Bioinformatics and Single Cell Analysis Core (BSCAC)
The Bioinformatics and Single Cell Analysis Core (BSCAC) will play a central role in the Columbia University Digestive and Liver Disease Research Center (CU-DLDRC), providing its members with access to GI/liver/pancreatic-focused state-of-the-art bioinformatics analysis and efficient workflows for horizontal integration with other CU-DLDRC cores.
- The BSCAC will provide analysis of single-cell, single-nucleus RNA-sequencing (RNA-seq) for all digestive organs spatial transcriptomics for mouse and adult and pediatric human GI/liver/pancreatic samples. BSCAC has extensive experience in these analyses. Following initial quality control, the BSCAC will provide high resolution analysis of cell populations throughout all digestive organs; analysis of differential expressed genes as well as pathway analysis for specific cell populations.
- The BSCAC will provide analysis of spatial transcriptomics datasets to identify cell populations, differentially expressed genes and pathways. These services will be phased in once spatial transcriptomics platforms reach 10 micron resolution.
- The BSCAC will analyze cell-cell interactions and regulatory processes that mediate disease progression and provide opportunities for diagnostic and/or therapeutic interventions, with a particular focus on identifying transcriptional regulators in scRNA-seq/sn-RNA-seq and spatial transcriptomics dataset by ARACNe and VIPER.
- The BSCAC will offer comprehensive solutions for the analysis of transcription and transcriptional regulators through single cell ATAC-seq as wwll as cell- and organoid-based CRISPR/Cas9 and drug screens, using cost-efficient plate-seq analysis platforms.
The anticipated start date for BSCAC operation is Spring 2022. An update will be provided on this website in December ’21. Once the core starts, a detailed list of services and fee schedule will be provided through this website and the iLab system.
BSCAC is already working with CU-DLDRC investigators on developing bioinformatics and single cells analyses – please contact Peter Sims or Robert Schwabe for specific projects or needs.