ISH Quantification
ISH QUANTIFICATION
(Designed for RNAscope®)
Product Overview
Indica Labs In-situ Hybridization (ISH) module is recognized as the fastest, most accurate and user friendly analysis tool for quantifying nucleic acid probes across tissues and cell lines. This module measures up to dual chromogenic and/or silver-labeled DNA or RNA ISH probes on a cell-by-cell basis. This allows the user to rapidly contextualize the gene expression profile of every cell across the tissue. HALO® ISH analysis is designed to work with single or dual RNA ISH assays including RNAscope™ and supports the H-score protocol for RNAscope as recommended by the manufacturer, ACD, a Bio-techne brand.
Advance your RNAscope image analysis by downloading the latest Quantitative RNAscope Image Analysis Guide from Indica Labs and ACD, a Bio-techne brand and view the latest high-impact publications using HALO RNAscope image analysis.
Three examples of ISH quantification are shown in the slider above. In the first example, a kidney section is probed with a single RNA ISH probe (brown) and hematoxylin counterstain. Negative cells are white in the markup image and cells positive for RNA probe are labeled in different shades of red according to their RNAscope score – cells with between 1-3 probe = +1 (light pink), 4-9 spots = +2 (dark pink), 10-13 spots = +3 (light red) and >14 spots = +4 (dark red) as shown in the image below.
The second example is a dual RNA ISH assay in tumor using red and blue probes. Negative cells are identified using a white overlay mask. Cells positive for the red probe only are shown in different shades of red according to their RNAscope score as described for the single probe assay above. Cells positive for the blue probe only are shown in different shades of green according to their RNAscope score. Cells positive for both markers are in shades of yellow representing the ratio of red: blue probe.
The last example is a dual DNA ISH assay. Like the dual RNA ISH assay, cells containing red probe only are in shades of red, black probe only are in shades of green, cells with both probes are in shades of yellow, and probes with no probe are white.
The module reports the total number of cells, total number of spots, total area of spots, the average number of spots per cell and per unit area of tissue, the average area of spots per cell and per unit area of tissue, as well as the number and percentage of cells with RNAscope score of 0, 1+, 2+, 3+ and 4+. When two probes are present, the module also reports the ratio of probe 1: probe 2. Histograms are automatically generated representing the frequency distribution of probes per cell [Figure 1) and RNAscope cell scoring [Figure 2] as shown below.
Figure 1 shows a distribution curve of probe number on a cell by cell basis, in this example most cells were shown to have between 0-5 copies per cell.
Figure 2. This bar chart shows the numbers of cells that were categorized as 0, 1+, 2+, 3+ and 4+ respectively. The chart shows that a slim majority of cells were positive for RNA probe expression.
The ISH quantification module integrates seamlessly into the HALO® platform which is compatible with a number of third party systems and file formats.
Contact info@indicalab.com for product demonstration and pricing information or upload some images for a free trial.
ISH QUANTIFICATION
(Designed for RNAscope®)
Indica Labs In-situ Hybridization (ISH) module is recognized as the fastest, most accurate and user friendly analysis tool for quantifying nucleic acid probes across tissues and cell lines. This module measures up to dual chromogenic and/or silver-labeled DNA or RNA ISH probes on a cell-by-cell basis. This allows the user to rapidly contextualize the gene expression profile of every cell across the tissue. HALO® ISH analysis is designed to work with single or dual RNA ISH assays including RNAscope™ and supports the H-score protocol for RNAscope as recommended by the manufacturer, ACD, a Bio-techne brand.
Advance your RNAscope image analysis by downloading the latest Quantitative RNAscope Image Analysis Guide from Indica Labs and ACD, a Bio-techne brand and view the latest high-impact publications using HALO RNAscope Image analysis.
Three examples of ISH quantification are shown in the slider above. In the first example, a kidney section is probed with a single RNA ISH probe (brown) and hematoxylin counterstain. Negative cells are white in the markup image and cells positive for RNA probe are labeled in different shades of red according to their RNAscope score – cells with between 1-3 probe = +1 (light pink), 4-9 spots = +2 (dark pink), 10-13 spots = +3 (light red) and >14 spots = +4 (dark red) as shown in the image below.
The second example is a dual RNA ISH assay in tumor using red and blue probes. Negative cells are identifed using a white overlay mask. Cells positive for the red probe only are shown in different shades of red according to their RNAscope score as described for the single probe assay above. Cells positive for the blue probe only are shown in different shades of green according to their RNAscope score. Cells positive for both markers are in shades of yellow representing the ratio of red: blue probe.
The last example is a dual DNA ISH assay. Like the dual RNA ISH assay, cells containing red probe only are in shades of red, black probe only are in shades of green, cells with both probes are in shades of yellow, and probes with no probe are white.
The module reports the total number of cells, total number of spots, total area of spots, the average number of spots per cell and per unit area of tissue, the average area of spots per cell and per unit area of tissue, as well as the number and percentage of cells with RNAscope score of 0, 1+, 2+, 3+ and 4+. When two probes are present, the module also reports the ratio of probe 1: probe 2. Histograms are automatically generated representing the frequency distribution of probes per cell [Figure 1) and RNAscope cell scoring [Figure 2] as shown below.
Figure 1 shows a distribution curve of probe number on a cell by cell basis, in this example most cells were shown to have between 0-5 copies per cell.
Figure 2. This bar chart shows the numbers of cells that were categorized as 0, 1+, 2+, 3+ and 4+ respectively. The chart shows that a slim majority of cells were positive for RNA probe expression.
