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ACD can configure probes for the various manual and automated assays for INS for RNAscope Assay, or for Basescope Assay compatible for your species of interest.

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Spatial mapping of cancer tissues by OMICS technologies

Biochimica et biophysica acta. Reviews on cancer

2021 Nov 30

Ahmed, R;Augustine, R;Valera, E;Ganguli, A;Mesaeli, N;Ahmad, IS;Bashir, R;Hasan, A;
PMID: 34861353 | DOI: 10.1016/j.bbcan.2021.188663

Spatial mapping of heterogeneity in gene expression in cancer tissues can improve our understanding of cancers and help in the rapid detection of cancers with high accuracy and reliability. Significant advancements have been made in recent years in OMICS technologies, which possess the strong potential to be applied in the spatial mapping of biopsy tissue samples and their molecular profiling to a single-cell level. The clinical application of OMICS technologies in spatial profiling of cancer tissues is also advancing. The current review presents recent advancements and prospects of applying OMICS technologies to the spatial mapping of various analytes in cancer tissues. We benchmark the current state of the art in the field to advance existing OMICS technologies for high throughput spatial profiling. The factors taken into consideration include spatial resolution, types of biomolecules, numbers of different biomolecules detected from the same assay, labeled versus label-free approaches, and approximate time required for each assay. Further advancements are still needed for the widespread application of OMICs technologies in performing fast and high throughput spatial mapping of cancer tissues as well as their effective use in research and clinical applications.
Sex-specific pubertal and metabolic regulation of Kiss1 neurons via Nhlh2

eLife

2021 Sep 08

Leon, S;Talbi, R;McCarthy, EA;Ferrari, K;Fergani, C;Naule, L;Choi, JH;Carroll, RS;Kaiser, UB;Aylwin, CF;Lomniczi, A;Navarro, VM;
PMID: 34494548 | DOI: 10.7554/eLife.69765

Hypothalamic Kiss1 neurons control gonadotropin-releasing hormone release through the secretion of kisspeptin. Kiss1 neurons serve as a nodal center that conveys essential regulatory cues for the attainment and maintenance of reproductive function. Despite this critical role, the mechanisms that control kisspeptin synthesis and release remain largely unknown. Using Drop-Seq data from the arcuate nucleus of adult mice and in situ hybridization, we identified Nescient Helix-Loop-Helix 2 (Nhlh2), a transcription factor of the basic helix-loop-helix family, to be enriched in Kiss1 neurons. JASPAR analysis revealed several binding sites for NHLH2 in the Kiss1 and Tac2 (neurokinin B) 5' regulatory regions. In vitro luciferase assays evidenced a robust stimulatory action of NHLH2 on human KISS1 and TAC3 promoters. The recruitment of NHLH2 to the KISS1 and TAC3 promoters was further confirmed through chromatin immunoprecipitation. In vivo conditional ablation of Nhlh2 from Kiss1 neurons using Kiss1Cre:Nhlh2fl/fl mice induced a male-specific delay in puberty onset, in line with a decrease in arcuate Kiss1 expression. Females retained normal reproductive function albeit with irregular estrous cycles. Further analysis of male Kiss1Cre:Nhlh2fl/fl mice revealed higher susceptibility to metabolic challenges in the release of luteinizing hormone and impaired response to leptin. Overall, in Kiss1 neurons, Nhlh2 contributes to the metabolic regulation of kisspeptin and NKB synthesis and release, with implications for the timing of puberty onset and regulation of fertility in male mice.
Knockdown of circROBO2 attenuates acute myocardial infarction through regulating the miR-1184/TRADD axis

Molecular medicine (Cambridge, Mass.)

