Project description:Mapping 6mA at single-base resolution across multiple eukaryotic genomes reveals its genomic distribution patterns, indicating a function in transcriptional regulation.

2017-09-01 | GSE68860 | GEO

Polony gels enable amplifiable DNA stamping and spatial transcriptomics of chronic pain

Project description:Despite wide applications in tissue mapping and vastly improved imaging and omics technologies, spatial, genome-wide assays of gene expression are yet to reliably achieve the resolution and sensitivity approaching dissociative single-cell RNA sequencing. Here, we introduce Pixel-seq, a spatial barcoding method using “continuous” polony gels of ≤ 1 µm feature resolution for capturing tissue RNAs and precise aggregation of mapped transcripts into individual cells. The single-cell assay was demonstrated on mapping the most common brain structures, neuron layers and clusters, creating a three-dimensional atlas of the mouse parabrachial nucleus, and discovering neuropathic pain-associated gene regulation, glial transcriptomic dynamics, and cell-cell communication in the homeostatic adult brain. Our results highlight the necessity of the non-dissociative single-cell sequencing for mapping structural and functional heterogeneity in tissues.

2022-10-31 | GSE186097 | GEO

RETrace: simultaneous retrospective lineage tracing and methylation profiling of single cells

Project description:Retrospective lineage tracing harnesses naturally occurring mutations in cells to elucidate single cell development. Common single cell phylogenetic fate mapping methods have utilized highly mutable microsatellite loci found within the human genome. Such methods were limited by the introduction of in vitro noise through polymerase slippage inherent in DNA amplification, which we characterized to be approximately 10-100 higher than in vivo replication mutation rate. Here, we present RETrace, a method for simultaneously capturing both microsatellites and methylation-informative cytosines to characterize both lineage and cell type, respectively, from the same single cell. An important unique feature of RETrace was the introduction of linear amplification of microsatellites in order to reduce in vitro amplification noise. We further coupled microsatellite capture with single-cell reduced representation bisulfite sequencing (scRRBS), to measure the CpG methylation status on the same cell for cell type inference. When compared to existing retrospective lineage tracing methods, RETrace achieved higher accuracy (88% triplet accuracy from an ex vivo HCT116 tree) at a higher cell division resolution (lowering the required number of cell division difference between single cells by approximately 100 divisions). Simultaneously, RETrace demonstrated the ability to capture on average 150,000 unique CpGs per single cell in order to accurately determine cell type. We further formulated additional developments that would allow high-resolution mapping on microsatellite stable cells or tissues with RETrace. Overall, we present RETrace as a foundation for multi-omics lineage mapping and cell typing of single cells.

2020-02-23 | GSE136089 | GEO

Epigenome characterization at single base-pair resolution

Project description:We have combined standard micrococcal (MNase) digestion of nuclei with a modified protocol for construction paired-end DNA sequencing libraries to map both nucleosomes and subnucleosome-sized particles at single base-pair resolution throughout the budding yeast genome. We found that partially unwrapped nucleosomes and subnucleosome-sized particles can occupy the same position within a cell population, suggesting dynamic behavior. By varying the time of MNase digestion, we have been able to observe changes that reflect differential sensitivity of particles, including eviction of nucleosomes. Our protocol and mapping method provide a general strategy for characterizing full epigenomes. We used micrococcal nuclease mapping, chromatin immunoprecipitation and paired-end sequencing to determine the structure of yeast centromeres at single base-pair resolution.

2011-10-26 | E-GEOD-30551 | biostudies-arrayexpress

Mus musculus

Project description:Cell cycle dynamics of chromosomal organisation at single-cell resolution

| PRJNA369960 | ENA

Single-cell 5-formylcytosine Landscapes of Mammalian Early Embryos at Single-base Resolution

Project description:Active DNA demethylation in mammals involves Ten-eleven translocation (TET) family proteins-mediated oxidation of 5-methylcytosine (5mC). However, base-resolution landscapes of 5-formylcytosine (5fC, an oxidized derivative of 5mC) at the single-cell level remains unexplored. Here we present “CLEVER-seq”, which is a single-cell, single-base resolution 5fC sequencing technology, based on biocompatible, selective chemical labeling of 5fC and subsequent C-to-T conversion during amplification and sequencing. CLEVER-seq of mouse early embryos reveals the highly patterned genomic distribution and parental specific dynamics of 5fC during mouse early pre-implantation development and synergistic 5fC production in paternal and maternal genomes. Integrated analysis demonstrates that promoter 5fC production precedes the expression upregulation of a clear set of developmentally and metabolically critical genes. Collectively, our work reveals the dynamics of active DNA demethylation during early mouse pre-implantation development and provides an important resource for further functional studies of epigenetic reprogramming in single cells.

2024-04-11 | GSE263008 | GEO

Mus musculus

Project description:Lineage dynamics of pancreatic development at single cell resolution

| PRJNA393711 | ENA

A Single-Cell Resolution Atlas of expanding hematopoietic organ in zebrafish

Project description:A Single-Cell Resolution Atlas of expanding hematopoietic organ in zebrafish

| PRJNA610520 | ENA