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Distinct immune escape and microenvironment between RG-like and pri-OPC-like glioma revealed by single-cellRNA-seq analysis

Frontiers of Medicine 2024, Volume 18, Issue 1,   Pages 147-168 doi: 10.1007/s11684-023-1017-7

Abstract: By conducting single-cell RNA-seq analyses on 26 gliomas, we reported their classification into primitiveoligodendrocyte precursor cell (pri-OPC)-like and radial glia (RG)-like tumors and validated it in aFor example, glial/glioma stem cell markers OLIG1/PTPRZ1 and B cell-specific receptors

Keywords： single-cell RNA-seq     glioma     radial glia     primitive oligodendrocyte precursor cell     immune escape    

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Single-cell RNA-seq reveals the transcriptional program underlying tumor progression and metastasis in

Frontiers of Medicine 2024, Volume 18, Issue 4,   Pages 690-707 doi: 10.1007/s11684-024-1081-7

Abstract: The ‘starter’ population exhibited high expression levels of multiple cell cycle-related genes, indicatingthe important role of cell cycle upregulation in NB tumor progression.

Keywords： single-cell RNA sequencing     metastasis     neuroblastoma     epithelial-to-mesenchymal transition    

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Effects of vitrification and cryostorage duration on single-cell RNA-Seq profiling of vitrified-thawed

Ying Huo, Peng Yuan, Qingyuan Qin, Zhiqiang Yan, Liying Yan, Ping Liu, Rong Li, Jie Yan, Jie Qiao

Frontiers of Medicine 2021, Volume 15, Issue 1,   Pages 144-154 doi: 10.1007/s11684-020-0792-7

Abstract: RNA-Seq profiles of 3 fresh oocytes and 13 surviving vitrified-thawed oocytes (3, 3, 4, and 3 oocyteswere cryostored for 1, 2, 3, and 12 months) were analyzed at a single-cell resolution.

Keywords： human metaphase II oocyte     vitrification     cryostorage duration     single-cell RNA-Seq     lncRNA    

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Single-cell RNA-seq data analysis on the receptor ACE2 expression reveals the potential risk of different

Xin Zou, Ke Chen, Jiawei Zou, Peiyi Han, Jie Hao, Zeguang Han

Frontiers of Medicine 2024, Volume 18, Issue 1,   Pages 185-192 doi: 10.1007/s11684-020-0754-0

Abstract: To construct a risk map of different human organs, we analyzed the single-cell RNA sequencing (scRNA-seqThrough scRNA-seq data analyses, we identified the organs at risk, such as lung, heart, esophagus, kidney, bladder, and ileum, and located specific cell types (i.e., type II alveolar cells (AT2), myocardial

Keywords： 2019-nCoV     ACE2     single-cell RNA-seq    

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PathogenTrack and Yeskit: tools for identifying intracellular pathogens from single-cell RNA-sequencing

Frontiers of Medicine 2022, Volume 16, Issue 2,   Pages 251-262 doi: 10.1007/s11684-021-0915-9

Abstract: Taking advantage of single-cell RNA-sequencing (scRNA-seq) analysis, we can assess the transcriptomicfeatures at the single-cell level.Still, the tools used to interpret pathogens (such as viruses, bacteria, and fungi) at the single-celldata to identify intracellular pathogens at the single-cell level.the state-of-the-art tools such as Viral-Track, and the first tools for identifying bacteria at the single-cell

Keywords： scRNA-seq     intracellular pathogen     microbe     COVID-19     SARS-CoV-2    

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Distinct mononuclear diploid cardiac subpopulation with minimal cell–cell communications persists in

Frontiers of Medicine 2023, Volume 17, Issue 5,   Pages 939-956 doi: 10.1007/s11684-023-0987-9

Abstract: end, 12 645 cardiac cells were generated from embryonic day 17.5 and postnatal days 2 and 8 mice by single-cellRNA sequencing.MNDCMs having interactions with macrophages and non-proliferative MNDCMs (non-pMNDCMs) with minimal cell–cell Single-nucleus RNA sequencing and immunohistochemical staining further proved that the Myl4single-cell transcriptomic data.

