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15 protocols using nanozoomer s210 digital slide scanner

1

Pappenheim Staining for Cell Morphology

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For microscopic analysis of cytospins, 5 × 104 cells were centrifuged for 10 min at 800 rpm on microscopic slides using the Thermo Shandon Cytospin 4 centrifuge (Thermo Fisher Scientific, Waltham, MA, USA). For the Pappenheim staining, cells were stained 5 min in May-Grünwald dye, washed, and then stained for 20 min in Giemsa dye (Sigma-Aldrich). Cytospins were visualized with a NanoZoomer S210 digital slide scanner (Hamamatsu, Hamamatsu City, Japan) using 40× magnification. Cell morphology was assessed with the NDP.view2 2.8.24 viewing software U12388-01 (Hamamatsu).
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2

Multiplex IHC Analysis of LUSC Samples

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Diagnostic blocks were obtained for 10 patients with LUSC in the validation cohort. Tissue blocks were fixed with formalin, embedded in paraffin, then serially sectioned into sections of 4-μm in thickness. Serial sections from the validation cohort were subjected to H&E staining and multiplex IHC using the T-cell panel: anti-CD8 (type: mouse monoclonal, clone: 4B11, source: Leica Microsystems Ltd., used at 1:100 dilution); anti-CD4 (type: mouse monoclonal, clone name: 4B12, source: Leica Microsystems Ltd., used at 1:50 dilution); anti-FOXP3 [type: mouse monoclonal, clone: 236A/E3, source: kindly gifted by Dr. G. Roncador (CNIO, Madrid, Spain), used at 1:2 dilution] and the B-cell panel: anti-CXCR5 (type: rabbit polyclonal, catalog no. ABN200, source: Merck Life Science UK Limited, used at 1:1,000 dilution); anti-CD79b (type: mouse monoclonal, clone: B29/123, source: LRF Immunodiagnostics Unit, John Radcliffe Hospital, used at 1:25 dilution); anti-CD20 (type: mouse monoclonal, clone: L26, source: Agilent Technologies LDA UK Ltd., used at 1:100 dilution); anti-P40 (type: mouse monoclonal, clone: BC28, source: Biocare Medical, used at 1:100 dilution). All slides were scanned using the NanoZoomer S210 digital slide scanner (C13239–01) and the NanoZoomer digital pathology system v.3.1.7 (Hamamatsu) at ×40 (228 nm/pixel resolution).
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3

BRAF V600E Immunohistochemistry Protocol

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The formalin fixed paraffin embedded (FFPE) biopsy sections (3 μm thick) were placed on 3-aminopropyletxylene-covered slides. Subsequently, sections were stained with mouse monoclonal antibody against BRAF V600E (1/100 dilution; clone VE1) following the Ventana Medical Systems' protocol and as previously described [9 (link)]. Briefly, staining was performed on a Ventana BenchMark Ultra (Ventana Medical Systems, Inc., Tucson, AZ, USA). The staining protocol included the use of Cell Conditioning 1 for 64 minutes; pre-peroxidase inhibition with 3% hydrogen peroxide for 10 minutes at 37°C and primary antibody incubation for 70 minutes. Amplification kit was applied for 4 minutes at 37°C to increase the signal intensity. The OptiView DAB IHC Detection kit was used to detect BRAF V600E protein expression. Tissues were counterstained with hematoxylin for 16 minutes and Bluing Reagent for 4 minutes. Then, stained sections were scanned by NanoZoomer S210 Digital slide scanner (Hamamatsu Photonics, Japan). The scoring of VE1 antibody staining was performed by visual inspection of two independent researchers. The scores range from 0 to 3 (0 for negative staining and 1–3 for different levels of positive staining).
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4

Pirin Immunohistochemistry for FFPE Samples

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Sections (4 μm thick) from Formaldehyde Fixed Paraffin Embedded (FFPE) blocks were subjected to antigen retrieval in citrate buffer (pH 6.1) and steam for 105 min, and then analyzed by Pirin immunohistochemistry with an anti-Pirin antibody (PA5-29777: Thermo Fisher Scientific, Waltham, MA, USA) and using the EnvisionTMG|2 Sistema/AP Kit (Dako Corporation, Denmark). The slides were counterstained with hematoxylin and images were obtained using a NanoZoomer S210 Digital slide scanner (Hamamatsu C13239-01). The staining intensity was evaluated as negative, low or high expression after independent examination by two observers. Discordant assessments were reviewed jointly to obtain a conclusive consensus evaluation.
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5

