The Stanford Tissue Mapping Center within HuBMAP is leading the 3D single cell characterization of bowel and colon tissues through highly multi-plexed `omic' profiling and histological and antibody- tagged epitope imaging. Our goal is to identify the single cell gene transcription profiles that establish the identity of each cellular population in colon and small bowel tissue and understand the relevance of the spatial organization of different cell types to bowel function.
In the first 2 years of the project we have collected 2 sets of open access bowel tissues (small bowel: ileum, jejunum, mid-jejunum, duodenum, large bowel: ascending, transverse, descending, rectum) and 1 set of heart tissue from healthy donors. We have already generated and shared the single nuclei (sn) RNAseq and CODEX data (among other omic datas) for the first patient and we are actively generating this data on the second patient. By integrating the snRNAseq and CODEX data, we intend to spatially reconstruct the transcriptomic and epigenetic cellular landscape of the bowel tissues by running the 2 assays on adjacent tissues. However, the goal of overlapping the datasets on to one another by anchoring the single nuclei data to the CODEX data may prove intractable because CODEX is limited to targeting ~50 protein markers which: 1) may not be detected in both technologies and 2) may not be associated with reads from sequenced single cells. Though we are not abandoning the integration of snRNAseq- CODEX approach, we are still considering other technologies which can simultaneously detect RNA and protein spatially.