2021 Mar 03

Chen, TP;Zhang, NJ;Wang, HJ;Hu, SG;Geng, X;
PMID: 33658002 | DOI: 10.1186/s10020-021-00275-6

Studies have found that circular RNAs (circRNAs) play key roles in cardiovascular diseases. However, the function of circROBO2 in acute myocardial infarction (AMI) is unclear. This study aimed to investigate the pathogenesis of circROBO2 in AMI. qRT-PCR and Western blot were used to determine the expression levels of circROBO2, miR-1184, and TRADD in AMI and sham-operated mouse models at mRNA and protein level, respectively. The relationship among miR-1184, circROBO2 and TRADD was evaluated by RNA immunoprecipitation (RIP) analysis and luciferase reporter gene analysis. The roles of circROBO2, miR-1184, and TRADD in myocardial cell apoptosis were evaluated using flow cytometry. Ultrasound echocardiography, serum creatine kinase MB (CK-MB) and lactate dehydrogenase (LDH), myocardial infarction area, and myocardial cell apoptosis were measured to examine the effects of circROBO2 on myocardial injury. The expression levels of miR-1184 were significantly reduced, and the expression levels of circROBO2 and TRADD were significantly increased in MI group. CircROBO2 acted as a sponge for miR-1184 by upregulating the expression of TRADD. In addition, overexpression of miR-1184 enhanced the protective effect of knockdown of circROBO2 by partially inhibiting the expression of TRADD in vivo and in vitro. Knockdown of circROBO2 reduced the apoptosis of cardiomyocytes by increasing the expression levels of miR-1184, which in turn decreased the expression levels of TRADD in the myocardium post-MI.
EZH2 is required for parathyroid and thymic development through differentiation of the third pharyngeal pouch endoderm

Disease models & mechanisms

2021 Feb 19

Caprio, C;Lania, G;Bilio, M;Ferrentino, R;Chen, L;Baldini, A;
PMID: 33608392 | DOI: 10.1242/dmm.046789

The Ezh2 gene encodes a histone methyltransferase of the Polycomb Repressive Complex 2 that methylates histone H3 lysine 27. In this work we asked whether EZH2 has a role in the development of the pharyngeal apparatus and whether it regulates the expression of the Tbx1 gene, which encodes a key transcription factor required in pharyngeal development. To these ends, we performed genetic in vivo experiments with mouse embryos and we used mouse embryonic stem cell (ESC)-based protocols to probe endoderm and cardiogenic mesoderm differentiation. Results showed that EZH2 occupies the Tbx1 gene locus in mouse embryos, and that suppression of EZH2 was associated with reduced expression of Tbx1 in differentiated mESCs. Conditional deletion of Ezh2 in the Tbx1 expression domain, which includes the pharyngeal endoderm, did not cause cardiac defects but revealed that the gene has an important role in the morphogenesis of the 3rd pharyngeal pouch (PP). We found that in conditionally deleted embryos the 3rd PP was hypoplastic, had reduced expression of Tbx1, lacked the expression of Gcm2, a gene that marks the parathyroid domain, but expressed FoxN1, a gene marking the thymic domain. Consistently, the parathyroids did not develop, and the thymus was hypoplastic. Thus, Ezh2 is required for parathyroid and thymic development, probably through a function in the pouch endoderm. This discovery also provides a novel interpretational key for the finding of Ezh2 activating mutations in hyperparathyroidism and parathyroid cancer.
Down-regulation of habenular calcium-dependent secretion activator 2 induces despair-like behavior

Scientific reports

2021 Feb 12

Yoo, H;Yang, SH;Kim, JY;Yang, E;Park, HS;Lee, SJ;Rhyu, IJ;Turecki, G;Lee, HW;Kim, H;
PMID: 33580180 | DOI: 10.1038/s41598-021-83310-0

