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Imagej software

Manufactured by GE Healthcare
Sourced in United States, United Kingdom, China

ImageJ is a free, open-source image processing software used for scientific image analysis. It provides a wide range of tools and features for tasks such as image display, enhancement, measurement, and processing. ImageJ is designed to be highly customizable and can be extended through the use of plugins.

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32 protocols using imagej software

1

Western Blot Analysis of MMP-2, MMP-9, and p38 MAPK

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After incubated with various concentrations of oxymatrine or SB203580 (Sigma-Aldrich, St Louis, MO; 10 μM), cells were suspended in 100μl of lysis buffer. After separating on 10 % SDS-polyacrylamide gel electrophoresis, proteins were transferred onto PVDF membranes. The membranes were subsequently blocked in defatted milk to reducing non-specific binding at 37˚C for 1 h and then incubated with different antibodies (MMP-2, MMP-9, p38, p-p38 and β-actin) in TBST containing 5% defatted milk at 4˚C overnight. Then membranes were incubated with corresponding second anti-body for 1 h at room temperature. The bands were measured with an enhanced chemiluminescence kit (Millipore, Billerica, MA, USA) and exposed by autoradiography. The densitometric analysis was carried out with Image J software (GE Healthcare, Buckinghamshire, UK).
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2

Revealing ER Stress and Autophagy Markers

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Following the desired treatments, CHO cells were washed and harvested on ice, and then lyzed with ice-cold protein extraction buffer (Beyotime, Nanjing, China). The protein concentration was determined using BCA protein assay kit (ComWin, Beijing, China). Equal amounts of protein were loaded into gel wells, separated by electrophoresis on SDS-polyacrylamide gels and transferred onto PVDF transfer membrane (Millipore, Bedford, MA). The transferred blots were blocked with blocking agents (5% w/v BSA and 0.05% Tween-20 in TBS) for 1 h at room temperature. Blots were then incubated in a certain proportion of specific primary antibodies: anti-GRP78 (ab25192 Rabbit monoclonal, Abcam), anti-ATF-6 (ab203119 Rabbit polyclonal, Abcam), anti-PERK (C33E10 Rabbit polyclonal, Abcam), anti-IRE1 (ab37073 Rabbit polyclonal, Abcam), anti-CHOP (ab11419 Mouse monoclonal, Abcam), anti-Beclin1 (ab55878 Rabbit polyclonal, Abcam), anti-LC3B (ab81785 Rabbit polyclonal, Abcam) (1:1000) overnight at 4°C. These membranes were rinsed 3 times for 10 min each with TBS-Tween (Sigma, St. Louis, MO, USA) and incubated with HRP conjugated secondary antibodies (1:5000) (CWBio, Beijing, China). After washing, protein bands were visualized by an enhanced chemiluminescence detection kit (ComWin, Beijing, China). Each band density was quantified using Image J software (GE Healthcare, Piscataway, New Jersey, USA).
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3

Quantitative Western Blot Analysis of Cervical Cancer Cell Signaling

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1×106 cervical cancer cells were suspended in 250 µl of lysis buffer (40mmol/l Tris-HCl, 1 mmol/l EDTA, 150 mmol/l KCl, 100 mmol/l NaVO3, 1% Triton X-100, 1 mmol/l PMSF, pH 7.5). The nuclear lysates were harvested with NucBuster Protein Extration Kit (Novagen, Germany) according to manufacturer’s instructions. The proteins (50 µg) were separated by 10% SDS-polyacrylamide gel electrophoresis and transferred onto PVDF membranes. The membranes were subsequently blocked in non-fat milk (5% in Tris-buffered saline with TWEEN-20, TBST) buffer at 37°C for 1 h to block non-specific binding and were then incubated overnight with antibodies against p38, p-p38, MMP2, MMP9, TIMP-1, TIMP-2, NF-κB-p50, p65/RelA, Histone H1 or β-actin in TBST containing 5% defatted milk at 4°C. Then second antibodies were incubated. The bands were detected with an enhanced chemiluminescence kit (Amersham, ECL Plus, Freiburg, Germany) and exposed by autoradiography. The densitometry analysis was performed using Image J software (GE Healthcare, Buckinghamshire, UK).
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4

MCR-1 Expression Quantification

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After treatment with DHA (0, 4-32 μg/mL) for 3 or 6 h, bacterial cultures were collected to prepare western blot assays sample. The membrane was blocked, and incubated with primary antibody against MCR-1 (prepared from mouse) and goat anti-mouse IgG secondary antibody (HRP). Finally, the membrane was visualized with an enhanced chemiluminescence substrate and the blots were quantified using ImageJ software (GE Healthcare Life Sciences, UK). Moreover, the samples of culture supernatant and bacterial precipitation from E. coli W3110 (pUC19-mcr-1) were separated by SDS–PAGE and stained with Coomassie brilliant blue.
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5

