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Ini 1

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The INI-1 is a laboratory equipment designed for the measurement and analysis of various parameters. It is capable of performing a range of functions essential for research and testing purposes. The core function of the INI-1 is to provide accurate and reliable data for scientific applications.

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Lab products found in correlation

Benchmark xt, by Roche (2 mentions) Cytokeratin ae1 3, by Merck Group (2 mentions) Calretinin, by Biocare Medical (2 mentions) Desmin, by Agilent Technologies (2 mentions) S100 protein, by Roche (2 mentions) Chromogranin a, by Agilent Technologies (1 mentions) Glial fibrillary acidic protein (gfap), by BioGenex (1 mentions) Hep par 1, by Agilent Technologies (1 mentions) Ventana staining system, by Roche (1 mentions) Bond polymer refine detection system, by Leica (1 mentions) Hpa001906, by Merck Group (1 mentions) E cadherin clone eccd 2, by Thermo Fisher Scientific (1 mentions) Ventanabenchmark xt automatic, by Roche (1 mentions) Bcor c 10, by Santa Cruz Biotechnology (1 mentions) Myogenin f5d, by Agilent Technologies (1 mentions) Ae1 ae3, by Agilent Technologies (1 mentions) Ultraview universal dab detection kit, by Roche (1 mentions) Ema e29, by Agilent Technologies (1 mentions) Cd34 qbend 10, by Agilent Technologies (1 mentions) Desmin d33, by Agilent Technologies (1 mentions)

8 protocols using ini 1

1

Comprehensive Immunohistochemical Analysis of Tumors

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Immunohistochemistry (IHC) was performed using Envision+ Dual Link, Peroxidase (Dakocytomation) or standard streptavidin technique (Jackson) with a 3-3’-diaminobenzadine (DAB) chromogen. The primary anti-bodies utilized for classification of this tumor were as follows: CD99 (M; O13; Signet), desmin (M; 33; Accurate Chemical & Scientific), smooth muscle actin (SMA) (M; IA4; Dako), chromogranin A (R; Dako), epithelial membrane antigen (EMA) (M; E29; Cell Marque), S-100 (P; Dako), vimentin (M; V9; BioGenex), cytokeratin cocktail (M; AE1 and AE3 and CAM 5.2, KA4 and UC2/PR-10-11; Becton-Dickerson and Zymed/ThermoFisher Scientific), CD45 (M; PD7/26 and 2B11; Cell Marque); CD138 (M; MI15; Dako), CD31 (M; JC/70A; Cell Marque), CD34 (M; QBEnd/10; Dako), PLAP (M; 8A9; Dako), CD68 (M; KPI; Cell Marque), CD117 (R; Diagnostics Biosystems), GFAP (M; GA-5 Biogenex), INI-1 (M; BAF47; BD Bioscience), and WT-1 (M;6F-H2; Dako).
Donahue J.E., Yakirevich E., Zhong S., Treaba D.O., Lakis N.S., Ali S.M., de la Monte S.M, & Mangray S. (2017). Primary Spinal Epidural CIC-DUX4 Undifferentiated Sarcoma in a Child. Pediatric and developmental pathology : the official journal of the Society for Pediatric Pathology and the Paediatric Pathology Society, 21(4), 411-417.
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2

Immunohistochemical Staining of FFPE Tissue

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Immunohistochemical staining was performed on 5-micron cut sections of formalin-fixed, paraffin-embedded (FFPE) tissue blocks of all cases on Ventana staining system (Ventana Medical Systems, Tucson AZ, USA). All cases were stained with INI1 (monoclonal mouse antibody; 1:400; BD Bioscience, San Jose, CA, USA), Hep-par1 (mouse monoclonal antibody; 1:200; Dako, Santa Clara, CA, USA), Arginase (rabbit monoclonal antibody; 1:100; Sigma-Aldrich, St. Louis, MO, USA) and glypican-3 (mouse monoclonal antibody; ready to use; Sigma-Aldrich, St. Louis, MO, USA) antibodies.
Fazlollahi L., Hsiao S.J., Kochhar M., Mansukhani M.M., Yamashiro D.J, & Remotti H.E. (2019). Malignant Rhabdoid Tumor, an Aggressive Tumor Often Misclassified as Small Cell Variant of Hepatoblastoma. Cancers, 11(12), 1992.
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3

