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
A comparison of single-cell trajectory inference methods.
TL;DR: The authors comprehensively benchmark the accuracy, scalability, stability and usability of 45 single-cell trajectory inference methods and develop a set of guidelines to help users select the best method for their dataset.
Journal ArticleDOI
Transcriptional Heterogeneity and Lineage Commitment in Myeloid Progenitors
Franziska Paul,Yaâara Arkin,Amir Giladi,Diego Adhemar Jaitin,Ephraim Kenigsberg,Hadas Keren-Shaul,Deborah R. Winter,David Lara-Astiaso,Meital Gury,Assaf Weiner,Eyal David,Nadav Cohen,Felicia Kathrine Bratt Lauridsen,Simon Haas,Andreas Schlitzer,Andreas Schlitzer,Alexander Mildner,Florent Ginhoux,Steffen Jung,Andreas Trumpp,Bo Torben Porse,Amos Tanay,Ido Amit +22 more
TL;DR: This work comprehensively map myeloid progenitor subpopulations by transcriptional sorting of single cells from the bone marrow, showing unexpected transcriptional priming toward seven differentiation fates but no progenitors with a mixed state.
Journal ArticleDOI
Forcing cells to change lineages
Thomas Graf,Tariq Enver +1 more
TL;DR: The ability to produce stem cells by induced pluripotency (iPS reprogramming) has rekindled an interest in earlier studies showing that transcription factors can directly convert specialized cells from one lineage to another.
Journal ArticleDOI
chromVAR: inferring transcription-factor-associated accessibility from single-cell epigenomic data
TL;DR: chromVAR as mentioned in this paper is an R package for analyzing sparse chromatin-accessibility data by estimating gain or loss of accessibility within peaks sharing the same motif or annotation while controlling for technical biases.
Journal ArticleDOI
Metabolic requirements for the maintenance of self-renewing stem cells
Keisuke Ito,Toshio Suda +1 more
TL;DR: Investigation into the molecular mechanisms and metabolic pathways underlying stem cell self-renewal and differentiation hold great therapeutic promise.