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Image studio version 2

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Image Studio version 2.1 is a software suite designed for image analysis and data visualization. It provides tools for quantifying and analyzing images captured with LI-COR's imaging systems. The software supports a range of file formats and offers features for image processing, data analysis, and report generation.

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Lab products found in correlation

Odyssey blocking buffer, by LI COR (4 mentions) Odyssey infrared imaging system, by LI COR (4 mentions) Ripa buffer, by Cell Signaling Technology (4 mentions) Nitrocellulose membrane, by Avantor (2 mentions) Irdye 800cw donkey anti rabbit, by LI COR (2 mentions) Laemmli buffer, by Boston BioProducts (2 mentions) Anti his tag antibody rb, by Novus Biologicals (2 mentions) Dithiothreitol (dtt), by Merck Group (2 mentions) Mini protean tgx, by Bio-Rad (2 mentions) Irdye 680rd donkey anti rabbit, by LI COR (2 mentions) Rabbit anti β actin antibody, by Cell Signaling Technology (2 mentions) Mini protean tgx precast gel, by Bio-Rad (2 mentions) Irdye 800cw donkey anti mouse, by LI COR (2 mentions) Immobilon fl pvdf transfer membranes, by Thermo Fisher Scientific (2 mentions) Mouse anti runx1 sc 365644, by Santa Cruz Biotechnology (2 mentions) Mouse anti p runx1 sc 293146, by Santa Cruz Biotechnology (2 mentions) Mouse anti jnk sc 7345 mouse anti p jnk sc 6254, by Santa Cruz Biotechnology (2 mentions) Bca assay kit, by Thermo Fisher Scientific (2 mentions) Odyssey image station, by LI COR (1 mentions) Il 1β, by Abcam (1 mentions)

Close spelling variants of this product

Image Studio (447 citations) Image Studio 2.0 (26 citations) Image Studio software version 2.1 (4 citations) Image studio light (version 5.2). (3 citations)

12 protocols using image studio version 2

1

Western Blot Analysis of ApoE Fractions

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We used WB to detect ApoE positive fractions collected from the heparin binding columns. Fractions were diluted in 10 μL RIPA buffer (Cell Signaling Technology), 4 μL DTT (1 M, Sigma Aldrich) and 10 μl Laemmli buffer (Boston Bioproducts) to a final volume of 40 μl and denatured 5 min. at 60°C. Samples were separated electrophoretically for 1h at 70 V using 4–20% pre-cast gradient gels (Mini-PROTEAN® TGX™, Bio-Rad) and SDS-Tris-Glycine buffer. Proteins were transferred to nitrocellulose membranes (VWR; 27376–991) for 1 hour at 70 V. Membranes were blocked 1 hour with Odyssey Blocking Buffer (LI-COR Biosciences, Lincoln, NE), and probed either 1 h room temperature (R.T.) or over-night at 4°C with anti-his tag antibody (rb, 1:5000, Novus biologicals), and 1 hour R.T. with IRDye 800CW donkey anti-rabbit (1:10000, LI-COR Biosciences) antibodies. Immunoreactive bands were visualized using the Odyssey Infrared Imaging System and visualized on the Image Studio version 2.1 (LI-COR Biosciences). A composite of individual gels was used to generate Figure 2. All western blotting reported in Figure 2 are representative of two independent experiments.
Arboleda-Velasquez J.F., Lopera F., O’Hare M., Delgado-Tirado S., Marino C., Chmielewska N., Saez-Torres K.L., Amarnani D., Schultz A.P., Sperling R.A., Leyton-Cifuentes D., Chen K., Baena A., Aguillon D., Rios-Romenets S., Giraldo M., Guzmán-Vélez E., Norton D.J., Pardilla-Delgado E., Artola A., Sanchez J.S., Acosta-Uribe J., Lalli M., Kosik K.S., Huentelman M.J., Zetterberg H., Blennow K., Reiman R.A., Luo J., Chen Y., Thiyyagura P., Su Y., Jun G.R., Naymik M., Gai X., Bootwalla M., Ji J., Shen L., Miller J.B., Kim L.A., Tariot P.N., Johnson K.A., Reiman E.M, & Quiroz Y.T. (2019). Resistance to autosomal dominant Alzheimer’s in an APOE3-Christchurch homozygote: a case report. Nature medicine, 25(11), 1680-1683.
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2