RNAscope Data Analysis Guide by ACD, a Bio-techne brand
PUBLICATIONS
Here are a few publications that cite use of our ISH and FISH modules. Your publication not on the list? Drop us an email to let us know about it!
| Title | Authors | Year | Journal | Application | HALO Modules | |
|---|---|---|---|---|---|---|
| Glucose-Dependent Insulinotropic Polypeptide Receptor-Expressing Cells in the Hypothalamus Regulate Food Intake | Adriaenssens AE, Biggs EK, Darwish T, Tadross J, Sukthankar T, Girish M, Polex-Wolf J, Lam BY, Zvetkova I, Pan W, Chiarugi D, Yeo GSH, Blouet C, Gribble FM, Reimann F | 2019 | Cell Metabolism | Metabolism | ISH/FISH | |
| Fully automated RNAscope in situ hybridization assays for formalin‐fixed paraffin‐embedded cells and tissues | Anderson CM, Zhang B, Miller M, Butko E, Wu X, Laver T, Kernag C, Kim J, Luo Y, Lamparski H | 2016 | Journal of Cellular Biochemistry | Oncology, Gastroenterology, Infectious Disease | ISH/FISH | |
| TGFβ inhibition restores a regenerative response in acute liver injury by suppressing paracrine senescence | Bird TG, Müller M, Boulter L, Vincent DF, Ridgway RA, Elena Lopez-Guadamillas E, Lu W-Y, Jamieson T, Govaere O, Campbell AD, Ferreira-Gonzalez S, Cole AM, Hay T, Simpson KJ, Clark W, Hedley A, Clarke M, Gentaz P, Nixon C, Bryce S, Kiourtis C, Sprangers J, Nibbs RJB, Van Rooijen N, Bartholin L, McGreal SR, Apte U, Barry ST, Iredale JP, Clarke AR, Serrano M, Roskams TA, Sansom OJ, Forbes SJ | 2018 | Science Translational Medicine | Metabolism | ISH/FISH | |
| Food Perception Primes Hepatic ER Homeostasis via Melanocortin-Dependent Control of mTOR Activation | Brandt C, Nolte H, Henschke S, Ruud LE, Awazawa M, Morgan DA, Gabel P, Sprenger H-G, Hess ME, Günther S, Langer T, Rahmouni K, Fenselau H, Krüger M, Brüning JC | 2018 | Cell | Neuroscience, Metabolism | ISH/FISH | |
| Detection and quantification of Parascaris P-glycoprotein drug transporter expression with a novel mRNA hybridization technique | Chelladurai JJ, Brewer MT | 2019 | Veterinary Parasitology | Infectious Disease | ISH/FISH | |
| IL-7-dependent compositional changes within the γδ T cell pool in lymph nodes during ageing lead to an unbalanced anti-tumour response | Chen H-C, Eling N, Martinez-Jimenez CP, O'Brien LM, Carbonaro V, Marioni JC, Odom DT, de la Roche M | 2019 | EMBO Reports | Oncology, Immuno-oncology | ISH/FISH | |
| Gene Signature of Proliferating Human Pancreatic α-Cells | Dominguez Gutierrez G, Xin Y, Okamoto H, Kim J, Lee A-H, Ni M, Adler C, Yancopoulos GD, Murphy AJ, Gromada J | 2018 | Endocrionology | Metabolism | ISH/FISH | |
| Assessment of PD-L1 mRNA and protein expression in non-small cell lung cancer, head and neck squamous cell carcinoma and urothelial carcinoma tissue specimens using RNAScope and immunohistochemistry | Duncan DJ, Scott M, Scorer P, Barker C | 2019 | PLOS One | Oncology, Immuno-oncology | ISH/FISH | |
| APNG as a prognostic marker in patients with glioblastoma | Fosmark S, Hellwege S, Dahlrot RH, Jensen KL, Derand H, Lohse J, Sørensen MD, Hansen S, Kristensen BW | 2017 | PLOS One | Oncology | ISH/FISH | |
| Lipid Source and Peroxidation Status Alter Immune Cell Recruitment in Broiler Chicken Ileum | Fries-Craft KA, Meyer MM, Lindblom SC, Kerr BJ, Bobeck EA | 2021 | The Journal of Nutrition | Immunology | ISH/FISH | |
| G-protein-independent coupling of MC4R to Kir7. 1 in hypothalamic neurons | Ghamari-Langroudi M, Digby GJ, Sebag JA, Millhauser GL, Palomino R, Matthews R, Gillyard T, Panaro BL, Tough IR, Cox HM, Denton JS, Cone RD | 2015 | Nature | Metabolism | ISH/FISH | |
| A phase II study of the dual mTOR inhibitor MLN0128 in patients with metastatic castration resistant prostate cancer | Graham L, Banda K, Torres A, Carver BS, Chen Y, Pisano K, Shelkey G, Curley T, Scher HI, Lotan TL, Hsieh AC, Rathkopf DE | 2018 | Investigational New Drugs | Oncology | ISH/FISH | |
| Expression of cholecystokinin by neurons in mouse spinal dorsal horn | Guitierrez-Mecinas M, Bell AM, Shepherd F, Polgar E, Watanabe M, Furuta T, Todd AJ | 2019 | The Journal of Comparitive Neurology | Neuroscience | ISH/FISH | |
| Ultrasensitive automated RNA in situ hybridization for kappa and lambda light chain mRNA detects B-cell clonality in tissue biopsies with performance comparable or superior to flow cytometry | Guo L, Wang Z, Anderson CA, Doolittle E, Kernag S, Cotta CV, Ondrejka SL, Ma X-J, Cook JR | 2018 | Modern Pathology | Classifier, ISH/FISH | ||
| A distinct repertoire of cancer-associated fibroblasts is enriched in cribriform prostate cancer | Hesterberg AB, Rios BL, Wolf EM, Tubbs C, Wong HY, Schaffer KR, Lotan TL, Giannico GA, Gordetsky JB, Hurley PJ | 2021 | Journal of Pathology:Clinical Research | Oncology | Classifier, ISH/FISH | |
| Neurexin 3 transmembrane and soluble isoform expression and splicing haplotype are associated with neuron inflammasome and Alzheimer's disease | Hishimoto A, Pletnikova O, Lang DL, Troncoso JC, Egan JM, Liu Q-R | 2019 | Alzheimer's Research & Therapy | Neuroscience | ISH/FISH | |
