scholarly journals Characterizing cellular heterogeneity in chromatin state with scCUT&Tag-pro

2021 ◽  
Author(s):  
Bingjie Zhang ◽  
Avi Srivastava ◽  
Eleni Mimitou ◽  
Tim Stuart ◽  
Ivan Raimondi ◽  
...  
Keyword(s):  
New Technologies ◽  
Developmental Trajectories ◽  
Single Cells ◽  
Surface Proteins ◽  
Cellular Heterogeneity ◽  
Integrated Analysis ◽  
Chromatin States ◽  
Multiple Binding ◽  
Genomic Characterization ◽  
Cell Type Specific

AbstractNew technologies that profile chromatin modifications at single-cell resolution offer enormous promise for functional genomic characterization. However, the sparsity of these measurements and the challenge of integrating multiple binding maps represent significant challenges. Here we introduce scCUT&Tag-pro, a multimodal assay for profiling protein-DNA interactions coupled with the abundance of surface proteins in single cells. In addition, we introduce scChromHMM, which integrates data from multiple experiments to infer and annotate chromatin states based on combinatorial histone modification patterns. We apply these tools to perform an integrated analysis across nine different molecular modalities in circulating human immune cells. We demonstrate how these two approaches can characterize dynamic changes in the function of individual genomic elements across both discrete cell states and continuous developmental trajectories, nominate associated motifs and regulators that establish chromatin states, and identify extensive and cell type-specific regulatory priming. Finally, we demonstrate how our integrated reference can serve as a scaffold to map and improve the interpretation of additional scCUT&Tag datasets.

scholarly journals Single-cell genomics reveals region-specific developmental trajectories underlying neuronal diversity in the prenatal human hypothalamus

2021 ◽  
Author(s):  
Brian Herb ◽  
Hannah J Glover ◽  
Aparna Bhaduri ◽  
Alex M Casella ◽  
Tracy L Bale ◽  
...  
Keyword(s):  
Developmental Trajectories ◽  
Single Cells ◽  
Neuronal Diversity ◽  
Cell Type ◽  
Human Hypothalamus ◽  
Paired Samples ◽  
Cell Type Specific ◽  
Gene Regulatory ◽  
Stem Cell Populations ◽  
Temporal Trajectory

The hypothalamus is critically important for regulating most autonomic, metabolic, and behavioral functions essential for life and species propagation, yet a comprehensive understanding of neuronal subtypes and their development in the human brain is lacking. Here, we characterized the prenatal human hypothalamus by sequencing the transcriptomes of 45,574 single-cells from 12 embryos, spanning gestational weeks 4 through 25. These cells describe a temporal trajectory from proliferative stem cell populations to maturing neurons and glia, including 38 distinct excitatory and inhibitory neuronal subtypes. Merging these data with paired samples from the cortex and ganglionic eminences (GE) revealed two distinct neurogenesis pathways, one shared between GE and hypothalamus and a second unique to cortex. Gene regulatory network modeling predicted that these distinct maturation trajectories involve the activation of region- and cell type-specific transcription factor networks. These results provide the first comprehensive transcriptomic view of human hypothalamus development at cellular resolution.

scholarly journals STRIDE: accurately decomposing and integrating spatial transcriptomics using single-cell RNA sequencing

2021 ◽  
Author(s):  
Dongqing Sun ◽  
Yihan Xiao ◽  
Zhaoyang Liu ◽  
Taiwen Li ◽  
Qiu Wu ◽  
...  
Keyword(s):  
Single Cell ◽  
Three Dimensional ◽  
Cell Types ◽  
Computational Method ◽  
Cellular Heterogeneity ◽  
Integrated Analysis ◽  
Cell Type ◽  
Specificity And Sensitivity ◽  
Cell Type Specific ◽  
Spatial Locations

AbstractThe recent advances in spatial transcriptomics have brought unprecedented opportunities to understand the cellular heterogeneity in the spatial context. However, the current limitations of spatial technologies hamper the exploration of cellular localizations and interactions at single-cell level. Here, we present spatial transcriptomics deconvolution by topic modeling (STRIDE), a computational method to decompose cell-types from spatial mixtures by leveraging topic profiles trained from single-cell transcriptomics. STRIDE accurately estimated the cell-type proportions and showed balanced specificity and sensitivity compared to existing methods. We demonstrate STRIDE’s utility by applying it to different spatial platforms and biological systems. Deconvolution by STRIDE not only mapped rare cell-types to spatial locations but also improved the identification of spatial localized genes and domains. Moreover, topics discovered by STRIDE were associated with cell-type-specific functions, and could be further used to integrate successive sections and reconstruct the three-dimensional architecture of tissues. Taken together, STRIDE is a versatile and extensible tool for integrated analysis of spatial and single-cell transcriptomics and is publicly available at https://github.com/DongqingSun96/STRIDE.

