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7 protocols using ab243041

1

Immunoblot and Immunohistochemistry Antibody Protocols

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The following primary antibodies were used for either immunoblots (IB) or immunohistochemistry (IHC) experiments: chicken antiGFP (1:1,000, Aves Labs, GFP-1010), rabbit polyclonal anti-MOR (1:350, Millipore, AB5511), rabbit polyclonal anti-PDE1A (1:500, Proteintech, 12442–2-AP), rabbit polyclonal anti-PPP1R1B (1:1,000, Millipore, AB10518), goat anti-tdTomato (1:500, LifeSpan Biosciences, LS-C340696), mouse monoclonal anti-FOXP1 (1:500, Abcam, ab32010), rabbit polyclonal anti-FOXP1 (IHC:1:1,000, IB: 1:5,000 (Spiteri et al., 2007 (link)), rabbit polyclonal anti-Calbindin (1:500, Millipore AB1778 and 1:250, Swant CB-38a for DEG quantification), goat anti-FOXP2 (N-terminal) (1:500, Santa Cruz 21069), rabbit polyclonal anti-b-Tubulin (IB: 1:10,000, Abcam, ab243041), and mouse monoclonal anti-SOX4 (1:500, Abcam, ab243041). All IHC following secondary antibodies were used at a 1:1,000 dilutions Alexa Fluor 488 Donkey Anti-Chicken IgG (Thermo Fisher, 703–545-155), Alexa Fluor 555 Donkey Anti-Goat IgG (Thermo Fisher, A-21432), Alexa Fluor 647 Donkey Anti-Rabbit IgG (Thermo Fisher, 711–605-152), Alexa Fluor 647 Donkey Anti-Mouse IgG (Thermo Fisher, A-31571). For IB, the following secondary antibodies were used at a 1:10,000 dilution: IRDye 800CW Donkey anti-Rabbit IgG (Li-Cor, 925–32213) and IRDye 680RD Donkey anti-Rabbit IgG (Li-Cor, 925–68071).
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2

Immunoblot and Immunohistochemistry Antibody Protocols

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The following primary antibodies were used for either immunoblots (IB) or immunohistochemistry (IHC) experiments: chicken antiGFP (1:1,000, Aves Labs, GFP-1010), rabbit polyclonal anti-MOR (1:350, Millipore, AB5511), rabbit polyclonal anti-PDE1A (1:500, Proteintech, 12442–2-AP), rabbit polyclonal anti-PPP1R1B (1:1,000, Millipore, AB10518), goat anti-tdTomato (1:500, LifeSpan Biosciences, LS-C340696), mouse monoclonal anti-FOXP1 (1:500, Abcam, ab32010), rabbit polyclonal anti-FOXP1 (IHC:1:1,000, IB: 1:5,000 (Spiteri et al., 2007 (link)), rabbit polyclonal anti-Calbindin (1:500, Millipore AB1778 and 1:250, Swant CB-38a for DEG quantification), goat anti-FOXP2 (N-terminal) (1:500, Santa Cruz 21069), rabbit polyclonal anti-b-Tubulin (IB: 1:10,000, Abcam, ab243041), and mouse monoclonal anti-SOX4 (1:500, Abcam, ab243041). All IHC following secondary antibodies were used at a 1:1,000 dilutions Alexa Fluor 488 Donkey Anti-Chicken IgG (Thermo Fisher, 703–545-155), Alexa Fluor 555 Donkey Anti-Goat IgG (Thermo Fisher, A-21432), Alexa Fluor 647 Donkey Anti-Rabbit IgG (Thermo Fisher, 711–605-152), Alexa Fluor 647 Donkey Anti-Mouse IgG (Thermo Fisher, A-31571). For IB, the following secondary antibodies were used at a 1:10,000 dilution: IRDye 800CW Donkey anti-Rabbit IgG (Li-Cor, 925–32213) and IRDye 680RD Donkey anti-Rabbit IgG (Li-Cor, 925–68071).
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3

Immunohistochemical Analysis of Transcription Factors

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IHC was performed as described previously [80 (link)]. Paraffin-embedded clinical tissues were incubated with the following antibodies: anti-SOX9 (abcam, ab185966; 1:1000 dilution), anti-RUNX2 (abcam, ab192256; 1:1000 dilution), anti-TTF1 (abcam, ab76013; 1:250 dilution), anti-Ki67 (Proteintech, 27309-1-AP; 1:5000 dilution), anti-SOX4 (abcam, ab243041, 1:1000 dilution), anti-RUNX1 (abcam, ab240639, 1:2000 dilution), anti-SIX1 (abcam, ab252224, a:100 dilution), and anti-Clusterin (abcam, ab92548; 1:200 dilution). The immunostaining was reviewed and scored blindly. The scoring system for grading expression level was reported previously [81 (link)]. The score of each sample was multiplied by the grading of intensity and staining area.
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4