| Variability in Platelet-Derived Growth Factor Receptor Alpha Antibody Specificity May Impact Clinical Utility of Immunohistochemistry Assays | Holzer TR, Reising LO, Credille KM, Schade AE, Oakley | 2016 | Journal of Histochemistry & Cytochemistry | Oncology | Cytonuclear, ISH/FISH | |
| Development of resistance to FAK inhibition in pancreatic cancer is linked to stromal depletion | Jiang H, Liu X, Knolhoff BL, Hegde S, Lee KB, Jiang H, Fields RC, Pachter JA, Lim K-H, DeNardo DG | 2019 | Gut | Oncology | Cytonuclear, ISH/FISH | |
| Single-Cell Quantification of mRNA Expression in The Human Brain | Jolly S, Lang V, Koelzer VH, Frigerio CS, Magno L, Salinas PC, Whiting P, Palomer E | 2019 | Scientific Reports | Neuroscience | ISH/FISH | |
| A first-in-human, phase 1, dose-escalation study of ABBV-176, an antibody-drug conjugate targeting the prolactin receptor, in patients with advanced solid tumors | Lemech C, Woodward N, Chan N, Mortimer J, Naumovski L, Nuthalapati S, Tong B, Jiang F, Ansell P, Ratajczak CK, Sachdev J | 2020 | Investigational New Drugs | Oncology | ISH/FISH | |
| Mutant myocilin impacts sarcomere ultrastructure in mouse gastrocnemius muscle | Lynch JM, Dolman AJ, Guo C, Dolan K, Xiang C, Reda S, Li B, Prasanna G | 2018 | PLOS One | Gastroenterology, Myology | ISH/FISH | |
| Breast and pancreatic cancer interrupt IRF8-dependent dendritic cell development to overcome immune surveillance | Meyer MA, Baer JM, Knolhoff BL, Nywening TM, Panni RZ, Su X, Weilbaecher KN, Hawkins WG, Ma C, Fields RC, Linehan DC, Challen GA, Faccio R, Aft RL, DeNardo DG | 2018 | Nature Communications | Oncology, Immuno-oncology | ISH/FISH | |
| Gene expression of prostaglandin EP4 receptor in three canine carcinomas | Musser ML, Viall AK, Phillips RL, Hostetter JM, Johannes CM | 2020 | BMC Veterinary Research | Oncology | ISH/FISH | |
| Cholecystokinin-1 receptor agonist induced pathological findings in the exocrine pancreas of non-human primates | Nyborg NCB, Kirk RK, de Boer AS, Andersen DW, Bugge A, Wulff BS, Thorup I, Clausen TR | 2020 | Toxicology & Applied Pharmacology | Metabolism | ISH/FISH | |
| CD8+ T cells fail to limit SIV reactivation following ART withdrawal until after viral amplification | Okoye AA, Duell DD, Fukazawa Y, Varco-Merth B, Marenco A, Behrens H, Chaunzwa TM, Selseth AN, Gilbride RM, Shao J, Edlefsen PT, Geleziunas R, Pinkevych M, Davenport MP, Busman-Sahay K, Nekorchuk MD, Park H, Smedley JV, Axthelm MK, Estes JD, Hansen SG, Keele BF, Lifson JD, Picker LJ | 2021 | The Journal of Clinical Investigation | Immunology, Infectious Disease | ISH/FISH | |
| Differential Cytokine Gene Expression in Granulomas from Lungs and Lymph Nodes of Cattle Experimentally Infected with Aerosolized Mycobacterium bovis | Palmer MV, Thacker TC, Waters WR | 2016 | PLOS One | Infectious Disease | ISH/FISH | |
| The Fat Mass and Obesity-Associated Protein (FTO) Regulates Locomotor Responses to Novelty via D2R Medium Spiny Neurons | Ruud J, Alber J, Tokarska A, Engström Ruu L, Nolte H, Biglari N, Lippert R, Lautenschlager Ä, Cieślak PE, Szumiec Ł, Hess ME, Brönneke HS, Krüger M, Nissbrandt H, Korotkova T, Silberberg G, Rodriguez Parkitna J, Brüning J | 2019 | Cell Reports | Neuroscience, Metabolism | ISH/FISH | |
| NPY mediates the rapid feeding and glucose metabolism regulatory functions of AgRP neurons | Ruud LE, Pereira MMA, de Solis AJ, Fenselau H, Bruning JC | 2020 | Nature Communications | Metabolism | ISH/FISH | |
| Quantitative digital pathology reveals association of cell-specific PNPLA3 transcription with NAFLD disease activity | Sandhu B, Perez Matos MC, Tran S, Zhong A, Csizmadia E, Kim M, Herman MA, Nasser I, Lai M, Jiang ZG | 2019 | JHEP Reports | Fibrosis | ISH/FISH | |
| Alpha-synuclein is a DNA binding protein that modulates DNA repair with implications for Lewy body disorders | Schaser AJ, Osterberg VR, Dent SE, Stackhouse TL, Wakeham CM, Boutros SW, Weston LJ, Owen N, Weissman TA, Luna E, Raber J, Luk KC, McCullough AK, Woltjer RL, Unni VK | 2019 | Scientific Reports | Neuroscience | ISH/FISH | |
| Age-determined expression of priming protease TMPRSS2 and localization of SARS-CoV-2 infection in the lung epithelium | Schuler BA, Habermann AC, Plosa EJ, Taylor CJ, Jetter C, Kapp ME, Benjamin JT, Gullerman P, Nichols DS, Braunstein LZ, Hackett A, Koval M, Guttentag SH, Blackwell TS, Webber SA, Banovich NE, Kropski JA, Sucre JMS | 2020 | The Journal of Clincial Invesitgation | Infectious Disease | ISH/FISH | |
| Small Molecule IL-36γ Antagonist as a Novel Therapeutic Approach for Plaque Psoriasis | Todorović V, Su Z, Putman CB, Kakavas SJ, Salte KM, McDonald HA, Wetter JB, Paulsboe SE, Sun Q, Gerstein CE, Medina L, Sielaff B, Sadhukhan R, Stockmann H, Richardson PL, Qiu W, Argiriadi MA, Henry RF, Herold JM, Shotwell JB, McGaraughty SP, Honore P, Gopalakrishnan SM, Sun CC, Scott VE | 2019 | Scientific Reports | Immunology, Dermatology | ISH/FISH | |
