Journal ArticleDOI
Derivation of Intermediate Pluripotent Stem Cells Amenable to Primordial Germ Cell Specification
Leqian Yu,Yulei Wei,Yulei Wei,Hai Xi Sun,Ahmed K. Mahdi,Carlos A. Pinzon Arteaga,Masahiro Sakurai,Daniel A. Schmitz,Canbin Zheng,Canbin Zheng,Emily D. Ballard,Jie Li,Noriko Tanaka,Aoi Kohara,Daiji Okamura,A. Mutto,Ying Gu,Pablo J. Ross,Jun Wu +18 more
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TLDR
By modulating fibroblast growth factor (FGF), transforming growth factor β (TGF-β), and WNT pathways, PSCs are derived from mice, horses, and humans (designated as XPSCs) that are permissive for direct PGC-like cell induction in vitro and are capable of contributing to intra- or inter-species chimeras in vivo.About:
This article is published in Cell Stem Cell.The article was published on 2021-03-04. It has received 89 citations till now. The article focuses on the topics: Induced pluripotent stem cell & Stem cell.read more
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Integrative Genomics Viewer
James T. Robinson,Helga Thorvaldsdottir,Wendy Winckler,Mitchell Guttman,Eric S. Lander,Eric S. Lander,Gad Getz,Jill P. Mesirov +7 more
TL;DR: The sheer volume and scope of data posed by this flood of data pose a significant challenge to the development of efficient and intuitive visualization tools able to scale to very large data sets and to flexibly integrate multiple data types, including clinical data.
Journal ArticleDOI
Blastocyst-like structures generated from human pluripotent stem cells
Leqian Yu,Yulei Wei,Yulei Wei,Jialei Duan,Daniel A. Schmitz,Masahiro Sakurai,Lei Wang,Kunhua Wang,Shuhua Zhao,Gary C. Hon,Jun Wu +10 more
TL;DR: In this article, the authors developed an effective three-dimensional culture strategy with successive lineage differentiation and self-organization to generate blastocyst-like structures in vitro, which they termed human blastoids.
Journal ArticleDOI
Mammalian in vitro gametogenesis.
TL;DR: Germ cells differentiate into sexually dimorphic gametes, oocytes, and spermatozoa, which unite to form new individuals as discussed by the authors, and therefore, germ cell development entails intricate regulations of genome f...
Journal ArticleDOI
Formative pluripotent stem cells show features of epiblast cells poised for gastrulation.
Xiaoxiao Wang,Yunlong Xiang,Yang Yu,Ran Wang,Yu Zhang,Qianhua Xu,Sun Hao,Zhen Ao Zhao,Xiangxiang Jiang,Xiaoqing Wang,Xukun Lu,Dandan Qin,Yujun Quan,Jiaqi Zhang,Ng Shyh-Chang,Hongmei Wang,Naihe Jing,Naihe Jing,Wei Xie,Lei Li +19 more
TL;DR: In this article, self-renewing formative pluripotent stem cells (fPSCs) were established from different mouse ESCs, pre-/early-gastrula epiblasts and induced PSCs.
Journal ArticleDOI
Cell competition constitutes a barrier for interspecies chimerism.
Canbin Zheng,Yingying Hu,Masahiro Sakurai,Carlos A. Pinzon-Arteaga,Jie Li,Yulei Wei,Yulei Wei,Daiji Okamura,Benjamin Ravaux,Haley Rose Barlow,Leqian Yu,Hai Xi Sun,Elizabeth H. Chen,Ying Gu,Jun Wu +14 more
TL;DR: In this paper, the authors developed an interspecies pluripotent stem cell (PSC) co-culture strategy and uncovered a previously unknown mode of cell competition between species, and found that genes related to the NF-κB signalling pathway, among others, were upregulated in less-fit "loser" human cells.
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Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2
TL;DR: This work presents DESeq2, a method for differential analysis of count data, using shrinkage estimation for dispersions and fold changes to improve stability and interpretability of estimates, which enables a more quantitative analysis focused on the strength rather than the mere presence of differential expression.
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The Sequence Alignment/Map format and SAMtools
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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Fast gapped-read alignment with Bowtie 2
TL;DR: Bowtie 2 combines the strengths of the full-text minute index with the flexibility and speed of hardware-accelerated dynamic programming algorithms to achieve a combination of high speed, sensitivity and accuracy.
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clusterProfiler: an R Package for Comparing Biological Themes Among Gene Clusters
TL;DR: An R package, clusterProfiler that automates the process of biological-term classification and the enrichment analysis of gene clusters and can be easily extended to other species and ontologies is presented.
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HISAT: a fast spliced aligner with low memory requirements
TL;DR: Tests showed that HISAT is the fastest system currently available, with equal or better accuracy than any other method, and requires only 4.3 gigabytes of memory.