Biomedical Engineering ETDs
Publication Date
Fall 12-17-2022
Abstract
Spatially resolved transcriptomics technologies investigate gene expression in the context of a tissue. While imaging-based technologies enable gene expression quantification at a single-cell level, only two NGS-based technologies are currently capable of single-cell resolution. Both Stereo-seq and Seq-Scope involve two rounds of sequencing: one to sequence the location of spatial barcodes and the other to obtain sequence of cDNA. Thus, the objective of the research study is to develop a technology that can capture transcripts from every cell of a tissue without the need for two rounds of sequencing. To this end, a capture surface or barcoded array (similar to 10x Genomics’ Visium platform) with feature sizes of 2.0µm and 0.6µm was manufactured. Spatial transcriptomics was performed on a fresh-frozen and FFPE mouse brain tissue section. The research study demonstrates successful capture of transcripts from the tissue. Furthermore, spatial domains and spatially variable genes identified were consistent with published literature.
Language
English
Keywords
Spatial transcriptomics, mouse brain stratification, spatial RNAseq, spatial sequencing
Document Type
Dissertation
Degree Name
Biomedical Engineering
Level of Degree
Doctoral
Department Name
Biomedical Engineering
First Committee Member (Chair)
Dr. Jeremy Edwards
Second Committee Member
Dr. Yan Guo
Third Committee Member
Dr. Adam Halasz
Fourth Committee Member
Dr. Shuang Luan
Recommended Citation
Swaminathan, Radha. "SPATIAL SINGLE-CELL IDENTIFICATION OF CELL LAYERS WITHIN MOUSE BRAIN USING A NOVEL SPATIALLY RESOLVED TRANSCRIPTOMICS TECHNOLOGY." (2022). https://digitalrepository.unm.edu/bme_etds/42