| A randomized, open-label study of the efficacy and safety of AZD4547 monotherapy versus paclitaxel for the treatment of advanced gastric adenocarcinoma with FGFR2 polysomy or gene amplification | Van Cutsem E, Bang Y-J, Mansoor W, Petty RD, Chao Y, Cunningham D, Ferry DR, N. R. Smith NR, Frewer P, Ratnayake J, Stockman PK, Kilgour E, and Landers D | 2017 | Annals of Oncology | Oncology | Classifier, ISH/FISH | |
| The human IL-15 superagonist N-803 promotes migration of virus-specific CD8+ T and NK cells to B cell follicles but does not reverse latency in ART-suppressed, SHIV-infected macaques | Webb GM, Molden J, Bushman-Sahay K, Abdulhaqq S, Wu HL, Weber WC, Bateman KB, Reed JS, Northrup M, Maier N,Tanaka S, Gao L, Davey B, Carpenter BL, Axthelm MK, Stanton JJ, Smedley J, Greene JM, Safrit JT, Estes JD, Skinner PJ, Sacha JB | 2020 | PLOS Pathogens | Infectious Disease | Cytonuclear, ISH/FISH | |
| RNA Sequencing of Single Human Islet Cells Reveals Type 2 Diabetes Genes | Xin Y, Kim J, Okamoto H, Ni M, Wei Y, Adler C, Murphy AJ, Yancopoulos GD, Lin C, Gromada J | 2016 | Cell Metabolism | Metabolism | ISH/FISH | |
| Expression of avian β-defensin mRNA in the chicken yolk sac | Zhang H, Wong EA | 2019 | Developmental & Comparative Immunology | Immunology | ISH/FISH | |
| Activation of the renal GLP‐1R leads to expression of Ren1 in the renal vascular tree | Bjørnholm KD, Ougaard ME, Skovsted GF, Knudsen LB, Pyke C | 2021 | Endocrinology, Diabetes, & Metabolism | Metabolism | ISH/FISH | |
| A Method to Pre-Screen Rat Mammary Gland Whole-Mounts Prior To RNAscope | Duderstadt EL, Sanders MA, Samuelson DJ | 2021 | Journal of Mammary Gland Biology and Neoplasia | ISH/FISH | ||
| Age-associated expression of p21and p53 during human wound healing | Chia CW, Sherman-Baust CA, Larson SA, Pandey R, Withers R, Karikkineth AC, Zukley LM, Campisi J, Egan JM, Sen R, Ferrucci L | 2021 | Aging Cell | Dermatology | Area Quantification, ISH/FISH, Multiplex IHC | |
| Immune-regulated IDO1-dependent tryptophan metabolism is source of one-carbon units for pancreatic cancer and stellate cells | Newman AC, Falcone M, Uribe AH, Zhang T, Athineos D, Pietzke M, Vazquez A, Blyth K, Maddocks ODK | 2021 | Molecular Cell | Immuno-oncology | Classifier, ISH/FISH | |
| VGLUT2 is a determinant of dopamine neuron resilience in a rotenone model of dopamine neurodegeneration | Buck SA, De Miranda BR, Logan RW, Fish KN, Greenamyre JT, Freyberg Z | 2021 | The Journal of Neuroscience | Neuroscience | ISH/FISH | |
| Mitigation of endemic GI-tract pathogen-mediated inflammation through development of multimodal treatment regimen and its impact on SIV acquisition in rhesus macaques | Bochart RM, Busman-Sahay K, Bondoc S, Morrow DW, Ortiz AM, Fennessey CM, Fischer MB, Shiel O, Swanson T, Shriver-Munsch CM, Crang HB, Armantrout KM, Barber-Axthelm AM, Langner C, Moats CR, Labriola CS, MacAllister R, Axthelm MK, Brenchley JM, Keele BF, Estes JD, Hansen SG, Smedley JV | 2021 | PLOS Pathogens | Infectious Disease | ISH/FISH, Multiplex IHC | |
| Mucosal IFNγ production and potential role in protection in Escherichia coli O157:H7 vaccinated and challenged cattle | Schaut RG, Palmer MV, Boggiatto PM, Kudva IT, Loving CL, Sharma VK | 2021 | Scientific Reports | Immunology | ISH/FISH | |
| Functionally distinct POMC-expressing neuron subpopulations in hypothalamus revealed by intersectional targeting | Biglari N, Gaziano I, Schumacher J, Radermacher J, Paeger L, Klemm P, Chen W, Corneliussen S, Wunderlich CM, Sue M, Vollmar S, Klöckener T, Sotelo-Hitschfeld T, Abbasloo A, Edenhofer F, Reimann F, Gribble FM, Fenselau H, Kloppenburg P, Wunderlich FT, Brüning JC | 2021 | Nature Neuroscience | Neuroscience | ISH/FISH | |
| Lawsonia intracellularis infected enterocytes lack sucrase-isomaltase which contributes to reduced pig digestive capacity | Helm E, Burrough E, Leite, F, Gabler, N | 2021 | Veterinary Research | Other | ISH/FISH | |
| The amino acid transporter SLC7A5 is required for efficient growth of KRAS-mutant colorectal cancer | Najumudeen AK, Ceteci F, Fey SK, Hamm G, Steven RT, Hall H, Nikula CJ, Dexter A, Murta T, Race AM, Sumpton D, Vlahov N, Gay DM, Knight JRP, Jackstadt R, Leach JDG, Ridgway RA, Johnson ER, Nixon C, Hedley A, Gilroy K, Clark W, Malla SB, Dunne PD, Rodriguez-Blanco G, Critchlow SE, Mrowinska A, Malviya G, Solovyev D, Brown G, Lewis DY, Mackay GM, Strathdee D, Tardito S, Gottlieb E, CRUK Rosetta Grand Challenge Consortium, Takats Z, Barry ST, Goodwin RJA, Bunch J, Bushell M, Campbell AD, Sansom OJ | 2021 | Nature Genetics | Oncology | ISH/FISH | |
| Robust and persistent reactivation of SIV and HIV by N-803 and depletion of CD8+ cells | McBrien JB, Mavigner M, Li LF, Smith SA, White E, Tharp GK, Walum H, Busman-Suhay K, Aguilera-Sandoval CR, Thayer WO, Spagnuolo RA, Kovarova M, Wahl A, Cervasi B, Margolis DM, Vanderford TH, Carnathan DG, Paiardini M, Lifson JD, Lee JH, Safrit JT, Bosinger SE, Estes JD, Derdeyn CA, Garcia JV, Kulpa DA, Chahroudi A, Silvestri G | 2020 | Nature | Other | ISH/FISH | |