Western Blot Analysis of EMT Markers

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Whole cell lysates were extracted with radioimmunoprecipitation assay buffer (R&D System, Minneapolis, MN) on ice for 20 min. Nuclear lysates were extracted as previously mentioned 5 (link). Cells were suspended in 100μl of lysis buffer. After separating on 10 % SDS-polyacrylamide gel electrophoresis, proteins were transferred onto PVDF membranes. The membranes were subsequently blocked in defatted milk to reduce non-specific binding at 37˚C for 1 h and then incubated with different antibodies (E-cadherin, N-cadherin, vimentin, Snail, Slug, Histone H1, ERK, p-ERK, NF-κB-p50, p65or beta-actin).
The bands were measured with an enhanced chemiluminescence kit (Millipore, Billerica, MA, USA) and exposed by autoradiography. The densitometric analysis was carried out with Image J software (GE Healthcare, Buckinghamshire, UK).
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6

CD73 Expression in GECs After P. gingivalis Infection

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CD73 protein expression in GECs was evaluated via Western blotting as previously performed [43,63,68]. Cell lysates of GECs infected with P. gingivalis for 1, 6, and 24 h were collected in 1x RIPA buffer with protease inhibitor cocktail (Thermo Fisher) and protein levels were determined by Bradford assay. The cell lysates in 1x Laemmli Sample Buffer were loaded onto a 10% SDS-Page gel at 140 V for 1 h. The separated proteins were transferred to a nitrocellulose membrane via wet transfer at 80 V for 1 h and blocked with 5% nonfat dry milk in Tris-buffered saline and 0.1% Tween-20. The membrane was incubated overnight at 4°C in 1:1,000 mouse CD73 (Abcam) and mouse GAPDH (Abcam) antibodies, washed, and incubated with secondary mouse HRP conjugated antibody for 1 h. Protein bands were visualized using enhanced chemiluminescence (GE Healthcare) and analyzed using NIH ImageJ software.
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7

Histone H3K9 Methylation Quantification

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Tissue was homogenized in lysis buffer (RIPA buffer, DTT; Cell Signaling, Danvers, MA, USA). Supernatant containing proteins was collected after 10 min centrifugation (10 000 g at 4°C). Protein concentration was assessed using the Pierce BCA Protein Assay Kit (Thermo Scientific, Rochester, NY, USA). Protein samples were denaturated at 70 °C for 10 min and run on a 4–12% Bis-Tris gel (NuPAGE Novex; Life Technologies, Grand Island, NY, USA), and then transferred to a polyvinylidene fluoride membrane (Millipore). The membrane was blocked with 5% nonfat dry milk and incubated overnight with the primary antibody (rabbit anti-H3K9me1 (1/1000; Abcam) and rabbit anti-H3 (1/1000; Cell Signaling). The membrane was washed with TBST and then incubated with secondary antibody anti-rabbit HRP (1:10 000; Cell Signaling) for 1 h. Detection and densitometric evaluations were performed using the ECL western blotting detection reagent (GE Healthcare, Piscataway, NJ, USA) and ImageJ software (Bethesda, MD, USA).
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8

Clonogenic Assay for KLK7 Expressing Cells

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To test the ability of single cells to grow into a colony, KLK7‐expressing cells (M74‐D6 and M74‐H) or vector control cells (M74‐mock) were plated at a low density (1000 cells/well) in six‐well plates and allowed to generate single colonies for 14 days. The colonies were washed twice in PBS, then stained with 0.5% (v/v) crystal violet/20% methanol, imaged, and quantified using an Image Quant™ LAS 4000 digital imaging system and the image j software (GE Healthcare, Piscataway, NJ, USA). At least three independent experiments were performed in duplicate.
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9

Western Blot Analysis Protocol

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Western blot analysis was done as previously described [28 (link)]. The primary and secondary antibodies are described in Table 4 (application WB). Chemiluminescent signal was detected using an ImageQuant LAS 4000 analyser (GE Healthcare) and the quantitative densitometric analysis was done using ImageJ software (U.S. National Institutes of Health).
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10

Western Blot Analysis of Apoptosis Markers

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Samples of tissues and cells were lysed in RIPA lysis buffer with phosphatase and protease inhibitors. Protein samples were subjected to 10% SDS-PAGE and transferred to PVDF membranes. 5% non-fat milk in 0.1% TBST buffer was used to blocked membranes at 4 °C overnight. The membranes were subsequently incubated with antibodies cleaved caspase-3 (Cell Signaling Technology #9661, 1:1000), BCL2L11 (Cell Signaling Technology #2933S, 1:1000), β-actin (Cell Signaling Technology #3700S, 1:2000). The protein–antibody complex was detected with HRP-conjugated secondary antibodies and enhanced chemiluminescence. Image J software (GE Healthcare, USA) was used to perform the analysis of western blot.
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