Calcium-dependent secretion activator 2 (CAPS2) regulates the trafficking and exocytosis of neuropeptide-containing dense-core vesicles (DCVs). CAPS2 is prominently expressed in the medial habenula (MHb), which is related to depressive behavior; however, how MHb neurons cause depressive symptoms and the role of CAPS2 remains unclear. We hypothesized that dysfunction of MHb CAPS neurons might cause defects in neuropeptide secretion and the activity of monoaminergic centers, resulting in depressive-like behaviors. In this study, we examined (1) CAPS2 expression in the habenula of depression animal models and major depressive disorder patients and (2) the effects of down-regulation of MHb CAPS2 on the animal behaviors, synaptic transmission in the interpeduncular nucleus (IPN), and neuronal activity of monoamine centers. Habenular CAPS2 expression was decreased in the rat chronic restraint stress model, mouse learned helplessness model, and showed tendency to decrease in depression patients who died by suicide. Knockdown of CAPS2 in the mouse habenula evoked despair-like behavior and a reduction of the release of DCVs in the IPN. Neuronal activity of IPN and monoaminergic centers was also reduced. These results implicate MHb CAPS2 as playing a pivotal role in depressive behavior through the regulation of neuropeptide secretion of the MHb-IPN pathway and the activity of monoaminergic centers.
CXCR7 ameliorates myocardial infarction as a β-arrestin-biased receptor

Scientific reports

2021 Feb 09

Ishizuka, M;Harada, M;Nomura, S;Ko, T;Ikeda, Y;Guo, J;Bujo, S;Yanagisawa-Murakami, H;Satoh, M;Yamada, S;Kumagai, H;Motozawa, Y;Hara, H;Fujiwara, T;Sato, T;Takeda, N;Takeda, N;Otsu, K;Morita, H;Toko, H;Komuro, I;
PMID: 33564089 | DOI: 10.1038/s41598-021-83022-5

Most seven transmembrane receptors (7TMRs) are G protein-coupled receptors; however, some 7TMRs evoke intracellular signals through β-arrestin as a biased receptor. As several β-arrestin-biased agonists have been reported to be cardioprotective, we examined the role of the chemokine receptor CXCR7 as a β-arrestin-biased receptor in the heart. Among 510 7TMR genes examined, Cxcr7 was the most abundantly expressed in the murine heart. Single-cell RNA-sequencing analysis revealed that Cxcr7 was abundantly expressed in cardiomyocytes and fibroblasts. Cardiomyocyte-specific Cxcr7 null mice showed more prominent cardiac dilatation and dysfunction than control mice 4 weeks after myocardial infarction. In contrast, there was no difference in cardiac phenotypes between fibroblast-specific Cxcr7-knockout mice and control mice even after myocardial infarction. TC14012, a specific agonist of CXCR7, significantly recruited β-arrestin to CXCR7 in CXCR7-expressing cells and activated extracellular signal-regulated kinase (ERK) in neonatal rat cardiomyocytes. Cxcr7 expression was significantly increased and ERK was activated in the border zone of the heart in control, but not Cxcr7 null mice. These results indicate that the abundantly expressed CXCR7 in cardiomyocytes may play a protective role in the heart as a β-arrestin-biased receptor and that CXCR7 may be a novel therapeutic target for myocardial infarction.
Effects of paclitaxel in mitochondrial function and cellular phenotype in human peripheral blood mononuclear cells and monocytes

The Journal of Pain

2021 May 01

Fonseca, M;Morgan, J;Brooks, T;Lycan, T;Strowd, R;Cubillos-Ruiz, J;Romero-Sandoval, E;
| DOI: 10.1016/j.jpain.2021.03.013