Keywords： mononuclear diploid cardiomyocytes     cell–cell communication     cardiac fibroblast     single-cell RNA sequencing    

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Microfluidic Barcode Biochips for High-Throughput Real-Time Biomolecule and Single-Cell Screening

Jiaoyan Qiu,Yanbo Liang,Chao Wang,Yang Yu,Yu Zhang,Hong Liu,Lin Han,

Engineering doi: 10.1016/j.eng.2024.06.016

Abstract: The real-time screening of biomolecules and single cells in biochips is extremely important for diseasemicrofluidics barcode biochip analytical approaches for the high-throughput screening of biomolecules and singlecells, including protein biomarkers, microRNA (miRNA), circulating tumor DNA (ctDNA), single-cell secretedproteins, single-cell exosomes, and cell interactions.Following this, we outline recent improvements in microfluidic devices for biomolecule and single-cell

Keywords： High-throughput     Microfluidic barcode biochip     Single-cell analysis     Biomolecules    

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Global transcriptome analysis for identification of interactions between coding and noncoding RNAs during human erythroid differentiation

Nan Ding,Jiafei Xi,Yanming Li,Xiaoyan Xie,Jian Shi,Zhaojun Zhang,Yanhua Li,Fang Fang,Sihan Wang,Wen Yue,Xuetao Pei,Xiangdong Fang

Frontiers of Medicine 2016, Volume 10, Issue 3,   Pages 297-310 doi: 10.1007/s11684-016-0452-0

Abstract: However, analysis focusing on the integration of the three RNA types has yet to be done.Results indicated that lncRNAs were promising cell marker candidates for erythroid differentiation.Integrated analysis revealed that noncoding RNAs potentially participated in controlling blood cell maturation

Keywords： erythroid differentiation     hematopoietic stem cell     RNA-seq     miRNA     lncRNA    

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Identification of transporter proteins for PQQ-secretion pathways by transcriptomics and proteomics analysis in

Hui Wan,Yu Xia,Jianghua Li,Zhen Kang,Jingwen Zhou

Frontiers of Chemical Science and Engineering 2017, Volume 11, Issue 1,   Pages 72-88 doi: 10.1007/s11705-016-1580-4

Abstract: used both two-dimensional fluorescence-difference gel electrophoresis tandem mass spectrometry and RNA

Keywords： 2D-DIGE     pqqB     pyrroloquinoline quinone     RNA-Seq     Vitamin C    

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A cytoprotective graphene oxide-polyelectrolytes nanoshell for single-cell encapsulation

Luanying He, Yulin Chang, Junhao Zhu, Ying Bi, Wenlin An, Yiyang Dong, Jia-Hui Liu, Shihui Wang

Frontiers of Chemical Science and Engineering 2021, Volume 15, Issue 2,   Pages 410-420 doi: 10.1007/s11705-020-1950-9

Abstract: Graphene oxide (GO) has been increasingly utilized in the fields of food, biomedicine, environment and other fields because of its benign biocompatible. We encapsulated two kinds of GO with different sizes on yeast cells with the assistance of polyelectrolytes poly (styrene sulfonic acid) sodium salt (PSS) and polyglutamic acid (PGA) (termed as Y@GO). The result does not show a significant difference between the properties of the two types of Y@GO (namely Y@GO1 and Y@GO2). The encapsulation layers are optimized as Yeast/PGA/PSS/PGA/GO/PGA/PSS based on the morphology, dispersity, colony-forming unit, and zeta potential. The encapsulation of GO increases the roughness of the yeast. It is proved that the Y@GO increases the survival time and enhance the activity of yeast cells. The GO shell improves the resistance of yeast cells against pH and salt stresses and extends the storage time of yeast cells.

