Results 141 to 150 of about 86,859 (350)

Granatum: a graphical single-cell RNA-Seq analysis pipeline for genomics scientists

Genome Medicine, 2017
Background Single-cell RNA sequencing (scRNA-Seq) is an increasingly popular platform to study heterogeneity at the single-cell level. Computational methods to process scRNA-Seq data are not very accessible to bench scientists as they require a ...
Xun Zhu, Thomas K. Wolfgruber, Austin Tasato, Cédric Arisdakessian, David G. Garmire, Lana X. Garmire   +5 more
doaj   +1 more source

The immune cell landscape in kidneys of patients with lupus nephritis. [PDF]

, 2019
Lupus nephritis is a potentially fatal autoimmune disease for which the current treatment is ineffective and often toxic. To develop mechanistic hypotheses of disease, we analyzed kidney samples from patients with lupus nephritis and from healthy control
Accelerating Medicines Partnership in SLE network, Anolik, Jennifer H, Apruzzese, William, Arazi, Arnon, Berthier, Celine C, Brenner, Michael B, Browne, Edward P, Buyon, Jill P, Chicoine, Adam, Dall'Era, Maria, Davidson, Anne, Diamond, Betty, Eisenhaure, Thomas M, Furie, Richard A, Hacohen, Nir, Hildeman, David A, Hoover, Paul J, Jonsson, A Helena, Kalunian, Kenneth C, Kamen, Diane L, Kretzler, Matthias, Lederer, James A, Li, Shuqiang, Lieb, David J, Liu, Yanyan, Massarotti, Elena, McInnis, Elizabeth A, Noma, Akiko, Nusbaum, Chad, Park, Meyeon, Payan-Schober, Fernanda, Pendergraft, William F, Petri, Michelle A, Putterman, Chaim, Rao, Deepak A, Raychaudhuri, Soumya, Slowikowski, Kamil, Smilek, Dawn E, Steelman, Scott, Sutherby, Danielle, Tosta, Patti, Wofsy, David, Woodle, E Steve, Zhang, Fan   +43 more
core  

Size‐Modulated Mesoderm‐Endoderm Divergence and Myocardial Cavitation in Micropatterned Cardioids

Advanced Science, EarlyView.
Micropatterned cardioids, CRISPR‐engineered reporter hiPSCs, deep‐tissue imaging, and single‐cell RNA sequencing are integrated to model mesoderm‐endoderm co‐development. Heart‐foregut crosstalk promotes single large cavitation inside cardioids, resembling early heart chamber formation. ABSTRACT The human heart, originating from the splanchnic mesoderm,
Plansky Hoang, David W. McKellar, Andrew Kowalczewski, Nhu Y. Mai, Meng Chai, Xiaojun L. Lian, Yi Zheng, Jeffrey Amack, Nathan Tucker, Iwijn De Vlaminck, Huaxiao Yang, Benjamin D. Cosgrove, Zhen Ma   +12 more
wiley   +1 more source

scRNA-seq Data Processing (Cell Ranger, v6.0.0) v1

, 2022
Merissa Olmer, Martin Lotz, P. Natarajan, Steven R. Head   +3 more
openalex   +1 more source

Hierarchical marker genes selection in scRNA-seq analysis

PLOS Computational Biology
When analyzing scRNA-seq data containing heterogeneous cell populations, an important task is to select informative marker genes to distinguish various cell clusters and annotate the clusters with biologically meaningful cell types. In existing analysis methods and pipelines, marker genes are typically identified using a one-vs-all strategy, examining ...
Yutong Sun, Peng Qiu
openaire   +3 more sources

Single‐Cell Transcriptomics Reveals FLS2‐Dependent Hypoxia Signaling and ERF13‐Mediated Transcription During flg22‐Triggered Immunity

Advanced Science, EarlyView.
This study employs sc‐RNA sequencing, genetics, and phenotyping to systematically map the cell‐type‐specific immune responses triggered by flg22. It reveals FLS2‐dependent transcriptional reprogramming in epidermal and mesophyll cells, and uncovers crosstalk between immune and hypoxia signaling pathways.
Yaping Zhou, Aizhi Qin, Mengfan Li, Qianli Zhao, Luyao Kong, Lulu Yan, Chunyang Li, Hao Liu, Yinpeng Zhang, Jiani Long, Mengyu Liao, Mengmeng Zhou, Xiaoli Fan, Baozhen Wang, Wenxuan Kang, Shui Wang, Zhixin Liu, Xuwu Sun   +17 more
wiley   +1 more source

Fibronectin1‐Expressing Subicular Circuits Selectively Govern the Retrieval of Novel Object Recognition

Advanced Science, EarlyView.
Fibronectin 1 (FN1)‐expressing subicular subpopulations encode novel object preference and selectively govern retrieval of novel object recognition (NOR) via affecting excitability of entorhinal‐projecting circuit through large conductance Ca2+‐activated potassium (BK) channel. ABSTRACT Novel object recognition (NOR), referring to the cognitive ability
Fan Fei, Jiaying Shi, Jing Xi, Yixiang Xu, Shuye Ying, Xukun Fan, Wangjialu Lu, Zhisheng Li, Menghan Li, Yu Wang, Li Cheng, Lin Yang, Lingyu Xu, Zhong Chen, Cenglin Xu, Yi Wang   +15 more
wiley   +1 more source

GSAE: an autoencoder with embedded gene-set nodes for genomics functional characterization

, 2018
Bioinformatics tools have been developed to interpret gene expression data at the gene set level, and these gene set based analyses improve the biologists' capability to discover functional relevance of their experiment design. While elucidating gene set
Chen, Hung-I Harry, Chen, Yidong, Chiu, Yu-Chiao, Huang, Yufei, Zhang, Songyao, Zhang, Tinghe   +5 more
core   +3 more sources

scDNA-scRNA-seq (SDR-seq) v1

scDNA-scRNA-seq (SDR-seq) is a method that enables a targeted readout of both genomic and transcriptomic targets in thousands of single cells per experiment. It combines an in-situ reverse transcription (RT) step of fixed cells with a multiplexed PCR in an emulsion-based droplets using the microfluidic Tapestri device from MissionBio.
Dominik Lindenhofer, Julia Bauman, John A. Hawkins, Donnacha Fitzgerald, Umut Yildiz, Haeyeon Jung, Anastasiia Korosteleva, Mikael Marttinen, Moritz Kueblbeck, Judith B. Zaugg, Kyung-Min Noh, Sascha Dietrich, Wolfgang Huber, Oliver Stegle, Lars M. Steinmetz   +14 more
openaire   +1 more source

Sphingomonas paucimobilis‐Driven Epithelial–Endothelial Transition in Adenomyosis Pathogenesis

Advanced Science, EarlyView.
This study identifies epithelial–endothelial transition (EET) as a novel adenomyosis pathogenic mechanism driven by Sphingomonas paucimobilis colonization. Systematic inhibitor experiments validate a TNFα→NF‐κB→MMP signaling cascade essential for EET. Critically, bacterial culture supernatant fails to induce pathological changes, demonstrating viable ...
Peigen Chen, Hao Shi, Junxian He, Ziyu Liu, Yuanyuan Zhu, Xiaoyan Liang, Guihua Liu, Xing Yang   +7 more
wiley   +1 more source