Liver biopsies from chronic hepatitis B (n = 26) and non-infected subjects (n = 8) were collected with informed consent to have a small part of their biopsy specimen, exceeding that needed for complete pathology examination, used for research purposes. The local ethical committee approved the use of this archival material (CE90/19) together with anonymised clinical and demographic data for the purposes of this study. Samples of each biopsy were stored in RNAlater (Thermo Fisher, Waltham, MA, USA) at −80 °C or fixed in 10% buffered formalin. Paraffin-embedded sections (5 μm) were stained with hematoxylin and eosin, Masson’s trichrome, and Gomori’s silver impregnation for reticulin fibres. Histological grading and staging scores were determined according to the Ishak scoring system [19 (link)]. Immunohistochemistry was performed on sections of fixed liver biopsies with a commercial streptavidin–biotin technique according to the manufacturer’s instructions on a BENCHMARK XT staining system (Ventana Medical Systems, Tucson, AZ, USA) using primary mouse monoclonal antibodies against HBcAg (clone LF161, Novocastra TM IHC Antibodies, Leica Biosystems, Wetzlar, Germany) or HBsAg (clone 3E7, Santa Cruz Biotechnology, Dallas, TX, USA).
Benchmark xt staining system
Manufactured by Roche
Sourced in United States
The BenchMark XT Staining System is an automated instrument designed for the staining of histological samples. It performs standardized immunohistochemistry and in situ hybridization protocols to enable consistent and reliable results.
Automatically generated - may contain errors
Lab products found in correlation
Rnalater, by Thermo Fisher Scientific (2 mentions)
Ultraview sish detection kit, by Roche (1 mentions)
Pr clone 1e2, by Roche (1 mentions)
Her2 pathway clone 4b5, by Roche (1 mentions)
Clone sp1, by Roche (1 mentions)
Optiview dab detection kit, by Roche (1 mentions)
Ki 67 clone 30 9, by Roche (1 mentions)
Ventana sp263, by Roche (1 mentions)
Autostainer link 48, by Agilent Technologies (1 mentions)
Envision dab detection system, by Agilent Technologies (1 mentions)
22c3 pharmdx, by Agilent Technologies (1 mentions)
Af1027, by R&D Systems (1 mentions)
Ultraview universal dab detection kit, by Roche (1 mentions)
7 protocols using benchmark xt staining system
1
Hepatitis B Liver Biopsy Protocol
2
Immunohistochemical Evaluation of Breast Cancer
Check if the same lab product or an alternative is used in the 5 most similar protocols
+ Expand
The immunohistochemistry analysis was performed using specific antibodies against ER, Clone SP1 (Ventana Medical Systems Inc., Tucson, AZ, USA); PR Clone 1E2 (Ventana Medical Systems); Ki67, Clone 30-9 (Roche Diagnostics K.K., Tokyo, Japan); AR Clone SP107 (Cell-MarqueTM, Rocklin, CA, USA); HER2 PATHWAY Clone 4B5 (Ventana Medical Systems). Immunostaining was performed using the Ventana Benchmark XT staining system with Optiview DAB detection kit. In cases of HER2 with equivocal immunohistochemical score (2+), we performed HER2 gene amplification by ultra-View SISH Detection Kit (Ventana Medical Systems). Evaluation of immunostaining and SISH for HER2 was based on American Society of Clinical Oncology/College of American Pathologists (ASCO/CAP) recommendations [6 (link)]. ER, PR and AR expression was considered positive if at least 10% immunostained tumor nuclei were detected in the sample [17 (link)]. Ki67 was scored low if <14% of tumor nuclei were positive and high if ≥14% of tumor nuclei were positive [35 (link)].
3
Immunohistochemistry Protocol for VWA5A
Check if the same lab product or an alternative is used in the 5 most similar protocols
+ Expand
From the TMA block of the validation set, 4 μm thick sections were taken to perform IHC for VWA5A. Monoclonal anti-VWA5A antibody (dilution 1:400; clone OTI3D6; Novus Biologicals, Centennial, CO, USA) was used, and immunostaining was performed using Benchmark automatic immunostaining device (Ventana BenchMark XT Staining System, Tucson, AZ) following the manufacturer’s guidelines. Interpretation of the IHC slides were done by a breast pathologist (K.J.) using histoscore (H-score) while blinded to the clinicopathological characteristics. H-score of 50 was used as a cut-off value discriminating VWA5A-high and VWA5A-low.
4
EGFR and PD-L1 Biomarker Analysis Protocol
Check if the same lab product or an alternative is used in the 5 most similar protocols
+ Expand
EGFR gene mutations were analyzed by a peptide nucleic acid (PNA) clamping-based sensitive method (PNA Clamp™ or PANAMutyper™ EGFR mutation detection kit) in formalin-fixed paraffin-embedded tissues (16 (link)-18 (link)). EGFR-activating mutations were defined as mutations associated with EGFR-TKI sensitivity, including exon 19 deletion, exon 21 L858R, and L861Q.