Western Blot Analysis of ApoE Fractions

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We used WB to detect ApoE positive fractions collected from the heparin binding columns. Fractions were diluted in 10 μL RIPA buffer (Cell Signaling Technology), 4 μL DTT (1 M, Sigma Aldrich) and 10 μl Laemmli buffer (Boston Bioproducts) to a final volume of 40 μl and denatured 5 min. at 60°C. Samples were separated electrophoretically for 1h at 70 V using 4–20% pre-cast gradient gels (Mini-PROTEAN® TGX™, Bio-Rad) and SDS-Tris-Glycine buffer. Proteins were transferred to nitrocellulose membranes (VWR; 27376–991) for 1 hour at 70 V. Membranes were blocked 1 hour with Odyssey Blocking Buffer (LI-COR Biosciences, Lincoln, NE), and probed either 1 h room temperature (R.T.) or over-night at 4°C with anti-his tag antibody (rb, 1:5000, Novus biologicals), and 1 hour R.T. with IRDye 800CW donkey anti-rabbit (1:10000, LI-COR Biosciences) antibodies. Immunoreactive bands were visualized using the Odyssey Infrared Imaging System and visualized on the Image Studio version 2.1 (LI-COR Biosciences). A composite of individual gels was used to generate Figure 2. All western blotting reported in Figure 2 are representative of two independent experiments.
Arboleda-Velasquez J.F., Lopera F., O’Hare M., Delgado-Tirado S., Marino C., Chmielewska N., Saez-Torres K.L., Amarnani D., Schultz A.P., Sperling R.A., Leyton-Cifuentes D., Chen K., Baena A., Aguillon D., Rios-Romenets S., Giraldo M., Guzmán-Vélez E., Norton D.J., Pardilla-Delgado E., Artola A., Sanchez J.S., Acosta-Uribe J., Lalli M., Kosik K.S., Huentelman M.J., Zetterberg H., Blennow K., Reiman R.A., Luo J., Chen Y., Thiyyagura P., Su Y., Jun G.R., Naymik M., Gai X., Bootwalla M., Ji J., Shen L., Miller J.B., Kim L.A., Tariot P.N., Johnson K.A., Reiman E.M, & Quiroz Y.T. (2019). Resistance to autosomal dominant Alzheimer’s in an APOE3-Christchurch homozygote: a case report. Nature medicine, 25(11), 1680-1683.
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3

Optimized Western Blot Imaging

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All the images were acquired and quantified using the Image Studio version 2.1 (LI-COR Biosciences, Lincoln, NE). All the blots were scanned at an intensity of 4.0. The brightness was adjusted uniformly across the entire blot using the Image studio software to visualize the bands for each experiment. Original complete blots are shown in supplementary data and citations for each antibody provided in the methods section.
Delgado-Tirado S., Amarnani D., Zhao G., Rossin E.J., Eliott D., Miller J.B., Greene W.A., Ramos L., Arevalo-Alquichire S., Leyton-Cifuentes D., Gonzalez-Buendia L., Isaacs-Bernal D., Whitmore H.A., Chmielewska N., Duffy B.V., Kim E., Wang H.C., Ruiz-Moreno J.M., Kim L.A, & Arboleda-Velasquez J.F. (2020). Topical delivery of a small molecule RUNX1 transcription factor inhibitor for the treatment of proliferative vitreoretinopathy. Scientific Reports, 10, 20554.
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4

Western Blot Analysis of RUNX1 and JNK

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Unless otherwise stated, cells for western blot analysis were treated for 72 hours before being lysed. Cells were lysed using RIPA buffer (Cell Signaling Technology, Danvers, MA, USA) and protein concentration measured using the bicinchoninic acid (BCA) assay kit (Thermo Fisher Scientific, Inc Waltham, MA, USA). A total of 10‐20 μg of protein was separated by 4‐20% Mini‐PROTEAN TGX precast gels (Bio‐Rad, Hercules, CA, USA) and transferred to Immobilon™‐FL PVDF transfer membranes (Thermo Fisher Scientific, Inc). Membranes were dried overnight, wetted with methanol, and blocked with Odyssey Blocking Buffer (LI‐COR Biosciences, Lincoln, NE, USA) for 1 hour prior to incubation with primary antibodies, mouse anti‐RUNX1 (sc‐365644), mouse anti‐p‐RUNX1 (sc‐293146), mouse anti‐JNK (sc‐7345) mouse anti‐p‐JNK (sc‐6254) (Santa Cruz Biotechnology) and rabbit anti‐β‐actin antibody (4970S, Cell Signaling Technology) for 4 hours at room temperature (RT). Membranes were subsequently washed with TBST and incubated with secondary antibodies (IRDye 680RD donkey anti‐rabbit and IRDye 800CW donkey anti‐mouse (dilution 1:4000) (LI‐COR Biosciences). After rinsing twice with TBST, immunoreactive bands were visualized using the Odyssey Infrared Imaging System, and band intensities normalized to β‐actin were quantified using Image Studio version 2.1 (LI‐COR Biosciences).
Whitmore H.A., Amarnani D., O'Hare M., Delgado‐Tirado S., Gonzalez‐Buendia L., An M., Pedron J., Bushweller J.H., Arboleda‐Velasquez J.F, & Kim L.A. (2020). TNF‐α signaling regulates RUNX1 function in endothelial cells. The FASEB Journal, 35(2), e21155.
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5

