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
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Developmental stage- and site-specific transitions in lineage specification and gene regulatory networks in human hematopoietic stem and progenitor cells
Anindita Roy,Anindita Roy,Guanlin Wang,Deena Iskander,O'Byrne S,Elliott N,Justin M. O'Sullivan,Georgina Buck,Georgina Buck,Elisabeth F. Heuston,Wei Wen,Alba Rodriguez Meira,Peng Hua,Karadimitiris A,Adam J. Mead,David M. Bodine,Irene Roberts,Irene Roberts,Bethan Psaila,Supat Thongjuea +19 more
TL;DR: In this paper, the authors compared 57,489 HSPCs from 5 different tissues spanning four developmental stages through the human lifetime and found significant site-and developmental stage-specific transitions in cellular architecture and gene regulatory networks.
Journal ArticleDOI
Single-cell RNA sequencing in osteoarthritis.
TL;DR: In this paper , a review summarizes the microstructural changes in articular cartilage, meniscus, synovium and subchondral bone that are mainly due to crosstalk among chondrocytes, osteoblasts, fibroblasts and endothelial cells during osteoarthritis progression.
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Lineage Commitment of Dermal Fibroblast Progenitors is Mediated by Chromatin De-Repression
Quan M. Phan,Lucia Salz,Sam S. Kindl,Jayden S. Lopez,Sean M. Thompson,Jasson Makkar,Iwona Driskell,Ryan R. Driskell +7 more
TL;DR: In this article , the authors used multimodal single-cell approaches, epigenetic assays, and allografting techniques to define a DFP state and the mechanisms that govern its differentiation potential.
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Benchmarking Algorithms for Gene Set Scoring of Single-cell ATAC-seq Data
TL;DR: In this article , the applicability and performance of RNA-seq Gene Set scoring (GSS) tools on scATAC-seq data remain to be investigated, and the impact of gene activity conversion, dropout imputation, and gene set collections on the results of GSS is evaluated.
References
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TL;DR: SAMtools as discussed by the authors implements various utilities for post-processing alignments in the SAM format, such as indexing, variant caller and alignment viewer, and thus provides universal tools for processing read alignments.
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TL;DR: The Spliced Transcripts Alignment to a Reference (STAR) software based on a previously undescribed RNA-seq alignment algorithm that uses sequential maximum mappable seed search in uncompressed suffix arrays followed by seed clustering and stitching procedure outperforms other aligners by a factor of >50 in mapping speed.