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Nih imagej software

Manufactured by Bio-Rad
Sourced in United States

NIH ImageJ is an open-source software program for image processing and analysis. It provides a wide range of tools for image manipulation, including the ability to view, edit, analyze, process, save and print digital images. The core function of NIH ImageJ is to enable users to perform various image analysis tasks on digital images.

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7 protocols using nih imagej software

1

Western Blot Analysis of Serum Proteins

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Equal volumes of serum from randomly chosen samples were heated with sample buffer (3.2% SDS, 32% glycerol, 0.16% bromophenol blue, 100 mM Tris–HCl, pH 6.8, 8% 2-mercaptoethanol). They were then electrophoresed on Criterion Stain-free 4–20% SDS-PAGE gels (Bio-Rad) and transferred onto nitrocellulose membranes at 100 V for 30 min. The membranes were blocked with PBS containing 5% nonfat dry milk and probed separately with each of the antibodies: anti-CKM (mouse monoclonal, 1:1,000, Santa Cruz, sc-365046), anti-COMP (mouse monoclonal, 1:1,000, Santa Cruz, sc374660), anti-EFEMP1 (mouse monoclonal, 1:1,000, Santa Cruz, sc-33722, 1:1,000), anti-FBLN1 (mouse monoclonal, 1:1,000, Santa Cruz, sc25281), anti-GSN (mouse monoclonal, 1:1,000, Abcam, ab11081), anti-PROS1 (rabbit monoclonal, 1:1,000, Santa Cruz, sc-52720). The membranes were washed three times in PBS containing 0.1% Tween 20 and incubated with horseradish peroxidase-conjugated secondary antibodies for 2 h at room temperature. Signals were detected using enhanced chemiluminescence and Gel Doc System (Bio-Rad). The blots were stripped and probed for the housekeeper protein transferrin. The signal intensity was quantified using Image Lab (Bio-Rad) and NIH ImageJ software (v1.45s).
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2

Quantifying Plasma Apolipoproteins and Enzymes

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Equal volumes of fasted plasmas were separated on SDS–PAGE gels and transferred onto 0.2 μM nitrocellulose membranes at 75 volts for 30 min. Membranes were blocked with Tris buffered saline (TBS) containing 5% non-fat dry milk and probed with anti-apoAI antibody (rabbit polyclonal 1:5,000 Merck #178422) and anti-apoC-I antibody (rabbit monoclonal 1:1,000 Abcam #ab198288) overnight at 4°C. They were then washed three times in TBS containing 0.1% Tween 20 and incubated with horseradish peroxidase-conjugated secondary antibody for 2 h at room temperature. Signals were detected using enhanced chemiluminescence and Gel Doc System (Bio-Rad). The signal intensity was quantified using Image Lab (Bio-Rad) and NIH ImageJ software (v1.45s). Plasma PON1 (Cloud-Clone, #SEA243Hu) and SERPINA1 (Abcam, #ab108799) were measured by ELISA following the manufacturer’s protocols.
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3

Protein Expression in Hippocampus and bEnd.3 Cells

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Hippocampal tissues and bEnd.3 cells were homogenized in RIPA lysis buffer containing 20 mM Tris, 150 mM NaCl, 1 mM EDTA, 1% Triton X-100, 1.5 μg/ml leupeptin, and 1 mM phenylmethylsulfonyl fluoride (PMSF). The samples were centrifuged at 12,000×g (4 °C) for 20 min, and the supernatants were harvested. Protein concentration was determined using a BCA kit. Proteins were separated by 10% sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) and transferred to a PVDF microporous membrane (Millipore, USA). The membranes were incubated with 5% non-fat milk at room temperature for 1 h and incubated overnight at 4 °C with primary antibodies: polyclonal rabbit anti-IL-17A receptor (1:500), monoclonal mouse anti-MMP-2 (1:1000), monoclonal mouse anti-MMP-9 (1:500), monoclonal mouse anti-claudin-5 (1:500) and monoclonal rabbit anti-occludin (1:1000). An antibody against GAPDH (1:1000) was also used as an internal standard. The membranes were incubated with goat anti-mouse secondary or goat anti-rabbit secondary antibodies at room temperature for 1 h and then detected with a chemiluminescent substrate. The relative densities of the protein bands were visualized and analysed by Image Lab software (Bio-Rad, Richmond, CA, USA) and NIH ImageJ software (Bethesda, MD, USA), respectively.
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4

