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
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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
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Full-length RNA-seq from single cells using Smart-seq2
Simone Picelli,Omid R. Faridani,Åsa K. Björklund,Gösta Winberg,Sven Sagasser,Rickard Sandberg +5 more
TL;DR: In this article, the authors presented a detailed protocol for Smart-seq2 that allows the generation of full-length cDNA and sequencing libraries by using standard reagents, and the entire protocol takes ∼2 d from cell picking to having a final library ready for sequencing; sequencing will require an additional 1-3 d depending on the strategy and sequencer.
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TL;DR: Harmony, for the integration of single-cell transcriptomic data, identifies broad and fine-grained populations, scales to large datasets, and can integrate sequencing- and imaging-based data.
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TL;DR: On a compendium of single-cell data from tumors and brain, it is demonstrated that cis-regulatory analysis can be exploited to guide the identification of transcription factors and cell states.
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ForceAtlas2, a Continuous Graph Layout Algorithm for Handy Network Visualization Designed for the Gephi Software
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Stem cells: units of development, units of regeneration, and units in evolution.
TL;DR: The review begins with a detailed examination of hematopoi-via the umbilical vein to the fetal liver between dpc 8.5 etic (blood-forming) stem cells, and the transcription pro-The earliest stem cells in ontogeny are totipotent, ex- files of each of these populations are quite distinct.