Evaluating SOX4 Expression in Retinoblastoma

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Immunohistochemistry (IHC) was performed on 4-μm-thick paraffin sections of human tissues using standard protocols with optimized conditions. Tissue samples for IHC assays were obtained from a cohort of 47 RB patients who had undergone treatment at the Zhongshan Ophthalmic Center. All RB samples were reviewed by specialized pathologists. The expression of SOX4 (Abcam, ab243041, 1:1000) was evaluated with the HRP-conjugated Goat anti-mouse IgG (H + L) (Servicebio, GB23301, 1:200) using semi-quantitative methods that considered both the proportion and intensity of stained tumor cells. The percentage of positively stained cells was counted in five randomly selected fields under a light microscope (×400), and staining intensity was graded as follows: negative (0), weak (1+), moderate (2+), or intense (3+). The percentage of stained cells was categorized as follows: ≤10% (grade 1), 11–50% (grade 2), or >50% (grade 3). The final IHC scores were calculated by multiplying the scores for the percentage of stained cells and staining intensity. In this study, the highest score obtained was 9, while the lowest was 0. SOX4 expression was deemed high when the IHC score was ≥ 4 and low when the IHC score was < 4. The significance of the difference was evaluated using Fisher’s exact test.
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5

Immunohistochemical Localization of SOX4

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Tissues were fixed in 10% formalin, embedded in paraffin and cut into thick sections (5 μm). Next, these sections were incubated with primary antibody against SOX4 (ab243041, 1:1000, Abcam) for 12 h at 4°C. Thereafter, the sections were continuously incubated with secondary antibody (ab205719, 1:2000, Abcam) for 1 h. After that, the slides were then stained by 3,3ʹ-Diaminobenzidine (DAB) solution (Sigma-Aldrich) and subsequently counterstained with hematoxylin (Sigma-Aldrich). Finally, images were obtained using a microscope with a magnification of ×200. All experiments were repeated three times.
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6

Western Blot Analysis of SOX4 Expression

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The RIPA lysis buffer (Beyotime Biotechnology, Shanghai, China) was supplemented to the cells and the total protein was extracted on the ice. After the samples were centrifuged, the supernatant was collected as the protein samples. BCA method was applied for protein quantification. Then, 5× loading buffer was mixed with the samples, and next the protein was denatured in boiling water. After SDS-PAGE, the protein was transferred on the PVDF membrane, and then the membrane was blocked in 3% bovine bull serum albumin (BSA) for 1 h. Then, the membranes were incubated with the primary antibodies including anti-SOX4 (ab243041, 1:1000, Abcam, Shanghai, China) and anti-GAPDH (ab8245, 1:3000, Abcam, Shanghai, China), respectively, overnight at 4°C. After the residual primary antibody on the membrane was rinsed off by TBST on a shaker, the membrane was incubated with HRP-labeled secondary antibody (goat anti-mouse IgG H&L, ab205719, 1:2500, Abcam, Shanghai, China) for 1 h at room temperature. After the residual secondary antibody on the membrane was washed off by TBST on the shaker, the Enhanced Chemiluminescence Western blotting Substrate (Dongguan Biotech, Shandong, China) was added on to the membrane to react with the protein-antibody complex, and the protein bands were developed. GAPDH was the internal reference.
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7

Protein Extraction and Quantification

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Cell lysis buffer (Abcam, Cambridge, Massachusetts, USA) was adopted to prepare protein samples. Protein supernatant was isolated from cell debris via centrifugation at 13 200g for 15 min. A BCA Kit (Pierce, Rockford, Illinois, USA) was adopted to quantify protein samples. Proteins were added to SDS-PAGE gel and shifted onto polyvinylidene fluoride membrane (Millipore, Billerica, Massachusetts, USA). Primary antibodies, including anti-CyclinD1 (ab16663; Abcam), anti-SOX4 (ab243041; Abcam), and anti-glyceraldehyde 3-phosphate dehydrogenase (ab8245; Abcam), were diluted in 3% BSA and then mixed with the membrane overnight at 4°C. The membrane was labeled with the secondary antibody for 2 h. Immunoreactive protein bands were determined by the ECL Kit.
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