Chemotherapy-induced neuropathy (CIPN) is a common complication of paclitaxel. CIPN affects the quality of life of cancer survivors and frequently leads to discontinuation of treatment. Paclitaxel affects neuronal microtubules and induces neuronal mitochondrial dysfunction. However, there is limited clinical information regarding paclitaxel's effects on monocytes. Preclinical studies suggest that paclitaxel-induced neuronal damage is driven by monocytes/macrophages. Therefore, we evaluated whether paclitaxel selectively induces mitochondrial dysfunction and a pro-inflammatory phenotype in human circulating monocytes. We conducted studies in human primary peripheral blood mononuclear cells (PBMCs) from cancer patients being treated with paclitaxel, and in vitro analysis in PBMC cells and monocytes, and THP-1 monocytes in the presence of paclitaxel (0.1, 1, 10 uM). We used flow cytometric markers to study mitochondrial reactive oxygen species (ROS) and mitochondrial membrane potential, namely MitoSox and DIOC6(3) respectively. We also measured mRNA levels of pro- and anti-inflammatory molecules using qRT-PCR. In vitro paclitaxel induced a depolarization state in mitochondria in THP-1, human primary monocytes, and primary human PBMCs, but it did not change MitoSox. Monocytes in PBMCs cells from patients treated with paclitaxel showed significative depolarization state in mitochondria when compared to cells from control patients. In THP-1 cells, paclitaxel enhanced mRNA levels of the pro-inflammatory cytokines IL-8 and TNF alpha. In human primary PBMCs, paclitaxel reduced the anti-inflammatory factors CD163 and IL-10, and enhanced the TNF alpha, COX-2 and MCP-1 mRNA levels. Our study provides evidence that paclitaxel can induce mitochondrial dysfunction in isolated human monocytes and in monocytes present in total PBMCs cells. The observed depolarizing changes are indicative of a pro-mitophagy state, which is in accordance with the paclitaxel-induced pro-inflammatory phenotype in these cells. Early detection of mitochondria dysfunction in human monocytes could be a predictable sign to CIPN development in cancer patients. Our research was supported by the Early-Career Investigator Award W81XWH-16-1-0438 of the Department of Defense, The Pershing Square Sohn Cancer Research Alliance, Weill Cornell Medicine Funds, Department of Anesthesiology-Wake Forest School of Medicine Funds, Comprehensive Cancer Center-Wake Forest School of Medicine Funds, NIDA R21CA248106, National Center for Advancing Translational Sciences (NCATS)-NIH through Grant Award Number UL1TR001420. The content is solely the responsibility of the authors and does not necessarily represent the official views of the NIH.
Free fatty-acid receptor 4 inhibitory signaling in delta cells regulates islet hormone secretion in mice

Molecular metabolism

2021 Jan 20

Croze, ML;Flisher, MF;Guillaume, A;Tremblay, C;Noguchi, GM;Granziera, S;Vivot, K;Castillo, VC;Campbell, SA;Ghislain, J;Huising, MO;Poitout, V;
PMID: 33484949 | DOI: 10.1016/j.molmet.2021.101166

Maintenance of glucose homeostasis requires the precise regulation of hormone secretion from the endocrine pancreas. Free fatty-acid receptor 4 (FFAR4/GPR120) is a G protein-coupled receptor whose activation in islets of Langerhans promotes insulin and glucagon secretion and inhibits somatostatin secretion. However, the contribution of individual islet cell types (α, β, and δ cells) to the insulinotropic and glucagonotropic effects of GPR120 remains unclear. As gpr120 mRNA is enriched in somatostatin-secreting δ cells, we hypothesized that GPR120 activation stimulates insulin and glucagon secretion via inhibition of somatostatin release. Glucose tolerance tests were performed in mice after administration of the selective GPR120 agonist Compound A. Insulin, glucagon and somatostatin secretion were measured in static incubations of isolated mouse islets in response to endogenous (ω-3 polyunsaturated fatty acids) and/or pharmacological (Compound A and AZ-13581837) GPR120 agonists. The effect of Compound A on hormone secretion was tested further in islets isolated from mice with global or somatostatin cell-specific knockout of gpr120. Gpr120 expression was assessed in pancreatic sections by RNA in situ hybridization. Cyclic AMP (cAMP) and calcium dynamics in response to pharmacological GPR120 agonists were measured specifically in α, β and δ cells in intact islets using cAMPER and GCaMP6 reporter mice, respectively. Acute exposure to Compound A increased glucose tolerance and circulating insulin and glucagon levels in vivo. Endogenous and/or pharmacological and GPR120 agonists reduced somatostatin secretion in isolated islets and concomitantly demonstrated dose-dependent potentiation of glucose-stimulated insulin secretion and arginine-stimulated glucagon secretion. Gpr120 was enriched in δ cells. Pharmacological GPR120 agonists reduced cAMP and calcium levels in δ cells but increased these signals in α and β cells. Compound A-mediated inhibition of somatostatin secretion was insensitive to pertussis toxin. The effect of Compound A on hormone secretion was completely absent in islets from mice with either global or somatostatin cell-specific deletion of gpr120 and was partially reduced upon blockade of somatostatin receptor signaling by cyclosomatostatin. Inhibitory GPR120 signaling in δ cells contributes to both insulin and glucagon secretion in part via mitigating somatostatin release.
Prenatal androgenization causes expression changes of progesterone and androgen receptor mRNAs in the arcuate nucleus of female mice across development