Immunohistochemical Characterization of Tumors

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When necessary, additional immunohistochemical stains were performed to facilitate the reclassification of tumors using the 2016 WHO classification system including molecular subgrouping of medulloblastomas. These immunohistochemical stains included: INI‐1 (BD Biosciences, 612111, 1:100), BRG1 (Santa Cruz Biotechnology, sc‐17796, 1:400), GFAP (Dako, 6F2, 1:400), synaptophysin (Dako, SY38, 1:100), neurofilament (Thermo Scientific, QL215385, 1:400), EMA (Dako, E29, 1:200), IDH1‐R132H (Dianova, DIA‐H09‐L), ATRX (Sigma, HPA001906, 1:100), H3K27M (Sigma, SAB5600095, 1:1000), GAB1 (Santa Cruz Biotechnology, sc‐133191, 1:400), YAP1 (Santa Cruz Biotechnology, sc‐101199, 1:200), LEF1 (abcam, EPR2029Y, 1:100), beta‐catenin (BD Biosciences, 610154, 1:1000) and p53 (Dako, DO‐7, 1:100). Staining was performed on the Leica Bond‐IIITM Autostainer using the Bond Polymer Refine Detection System (Leica Microsystems DS9800) with the DAB chromagen. Nuclei were counterstained with hematoxylin. Other immunostains that were previously performed as part of the initial clinical immunohistochemical workup included: vimentin, OLIG2, CD45, TdT, desmin, myoD1, myogenin, OCT4, HMB45, SOX10, AE1‐3, transthyretin, CD31 and CD34.
Viaene A.N., Pu C., Perry A., Li M.M., Luo M, & Santi M. (2020). Congenital tumors of the central nervous system: an institutional review of 64 cases with emphasis on tumors with unique histologic and molecular characteristics. Brain Pathology, 31(1), 45-60.
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4

Immunohistochemical Evaluation of INI1

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Tissues were fixed in 4% paraformaldehyde, dehydrated and embedded in paraffin. Immunohistochemistry was performed according to standard protocols on 3–4 µm sections. Sections were subjected to H&E and immunohistochemical staining with the following primary antibodies: INI1 (BD Transduction Laboratories, 612111, 1:400).
Custers L., Khabirova E., Coorens T.H., Oliver T.R., Calandrini C., Young M.D., Vieira Braga F.A., Ellis P., Mamanova L., Segers H., Maat A., Kool M., Hoving E.W., van den Heuvel-Eibrink M.M., Nicholson J., Straathof K., Hook L., de Krijger R.R., Trayers C., Allinson K., Behjati S, & Drost J. (2021). Somatic mutations and single-cell transcriptomes reveal the root of malignant rhabdoid tumours. Nature Communications, 12, 1407.
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5

Immunohistochemical Profiling of Tumor Markers

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Immunohistochemical labeling was performed on the Benchmark XT autostainer (Ventana Medical Systems Inc, Tucson, AZ) using the I-View detection kit. The standard antibodies used, vendors, pretreatments, and dilutions included: cytokeratin AE1/3 (Chemicon, steam, 1:4000), EMA (Ventana, 760–4259, steam, prediluted), WT1 (Cell Marque, clone 6F-H2, Steam, Prediluted), Calretinin (Biocare, Steam, Prediluted polyclonal), desmin (Dako M0760, clone D33, steam, 1:100), CD99 (Leica, Clone 12E7, steam, prediluted), S100 protein (Ventana, 760–2914, stream, prediluted), BAP-1 (Santa Cruz, clone C-4, steam, 1:200), and INI-1 (BD Transduction Laboratories, clone 25/BAF47, steam, 1:100).
Argani P., Harvey I., Nielsen G.P., Takano A., Suurmeijer A.J., Voltaggio L., Zhang L., Sung Y.S., Stenzinger A., Mechtersheimer G., Dickson B.C, & Antonescu C.R. (2020). EWSR1/FUS-CREB Fusions Define a Distinctive Malignant Epithelioid Neoplasm with Predilection for Mesothelial-Lined Cavities. Modern pathology : an official journal of the United States and Canadian Academy of Pathology, Inc, 33(11), 2233-2243.
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6