Diagnostic assays based on PD-L1 immunohistochemistry were performed according to the manufacturer’s instructions. The following antibodies and detection systems were utilized: mouse monoclonal primary anti–PD-L1 antibody, 22C3 pharmDx (prediluted, clone 22C3, Dako, Carpinteria, CA, USA) with an Autostainer Link 48 and an EnVision DAB Detection System (Agilent Technologies, Santa Clara, CA, USA); rabbit monoclonal primary anti-PD-L1 antibody, Ventana SP263 (prediluted, Ventana Medical Systems, Tucson, AZ, USA) with a Benchmark XT staining system and Ultra with OptiView Universal DAB Detection Kit (Ventana Medical Systems). The staining results were interpreted by expert lung pathologists. The percentage of tumor cells with membranous PD-L1 staining of any intensity (tumor proportion score, TPS) was categorized into three ranges and the corresponding groups (<1%, negative expression; 1–49%, weak expression; ≥50%, strong expression).
Diagnostic assays based on PD-L1 immunohistochemistry were performed according to the manufacturer’s instructions. The following antibodies and detection systems were utilized: mouse monoclonal primary anti–PD-L1 antibody, 22C3 pharmDx (prediluted, clone 22C3, Dako, Carpinteria, CA, USA) with an Autostainer Link 48 and an EnVision DAB Detection System (Agilent Technologies, Santa Clara, CA, USA); rabbit monoclonal primary anti-PD-L1 antibody, Ventana SP263 (prediluted, Ventana Medical Systems, Tucson, AZ, USA) with a Benchmark XT staining system and Ultra with OptiView Universal DAB Detection Kit (Ventana Medical Systems). The staining results were interpreted by expert lung pathologists. The percentage of tumor cells with membranous PD-L1 staining of any intensity (tumor proportion score, TPS) was categorized into three ranges and the corresponding groups (<1%, negative expression; 1–49%, weak expression; ≥50%, strong expression).
5
Immunohistochemical Evaluation of Biomarkers
Check if the same lab product or an alternative is used in the 5 most similar protocols
+ Expand
Immunoreactive markers were selected using three common candidate proteins from the machine learning algorithms subsequently validated by immunohistochemistry for 123 cases of independent needle biopsy FFPE samples which were obtained before chemotherapy. Standard immunohistochemistry procedures for the slides prepared by fixation in 10% neutral buffered formalin solution or 95% ethanol were performed using a benchmark automatic immunostaining device (Ventana BenchMark XT Staining System, Tucson, AZ, USA). The slides were incubated with anti-KIAA1522 (NBP1-90915, Novusbio) diluted 1:300, anti-PDCD6 (NBP1-19741, Novusbio) diluted 1:500, and anti-YARS (NBP1-86890, Novusbio) diluted 1:150. The immunohistochemical interpretation was evaluated by a semi-quantitative approach using an “H-score [17 (link)] in a blind and independent manner by two pathologists (H.J.O. and H.S.R.).
6
Immunohistochemical Profiling of HER2+ Breast Cancer
Check if the same lab product or an alternative is used in the 5 most similar protocols
+ Expand
Immunohistochemical staining was performed in formalin-fixed paraffin-embedded samples from 38 cases of HER2+ human BC obtained through needle biopsy prior to chemotherapy. The blocks were sectioned (thickness: 3 μm), and standard immunohistochemistry procedures for the slides prepared by fixation in 10% neutral buffered formalin solution or 95% ethanol were performed using a BenchMark automatic immunostaining device (Ventana BenchMark XT Staining System, Tucson, AZ, USA). Slides were incubated with anti-CD147 (GTX20666; GeneTex; dilution 1:75) and anti-CD276 (AF1027; R&D Systems; dilution 1:2,000). The immunohistochemical interpretation was evaluated by a semi-quantitative approach using an “H-score”41 (link) in blind and independent manner by two pathologists (HSR and MSJ).
7
Immunohistochemical Analysis of MUC4 Expression in Gastric Cancer
Check if the same lab product or an alternative is used in the 5 most similar protocols
+ Expand
Antral noncancerous mucosa was evaluated using IHC from 15 GC patients and 8 non-GC participants who consented to endoscopic biopsy. In the case of GC patients, cancer tissue was also stained. The antibody for detecting MUC4 (clone: 8G7) (1:100 dilution, Zeta Corporation, Arcadia, CA, USA) was used for IHC. The antibody we have used for IHC detects MUC4α region. The specificity of the antibody was evidenced by previous studies. Overall staining of sections (4 μm thick) was conducted via the BenchMark XT Staining system and ultraVIEW Universal DAB Detection Kit (Ventana Medical Systems, Inc., Tucson, AZ, USA). MUC4 expression was evaluated using light microscopy via multiplication of the intensity by area (%), where staining was observed in the epithelial glands (0 to 300):0, no staining;1+, faint/barely perceptible partial staining; 2+, weak to moderate staining; 3+, strong staining. In cancerous tissue, only strongly stained area loci were included for scoring. Each sample was scored in a blinded manner by a single pathologist (HSL).
About PubCompare
Our mission is to provide scientists with the largest repository of trustworthy protocols and intelligent analytical tools, thereby offering them extensive information to design robust protocols aimed at minimizing the risk of failures.
We believe that the most crucial aspect is to grant scientists access to a wide range of reliable sources and new useful tools that surpass human capabilities.
However, we trust in allowing scientists to determine how to construct their own protocols based on this information, as they are the experts in their field.
Ready to get started?
Sign up for free.
Registration takes 20 seconds.
Available from any computer
No download required
Revolutionizing how scientists
search and build protocols!