Multi-chromogen IHC for Bladder Tumors

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Formalin-fixed paraffin-embedded (FFPE) 3-μm sections were used for multi-chromogen sequential immunohistochemistry (IHC). IHC was performed using the Ventana Discovery Ultra (Roche Diagnostics). This system allows automated baking, deparaffinization, and cell conditioning. Chromogen sequential IHC was performed using RUO Discovery Universal (v21.00.0019). Primary antibodies were divided into two panels targeting CD3, HLA-E, and PD-L1 (1st section) and EpCAM, HLA-ABC, and PD-1 (immediately consecutive section) were used to stain bladder tumors from patients with NMIBC (n=11) and MIBC (n=8). All primary antibodies were incubated for 60 minutes at 37°C. OmniMap HRP or NP DISCOVERY (RUO) (Roche Diagnostics) were used as secondary antibodies. The signal was detected using Discovery OmniMap (Purple (CD3 or EpCAM), Teal (PD-L1 or HLA-ABC), or Yellow (HLA-E or PD-1) kits). Mayer’s hematoxylin was used for nuclear counterstaining. Whole tissue sections on the slide were converted into high-resolution digital data using a NanoZoomer S210 Digital slide scanner (Hamamatsu).
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6

Histological Profiling of Tissue Samples

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Representative 5-μm-thick sections from formalin-fixed paraffin embedded (FFPE) blocks were used for histochemical and immunohistochemical studies. Where available, immunohistochemical staining of cases at the NIH/NCI for glial fibrillary acidic protein (GFAP), epithelial membrane antigen (EMA), Ki-67, CD34, and OLIG2 was performed using automated immunohistochemistry Roche-Ventana Bench-Mark Ultra (Roche Diagnostics Corporation, Indianapolis, USA). Stained slides were scanned with the NanoZoomer S210 Digital Slide Scanner (Hamamatsu, Japan).
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7

Whole Slide Imaging Scanner Protocols

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Whole slide imaging magnification was performed using a Hamamatsu NanoZoomer S210 Digital slide scanner (C13239-01) (Hamamatsu Photonics, K.K., Japan). Images were inspected using NanoZoomer Digital Pathology (NDP) viewer software (NDP view.2) (U12388-01) (Hamamatsu Photonics, K.K., Japan).
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8

Histological and Immunohistochemical Analysis of Tumor Samples

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Sections (3 μm-thick) were cut from formalin-fixed paraffin-embedded (FFPE) tumor tissue blocks and stained with H&E or processed for immunohistochemistry (IHC) analysis. The latter was performed using an automated platform (Ventana BenchMark AutoStainer, Ventana Medical Systems, Tucson, AZ, USA) with the following primary antibodies: anti-Ki-67 (30-9) rabbit monoclonal primary antibody (cat:790-4286, Ventana Medical Systems); cleaved Caspase-3 (Asp175) polyclonal rabbit antibody (cat:9661, Cell Signaling, Danvers, MA, USA). Antigen retrieval was performed using ULTRA Cell Conditioning Solution (ULTRA CC1) antigen retrieval buffer (pH 8.5, Ventana Medical Systems) for all sections and the Ultraview detection system (Roche Diagnostic, Milano, Italy) was used for all analysis. Appropriate positive and negative controls were included for each immunohistochemical analysis. Image acquisition was performed with Hamamatsu NanoZoomer S210 Digital Slide Scanner (Iwata-City, Japan). The number of mitotic cells was assessed by counting number of mitoses per 10 high power fields (mitosis/10HPF) on standard Hematoxylin and Eosin (H&E) stained slides (40 × magnification). Only viable cells were considered in each HPF examined within the section.
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9

Histological Analysis of Intervertebral Disc Degeneration

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L6/S1 motion segments were fixed in zinc formaldehyde and histological staining including IHC was performed as described below. Following fixation, IVD samples were decalcified with 23% formic acid solution with three changes over 72 h. After decalcification, samples were dehydrated with 2-etoxyethanol and cleared with benzyl benzoate. Post dehydration and clearing, samples were infiltrated and embedded with a custom hydrophobic resin. Embedded samples were trimmed, and 5-μm thick sections were cut with a tungsten carbide knife and mounted on adhesive microscope slides. Thin sections were plasticized using xylene and stained with Alcian Blue (AB) and Picrosirius Red (PSR) [35, 36] . Briefly, slides were stained with Weigert's hematoxylin for 10 min before staining with AB solution for 30 min and PSR for 1 h as described [35] . Slides were imaged at 20X on the Hamamatsu NanoZoomer S210 Digital Slide scanner and degenerated grades scored via standardized grading system [37] by 3 separate graders and averaged. This comprehensive scoring system accounted for the entire IVD regions of NP (cellularity, morphology, fibrosis, matrix organization), AF (cellularity, bulging, lamellar organization, clefts/fissures), the cartilage endplates (cellularity, fissures/microfractures, Schmorl's nodes), and interfaces of these different regions.
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10

FOXF1 Immunohistochemistry in NP, AF, CEP

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For FOXF1, thin sections were deplasticized using xylene for iIHC. FOXF1 (GeneTex GTX48981) rabbit polyclonal antibody was used at a dilution of 1:500 and detected with a polymer, horseradish peroxidase linked anti-rabbit secondary. DAB (diaminobenzadine) was used as the visualization chromogen. Images were then scanned using the Hamamatsu NanoZoomer S210 Digital Slide scanner and quantified by % positive cells over total cells in each NP, AF, and CEP region.
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