Ventana benchmark ultra

Manufactured by Roche

Sourced in United States, Switzerland, France, Italy, Germany, Azerbaijan, United Kingdom, Japan

The Ventana Benchmark Ultra is a fully automated, open platform slide stainer designed for immunohistochemistry (IHC) and in situ hybridization (ISH) assays. It provides consistent and reliable sample processing for routine and advanced laboratory testing.

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285 protocols using ventana benchmark ultra

Multiplex IHC Analysis of FFPE Tissue

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Five-micron sections of FFPE tissue were assessed for PD-L1 expression, TILs, JAK1, and phosphorylated JAK1 protein expression using the following antibodies and detection methods following the manufacturer's protocol: PD-L1 (1:3 dilution, clone SP142 [Springer Biosciences], Leica Bond [Leica Biosystems]), CD3 (predilute, clone 2GV6, Ventana and Ventana BenchMark Ultra [Ventana Medical Systems]), and CD8 (1:25, clone CD8/144B [Dako], Ventana BenchMark Ultra [Ventana Medical Systems]), JAK1 (1:500), and phosphorylated JAK1Tyr1034/1035 (1:100) (Cell Signaling Technologies Inc.).

Takahashi N., Rajapakse V.N., Pongor L., Kumar S., Tlemsani C., Erwin-Cohen R., Young H.A., Hewitt S., Wei J.S., Khan J., Villarino A.V., Trepel J.B, & Thomas A. (2020). Dynamics of genomic and immune responses during primary immunotherapy resistance in mismatch repair–deficient tumors. Cold Spring Harbor Molecular Case Studies, 6(5), a005678.

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Optimized NKX3.1 IHC Protocol

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The NKX3.1 immunohistochemistry was performed on the Ventana Benchmark Ultra platform in Royal Derby Hospital, United Kingdom and Memorial Sloan Cancer Center, USA. In Royal Derby Hospital, the manufacturers recommended protocol was used. The antibody (antibody clone EP356) supplied by Cell Marque was ready to use and was optimally diluted by the manufacturer for use on the Ventana Benchmark Ultra in combination with Ventana detection kits and accessories. No further dilution or titration was carried out. The recommended staining protocol with ultraView detection kit included deparaffinization, antigen retrieval with Cell Conditioning 1, a primary antibody incubation time of 32 minutes at 36°C, counterstaining with Haematoxylin II for 8 minutes and post counterstaining bluing for 4 minutes. In Memorial Sloan Cancer Center, a similar protocol was used with some modifications. Normal prostatic tissue and a prostatic adenocarcinoma were used as a positive control and positive staining was identified as strong, crisp, nuclear staining with a clean background.

Hawari R., Fernandes L., Park K.J, & McCluggage W.G. (2021). SKENE’S GLAND DERIVATIVES IN THE FEMALE GENITAL TRACT AND CERVICAL ADENOID BASAL CARCINOMA ARE CONSISTENTLY POSITIVE WITH PROSTATIC MARKER NKX3.1.. International journal of gynecological pathology : official journal of the International Society of Gynecological Pathologists, 40(4), 400-407.

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Automated FOXD1 Immunohistochemistry Protocol

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Immunohistochemistry was performed with an automated, validated, and accredited staining system (Ventana Benchmark ULTRA, Ventana Medical Systems, Tucson, AZ, USA) using an ultraview Universal Alkaline Phosphatase Red Detection Kit (Ventana reference no. 760-501). Following deparaffinization and heat-induced antigen retrieval (CC1 for 32 min), the tissue samples were incubated for 32 min with the FOXD1 antibody (1:800 dilution, Abcam, Waltham, MA, USA, #129324). Counterstain was done by hematoxylin II stain for 12 min and a blue coloring reagent for 8 min according to the manufacturer’s instructions (Ventana Benchmark ULTRA, Ventana Medical Systems, Tucson, AZ, USA). For each slide, healthy kidney tissue was used as a positive control.

van den Bosch Q.C., Nguyen J.Q., Brands T., van den Bosch T.P., Verdijk R.M., Paridaens D., Naus N.C., de Klein A., Kiliç E, & Brosens E. (2022). FOXD1 Is a Transcription Factor Important for Uveal Melanocyte Development and Associated with High-Risk Uveal Melanoma. Cancers, 14(15), 3668.