scholarly journals Integrated analysis of glycan and RNA in single cells

2020 ◽  
Author(s):  
Fumi Minoshima ◽  
Haruka Ozaki ◽  
Hiroaki Tateno
Keyword(s):  
Stem Cells ◽  
Single Cell ◽  
Pluripotent Stem Cells ◽  
Neural Progenitor Cells ◽  
Single Cells ◽  
Cellular Heterogeneity ◽  
Integrated Analysis ◽  
Single Cell Sequencing ◽  
Induced Pluripotent ◽  
The Relationship

ABSTRACTSingle-cell sequencing has emerged as an indispensable technology to dissect cellular heterogeneity but never been applied to the simultaneous analysis of glycan and RNA. Using oligonucleotide-labeled lectins, we developed a sequencing-based method to jointly analyze glycome and transcriptome in single cells. We analyzed the relationship between the two modalities to uncover the heterogeneity of human induced pluripotent stem cells during differentiation into neural progenitor cells at the single-cell resolution.

scholarly journals ItChIP-simultaneous indexing and tagmentation-based ChIP-seq

2019 ◽  
Author(s):  
Shanshan Ai ◽  
Haiqing Xiong ◽  
Chen C. Li ◽  
Yingjie Luo ◽  
Yaxi Liu ◽  
...  
Keyword(s):  
Single Cell ◽  
Cell Fate ◽  
Cell Biology ◽  
Low Cost ◽  
Single Cells ◽  
Chromatin States ◽  
Cell Measurement ◽  
Cell Type Specific ◽  
Cost Efficient ◽  
Chromatin Profiling

Abstract Single-cell measurement of chromatin states, including histone modifications and non-histone protein binding, remains challenging. We present a low-cost, efficient ChIP-seq (simultaneous indexing and tagmentation-based ChIP-seq, itChIP), compatible to both low-input and single cells for profiling chromatin states. This single-cell itChIP approach combines chromatin opening, simultaneous cellular indexing and chromatin tagmentation in a single tube, processing samples with tens of single cells in rarity or with thousands of single cells per assay, and the entire procedure can be finished in two days. The sc-itChIP data acquire ~9,000 unique reads per cell, sufficiently capturing the earliest epigenetic priming along cell fate transition and the basis for cell-type specific enhancer usage. Our results demonstrate that itChIP is a generalizable technology for single-cell chromatin profiling of epigenetically heterogeneous cell populations in many biological processes. This step-by-step protocol is related to the publication “Profiling chromatin state by single-cell itChIP-seq” in Nature Cell Biology.

scholarly journals TUP1, CPH1 and EFG1 Make Independent Contributions to Filamentation in Candida albicans

Genetics ◽  
2000 ◽  
Vol 155 (1) ◽  
pp. 57-67 ◽  
Author(s):  
Burkhard R Braun ◽  
Alexander D Johnson
Keyword(s):  
Candida Albicans ◽  
Environmental Conditions ◽  
Target Genes ◽  
Single Cells ◽  
Filamentous Growth ◽  
Surface Proteins ◽  
Pathway Expression ◽  
Separate Pathway ◽  
The Common ◽  
Growth Pathway

Abstract The common fungal pathogen, Candida albicans, can grow either as single cells or as filaments (hyphae), depending on environmental conditions. Several transcriptional regulators have been identified as having key roles in controlling filamentous growth, including the products of the TUP1, CPH1, and EFG1 genes. We show, through a set of single, double, and triple mutants, that these genes act in an additive fashion to control filamentous growth, suggesting that each gene represents a separate pathway of control. We also show that environmentally induced filamentous growth can occur even in the absence of all three of these genes, providing evidence for a fourth regulatory pathway. Expression of a collection of structural genes associated with filamentous growth, including HYR1, ECE1, HWP1, ALS1, and CHS2, was monitored in strains lacking each combination of TUP1, EFG1, and CPH1. Different patterns of expression were observed among these target genes, supporting the hypothesis that these three regulatory proteins engage in a network of individual connections to downstream genes and arguing against a model whereby the target genes are regulated through a central filamentous growth pathway. The results suggest the existence of several distinct types of filamentous forms of C. albicans, each dependent on a particular set of environmental conditions and each expressing a unique set of surface proteins.

scholarly journals Integrated analysis of glycan and RNA in single cells

iScience ◽  
2021 ◽  
pp. 102882
Author(s):  
Fumi Minoshima ◽  
Haruka Ozaki ◽  
Haruki Odaka ◽  
Hiroaki Tateno
Keyword(s):  
Single Cells ◽  
Integrated Analysis

scholarly journals Cryopreservation of human cancers conserves tumour heterogeneity for single-cell multi-omics analysis

2021 ◽  
Vol 13 (1) ◽  
Author(s):  
Sunny Z. Wu ◽  
Daniel L. Roden ◽  
Ghamdan Al-Eryani ◽  
Nenad Bartonicek ◽  
Kate Harvey ◽  
...  
Keyword(s):  
Single Cell ◽  
Rna Sequencing ◽  
High Throughput ◽  
Single Cells ◽  
Cellular Heterogeneity ◽  
Tumour Heterogeneity ◽  
Fresh Tissue ◽  
Human Cancers ◽  
Cryopreserved Cell ◽  
Single Cell Rna Sequencing

