Hedgehog Signaling pathway in Thymic Differentiation - An in situ Single Cell Resolution Investigation

Date: 1 February 2024
Time: 8:00 – 9:00 PST | 11:00 – 12:00 EST | 16:00 – 17:00 GMT
Location: Webinar

Learn about applications of the ACD RNAscope™ HiPlex assay


The thymus is a vital organ of the immune system, responsible for the maturation and selection of T lymphocytes, which play a critical role in adaptive immunity. The Hedgehog (Hh) signaling pathway has been implicated in thymic differentiation and the maintenance of T-cell progenitors. However, the precise mechanisms by which Hh signaling regulates thymocyte development are not yet fully understood. This question was addressed using the ACD RNAscope™ HiPlex assay, a single-cell resolution gene expression profiling technology, to investigate the expression patterns of Hh signaling pathway components in thymic tissue. Twelve transcripts in thymus from wildtype and Gli1 knock-out mice were analyzed using Indica Labs HALO software. The results reveal dynamic changes in the expression of Hh pathway genes during thymic differentiation, with significant changes observed between thymic compartments. Overall, these findings provide new insights into the role of Hh signaling pathway in thymic differentiation and highlight the potential of ACD’s HiPlex assay for studying complex cellular processes at single-cell resolution.

Learning Objectives

  • Experience using the HiPlex assay will be shared
  • Learn about creation of classifiers for the identification of thymic medulla vs thymic cortex
  • Learn about using the Indica Labs FISH v3.1.2 module in RNAscope HiPlex ISH analysis


Dr. Julia Jones
Scientific Manager
Cancer Research UK Cambridge Institute

Julia has a BSc Biomedical Science from Southampton University and a PhD in Neuroscience from University of Cambridge (Babraham Institute) and has experience in the Pharmaceutical Industry at Eli Lilly and GlaxoSmithKline.

Julia joined CRUK-Cambridge Institute (CI) Histopathology/ISH core facility at the beginning of 2007 as a Scientific Officer and set up the in situ Hybridization service. Julia is now the Scientific Manager for ISH and line manages two members of staff. Current methods offered by the ISH Service include automated branched-DNA ISH for detection of messenger RNA and non-coding RNA, Locked Nucleic Acid ISH for detection of microRNA, and FISH for detecting DNA. The service also offers two different methods for detecting single nucleotide polymorphisms in RNA.

Julia is co-organizer of the biennial symposium: Applications of in situ Hybridization in Research and Disease.