Western Blot Analysis of RUNX1 and JNK

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Unless otherwise stated, cells for western blot analysis were treated for 72 hours before being lysed. Cells were lysed using RIPA buffer (Cell Signaling Technology, Danvers, MA, USA) and protein concentration measured using the bicinchoninic acid (BCA) assay kit (Thermo Fisher Scientific, Inc. Waltham, MA, USA). A total of 10–20 μg of protein was separated by 4–20% Mini-PROTEAN TGX precast gels (Bio-Rad, Hercules, CA, USA) and transferred to Immobilon™-FL PVDF transfer membranes (Thermo Fisher Scientific, Inc.). Membranes were dried overnight, wetted with methanol and blocked with Odyssey Blocking Buffer (LI-COR Biosciences, Lincoln, NE, USA) for 1 h prior to incubation with primary antibodies, mouse anti-RUNX1 (sc-365644), mouse anti-p-RUNX1 (sc-293146), mouse anti-JNK (sc-7345) mouse anti-p-JNK (sc-6254) (Santa Cruz Biotechnology) and rabbit anti-β-actin antibody (4970S, Cell Signaling Technology) for 4 hours at room temperature (RT). Membranes were subsequently washed with TBST and incubated with secondary antibodies (IRDye 680RD donkey anti-rabbit and IRDye 800CW donkey anti-mouse (dilution 1:4000) (LI-COR Biosciences). After rinsing twice with TBST, immunoreactive bands were visualized using the Odyssey Infrared Imaging System, and band intensities normalized to β-actin were quantified using Image Studio version 2.1 (LI-COR Biosciences).
Whitmore H.A., Amarnani D., O'Hare M., Delgado‐Tirado S., Gonzalez‐Buendia L., An M., Pedron J., Bushweller J.H., Arboleda‐Velasquez J.F, & Kim L.A. (2020). TNF‐α signaling regulates RUNX1 function in endothelial cells. The FASEB Journal, 35(2), e21155.
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6

Astrocyte and Neuron Protein Extraction

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Protein was extracted from primary murine astrocyte and neuron co-cultures using MPER while TPER was used to extract protein from human hippocampal tissue (Thermo Scientific, CA, USA). Bradford protein assay determined protein concentrations of MPER- or TPER- soluble fractions. Protein extracts were subsequently immunoblotted with the following antibodies: GLT-1 (a kind gift from Dr. Jeffrey David Rothstein, Johns Hopkins University), IL1-β (Biovision, CA, USA), tubulin and GAPDH (Abcam, MA, USA) were used to control for protein loading or to confirm no cross-contamination of each fraction. Band intensity was measured using the Odyssey Image station and Image Studio (version 2.1, Li-Cor Biosciences, NE, USA) and normalized by corresponding loading control protein.
Zumkehr J., Rodriguez-Ortiz C.J., Medeiros R, & Kitazawa M. (2018). Inflammatory cytokine, IL-1β, regulates glial glutamate transporter via microRNA-181a in vitro.. Journal of Alzheimer's disease : JAD, 63(3), 965-975.
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7

Western Blot Analysis of Carbonic Anhydrases

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Fifteen micrograms of protein per sample was separated on a Bio-Rad Mini-protein 4–15% precast 12-well 20 µl gels (4,561,085, Bio-Rad, CA) and electrophoretically transferred to Odyssey Nitrocellulose membrane (P/N 926–31,092, LI-COR, NE). Membranes were blocked with Odyssey TBS Blocking Buffer (P/N 927–50,000, LI-COR, NE) and incubated with primary antibody against CA-IX (1:1000, M75 mouse monoclonal CA-IX, Bioscience Slovakia), ER alpha (1:2000, Rabbit polyclonal ab 75,635, Abcam), CA-XII (1:10,000, rabbit Anti-CA12 antibody [EPR14861]—C-terminal, ab195233), CA-II (1:1000, rabbit Anti-Carbonic Anhydrase II antibody [EPR5195], ab124687), β-Actin (1:2000, (8H10D10) Mouse mAb #3700- Cell Signaling), and GAPDH (1:4000, rabbit monoclonal ab 181,602, Abcam). For visualization, IRDye Fluorescent secondary antibodies (LI-COR) were used: IRDye 680RD Goat Anti-mouse IgG (H + L), IRDye 680RD Donkey anti-rabbit IgG (H + L), IRDye 800CW goat anti- mouse IgG(H + L), and IRDye 800CW donkey anti-rabbit IgG(H + L). Membranes were imaged on LI-COR Odyssey Blot Imager and quantified using Image Studio Version 2.1(LI-COR). Uncropped versions of western blots are available in Supplementary.
Russell S., Xu L., Kam Y., Abrahams D., Ordway B., Lopez A.S., Bui M.M., Johnson J., Epstein T., Ruiz E., Lloyd M.C., Swietach P., Verduzco D., Wojtkowiak J, & Gillies R.J. (2022). Proton export upregulates aerobic glycolysis. BMC Biology, 20, 163.
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8

