Resource Core C - Skin Genomics, Transcriptomics, and Epigenetics Core

Summary – Resource Core C
The results of surveying the Research Community of the SBDRC at Mount Sinai indicated that a top strategic
priority is access to state-of-the-art and integrated methods for genomics, transcriptomics, and epigenetic
analysis of the skin in normal homeostasis and in disease. Core C will provide state-of-the-art start-to-finish
technologies for these cutting-edge approaches. The Core will leverage existing campus resources, such as
instrumentation and extensive expertise at both faculty and researcher levels, to provide technical and
intellectual support to the SBDRC Research Community. Core personnel will be embedded in skin research
labs where they will become familiarized with skin as a biological system and the questions being asked; this
will help to ensure that they can most effectively advise lab personnel on experimental design and services to
address the biological questions; conversely lab personnel will become more familiar with the technological
approaches available to them. Specifically, Core C will provide SBDRC investigators with consultation and
services centered on NexGen technologies. A robust organizational hub (the Smartsheet dashboard) will be
utilized for specimen and project in-take, both internally and externally. As part of Aim 1, Core C will facilitate
access to genomics (exome sequencing, whole genome sequencing and targeted capture) and transcriptomic
technologies (bulk RNA-seq, poly(A) RNA-seq, small RNA-seq) in healthy and diseased skin. Access to long-
read single molecule sequencing (SMRT/PacBio) will facilitate the analysis of structural changes in DNA and
the precise identification of RNA isoforms due to altered splicing. Services in Aim 2 will focus on state-of-the
art epigenomic studies to identify regulatory elements operating in the skin (ATAC-seq, ChIP-seq, CUT&RUN).
Interactions across regulatory elements (enhancers and promoters) will be identified by Hi-C. Integration with
transcriptomic findings will confirm target genes and identify altered networks operating in skin homeostasis
and disease. Aim 3 will focus on cellular heterogeneity, providing single cell technologies for transcript
(scRNA-seq) and epigenetic (scATAC-seq) analyses in single cells. CITE-Seq will provide simultaneous
epitope and transcriptome measurements of single cells. Services from Aim 3 will also include spatial
transcriptomics technology permitting the spatial resolution of RNA-seq data, and thereby the locations of all
mRNAs in individual tissue sections. As novel “omics” technologies are developed that would enhance skin
biology research, they will be incorporated into this Core’s activities. Data will be distributed to Core D where
computational biologists will perform rigorous analysis, visualization and data management. Overall, Core C is
an essential and integral component of the Center with the goal of facilitating scientific discoveries in skin
biology and skin disease areas by providing cutting-edge multi-omics studies to skin researchers.

Grant Number: 5P30AR079200-05
NIH Institute/Center: NIH
Principal Investigator: Anne Bowcock