Western Blot Analysis of C3 and Acrolein

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Serum (equal volumes) or protein lysates (10 µg) were heated with sample buffer (3.2% SDS, 32% glycerol, 0.16% bromophenol blue, 100 mM Tris-HCl, pH 6.8, 8% 2-mercaptoethanol). They were then electrophoresed on Criterion Stain-free 4–20% SDS-PAGE gels (Bio-Rad) and transferred onto nitrocellulose membranes at 100 volts for 30 min. The membranes were blocked with TBS containing 5% nonfat dry milk and probed with anti-C3 antibody (Santa Cruz, sc-28294, 1:1,000) or anti-acrolein antibody (NOVUS, NB200–556, 1:1,000) overnight at 4 °C. They were then washed three times in TBS containing 0.1% Tween 20 and incubated with horseradish peroxidase-conjugated secondary antibody for 2 h at room temperature. Signals were detected using enhanced chemiluminescence and Gel Doc System (Bio-Rad). The blots were stripped and probed for housekeeper proteins transferrin (serum) or β-actin (tissue lysate). The signal intensity was quantified using Image Lab (Bio-Rad) and NIH ImageJ software (v1.45 s).
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5

Western Blot Analysis of CDH4 and α-Synuclein

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Protein lysates (10μg for tissue, 20μg for cells) were heated at 95°C for 5 min in sample buffer (3.2% SDS, 32% glycerol, 0.16% bromophenol blue, 100 mM Tris-HCl, pH 6.8, 8% 2-mercaptoethanol) and then electrophoresed on Criterion stain-free 4-20% SDS-PAGE gels (Bio-Rad). The gels were transferred onto nitrocellulose membranes at 90 volts for 90 min. The membranes were blocked with TBS containing 5% w/v non-fat dry milk and probed with anti-CDH4 antibody (Abcam, ab109242, 1 : 2,000) or anti-α-synuclein (BD Biosciences, #610787, 1 : 2,000) overnight at 4°C. They were then washed three times in TBS containing 0.1% Tween 20 and incubated with horseradish peroxidase-conjugated secondary antibody for 2 h at room temperature. Signals were detected using enhanced chemiluminescence and Gel Doc System (Bio-Rad). The blots were stripped and probed for housekeeper protein β-actin. The signal intensity was quantified using Image Lab (Bio-Rad) and NIH ImageJ software (v1.45 s).
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6

CRC Biobank Tissue Extraction and Quantification

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The CRC sample biobank used is described elsewhere.70 (link) Briefly, tissue samples were obtained following patient's written informed consent according to a protocol approved by the Institutional Human Subject Review Board of the Centre Hospitalier Universitaire de Sherbrooke (CHUS; protocol 07-089). Tissue extracts were prepared as described previously.71 (link) Densitometric analyses were performed using a combination of the NIH Image J software and QuantiOne imaging system from Bio-Rad (Hercules, CA, USA). All immunoblotting data were normalized first using the GAPDH signal on the same membrane and then using the same IEC-6 sample loaded on every experiment to establish tumor/normal tissue ratios for each patient.
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7

Western Blot Analysis of Microglial Proteins

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Cellular proteins were extracted from the primary microglial cells using RIPA buffer. The homogenates were centrifuged for 15 min at 12,000 g at 4°C. The quantity of protein in each supernatant was determined using a BCA protein assay kit. Proteins (60 µg) were denatured with sodium dodecyl sulfate (SDS) sample buffer and separated using 10% SDS-polyacrylamide gel electrophoresis (PAGE). The proteins were transferred to a polyvinylidene fluoride (PVDF) microporous membrane (Millipore, Bedford, MA), which was then blocked with 5% skim milk for one hour at room temperature. The membrane was incubated with primary antibody (rabbit anti-Iba1 and/or anti-GAPDH) overnight at 4°C. After addition of the antirabbit secondary antibody for 1 hour, the protein bands on the membranes were detected with ECL kits (Thermo Fisher Scientific, Rockford, IL, USA). The relative density of the protein bands was evaluated by densitometry using Image Lab software (Bio-Rad, Richmond, CA, USA), and quantified by NIH ImageJ software (Bethesda, MD, USA).
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