Integrative Single-Cell RNA-Seq and ATAC-Seq Analysis of Human Developmental Hematopoiesis
Anna Maria Ranzoni,Andrea Tangherloni,Andrea Tangherloni,Andrea Tangherloni,Ivan Berest,Simone Giovanni Riva,Simone Giovanni Riva,Simone Giovanni Riva,Brynelle Myers,Paulina M. Strzelecka,Jiarui Xu,Jiarui Xu,Jiarui Xu,Elisa Panada,Elisa Panada,Irina Mohorianu,Judith B. Zaugg,Ana Cvejic,Ana Cvejic,Ana Cvejic +19 more
TLDR
In this paper, the authors applied single-cell RNA sequencing (scRNA-seq) and single cell assay for transposase-accessible chromatin sequencing to over 8,000 human immunophenotypic blood cells from fetal liver and bone marrow.About:
This article is published in Cell Stem Cell.The article was published on 2021-03-04 and is currently open access. It has received 122 citations till now. The article focuses on the topics: ATAC-seq & Chromatin.read more
Citations
More filters
Journal ArticleDOI
CellRank for directed single-cell fate mapping
Pingmin Wei,Yangyang Li +1 more
TL;DR: In this article , a trajectory inference approach for single-cell fate mapping in diverse scenarios, including regeneration, reprogramming and disease, for which direction is unknown, is presented, which combines the robustness of trajectory inference with directional information from RNA velocity, taking into account the gradual and stochastic nature of cellular fate decisions.
Journal ArticleDOI
Single‐cell RNA sequencing technologies and applications: A brief overview
Chang, Elizabeth,F. Krüpe +1 more
TL;DR: In this article , the authors provide a concise overview about the scRNA-seq technology, experimental and computational procedures for transforming the biological and molecular processes into computational and statistical data, and highlight a few examples on how scRNAseq can provide unique information for better understanding health and diseases.
Journal ArticleDOI
Unraveling B cell trajectories at single cell resolution.
TL;DR: In this paper , the adoption of single cell approaches to identify different B cell gene signatures and biomarkers in normal and diseased tissues, and subsequent benefits for future therapeutic discoveries are discussed.
Journal ArticleDOI
Enhancers in disease: molecular basis and emerging treatment strategies.
TL;DR: In this article, the authors review how these enhancer disruptions have recently been implicated in congenital disorders, cancers, and common complex diseases and address the implications for diagnosis and treatment, and show that enhancer-targeting drugs and gene editing approaches show great therapeutic promise for a range of diseases.
Journal ArticleDOI
Transitions in lineage specification and gene regulatory networks in hematopoietic stem/progenitor cells over human development.
Anindita Roy,Anindita Roy,Anindita Roy,Guanlin Wang,Deena Iskander,Sorcha O’Byrne,Natalina Elliott,Jennifer O'Sullivan,Gemma Buck,Gemma Buck,Elisabeth F. Heuston,Wei Xiong Wen,Alba Rodriguez Meira,Peng Hua,Anastasios Karadimitris,Adam J. Mead,Adam J. Mead,David M. Bodine,Irene Roberts,Irene Roberts,Irene Roberts,Bethan Psaila,Bethan Psaila,Supat Thongjuea,Supat Thongjuea +24 more
TL;DR: In this article, the authors compare 57,489 HSPCs from 5 different tissues spanning four developmental stages through the human lifetime, and demonstrate the utility of this dataset for understanding aberrant hematopoiesis through comparison to two cancers that present at distinct time points in postnatal life.
References
More filters
Journal ArticleDOI
Primed and ready: understanding lineage commitment through single cell analysis
TL;DR: This work reviews recent single cell expression profiling, imaging, and clonal tracking studies that have provided new insights into commitment, focusing on the hematopoietic system, and suggests how new technologies may illuminate the understanding of lineage commitment in the near future.
Journal ArticleDOI
Dynamic shifts in occupancy by TAL1 are guided by GATA factors and drive large-scale reprogramming of gene expression during hematopoiesis
Weisheng Wu,Christapher S. Morrissey,Cheryl A. Keller,Tejaswini Mishra,Maxim Pimkin,Gerd A. Blobel,Mitchell J. Weiss,Ross C. Hardison +7 more
TL;DR: It is found that sites of occupancy shift dramatically during commitment to the erythroid lineage, vary further during terminal maturation, and are strongly associated with changes in gene expression.
Journal ArticleDOI
The E-Id Protein Axis Specifies Adaptive Lymphoid Cell Identity and Suppresses Thymic Innate Lymphoid Cell Development
Masaki Miyazaki,Masaki Miyazaki,Kazuko Miyazaki,Kazuko Miyazaki,Kenian Chen,Yi Jin,Jacob Turner,Amanda J. Moore,Rintaro Saito,Kenichi Yoshida,Seishi Ogawa,Hans Reimer Rodewald,Yin C. Lin,Hiroshi Kawamoto,Cornelis Murre +14 more
TL;DR: This work demonstrated that E proteins establish T cell identity and suppress the development of thymic ILCs by modulating enhancer repertoires of genes associated with Notch signaling and TCR&bgr; locus assembly.
Posted ContentDOI
SnapATAC: A Comprehensive Analysis Package for Single Cell ATAC-seq
Rongxin Fang,Rongxin Fang,Sebastian Preissl,Yang Li,Xiaomeng Hou,Jacinta Lucero,Xinxin Wang,Amir Motamedi,Andrew K. Shiau,Xinzhu Zhou,Fangming Xie,Eran A. Mukamel,Kai Zhang,Yanxiao Zhang,M. Margarita Behrens,Joseph R. Ecker,Bing Ren,Bing Ren,Bing Ren +18 more
TL;DR: SnapATAC is introduced, a software package for analyzing scATAC-seq datasets that can efficiently dissect cellular heterogeneity in an unbiased manner and map the trajectories of cellular states and incorporates existing tools into a comprehensive package for analyze single cell ATac-seq dataset.
Journal ArticleDOI
Noncanonical NF‐κB Signaling Regulates Hematopoietic Stem Cell Self‐Renewal and Microenvironment Interactions
Chen Zhao,Yan Xiu,John M. Ashton,Lianping Xing,Yoshikazu Morita,Craig T. Jordan,Brendan F. Boyce +6 more
TL;DR: It is found that d KO HSPCs have profoundly impaired engraftment and self‐renewal activity after transplantation into wild‐type recipients and increased dKO HSPC proliferation was associated with impaired expression of niche adhesion molecules by bone‐lining cells and increased inflammatory cytokine expression by bone marrow cells.