Abstract Background High throughput single-cell RNA sequencing (scRNA-Seq) has emerged as a powerful tool for exploring cellular heterogeneity among complex human cancers. scRNA-Seq studies using fresh human surgical tissue are logistically difficult, preclude histopathological triage of samples, and limit the ability to perform batch processing. This hindrance can often introduce technical biases when integrating patient datasets and increase experimental costs. Although tissue preservation methods have been previously explored to address such issues, it is yet to be examined on complex human tissues, such as solid cancers and on high throughput scRNA-Seq platforms. Methods Using the Chromium 10X platform, we sequenced a total of ~ 120,000 cells from fresh and cryopreserved replicates across three primary breast cancers, two primary prostate cancers and a cutaneous melanoma. We performed detailed analyses between cells from each condition to assess the effects of cryopreservation on cellular heterogeneity, cell quality, clustering and the identification of gene ontologies. In addition, we performed single-cell immunophenotyping using CITE-Seq on a single breast cancer sample cryopreserved as solid tissue fragments. Results Tumour heterogeneity identified from fresh tissues was largely conserved in cryopreserved replicates. We show that sequencing of single cells prepared from cryopreserved tissue fragments or from cryopreserved cell suspensions is comparable to sequenced cells prepared from fresh tissue, with cryopreserved cell suspensions displaying higher correlations with fresh tissue in gene expression. We showed that cryopreservation had minimal impacts on the results of downstream analyses such as biological pathway enrichment. For some tumours, cryopreservation modestly increased cell stress signatures compared to freshly analysed tissue. Further, we demonstrate the advantage of cryopreserving whole-cells for detecting cell-surface proteins using CITE-Seq, which is impossible using other preservation methods such as single nuclei-sequencing. Conclusions We show that the viable cryopreservation of human cancers provides high-quality single-cells for multi-omics analysis. Our study guides new experimental designs for tissue biobanking for future clinical single-cell RNA sequencing studies.

scholarly journals Cellular lensing and near infrared fluorescent nanosensor arrays to enable chemical efflux cytometry

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Soo-Yeon Cho ◽  
Xun Gong ◽  
Volodymyr B. Koman ◽  
Matthias Kuehne ◽  
Sun Jin Moon ◽  
...  
Keyword(s):  
Near Infrared ◽  
Single Cells ◽  
Microfluidic Channel ◽  
Human Monocyte ◽  
Cellular Heterogeneity ◽  
Label Free ◽  
Nanotube Array ◽  
Chemical Cytometry ◽  
Rich Information ◽  
Non Destructive

AbstractNanosensors have proven to be powerful tools to monitor single cells, achieving spatiotemporal precision even at molecular level. However, there has not been way of extending this approach to statistically relevant numbers of living cells. Herein, we design and fabricate nanosensor array in microfluidics that addresses this limitation, creating a Nanosensor Chemical Cytometry (NCC). nIR fluorescent carbon nanotube array is integrated along microfluidic channel through which flowing cells is guided. We can utilize the flowing cell itself as highly informative Gaussian lenses projecting nIR profiles and extract rich information. This unique biophotonic waveguide allows for quantified cross-correlation of biomolecular information with various physical properties and creates label-free chemical cytometer for cellular heterogeneity measurement. As an example, the NCC can profile the immune heterogeneities of human monocyte populations at attomolar sensitivity in completely non-destructive and real-time manner with rate of ~600 cells/hr, highest range demonstrated to date for state-of-the-art chemical cytometry.

scholarly journals Comprehensive analysis of single cell ATAC-seq data with SnapATAC

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Rongxin Fang ◽  
Sebastian Preissl ◽  
Yang Li ◽  
Xiaomeng Hou ◽  
Jacinta Lucero ◽  
...  
Keyword(s):  
Single Cell ◽  
Single Cell Analysis ◽  
Expression Patterns ◽  
Regulatory Elements ◽  
Cellular Heterogeneity ◽  
Specific Gene ◽  
Open Chromatin ◽  
Cell Type ◽  
Process Data ◽  
Cell Type Specific

AbstractIdentification of the cis-regulatory elements controlling cell-type specific gene expression patterns is essential for understanding the origin of cellular diversity. Conventional assays to map regulatory elements via open chromatin analysis of primary tissues is hindered by sample heterogeneity. Single cell analysis of accessible chromatin (scATAC-seq) can overcome this limitation. However, the high-level noise of each single cell profile and the large volume of data pose unique computational challenges. Here, we introduce SnapATAC, a software package for analyzing scATAC-seq datasets. SnapATAC dissects cellular heterogeneity in an unbiased manner and map the trajectories of cellular states. Using the Nyström method, SnapATAC can process data from up to a million cells. Furthermore, SnapATAC incorporates existing tools into a comprehensive package for analyzing single cell ATAC-seq dataset. As demonstration of its utility, SnapATAC is applied to 55,592 single-nucleus ATAC-seq profiles from the mouse secondary motor cortex. The analysis reveals ~370,000 candidate regulatory elements in 31 distinct cell populations in this brain region and inferred candidate cell-type specific transcriptional regulators.

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