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Systematic reconstruction of cellular trajectories across mouse embryogenesis

Integrative analysis of single-cell RNA-sequencing datasets across mouse gastrulation and organogenesis identifies cell states and trajectories at successive developmental stages, along with transcription factors that could potentially mediate lineage choices.

Chengxiang Qiu
Junyue Cao
Jay Shendure
ResearchOpen Access14 Mar 2022
Nature Genetics

Volume: 54, P: 328-341
A global view of aging and Alzheimer’s pathogenesis-associated cell population dynamics and molecular signatures in human and mouse brains

Single-cell transcriptomes and single-cell chromatin accessibility profiles generated using EasySci provide a global view of aging and Alzheimer’s pathogenesis-associated cell population dynamics in human and mouse brains.

Andras Sziraki
Ziyu Lu
Junyue Cao
ResearchOpen Access30 Nov 2023
Nature Genetics

Volume: 55, P: 2104-2116
Publisher Correction: Expanding the binding specificity for RNA recognition by a PUF domain

Wei Zhou
Daniel Melamed
Stanley Fields
Amendments and CorrectionsOpen Access27 Jun 2022
Nature Communications

Volume: 13, P: 1
The single-cell transcriptional landscape of mammalian organogenesis

Data from single-cell combinatorial-indexing RNA-sequencing analysis of 2 million cells from mouse embryos between embryonic days 9.5 and 13.5 are compiled in a cell atlas of mouse organogenesis, which provides a global view of developmental processes occurring during this critical period.

Junyue Cao
Malte Spielmann
Jay Shendure
Research20 Feb 2019
Nature

Volume: 566, P: 496-502
HSF1 critically attunes proteotoxic stress sensing by mTORC1 to combat stress and promote growth

Dai and colleagues reveal that proteotoxic stress causes JNK-mediated disintegration of the mTORC1 complexes, whereas heat shock factor 1 (HSF1) counteracts this response to promote stress resistance and growth.

Kuo-Hui Su
Junyue Cao
Chengkai Dai
Research04 Apr 2016
Nature Cell Biology

Volume: 18, P: 527-539
Dissecting key regulators of transcriptome kinetics through scalable single-cell RNA profiling of pooled CRISPR screens

mRNA kinetics are described by combining single-cell combinatorial indexing with metabolic labeling and pooled CRISPR screens.

Zihan Xu
Andras Sziraki
Junyue Cao
ResearchOpen Access25 Sept 2023
Nature Biotechnology

Volume: 42, P: 1218-1223
Single-cell, whole-embryo phenotyping of mammalian developmental disorders

A study reports single-cell RNA-sequencing profiles for more than 1.6 million cell nuclei from 101 whole mouse embryos including 22 mutant and 4 wild-type genotypes, from one experiment.

Xingfan Huang
Jana Henck
Malte Spielmann
ResearchOpen Access15 Nov 2023
Nature

Volume: 623, P: 772-781
A single-cell time-lapse of mouse prenatal development from gastrula to birth

Single-cell transcriptome profiling of mouse embryos and newborn pups is combined with previously published data to construct a tree of cell-type relationships tracing development from zygote to birth.

Chengxiang Qiu
Beth K. Martin
Jay Shendure
ResearchOpen Access14 Feb 2024
Nature

Volume: 626, P: 1084-1093
Expanding the binding specificity for RNA recognition by a PUF domain

The PUF RNAbinding domain has an eight-repeat structure with the ability to bind an eight-base RNA sequence. Here the authors generate a comprehensive library of variants of a PUF domain to find an RNA binding code and design PUF domains that recognize an arbitrary RNA sequence.

Wei Zhou
Daniel Melamed
Stanley Fields
ResearchOpen Access24 Aug 2021
Nature Communications

Volume: 12, P: 1-15
Detecting protein and post-translational modifications in single cells with iDentification and qUantification sEparaTion (DUET)

Yandong Zhang, et al. develop iDentification and qUantification sEparaTion (DUET) to quantify target protein and its post-translational modification isoforms in single cells. Using their method, they report heterogeneities in the ubiquitination levels of histone H2B in single yeast cells and reveal the cell-cycle dynamics of H2B monoubiquitination.

Yandong Zhang
Changho Sohn
Long Cai
ResearchOpen Access03 Aug 2020
Communications Biology

Volume: 3, P: 1-6
Sci-fate characterizes the dynamics of gene expression in single cells

Gene expression dynamics in single cells are tracked by labeling newly synthesized RNA in indexed cells.

Junyue Cao
Wei Zhou
Jay Shendure
Research13 Apr 2020
Nature Biotechnology

Volume: 38, P: 980-988
Optimized single-nucleus transcriptional profiling by combinatorial indexing

This protocol presents an optimized version of the single-cell combinatorial indexing RNA sequencing protocol that is faster, less expensive and suitable for profiling tissues rich in RNases, as well as a ‘Tiny-Sci’ protocol for limited input samples.

Beth K. Martin
Chengxiang Qiu
Jay Shendure
Protocols19 Oct 2022
Nature Protocols

Volume: 18, P: 188-207
Author Correction: Detecting protein and post-translational modifications in single cells with iDentification and qUantification sEparaTion (DUET)

Yandong Zhang
Changho Sohn
Long Cai
Amendments and CorrectionsOpen Access18 Aug 2020
Communications Biology

Volume: 3, P: 1

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