Multimodal Tissue Profiling Protocol

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Tissues and organoids were fixed in 4% paraformaldehyde, dehydrated and embedded in paraffin. Immunohistochemistry was performed according to standard protocols on 3–4 µm sections. Sections were subjected to H&E, immunohistochemical as well as immunofluorescence staining. The following primary antibodies were used for immunohistochemical staining: desmin (Leica Novacastra, NCL-L-Des-Der11, 1:100), INI-1 (BD Transduction Laboratories, 612111, 1:400), P53 (Dako, M7001, 1:6000). For immunofluorescence on tissues: SIX2 (Proteintech, 11562-1-AP, 1:200), E-cadherin clone ECCD-2 (ThermoFisher, 13-1900, 1:200), CD90 clone EPR3133 (Abcam, 133350, 1:100) were used. Imaging was performed using Leica DM6 microscope.
Calandrini C., Schutgens F., Oka R., Margaritis T., Candelli T., Mathijsen L., Ammerlaan C., van Ineveld R.L., Derakhshan S., de Haan S., Dolman E., Lijnzaad P., Custers L., Begthel H., Kerstens H.H., Visser L.L., Rookmaaker M., Verhaar M., Tytgat G.A., Kemmeren P., de Krijger R.R., Al-Saadi R., Pritchard-Jones K., Kool M., Rios A.C., van den Heuvel-Eibrink M.M., Molenaar J.J., van Boxtel R., Holstege F.C., Clevers H, & Drost J. (2020). An organoid biobank for childhood kidney cancers that captures disease and tissue heterogeneity. Nature Communications, 11, 1310.
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7

Immunohistochemical Profiling of Tumor Markers

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Immunohistochemical labeling was performed on the Benchmark XT autostainer (Ventana Medical Systems Inc, Tucson, AZ) using the I-View detection kit. The standard antibodies used, vendors, pretreatments, and dilutions included: cytokeratin AE1/3 (Chemicon, steam, 1:4000), EMA (Ventana, 760–4259, steam, prediluted), WT1 (Cell Marque, clone 6F-H2, Steam, Prediluted), Calretinin (Biocare, Steam, Prediluted polyclonal), desmin (Dako M0760, clone D33, steam, 1:100), CD99 (Leica, Clone 12E7, steam, prediluted), S100 protein (Ventana, 760–2914, stream, prediluted), BAP-1 (Santa Cruz, clone C-4, steam, 1:200), and INI-1 (BD Transduction Laboratories, clone 25/BAF47, steam, 1:100).
Argani P., Harvey I., Nielsen G.P., Takano A., Suurmeijer A.J., Voltaggio L., Zhang L., Sung Y.S., Stenzinger A., Mechtersheimer G., Dickson B.C, & Antonescu C.R. (2020). EWSR1/FUS-CREB Fusions Define a Distinctive Malignant Epithelioid Neoplasm with Predilection for Mesothelial-Lined Cavities. Modern pathology : an official journal of the United States and Canadian Academy of Pathology, Inc, 33(11), 2233-2243.
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8

Immunohistochemical Analysis of Soft Tissue Tumors

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Sections were cut at 4 μm thick from formalin-fixed-paraffin-embedded (FFPE) tissue and immunostained using a VentanaBenchmark XT automatic stainer (Ventana, Tuscon, AZ, USA). Signals were revealed using the ultraView Universal Dab Detection kit (Ventana). The following antibodies were used: CD99 (12E7, Dako), EMA (E29, 1:50, Dako), desmin (D33, 1:80, Dako), cytokeratin AE1/AE3 (AE1/AE3, 1:50, Dako), caldesmon (h-CD, 1:100, Dako), myogenin (F5D, 1:100, Dako), S100 protein (Z0311, 1:800, Dako), CD34 (QBend-10, 1:25, Dako), INI1 (25, 1:50, BD Transduction Laboratories), BCOR (C-10, 1:50, Santa Cruz), ETV4 (16, 1:50, Santa Cruz). Immunohistochemistry for NTRK1 was performed using a 32 min incubation with the NTRK1 antibody (ab76291, clot EP1058Y, Abcam, dilution 1:200) on a Ventana ULTRA machine with Cell Conditioning Solution 1 pre-treatment for 64 min.
Alholle A., Karanian M., Brini A.T., Morris M.R., Kannappan V., Niada S., Niblett A., Ranchère-Vince D., Pissaloux D., Delfour C., Gonzalez A.M., Antonescu C.R., Sumathi V., Tirode F, & Latif F. (2018). Genetic analyses of undifferentiated small round cell sarcoma identifies a novel sarcoma subtype with a recurrent CRTC1-SS18 gene fusion. The Journal of pathology, 245(2), 186-196.
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