| Chronic stress differentially alters mRNA expression of opioid peptides and receptors in the dorsal hippocampus of female and male rats | Johnson MA, Contoreggi NH, Kogan JF, Bryson M, Rubin BR, Gray JD, Kreek MJ, McEwen BS, Milner TA | 2021 | The Journal of Comparative Neurology | Neruoscience | ISH/FISH | |
| Monocyte and macrophage derived myofibroblasts: Is it fate? A review of the current evidence | Vierhout M, Ayoub A, Naiel S, Yazdanshenas P, Revill S, Reihani A, Dvorkin-Gheva A, Shi W, Ask K | 2021 | Wound Repair and Regeneration | Review | ISH/FISH | |
| Orexin receptors 1 and 2 in serotonergic neurons differentially regulate peripheral glucose metabolism in obesity | Xiao X Yeghiazaryan G, Hess S, Klemm P, Sieben A, Kleinridders A, Morgan D, Wunderlich F. Rahmouni K. Kong D, Scammell T, Lowell B, Kloppenburg P, Brüning J, Hausen A. | 2021 | Nature Communications | Metabolism | ISH/FISH | |
| Functional heterogeneity of POMC neurons relies on mTORC1 signaling | Saucisse N, Mazier W, Simon V, Binder E, Catania C, Bellocchio L, Romanov R, Leon S, Matias I, Zizzari P, Quarta C, Cannich A, Meece K, Gonzales D, Clark S, Becker J, Yeo G, Fioramonti X, Merkle F, Wardlaw S, Harkany T, Massa F, Marsicano G, Cota D | 2021 | Cell Reports | Neuroscience | ISH/FISH | |
| Transcriptomic analysis links diverse hypothalamic cell types to fibroblast growth factor 1-induced sustained diabetes remission | Bentsen MA, Rausch DM, Mirzadeh Z, Muta K, Scarlett JM, Brown JM, Herranz-Perez V, Baquero AF, Thompson J, Alonge KM, Faber CL, Kaiyala KJ, Bennett C, Pyke C, Ratner C, Egerod KL, Holst B, Meek TH, Kutlu B, Zhang Y, Sparso T, Grove KL, Morton GJ, Kornum BR, Garcia-Verdugo J-M, Secher A, Jorgensen R, Schwartz MW, Pers TH | 2020 | Nature Communications | Metabolism | ISH/FISH | |
| PPAR-gamma induced AKT3 expression increases levels of mitochondrial biogenesis driving prostate cancer | Galbraith L, Mui E, Nixon C, Hedley A, Strachan D, MacKay G, Sumpton D, Sansom O, Leung H, Ahmad I | 2021 | Oncogene | Oncology | ISH/FISH | |
| HIV-1-induced cytokines deplete homeostatic innate lymphoid cells and expand TCF7-dependent memory NK cells | Wang Y, Lifschitz L, Gellatly K, Vinton CL, Busman-Sahay K, McCauley S, Vangala P, Kim K, Derr, Jaiswall S, Kucukural A, McDonel P, Hunt PW, Greenough T, Houghton J, Somsouk M, Estes JD, Brenchley JM, Garber M, Deeks SG, Luban J |
2020 | Nature Immunology |
Immunology, Infectious Disease |
Area Quantification, Cytonuclear, ISH/FISH |
|
| Mechanism of Nucleic Acid Sensing in Retinal Pigment Epithelium (RPE): RIG-I Mediates Type I Interferon Response in Human RPE | Schustak J, Twarog M, Wu X, Huang Q, Bao Y | 2021 | Journal of Immunology Research | Area Quantification, ISH/FISH | ||
| Alteration of Colonic Mucin Composition and Cytokine Expression in Acute Swine Dysentery | Lin S J-H, Arruda B, Burrough E | 2021 | Veterinary Pathology | Immunology | Area Quantification, ISH/FISH | |
| CTLA-4 and PD-1 dual blockade induces SIV reactivation without control of rebound after antiretroviral therapy interruption | Harper J, Gordon S, Chan CN, Wang H, Lindemuth E, Galardi C, Falcinelli SD, Raines SLM, Read JL, Nguyen K, McGary CS, Nekorchuk M, Busman-Sahay K, Schawalder J, King C, Pino M, Micci L, Cervasi B, Jean S, Sanderson A, Johns B, Koblansky AA, Amrine-Madsen H, Lifson J, Margolis DM, Silvestri G, Bar KJ, Favre D, Estes JD, Paiardini | 2020 | Nature Medicine | Immunology, Infectious Disease | Cytonuclear, ISH/FISH | |
| Three subtypes of lung cancer fibroblasts definedistinct therapeutic paradigms | Hu H, Peotrowska Z, Hare P, Chen H, Mulvey H, Mayfield A, Noeen S, Kattermann K, Greenberg M, Williams A, Riley A, Wilson J, Mao Y, Huang R, Banwait M, Ho J, Crowther G, Hariri L, Sequist L, Benes C, Niederst M, Engelman J | 2021 | Cancer Cell | Oncology | Cytonuclear, ISH/FISH | |
| Detection of Epstein–Barr Virus in Periodontitis: A Review of Methodological Approaches | Tonoyan L, Chevalier M, Vincent-Bungnas S, Marsault R, Doglio A | 2021 | Mircroorganisms | Review | ISH/FISH, ISH-IHC/FISH-IF | |
| Detection of engineered T cells in FFPE tissue by multiplex in situ hybridization and immunohistochemistry | Wright JH, Huang L-Y, Weaver S, Archila LD, McAfee MS, Hirayama AV, Chapuis AG, Bleakley M, Rongvaux A, Turtle CJ, Chanthaphavong S, Campbell JS, Pierce RH | 2020 | Journal of Immunological Methods | Immunology | ISH/FISH, ISH-IHC/FISH-IF | |
| Oncogenic BRAF, unrestrained by TGF?-receptor signalling, drives right-sided colonic tumorigenesis | Leach J, Vlahov N, Tsantoulis P, et al | 2021 | Nature Communications | Oncology | ISH/FISH, Highplex FL | |
| Glucagon Receptor Inhibition Reduces Hyperammonemia and Lethality in Male Mice with Urea Cycle Disorder | Cavino K, Sung B, Su Q, Na E, Kim J, Cheng X, Gromada J, Okamoto H | 2020 | Endocrinology | Metabolism | ISH/FISH, Multiplex IHC | |