Journal of Neuroendocrinology

2021 Oct 18

Watanabe, Y;Prescott, M;Campbell, R;Jasoni, C;
| DOI: 10.1111/jne.13058

Prenatal exposure to excess androgens is associated with the development of polycystic ovary syndrome (PCOS). In prenatally androgenised (PNA) mice, a model of PCOS, progesterone receptor (PR) protein expression is reduced in arcuate nucleus (ARC) GABA neurons. This suggests a mechanism for PCOS-related impaired steroid hormone feedback and implicates androgen excess in inducing transcriptional repression of the PR-encoding gene _Pgr_ in the ARC. However, the androgen sensitivity of ARC neurons and the relative gene expression of progesterone receptors over development and following prenatal androgen exposure remain unknown. Here we used RT-qPCR of microdissected ARC to determine the relative androgen receptor (_Ar_) and progesterone receptor (_Pgr_) gene expression in PNA and control mice at 5 developmental timepoints. In two-way ANOVA analysis, none of the genes examined showed expression changes with a statistically significant interaction between treatment and age, although _PgrA_ showed a borderline interaction. For all genes, there was a statistically significant main effect of age on expression levels, reflecting a general increase in expression with increasing age, regardless of treatment. For _PgrB_ and _Ar_, there was a statistically significant main effect of treatment, indicating a change in expression following PNA - increased for _PgrB_ and decreased for _Ar_ - regardless of age. For _PgrA_ there was a borderline main effect of treatment, suggesting a possible change in expression following PNA, regardless of age. _PgrAB_ gene expression changes showed no significant main effect of treatment. We additionally examined androgen and progesterone responsiveness specifically in P60 ARC GABA neurons by using RNAScope _in situ_ hybridization. This analysis revealed that _Pgr_ and _Ar_ were expressed in the majority of ARC GABA neurons in normal adult females. However, our RNAScope analysis did not show significant changes in _Pgr_ or _Ar_ expression within ARC GABA neurons following PNA. Lastly, as GABA drive to GnRH neurons is increased in PNA, we hypothesised that PNA mice would show increased expression of glutamic acid decarboxylase (GAD), the rate-limiting enzyme in GABA production. However, RT-qPCR showed that the expression of GAD encoding genes (_Gad1_ and _Gad2_) was unchanged in adult PNA mice compared to controls. Our findings indicate that PNA treatment can impact _Pgr_ and _Ar_ mRNA expression in adulthood. This may reflect altered circulating steroid hormones in PNA mice or PNA-induced epigenetic changes in the regulation of _Pgr_ and _Ar_ gene expression in ARC neurons.
Upregulation of TRPM3 in bladder afferents is involved in chronic pain in CYP-induced cystitis

Pain

2022 Feb 21

Zhao, M;Liu, L;Chen, Z;Ding, N;Wen, J;Liu, J;Ge, N;Zhang, X;
| DOI: 10.1097/j.pain.0000000000002616

