Results 31 to 40 of about 1,093 (205)

Quantification and statistical modeling of droplet-based single-nucleus RNA-sequencing data

Biostatistics, 2023
Summary In complex tissues containing cells that are difficult to dissociate, single-nucleus RNA-sequencing (snRNA-seq) has become the preferred experimental technology over single-cell RNA-sequencing (scRNA-seq) to measure gene expression.
Albert Kuo, Kasper D Hansen, Stephanie C Hicks   +2 more
openaire   +2 more sources

Characterizing the composition of iPSC derived cells from bulk transcriptomics data with CellMap

Scientific Reports, 2022
Induced pluripotent stem cell (iPSC) derived cell types are increasingly employed as in vitro model systems for drug discovery. For these studies to be meaningful, it is important to understand the reproducibility of the iPSC-derived cultures and their ...
Zhengyu Ouyang, Nathanael Bourgeois-Tchir, Eugenia Lyashenko, Paige E. Cundiff, Patrick F. Cullen, Ravi Challa, Kejie Li, Xinmin Zhang, Fergal Casey, Sandra J. Engle, Baohong Zhang, Maria I. Zavodszky   +11 more
doaj   +1 more source

A single-nucleus RNA-sequencing pipeline to decipher the molecular anatomy and pathophysiology of human kidneys

Nature Communications, 2019
Single-cell studies in solid tissues remain challenging and have benefited from the development of single-nuclei RNA sequencing strategies. Here Lake et al.
Blue B. Lake, Song Chen, Masato Hoshi, Nongluk Plongthongkum, Diane Salamon, Amanda Knoten, Anitha Vijayan, Ramakrishna Venkatesh, Eric H. Kim, Derek Gao, Joseph Gaut, Kun Zhang, Sanjay Jain   +12 more
doaj   +1 more source

Protein pyrophosphorylation by inositol pyrophosphates — detection, function, and regulation

FEBS Letters, EarlyView.
Protein pyrophosphorylation is an unusual signaling mechanism that was discovered two decades ago. It can be driven by inositol pyrophosphate messengers and influences various cellular processes. Herein, we summarize the research progress and challenges of this field, covering pathways found to be regulated by this posttranslational modification as ...
Sarah Lampe, Tanmay Kumar Mohanty, Rashna Bhandari, Dorothea Fiedler   +3 more
wiley   +1 more source

FlsnRNA-seq: protoplasting-free full-length single-nucleus RNA profiling in plants

Genome Biology, 2021
The broad application of single-cell RNA profiling in plants has been hindered by the prerequisite of protoplasting that requires digesting the cell walls from different types of plant tissues. Here, we present a protoplasting-free approach, flsnRNA-seq,
Yanping Long, Zhijian Liu, Jinbu Jia, Weipeng Mo, Liang Fang, Dongdong Lu, Bo Liu, Hong Zhang, Wei Chen, Jixian Zhai   +9 more
doaj   +1 more source

An upstream open reading frame regulates expression of the mitochondrial protein Slm35 and mitophagy flux

FEBS Letters, EarlyView.
This study reveals how the mitochondrial protein Slm35 is regulated in Saccharomyces cerevisiae. The authors identify stress‐responsive DNA elements and two upstream open reading frames (uORFs) in the 5′ untranslated region of SLM35. One uORF restricts translation, and its mutation increases Slm35 protein levels and mitophagy.
Hernán Romo‐Casanueva, Ariann E. Mendoza‐Martínez, P. Abril Medina‐Flores, Carlos Campero‐Basaldua, Alexander DeLuna, Soledad Funes   +5 more
wiley   +1 more source

Single-nuclei transcriptomics enable detection of somatic variants in patient brain tissue

Scientific Reports, 2023
Somatic variants are a major cause of human disease, including neurological disorders like focal epilepsies, but can be challenging to study due to their mosaicism in bulk tissue biopsies.
Sydney E. Townsend, Jesse J. Westfall, Jason B. Navarro, Daniel C. Koboldt, Elaine R. Mardis, Katherine E. Miller, Tracy A. Bedrosian   +6 more
doaj   +1 more source

Transferrin receptor 1‐mediated iron uptake supports thermogenic activation in human cervical‐derived adipocytes

FEBS Letters, EarlyView.
In this study, we found that human cervical‐derived adipocytes maintain intracellular iron level by regulating the expression of iron transport‐related proteins during adrenergic stimulation. Melanotransferrin is predicted to interact with transferrin receptor 1 based on in silico analysis.
Rahaf Alrifai, Mizuki Seo, Gyath Karadsheh, Fachrur Rizal Mahendra, Máté Á Demény, Ferenc Győry, János András Mótyán, László Fésüs, Endre Kristóf, Rini Arianti   +9 more
wiley   +1 more source

Neuronal subtypes and diversity revealed by single-nucleus RNA sequencing of the human brain [PDF]

Science, 2016
Single-nucleus gene expression Identifying the genes expressed at the level of a single cell nucleus can better help us understand the human brain. Blue et al. developed a single-nuclei sequencing technique, which they applied to cells in classically defined Brodmann areas from a postmortem brain ...
Lake, Blue B, Ai, Rizi, Kaeser, Gwendolyn E, Salathia, Neeraj S, Yung, Yun C, Liu, Rui, Wildberg, Andre, Gao, Derek, Fung, Ho-Lim, Chen, Song, Vijayaraghavan, Raakhee, Wong, Julian, Chen, Allison, Sheng, Xiaoyan, Kaper, Fiona, Shen, Richard, Ronaghi, Mostafa, Fan, Jian-Bing, Wang, Wei, Chun, Jerold, Zhang, Kun   +20 more
openaire   +4 more sources

Valosin‐containing protein counteracts ATP‐driven dissolution of FUS condensates through its ATPase activity in vitro

FEBS Letters, EarlyView.
Biomolecular condensates formed by fused in sarcoma (FUS) are dissolved by high ATP concentrations yet persist in cells. Using a reconstituted system, we demonstrate that valosin‐containing protein (VCP), an AAA+ ATPase, counteracts ATP‐driven dissolution of FUS condensates through its D2 ATPase activity.
Hitomi Kimura, Shin‐ichi Tate, Kyota Yasuda   +2 more
wiley   +1 more source