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Platform for genotyping and phenotyping each cell in a high throughput assay

在高通量检测中对每个细胞进行基因分型和表型分析的平台

基本信息

批准号：
10153373
负责人：
Benjamin Biron Yellen
金额：
$ 83.2万
依托单位：
CELLDOM, INC.
依托单位国家：
美国
项目类别：
财政年份：
2019
资助国家：
美国
起止时间：
2019-01-01 至 2023-08-31
项目状态：
已结题

来源：
https://reporter.nih.gov/project-details/10153373
关键词：
Address Award Bar Codes Biological Biological Assay Cell Culture Techniques Cell physiology Cells Cleaved cell Communities Complementary DNA DNA DNA Library DNA Primers Data Data Set Development Diagnostic Disease Drug resistance Enzymes Epigenetic Process Exposure to Fluorescence Gene Expression Genetic Transcription Genomics Genotype Goals Human Image In Vitro Individual Kinetics Knowledge Letters Libraries Link Measurement Measures Methods Microfluidic Microchips Microfluidics Microscopy Pattern Phase Phenotype Preparation Property Recurrence Resistance Resolution Serum Solid Surface Temperature Testing Therapeutic Time Touch sensation Transcript Work base cDNA Library chronic infection clinical diagnostics cost deep sequencing design digital drug development drug discovery experimental study extracellular fascinate fluorescence imaging genomic data genomic platform genomic tools high resolution imaging high throughput screening innovation instrument interest lead optimization live cell imaging miniaturize multidimensional data nervous system disorder nuclease personalized medicine preclinical development programs seal single cell analysis single-cell RNA sequencing success targeted sequencing tool tool development transcriptome transcriptome sequencing transcriptomics tumor

项目摘要

ABSTRACT One of the recurring questions that continues to pique the interest of academics and clinicians is to understand the functional, transcriptional, and epigenetic programs of rare cells often implicated in tumor recurrence, neurological disorders, chronic infections, and other diseases. Massively parallel single cell genomic tools can partially address this market need; however, the scientific community has made it clear that digital transcript counting is insufficient, and there is strong pull for instruments that provide more comprehensive, multi- dimensional single cell datasets. In particular, there is a need for high-throughput single cell phenotyping tools, which has lagged behind genomics tool development due to the increased difficulty of working with live cells. To meet this demand, Celldom is developing a platform that combines image-based phenotyping with single cell transcriptomics at the massive scales necessary to measure both live cell function and gene expression at the desired endpoint. We achieve this convergence by utilizing efficient microfluidic trap arrays patterned with locally printed DNA barcodes, which allows us to both take images of single cells and prepare barcoded scRNA-seq libraries of the same cells. Building on the solid progress in our Phase I award, in which we demonstrated that the steps in our workflow are all technically feasible and compatible, which include the ability to print DNA barcodes inside sealed microfluidic chips, trap single cells in an array, acquire high-resolution images of each cell, and finally prepare cDNA libraries from barcoded primers attached to surfaces, in this Phase II, we will unify this workflow and demonstrate the ultimate goal of deploying our approach in a drug discovery platform that combines time lapse imaging and high-resolution transcriptome analysis of single cells. Our work plan is summarized in three specific aims. Our first aim is to show that thousands of uniquely barcoded PCR primers can be printed inside our chips in one unique primer per chamber format, and that these chips can be used in the preparation of high quality scRNA-seq libraries with low chamber cross-contamination. Our second aim is to demonstrate that this transcriptomics workflow can be successfully implemented after extended duration in vitro cell culture, during which time the barcodes are continually exposed to enzymes present in the serum and any extracellular secretions. Our third aim is to show that knowledge of the specific barcodes allows the transcripts derived from specific chambers to be selectively enriched during the pooled amplification steps – this will be used to demonstrate targeted sequencing of high-priority clones, which is of particular interest to our target customers. After all three aims have been individually demonstrated, they will be combined in a final demonstration showing the ability to identify drug-resistant clones and probe their transcriptomic signatures at high resolution. We expect this demonstration will excite potential customers and entice them to purchase Celldom instruments for drug development applications, therapeutics, and clinical diagnostics.

摘要