The TRPM3 channel is a recently recognized noxious heat sensor that is involved in inflammatory thermal hyperalgesia. To examine its involvement in the development of hyperalgesia in interstitial cystitis/painful bladder syndrome (IC/PBS), rats with cyclophosphamide (CYP)-induced chronic cystitis were used as a model of IC/PBS. Mechanical and thermal hyperalgesia in lower abdominal region overlying the bladder in CYP rats were measured using von Frey filaments and radiant heat, respectively. TRPM3 expression at the mRNA, protein, and functional levels in dorsal root ganglion (DRG) neurons innervating the bladder was detected using RNA in situ hybridization (RNAscope), western blotting, immunohistochemistry, and Ca2+ imaging, respectively. TRPM3 channels were expressed on most of the bladder primary afferent nerve terminals containing calcitonin gene-related peptide (CGRP) and their cell bodies in L6-S1 DRGs. Activation of TRPM3 in the bladder wall by its specific agonists pregnenolone sulphate (PS) or CIM0216 induced spontaneous bladder pain, CGRP release and neurogenic inflammation which was evidenced by edema, plasma extravasation, inflammatory cell accumulation, and mast cell infiltration. In CYP rats, pretreatment with the TRPM3 antagonist primidone (2 mg/kg, i.p.) significantly alleviated the mechanical and thermal hyperalgesia, bladder submucosal edema, mast cell infiltration and bladder hyperactivity. CYP-induced cystitis was associated with TRPM3 upregulation at the mRNA, protein, and functional levels in bladder afferent neurons. Our results suggest that upregulation of TRPM3 channels is involved in the development of chronic pain in CYP-induced cystitis, and targeting TRPM3 may be a pharmacological strategy for treating bladder pain in IC/PBS.
Interferon Lambda Signals in Maternal Tissues to Exert Protective and Pathogenic Effects in a Gestational Stage-Dependent Manner

mBio

2022 Jun 28

Casazza, RL;Philip, DT;Lazear, HM;
PMID: 35471083 | DOI: 10.1128/mbio.03857-21

Interferon lambda (IFN-λ) (type III IFN) is constitutively secreted from human placental cells in culture and reduces Zika virus (ZIKV) transplacental transmission in mice. However, the roles of IFN-λ during healthy pregnancy and in restricting congenital infection remain unclear. Here, we used mice lacking the IFN-λ receptor (Ifnlr1-/-) to generate pregnancies lacking either maternal or fetal IFN-λ responsiveness and found that the antiviral effect of IFN-λ resulted from signaling exclusively in maternal tissues. This protective effect depended on gestational stage, as infection earlier in pregnancy (E7 rather than E9) resulted in enhanced transplacental transmission of ZIKV. In Ifnar1-/- dams, which sustain robust ZIKV infection, maternal IFN-λ signaling caused fetal resorption and intrauterine growth restriction. Pregnancy pathology elicited by poly(I·C) treatment also was mediated by maternal IFN-λ signaling, specifically in maternal leukocytes, and also occurred in a gestational stage-dependent manner. These findings identify an unexpected effect of IFN-λ signaling, specifically in maternal (rather than placental or fetal) tissues, which is distinct from the pathogenic effects of IFN-αβ (type I IFN) during pregnancy. These results highlight the complexity of immune signaling at the maternal-fetal interface, where disparate outcomes can result from signaling at different gestational stages. IMPORTANCE Pregnancy is an immunologically complex situation, which must balance protecting the fetus from maternal pathogens with preventing maternal immune rejection of non-self fetal and placental tissue. Cytokines, such as interferon lambda (IFN-λ), contribute to antiviral immunity at the maternal-fetal interface. We found in a mouse model of congenital Zika virus infection that IFN-λ can have either a protective antiviral effect or cause immune-mediated pathology, depending on the stage of gestation when IFN-λ signaling occurs. Remarkably, both the protective and pathogenic effects of IFN-λ occurred through signaling exclusively in maternal immune cells rather than in fetal or placental tissues or in other maternal cell types, identifying a new role for IFN-λ at the maternal-fetal interface.
Optogenetic stimulation of glutamatergic neurons in the cuneiform nucleus controls locomotion in a mouse model of Parkinson's disease