| Cross-Platform Comparison of Computer-assisted Image Analysis Quantification of In Situ mRNA Hybridization in Investigative Pathology | Holzer TR, Hanson JC, Wray EM, Bailey JA, Kennedy KR, Finnegan PR, Nasir A, Credille KM | 2019 | Applied Immunohistochemistry & Molecular Morpholgy | Other | ISH/FISH | |
| EBV+ tumors exploit tumor cell-intrinsic and -extrinsic mechanisms to produce regulatory T cell-recruiting chemokines CCL17 and CCL22 | Jorapur A, Marshall L, Jacobson S, Xu M, Marubayashi S, Zibinsky M, Hu D, Robles O, Jackson J, Baloche V, Busson P, Wustrow D, Brockstedt D, Talay O, Kassner P, Cutler G | 2022 | PLOS Pathogens | Oncology | ISH/FISH | |
| Genome Sequence and Experimental Infection of Calves with Bovine Gammaherpesvirus 4 (BoHV-4) | Bauermann F, Falkenberg S, Martins M, Dassanayake R, Neill J, Ridpath J, Silveira S, Palmer M, Buysse A, Mohr A, Flores E, Diel D | 2022 | Research Square | Infectious Disease, Other | ISH/FISH | |
| AAV9/MFSD8 gene therapy is effective in preclinical models of neuronal ceroid lipofuscinosis type 7 disease | Chen X, Dong T, Hu Y, Shaffo F, Belur N, Mazzulli J, Gray S |
2022 | The Journal of Clinical Investigation |
Neuroscience |
Area Quantification, ISH/FISH |
|
| Vertical transmission of attaching and invasive E. coli from the dam to neonatal mice predisposes to more severe colitis following exposure to a colitic insult later in life | Brand M, Proctor A, Hostetter J, Zhou N, Friedberg I, Jergens A, Phillips G, Wannemuehler M |
2022 | PLOS ONE |
Other | ISH/FISH |
|
| Epicardium-derived cells organize through tight junctions to replenish cardiac muscle in salamanders | Eroglu E, Yen C, Witman N, Elewa A, Araus A, Wang H, Szattler T, Umeano C, Sohlmer J, Goedel A, Simon A, Chien K |
2022 | Nature Cell Biology |
Myology |
ISH/FISH, ISH-IHC/FISH-IF |
|
| TGFβ1 Induces Senescence and Attenuated VEGF Production in Retinal Pericytes | Avarmovic D, Archaimbault S, Kemble A, Gruener S, Lazendic M, Westenskow P | 2022 | Biomedicines | Other | ISH/FISH | |
| Satellite repeat RNA expression in epithelial ovarian cancer associates with a tumor immunosuppressive phenotype | Porter R, Sun S, Flores M, Berzolla E, You E, Phillips I, KC N, Desai N, Tai E, Szabolcs A, Lang E, Pankaj A, Raabe M, Thapar V, Xu K, Nieman L, Rabe D, Kolin D, Stover E, Pepin D, Stott S, Deshpande V, Liu J, Solovyov A, Matulonis U, Greenbaum B, Ting D | 2022 | The Journal of Clinical Investigation | Immuno-oncology | ISH/FISH, ISH-IHC/FISH-IF | |
| Distinct Encoding of Reward and Aversion by Peptidergic BNST Inputs to the VTA | Soden M, Yee J, Cuevas B, Rastani A, Elum J, Zweifel L | 2022 | Frontiers in Neural Circuits | Neuroscience | ISH/FISH | |
| Age-associated expression of p21 and p53 during human wound healing | Chia CW, Sherman-Baust CA, Larson SA, Pandey R, Withers R, Karikkineth AC, Zukley LM, Campisi J, Egan JM, Sen R, Ferrucci L | 2021 | Aging Cell | Dermatology | Area Quantification, ISH/FISH, Multiplex IHC | |
| Hyperpolarised 13C-MRI identifies the emergence of a glycolytic cell population within intermediate-risk human prostate cancer | Sushentsev N, McLean M, Warren A, Benjamin A, Brodie C, Frary A, Gill A, Jones J, Kaggie J, Lamb B, Locke M, Miller J, Mills I, Priest A, Robb F, Shah N, Schulte R, Graves M, Gnanapragasam V, Brindle K, Barrett T, Gallacher F | 2022 | Nature Communications | Oncology | ISH/FISH, Membrane, Multiplex IHC | |
| Adult re-expression of IRSp53 rescues NMDA receptor function and social behavior in IRSp53-mutant mice | Noh Y, Yook C, Kang J, Lee S, Kim Y, Yang E, Kim H, Kim E | 2022 | Communications Biology | Neuroscience | ISH/FISH, Figure Maker | |
| The NALCN channel regulates metastasis and nonmalignant cell dissemination | Rahrmann E, Shorthouse D, Jassim A, Hu L, Ortiz M, Mahler-Araujo B, Vogel P, Paez-Ribes M, Fatemi A, Hannon G, Iyer R, Blundon J, Lourenco F, Kay J, Nazarian R, Hall B, Zakharenko S, Winton D, Zhu L, Gilbertson R | 2022 | Nature Genetics | Oncology | ISH/FISH, Multiplex IHC | |
| Relaxin/insulin-like family peptide receptor 4 (Rxfp4) expressing hypothalamic neurons Q8 modulate food intake and preference in mice | Lewis J, Woodward O, Nuzzaci D, Smith C, Adriaenssens A, Billing L, Brighton C, Phillips B, Tadross J, Kinston S, Ciabatti E, Gottgens B, Tripodi M, Mornigold D, Baker D, Gribble F, Reimann F | 2022 | Molecular Metabolism | Metabolism | ISH/FISH, Highplex FL | |
| Regional epithelial cell diversity in the small intestine of pigs | Wiarda J, Becker S, Sivasankaran S, Loving C, | 2022 | Journal of Animal Science | Gastroenterology | ISH/FISH, Figure Maker | |
| Single cell analysis of cribriform prostate cancer reveals cell intrinsic and tumor microenvironmental pathways of aggressive disease | Wong H, Sheng Q, Hesterberg A, Croessmann S, Rios B, Giri K, Jackson J, Miranda A, Watkins E, Schaffer K, Donahue M, Winkler E, Penson D, Smith J, Herrell S, Luckenbaugh A, Barocas D, Kim Y, Graves D, Giannico G, Rathmell J, Park B, Gordetsky J, Hurley P | 2022 | Nature Communications | Oncology | ISH/FISH | |
