Single cell biology—a Keystone Symposia report

Abstract

Single cell biology has the potential to elucidate many critical biological processes and diseases, from development and regeneration to cancer. Single cell analyses are uncovering the molecular diversity of cells, revealing a clearer picture of the variation among and between different cell types. New techniques are beginning to unravel how differences in cell state-transcriptional, epigenetic, and other characteristics-can lead to different cell fates among genetically identical cells, which underlies complex processes such as embryonic development, drug resistance, response to injury, and cellular reprogramming. Single cell technologies also pose significant challenges relating to processing and analyzing vast amounts of data collected. To realize the potential of single cell technologies, new computational approaches are needed. On March 17-19, 2021, experts in single cell biology met virtually for the Keystone eSymposium "Single Cell Biology" to discuss advances both in single cell applications and technologies.

RevGel-seq: instrument-free single-cell RNA sequencing using a reversible hydrogel for cell-specific barcoding

“…Research in many areas of biology focus on single-cell studies, particularly single-cell RNA sequencing (scRNA-seq) mainly using microfluidic-based methods 1–4 , with the 10x Genomics Chromium instruments achieving particularly wide usage 5 . Comparative benchmarking has been reported for many of the available methods (including CEL-seq2, MARS-seq, Quartz-seq2, gmcSCRB-seq, Smart-seq2, C1HT-small, C1HT-medium, Chromium, ddSEQ, Drop-seq, ICELL8, and inDrop) 6, 7 .…”

“…Upon gelation the tandems are immobilized, cell lysis is triggered by detergent diffusion, and RNA molecules are captured on the adjacent barcode beads. After reverse transcription and preparation for cDNA sequencing, bioinformatic analysis reveals performance quality comparable to microfluidic-based technologies.Research in many areas of biology focus on single-cell studies, particularly single-cell RNA sequencing (scRNA-seq) mainly using microfluidic-based methods [1][2][3][4] , with the 10x Genomics Chromium instruments achieving particularly wide usage 5 . Comparative benchmarking has been reported for many of the available methods (including CEL-seq2, MARS-seq, Quartz-seq2, gmcSCRB-seq, Smart-seq2, C1HT-small, C1HT-medium, Chromium, ddSEQ, Drop-seq, ICELL8, and inDrop) 6, 7 .…”

“…A convenient stopping point after two hours has been established by freezing at the cell lysis step, with full preservation of gene expression profiles. Overall, our results show that RevGel-seq represents an accessible and efficient instrument-free alternative, enabling flexibility in terms of experimental design and timing of sample processing, while providing broad coverage of cell types.Research in many areas of biology focuses on single-cell studies, particularly single-cell RNA sequencing (scRNA-seq) mainly using microfluidic-based methods [1][2][3][4][5][6] , with the 10x Genomics Chromium instruments achieving particularly wide usage 7 . Comparative benchmarking has been reported for many of the available methods (including CEL-Seq2,…”

Melanocytes Exhibit Distinct Cell States Governed by A Gene Regulatory Network Under Stochastic Influence

“…While this diversity is evident at the organism level, it was not observed/detectable at the cellular level until the last decade. Lately, with the advent of single-cell sequencing (scRNA seq) technologies, more and more evidence has revealed heterogeneity within a previously thought homogeneous pool of cells 1 . This has revolutionized the field of cancer research by unravelling previously unknown cell states of the transformed cancer cell [2][3][4][5] .…”