Proceedings of the National Academy of Sciences of the United States of America

2021 Oct 26

Fougère, M;van der Zouwen, CI;Boutin, J;Neszvecsko, K;Sarret, P;Ryczko, D;
PMID: 34670837 | DOI: 10.1073/pnas.2110934118

In Parkinson's disease (PD), the loss of midbrain dopaminergic cells results in severe locomotor deficits, such as gait freezing and akinesia. Growing evidence indicates that these deficits can be attributed to the decreased activity in the mesencephalic locomotor region (MLR), a brainstem region controlling locomotion. Clinicians are exploring the deep brain stimulation of the MLR as a treatment option to improve locomotor function. The results are variable, from modest to promising. However, within the MLR, clinicians have targeted the pedunculopontine nucleus exclusively, while leaving the cuneiform nucleus unexplored. To our knowledge, the effects of cuneiform nucleus stimulation have never been determined in parkinsonian conditions in any animal model. Here, we addressed this issue in a mouse model of PD, based on the bilateral striatal injection of 6-hydroxydopamine, which damaged the nigrostriatal pathway and decreased locomotor activity. We show that selective optogenetic stimulation of glutamatergic neurons in the cuneiform nucleus in mice expressing channelrhodopsin in a Cre-dependent manner in Vglut2-positive neurons (Vglut2-ChR2-EYFP mice) increased the number of locomotor initiations, increased the time spent in locomotion, and controlled locomotor speed. Using deep learning-based movement analysis, we found that the limb kinematics of optogenetic-evoked locomotion in pathological conditions were largely similar to those recorded in intact animals. Our work identifies the glutamatergic neurons of the cuneiform nucleus as a potentially clinically relevant target to improve locomotor activity in parkinsonian conditions. Our study should open avenues to develop the targeted stimulation of these neurons using deep brain stimulation, pharmacotherapy, or optogenetics.

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Description
sense
Example: Hs-LAG3-sense
Standard probes for RNA detection are in antisense. Sense probe is reverse complent to the corresponding antisense probe.
Intron#
Example: Mm-Htt-intron2
Probe targets the indicated intron in the target gene, commonly used for pre-mRNA detection
Pool/Pan
Example: Hs-CD3-pool (Hs-CD3D, Hs-CD3E, Hs-CD3G)
A mixture of multiple probe sets targeting multiple genes or transcripts
No-XSp
Example: Hs-PDGFB-No-XMm
Does not cross detect with the species (Sp)
XSp
Example: Rn-Pde9a-XMm
designed to cross detect with the species (Sp)
O#
Example: Mm-Islr-O1
Alternative design targeting different regions of the same transcript or isoforms
CDS
Example: Hs-SLC31A-CDS
Probe targets the protein-coding sequence only
EnEmProbe targets exons n and m
En-EmProbe targets region from exon n to exon m
Retired Nomenclature
tvn
Example: Hs-LEPR-tv1
Designed to target transcript variant n
ORF
Example: Hs-ACVRL1-ORF
Probe targets open reading frame
UTR
Example: Hs-HTT-UTR-C3
Probe targets the untranslated region (non-protein-coding region) only
5UTR
Example: Hs-GNRHR-5UTR
Probe targets the 5' untranslated region only
3UTR
Example: Rn-Npy1r-3UTR
Probe targets the 3' untranslated region only
Pan
Example: Pool
A mixture of multiple probe sets targeting multiple genes or transcripts

Enabling research, drug development (CDx) and diagnostics

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