| Transcriptional and functional divergence in lateral hypothalamic glutamate neurons projecting to the lateral habenula and ventral tegmental area | Rossi M, Basiri M, Liu Y, Hashikawa Y, Hashikawa K, Fenno L, Kim Y, Ramakrishnan C, Deisseroth K, Stuber G | 2021 | Neuron | Neuroscience | ISH/FISH | |
| Genetic suppression of the dopamine D3 receptor in striatal D1 cells reduces the development of L-DOPA-induced dyskinesia | Lanza K, Centner A, Coyle M, Del Priore I, Manfredsson F, Bishop C | 2021 | Experimental Neurology | Neuroscience | ISH/FISH | |
| Systemic Nos2 Depletion and Cox inhibition limits TNBC disease progression and alters lymphoid cell spatial orientation and density | Somasundaram V, Ridnour L, Cheng R, Walke A, Kedei N, Bhattacharyya D, Wink A, Edmondson E, Butcher D, Warner A, Dorsey T, Scheiblin D, Heinz W, Bryant R, Kinders R, Lipkowitz S, Wong S, Pore M, Hewitt S, McVicar D, Anderson S, Chang J, Glynn S, Ambs S, Lockett S, Wink D | 2022 | Redox Biology | Oncology | Classifer, ISH/FISH, Spatial Analysis, Registration, ISH-IHC/FISH-IF | |
| An endogenous opioid circuit determines state-dependent reward consumption | Castro D, Oswell C, Zhang E, Pedersen C, Piantadosi S, Rossi M, Hunker A, Guglin A, Moron J, Zweifel L, Stuber G, Bruchas M | 2021 | Nature | Neuroscience | ISH/FISH | |
| Sex differences in the rodent hippocampal opioid system following stress and oxycodone associated learning processes | Chalangal J, Mazid S, Windisch K, Milner T | 2021 | Pharmacology Biochemistry and Behavior | Review | ISH/FISH | |
| Engineering Cancer Antigen-Specific T Cells to Overcome the Immunosuppressive Effects of TGF-_ | Silk J, Abbott R Adams K, Bennett A, Brett S, Cornforth T, Crossland K, Figueroa D, Jing J, O'Conner C, Pachnio A, Patasic L, Peredo C, Quattrini A, Quinn L, Rust A, Saini M, Sanderson J, Steiner D, Tavano B, Viswanathan P, Wiedermann G, Wong R, Jakobsen B, Britten C, Gerry A, Brewer J | 2021 | The Journal of Immunology | Immuno-oncology, other | ISH/FISH | |
| A single-cell atlas of mouse lung development | Negretti N, Plosa E, Benjamin J, Schuler B, Habermann A, Jetter C, Gulleman P, Bunn C, Hackett A, Ransom M, Taylor C, Nichols D, Matlock B, Guttentag S, Blackwell T, Banovich N, Kropski J, Sucre J | 2021 | Development | Other | ISH/FISH | |
| Glutaminase 2 Knockdown Reduces Hyperammonemia and Associated Lethality of Urea Cycle Disorder Mouse Model | Mao X, Chen H, Lin A, Kim S, Burczynski M, Na E, Halasz G, Sleeman M, Murphy A, Okamoto H, Cheng X | 2022 | Journal of Inherited Metabolic Disease | Metabolism | Area Quantification, ISH/FISH | |
| What Happens to the Preserved Renal Parenchyma After Clamped Partial Nephrectomy? | Xiong L, Nguyen J, Peng Y, Zhou Z, Ning K, Jia N, Nie J, Wen D, Wu Z, Roversi G, Palacios D, Abramczyk E, Munoz-Lopez C, Campbell J, Cao Y, Li Wencai, Zhang X, He Z, Li X, Huang J, Shou J, Wu J, Chen M, Chen X, Zheng J, Xu C, Zhong W, Li Z, Dong W, Zhou J, Zhang H, Luo J, Liu J, Sun G, Han H, Guo S, Dong P, Zhou F, Yu C, Campbell S, Zhang Z | 2022 | European Urology | Other | Area Quantification, ISH/FISH | |
| Adolescent intermittent ethanol exposure produces Sex-Specific changes in BBB Permeability: A potential role for VEGFA | Vore A, Barney T, Deak M, Varlinskaya E, Deak T | 2022 | Brain, Behavior, and Immunity | Neuroscience | ISH/FISH | |
| Relationship between impaired BMP signalling and clinical risk factors at early-stage vascular injury in the preterm infant | Heydarian M, Oak P, Zhang X, Kamgari N, Kindt A, Koschlig M, Pritzke T, Gonzalez-Rodriguez E, Forster K, Morty R, Hafner F, Hubener C, Flemmer A, Yildirim A, Sudheendra D, Tian X, Petrera A, Kirsten H, Ahnert P, Morrell N, Desai T, Sucre J, Spiekerkoetter E, Hilgendorff A | 2022 | Thorax | Other | ISH/FISH | |
| Spatiotemporal expression pattern of Progesterone Receptor Component (PGRMC) 1 in endometrium from patients with or without endometriosis or adenomyosis | Thieffry C, Van Wynendaele M, Samain L, Tyteca D, Pierreux C, Marbaix E, Henriet P | 2022 | The Journal of Steroid Biochemistry and Molecular Biology | Other | ISH/FISH, Highplex FL | |
| Quantitative Imaging Analysis of the Spatial Relationship between Antiretrovirals, Reverse Transcriptase Simian-Human Immunodeficiency Virus RNA, and Fibrosis in the Spleens of Nonhuman Primates | Devanathan A, White N, Desyaterik Y, De la Cruz G, Nekorchuk M, Terry M, Busman-Sahay K, Adamson L, Luciw P, Fedoriw Y, Estes J, Rosen E, Kashuba A | 2022 | Antimicrobial Agents and Chemotherapy | Infectious Disease | ISH/FISH | |
| CD123-directed allogeneic chimeric-antigen receptor T-cell therapy (CAR-T) in blastic plasmacytoid dendritic cell neoplasm (BPDCN): Clinicopathological insights | Pemmaraju N, Wilson N, Senapati J, Economides M, Guzman M, Neelapu S, Kazemimood R, Davis R, Jain N, Khoury J, Sugita M, Cai T, Smith J, Frattini M, Garton A, Roboz G, Konopleva M | 2022 | Leukemia Research | Immuno-oncology | ISH/FISH | |
