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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A Meta-Analytic Single-Cell Atlas of Mouse Bone Marrow Hematopoietic Development
TL;DR: In this article, the authors performed a meta-analysis of mouse bone marrow scRNAseq data and identified replicable signatures that define cell types based on genes and known cellular functions, and evaluated the conservation of signatures associated with erythroid and monocyte lineage development across species using co-expression networks.
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A reference single-cell regulomic and transcriptomic map of cynomolgus monkeys
TL;DR: In this paper , a compendium of cell types from the cynomolgus monkey Macaca fascicularis (denoted as ‘Monkey Atlas’) using both single-cell chromatin accessibility (scATAC-seq) and RNA sequencing (scRNAseq) data at the organism-wide level is presented.
References
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Scikit-learn: Machine Learning in Python
Fabian Pedregosa,Gaël Varoquaux,Alexandre Gramfort,Vincent Michel,Bertrand Thirion,Olivier Grisel,Mathieu Blondel,Peter Prettenhofer,Ron Weiss,Vincent Dubourg,Jake Vanderplas,Alexandre Passos,David Cournapeau,Matthieu Brucher,Matthieu Perrot,Edouard Duchesnay +15 more
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Heng Li,Bob Handsaker,Alec Wysoker,T. J. Fennell,Jue Ruan,Nils Homer,Gabor T. Marth,Gonçalo R. Abecasis,Richard Durbin +8 more
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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Alexander Dobin,Carrie A. Davis,Felix Schlesinger,Jorg Drenkow,Chris Zaleski,Sonali Jha,Philippe Batut,Mark Chaisson,Thomas R. Gingeras +8 more
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.