Immunohistochemical Analysis of Mouse Lung

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Mouse lungs were fixed in zinc-buffered formalin, processed, embedded in paraffin, cut into 5-μm sections, and mounted on glass slides. Citrate-mediated antigen retrieval was performed, and then the following antibodies were used for detection: anti-β-catenin (Cell Signaling Technology), anti-AQP5 (Calbiochem), anti-Ki67, (Abcam), anti-BrdU, anti-CC10, anti-Cyclin D1, anti-SPC, anti-NKX2.1 (also known as TTF-1) (Santa Cruz Biotechnology), and c-MYC (Epitomics).
β-Galactosidase activity driven by the BAT-GAL transgene was assessed in fresh-frozen sections incubated with 5-bromo-4-chloro-3-indolyl-β-d-galactoside (X-Gal) for 16 h as described previously (Maretto et al. 2003 (link)).
Fifty-microgram aliquots of cell proteins were probed with antisera against c-MYC (Epitomics), Cyclin D1, p-ERK1/2 (pT202/PY204), total ERK1/2 (Cell Signaling Technology), and anti-β-actin (Sigma). Immunoblots were visualized using the Odyssey Classic or Odyssey Fc, with data analyzed using either the Odyssey application software version 3.0.30 or Image Studio version 2.0 software (LI-COR Biosciences).
Juan J., Muraguchi T., Iezza G., Sears R.C, & McMahon M. (2014). Diminished WNT → β-catenin → c-MYC signaling is a barrier for malignant progression of BRAFV600E-induced lung tumors. Genes & Development, 28(6), 561-575.
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9

Syntaxin 6 Lipid Binding Assay

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Immunopreciptated 3XFLAG-syntaxin 6 and 3XFLAG-syntaxin 6 ΔYGRL were incubated with Sphingostrips (S-6000) or PIPstrips (P-6001) (Echelon Biosciences Inc., Salt Lake City, UT). Briefly, 3XFLAG-syntaxin 6 and 3XFLAG-syntaxin 6 ΔYGRL were immunopreciptated from HeLa cells as described above. Protein eluates were quantitated and 8.4 or 2.5 μg of protein was incubated for 24 h in Tris buffered saline (TBS) (50 mM Tris, pH 7.4, and 150 mM NaCl) with Sphingostrips or PIPstrips, respectively. Unbound proteins were removed by washing three times with TBS-0.1%Tween-20. The strips were then processed by blotting with mouse anti-FLAG M2 primary antibody and goat anti-mouse IRDye 680LT-conjugated secondary antibody in TBS. Images were taken using the Odyssey CLx and processed with Image Studio version 2.0 (LiCor Biosciences). Protein input for sphingostrips and PIPstrips was analyzed by SDS-PAGE and Western blot as described above. Fold increase in syntaxin 6-lipid binding was determined by normalization of densitometry as described below.
Kabeiseman E.J., Cichos K.H, & Moore E.R. (2014). The eukaryotic signal sequence, YGRL, targets the chlamydial inclusion. Frontiers in Cellular and Infection Microbiology, 4, 129.
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10

Investigation of HER2 and Signaling Pathways

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Immunoblotting was carried out to investigate key gene expression alterations of HER2 and downstream signalling pathways. Pelleted cells were washed with cold PBS and lysed with RIPA buffer with proteinase and phosphatase inhibitors (Thermo Scientific Pierce, Rockford, IL). Protein concentrations were determined by Bradford Dye Reagent (BioRad, Hercules, CA). About 10–20 μg/lane of whole cell lysates were separated by a gradient Tris–glycine gel (Life Technologies Corp, Grand Island, NY). Bands were transferred to a nitrocellulose film (BioRad), blocked and probed with targeted primary antibodies (Supplementary Table S1). After binding with secondary antibodies (LiCOR Biosciences), bands were visualized with an Odyssey CLx system and analysed by Image Studio version 2.0 (LiCOR Biosciences).
Yang-Kolodji G., Mumenthaler S.M., Mehta A., Ji L, & Tripathy D. (2015). Phosphorylated ribosomal S6 (p-rpS6) as a post-treatment indicator of HER2 signalling targeted drug resistance. Biomarkers : biochemical indicators of exposure, response, and susceptibility to chemicals, 20(5), 313-322.
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