| Localization of macrophage subtypes and neutrophils in the prostate tumor microenvironment and their association with prostate cancer racial disparities | Maynard J, Godwin T, Lu J, Vidal I, Lotan T, De Marzo A, Joshu C, Sfanos K | 2022 | The Prostate | Oncology | ISH/FISH, Multiplex IHC | |
| Molecular identification of spatially distinct anabolic responses to mechanical loading in murine cortical bone | Chlebek C, Moore J, Ross F, van der Meulen M | 2022 | Journal of Bone and Mineral Research | Other | ISH/FISH | |
| Sex-specific effects of ethanol consumption in older Fischer 344 rats on microglial dynamics and A_(1-42) accumulation | Marsland P, Vore A, DaPrano E, Paluch J, Blackwell A, Varlinskaya E, Deak T | 2022 | Alcohol | Neuroscience | ISH/FISH | |
| Estrogen receptor beta activity contributes to both tumor necrosis factor alpha expression in the hypothalamic paraventricular nucleus and the resistance to hypertension following angiotensin II in female mice | Woods C, Contoreggi N, Johnson M, Milner T, Wang G, Glass M, | 2022 | Neurochemistry International | Neuroscience | ISH/FISH | |
| Angiotensin II Infusion Results in Both Hypertension and Increased AMPA GluA1 Signaling in Hypothalamic Paraventricular Nucleus of Male but not Female Mice | Wang G, Woods C, Johnson M, Milner T, Glass M | 2022 | Neuroscience | Neuroscience | ISH/FISH | |
| Multiregional single-cell dissection of tumor and immune cells reveals stable lock-and-key features in liver cancer | Ma L, Heinrich S, Wang L, Keggenhoff F, Khatib S, Forgues M, Kelly M, Hewitt S, Saif A, Hernandez J, Mabry D, Kloeckner R, Greten T, Chaisaingmongkol J, Ruchirawat M, Marquardt J, Wang X | 2022 | Nature Communications | Oncology | ISH/FISH | |
| Mouse fetal growth restriction through parental and fetal immune gene variation and intercellular communications cascade | Kaur G, Porter C, Ashenberg O, Lee J, Riesenfeld S, Hofree M, Aggelakopoulou M, Subramanian A, Kuttikkatte S, Attfield K, Desel C, Davies J, Evans H, Avraham-Davidi I, Nguyen L, Dionne D, Neumann A, Jensen L, Barber T, Soilleux E, Carrington M, McVean G, Rozenblatt-Rosen O, Regev A, Fugger L | 2022 | Nature Communications | Other | ISH/FISH, Multiplex IHC | HALO, HALO Link |
| Autologous T cell therapy for MAGE-A4+ solid cancers in HLA-A*02+ patients: a phase 1 trial | Hong D, Van Tine B, Biswas S, McAlpine C, Johnson M, Olszanski A, Clarke J, Araujo D, Blumenschein G, Kebriaei P, Lin Q, Tipping A, Sanderson J, Wang R, Trivedi T, Annareddy T, Bai J, Rafail S, Sun A, Fernandes L, Navenot J-M, Bushman F, Everett J, Karadeniz D, Broad R, Isabelle M, Naidoo R, Bath N, Betts G, Wolchinsky Z, Batrakou D, Van Winkle E, Elefant E, Ghobadi A, Cashen A, Grand'Maison A, McCarthy P, Fracasso P, Norry E, Williams D, Druta M, Liebner D, Odunsi K, Butler M | 2023 | Nature Medicine | Immuno-oncology | ISH/FISH, Spatial Analysis, Highplex FL | HALO |
| Combined KRASG12C and SOS1 inhibition enhances and extends the anti-tumor response in KRASG12C-driven cancers by addressing intrinsic and acquired resistance | Thatikonda V, Lu H, Jurado S, Kostyrko K, Bristow C, Bosch K, Feng N, Gao S, Gerlach D, Gmachi M, Lieb S, Jeschko A, Machado A, Marszalek E, Mahendra M, Jaeger P, Sorokin A, Strauss S, Trapani F, Kopetz S, Vellano C, Petronczki M, Kraut N, Heffernan T, Marszalek J, Pearson M, Waizenegger I, Hofmann M | 2023 | bioRxiv | Oncology | ISH/FISH, Multiplex IHC, Highplex FL, Figure Maker | HALO |
| Prefrontal cortical protease TACE/ADAM17 is involved in neuroinflammation and stress-related eating alterations | Sharafeddin F, Ghaly M, Simon T, Ontiveros-Angel P, Figueroa J | 2023 | bioRxiv | Neuroscience | ISH/FISH | HALO |
| Long noncoding RNA LINC01594 inhibits the CELF6-mediated splicing of oncogenic CD44 variants to promote colorectal cancer metastasis. | Liu B, Song A, Gui P, Wang J, Pan Y, Li C, Li S, Zhang Y, Jiang T, Xu Y, Huo F, Pei D, Song J | 2023 | Research Square | Oncology | ISH/FISH | HALO |
| CD47-Dependent Regulation of Immune Checkpoint Gene Expression and MYCN mRNA Splicing in Murine CD8 and Jurkat T Cells | Kaur S, Awad D, Finney R, Meyer T, Singh S, Cam M, Karim B, Warner A, Roberts D | 2023 | International Journal of Molecular Sciences | Immuno-oncology | ISH/FISH | HALO |
| SARS-CoV-2 infection induces DNA damage, through CHK1 degradation and impaired 53BP1 recruitment, and cellular senescence | Gioia U, Tavella S, Martinez-Orellana P, Cicio G, Colliva A, Ceccon M, Cabrini M, Henriques A, Fumagalli V, Paldino A, Presot E, Rajasekharan S, Iacomino N, Pisati F, Matti V, Sepe S, Conte M, Barozzi S, Lavagnino Z, Carletti T, Volpe M, Cavalcante P, Iannacone M, Rampazzo C, Bussani R, Tripodo C, Zacchigna S, Marcello A, di Fagagna F | 2023 | Nature Cell Biology | Infectious Disease | ISH/FISH, Highplex FL | HALO |
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