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Immunohistochemical Staining of SOX10 in Melanoma

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From each tissue block, one paraffin section of 3 µm was cut and mounted on a Superfrost Plus slide (Thermo Fisher Scientific, Waltham, MA, USA). They were dried at 60 °C for 1 h. H&E stains were performed by Ventana HE 600 (Roche Diagnostics, Tucson, AZ, USA) and IHC by Ventana Benchmark Ultra (Roche Diagnostics). SOX10 IHC positivity was visualized with the SOX-10 Rabbit Monoclonal Primary Antibody (SP267; ready-to-use; 32 min; Roche Diagnostics) in combination with either the OptiView DAB IHC Detection Kit (Roche Diagnostics; brown chromogen) or the ultraView Universal Alkaline Phosphatase Red Detection Kit (Roche Diagnostics; red chromogen). Standard settings and regent kits of Ventana Benchmark Ultra (Roche Diagnostics) were used for antigen retrieval (Cc1, 32 min) and endogenous peroxidase blocking (only DAB stains). Immunohistochemical slides were counterstained with Mayer’s hematoxylin and bluing reagent. Internal controls were present in primary melanomas (SOX10 positivity in epidermis).

Nielsen P.S., Georgsen J.B., Vinding M.S., Østergaard L.R, & Steiniche T. (2022). Computer-Assisted Annotation of Digital H&E/SOX10 Dual Stains Generates High-Performing Convolutional Neural Network for Calculating Tumor Burden in H&E-Stained Cutaneous Melanoma. International Journal of Environmental Research and Public Health, 19(21), 14327.

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Immunohistochemical Localization of HLA Class I

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The cellular localization of HLA class I was assessed on paraffin-embedded sections obtained from non-transplantable donor kidneys and peritumoral tissue derived from nephrectomies performed for oncological reasons.
Immunohistochemistry was conducted using the OptiView Universal DAB Detection Kit and an automated staining system, the Ventana Benchmark ULTRA (Ventana Medical Systems, Oro Valley, AZ, USA), following previously established protocols.42 (link),43 (link) With this published protocol, the kidney samples were stained using an anti-HLA class I antibody (clone TP25.99SF, Bio-Techne). For verification purposes, an anti-HLA class I with a different clone (clone EMR8-5, Abcam, Cambridge, UK) was also employed.

Wu L., van Heugten M.H., van den Bosch T.P., Duimel H., López-Iglesias C., Hesselink D.A., Baan C.C, & Boer K. (2024). Polarized HLA Class I Expression on Renal Tubules Hinders the Detection of Donor-Specific Urinary Extracellular Vesicles. International Journal of Nanomedicine, 19, 3497-3511.

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Detection of Lymph Node Micrometastases

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Formalin-fixed, paraffin-embedded tissue blocks of the lymph nodes were retrieved from the tissue archives of the departments of pathology in the AMC and UMCG. Four new levels of each lymph node with a distance of 250 µm between the levels were investigated. Two 4 µm thick sections of each level were cut serially. One section was stained with H&E and one with an antibody against K19 (dilation 1:100, clone RCK108; Dako, Glostrup, Denmark). All staining procedures were performed in the UMCG. The K19 staining was performed using a Ventana Benchmark Ultra automated stainer (Ventana Medical Systems, Tucson, AZ, USA) after pretreatment with protease.
Micrometastases were defined as cells detected by immunostaining with morphologic features of adenocarcinoma. H&E and K19 immunolabeled slides were investigated by two experienced pathologists (ASHG and JJD) blinded to the demographic and clinicopathologic features of patients.

Mantel H.T., Wiggers J.K., Verheij J., Doff J.J., Sieders E., van Gulik T.M., Gouw A.S, & Porte R.J. (2015). Lymph Node Micrometastases are Associated with Worse Survival in Patients with Otherwise Node-Negative Hilar Cholangiocarcinoma. Annals of Surgical Oncology, 22, 1107-1115.

