chemiluminescence reagent (Solarbio, Beijing, China). Quantification of protein levels was determined using ImageJ software. The protein abundance was normalized by β-actin. All experiments were repeated three times.
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5

Immunoblotting Analysis of OSCC Cells

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The processed OSCC cells and the ground tumors were increased with the lysates including RIPA (Beyotime, China) and protease inhibitors (Beyotime, China). The extracted proteins were quantified through BCA method, mixed with appropriate loading, and heated at 100℃ for denaturation. Then same amount (50 μg) of proteins were added to 10% SDS-PAGE, separated by electrophoresis at constant pressure, and transferred to PVDF membrane (Millipore). Next, the membrane with protein was sealed with 5% skim milk for 2 h, exposed to primary antibodies, including ASC (Abcam, ab283684, 1:1000), IL-1β (Abcam, ab254360, 1:1000), IL-18 (Abcam, ab207324, 1:1000), Pro-IL-18 (Proteintech, 10,663–1-AP, 1:1000), NLRP3 (Abcam, ab263899, 1:1000), IL-6 (Abcam, ab9324, 1 µg/ml), Sox4 (Abcam, ab70598, 1:500), JAK2 (Abcam, ab108596, 1:1000), pJAK2 (Abcam, ab32101, 1:1000), STAT3 (Abcam, ab68153, 1:1000), pSTAT3 (Abcam, ab267373, 1:1000) at 4℃ overnight, and secondary antibodies (Abcam) for 1 h. Finally, western blotting was developed after processing with ECL kit (Thermo scientific), and the brightness of each strip can be controlled by adjusting the exposure time.
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6

Protein Quantification and Western Blotting

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The BCA kit (Beyotime Biotechnology, Shanghai, China) was utilised to measure the concentration of protein was quantified by using. After the electrophoresis, the PVDF membranes were used. We incubated the membranes with different specific primary antibodies at 4°C overnight after blocking with 5% non‐fat milk at a shaker for 2 h. Another day, the corresponding secondary antibodies were used at room temperature for 2 h. Finally, the relative levels were calculated with a Bio‐Imaging System. The product numbers of antibodies were listed: MAPK14 (ab170099, Abcam, 1:1000), MKK6 (ab33866, Abcam, 1:1000), FOXC1 (ab226219, Abcam, 1:2000), p‐MAPK14 phosphorylate T180 + Y182 (ab195049, Abcam, 1:1000), SOX4 (ab70598, Abcam, 1:1000), SOX13 (ab96776, Abcam, 1:1000), MMP10 (ab261733, Abcam, 1:1000), U2AF2(ab37530, Abcam, 1:250), Tubulin (ab6046, Abcam, 1:500) was used as a internal control. H3 (#4499, CST, 1:2000) was used as a nucleus internal control. The experiment was performed in triplicate.
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7

Protein Expression Analysis in Rat Lung Tissue

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RIPA buffer (Sigma, USA) was used to isolate protein from rat lung tissue samples, and there proteins were then separated by 10% SDS-PAGE, transferred to PVDF membranes (Millipore, MA, USA), and these were blocked for 2 h with 5% non-fat milk, followed by probing overnight with anti-GAPDH (ab8245, Abcam, UK), anti-SDC4 (ab74139, Abcam), anti-SOX4 (ab70598, Abcam), anti-OCT4 (ab200834, Abcam), and anti-Nanog (ab109250, Abcam), all diluted 1:1000. Following three washes, blots were probed with HRP-anti-rabbit IgG (1:2000, ab6721, Abcam) for 2 h, after which bands were detected using an enhanced chemiluminescence system (ECL, ThermoFisher, USA), with the Image Lab™ Software (Bio-Rad, USA) being used to analyze the data.
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