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Immunohistochemical Staining of LRIG Proteins

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Five-micrometer thick sections from formalin-fixed, paraffin-embedded biopsies were obtained from archival tissue. After sectioning, they were deparaffinized, rehydrated, and rinsed in water. The Ventana standard procedure was used for immunohistochemical staining in a Ventana BenchMark ULTRA (Ventana Medical Systems, Tucson, AZ, USA). CC1 buffer was used for antigen retrieval. The following antibodies were used: rabbit anti-LRIG1-Vina 16, 22 µg/mL; rabbit anti-LRIG2-151 14, 3 µg/mL; rabbit anti-LRIG3 207-221 34, 8.8 µg/mL.

Razumova Z., Oda H., Govorov I., Lundin E., Östensson E., Lindquist D, & Mints M. (2021). The Prognostic Role of LRIG Proteins in Endometrial Cancer. Cancers, 13(6), 1361.

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Detection of EBV-infected Tumors by EBER CISH

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For detection of Epstein-Barr virus (EBV)-infected tumours, the presence of EBV-encoded RNA (EBER) transcripts was analysed by chromogenic in situ hybridization on 4-μm-thick TMA sections with appropriate controls, performed on the Ventana Benchmark ULTRA automated platform (Ventana Medical Systems, Tucson, AZ, USA) following the manufacturer's protocol. The EBER 1 DNP probe (760-1209, Ventana Medical Systems) was used for detection, ISH iVIEW Blue Plus Detection kit (760-097, Ventana Medical Systems) was used to produce the chromogenic reaction, and slides were counterstained with Red Counterstain II (780-2218, Ventana Medical Systems).

Svensson M.C., Borg D., Zhang C., Hedner C., Nodin B., Uhlén M., Mardinoglu A., Leandersson K, & Jirström K. (2019). Expression of PD-L1 and PD-1 in Chemoradiotherapy-Naïve Esophageal and Gastric Adenocarcinoma: Relationship With Mismatch Repair Status and Survival. Frontiers in Oncology, 9, 136.

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Immunohistochemical Profiling of Lymphoma

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Immunohistochemical stains were performed on the cell blocks using Leica Bond (Leica Biosystems, Buffalo Grove, IL, USA) and Ventana Benchmark Ultra (Ventana Medical Systems, Tucson, AZ, USA) immunostainers with satisfactory negative and positive controls. The antibodies, clones, dilutions, and manufacturers are summarized in Table 2. Expression of BCL6, CD10 and MUM1 in the lymphoma cells was evaluated with a cutoff of 30% for each antibody. The cell-of-origin (COO) of the selected cases was classified into either germinal center B-cell (GCB) or non-GCB subtype according to the Hans algorithm.^{55 (link)} The cutoff for BCL2 and MYC expression was set at 50% and 40%, respectively, according to the literature.^{56 (link)} Ki67 was utilized to assess the proliferation rate of lymphoma cells (0–100%). The immunostains of other antibodies were graded as negative or positive.

Gisriel S.D., Yuan J., Braunberger R.C., Maracaja D.L., Chen X., Wu X., McCracken J., Chen M., Xie Y., Brown L.E., Li P., Zhou Y., Sethi T., McHenry A., Hauser R.G., Paulson N., Tang H., Hsi E.D., Wang E., Zhang Q.Y., Young K.H., Xu M.L, & Pan Z. (2022). Human herpesvirus 8-negative effusion-based large B-cell lymphoma: a distinct entity with unique clinicopathologic characteristics. Modern pathology : an official journal of the United States and Canadian Academy of Pathology, Inc, 35(10), 1411-1422.

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Immunohistochemical Analysis of p27Kip1

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Immunohistochemistry for p27^Kip1 was performed on archived formalin-fixed paraffin embedded tissue using a commercially available mouse monoclonal antibody (RRID: AB_11190322, https://scicrunch.org/resources/Any/search?q=AB_11190322&l=AB_11190322, clone SX53G8, predilute, catalog number LS-C389523, Ventana Medical Systems, Tucson, AZ, USA) on an automated staining platform—the Ventana BenchMark Ultra (Ventana Medical Systems) using the manufacturer’s protocol.

Seabrook A., Wijewardene A., De Sousa S., Wong T., Sheriff N., Gill A.J., Iyer R., Field M., Luxford C., Clifton-Bligh R., McCormack A, & Tucker K. (2022). MEN4, the MEN1 Mimicker: A Case Series of three Phenotypically Heterogenous Patients With Unique CDKN1B Mutations. The Journal of Clinical Endocrinology and Metabolism, 107(8), 2339-2349.

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