Keywords： GO     yeast     polyelectrolyte     cytoprotection     nanomaterials    

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BULKED SEGREGANT RNA SEQUENCING (BSR-SEQ) IDENTIFIES A NOVEL ALLELE ASSOCIATED WITH WEEPING TRAITS IN

Frontiers of Agricultural Science and Engineering 2021, Volume 8, Issue 2,

Abstract: Bulked segregant RNA sequencing was used and five QTLs on Chromosome 7 were identified.In addition, a reliable single nucleotide polymorphism marker was developed based on the variation in

Keywords： BSR-seq / PmUGT72B3 / Prunus mume / UDP-glycosyltransferase / weeping shoots / WGCNA    

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Emerging Trends for Microbiome Analysis: From Single-Cell Functional Imaging to Microbiome Big Data

Jian Xu, Bo Ma, Xiaoquan Su, Shi Huang, Xin Xu, Xuedong Zhou, Wei Huang, Rob Knight

Engineering 2017, Volume 3, Issue 1,   Pages 66-70 doi: 10.1016/J.ENG.2017.01.020

Abstract:

Method development has always been and will continue to be a core driving force of microbiome science. In this perspective, we argue that in the next decade, method development in microbiome analysis will be driven by three key changes in both ways of thinking and technological platforms: ① a shift from dissecting microbiota structureby sequencing to tracking microbiota state, function, and intercellular interaction via imaging; ② a shift from interrogating a consortium or population of cells to probing individual cells; and ③ a shift from microbiome data analysis to microbiome data science. Some of the recent method-development efforts by Chinese microbiome scientists and their international collaborators that underlie these technological trends are highlighted here. It is our belief that the China Microbiome Initiative has the opportunity to deliver outstanding “Made-in-China” tools to the international research community, by building an ambitious, competitive, and collaborative program at the forefront of method development for microbiome science.

Keywords： Microbiome     Methoddevelopment     Single-cell analysis     Big data     China Microbiome Initiative    

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A Single-Cell Landscape of Human Liver Transplantation Reveals a Pathogenic Immune Niche Associated with Article

Xin Shao,Zheng Wang,Kai Wang,Xiaoyan Lu,Ping Zhang,Rongfang Guo,Jie Liao,Penghui Yang,Xiao Xu,Xiaohui Fan

Engineering 2024, Volume 36, Issue 5,   Pages 193-208 doi: 10.1016/j.eng.2023.12.004

Abstract: Herein, we constructed a pioneering single-cell transcriptomic landscape of human transplanted liverscellular characteristics of transplanted livers and the EAD-associated pathogenic immune niche at the single-cell

Keywords： Human liver transplantation     Early allograft dysfunction     Pathogenic immune niche     Single-cell analysis     Cell–cell communication    

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BULKED SEGREGANT RNA SEQUENCING (BSR-SEQ) IDENTIFIES A NOVEL ALLELE ASSOCIATED WITH WEEPING TRAITS IN

Xiaokang ZHUO, Tangchun ZHENG, Zhiyong ZHANG, Suzhen LI, Yichi ZHANG, Lidan SUN, Weiru YANG, Jia WANG, Tangren CHENG, Qixiang ZHANG

Frontiers of Agricultural Science and Engineering   Pages 196-214 doi: 10.15302/J-FASE-2020379

Abstract: Bulked segregant RNA sequencing was used and five QTLs on Chromosome 7 were identified.In addition, a reliable single nucleotide polymorphism marker was developed based on the variation in

Keywords： BSR-seq     PmUGT72B3     Prunus mume     UDP-glycosyltransferase     weeping shoots     WGCNA    

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Dysregulated N-methyladenosine modification in peripheral immune cells contributes to the pathogenesis of amyotrophic lateral sclerosis

Frontiers of Medicine 2024, Volume 18, Issue 2,   Pages 285-302 doi: 10.1007/s11684-023-1035-5

Abstract: Methylated RNA immunoprecipitation sequencing (MeRIP-seq) and liquid chromatography–mass spectrometryThe single-cell transcriptomic dataset (GSE174332) of primary motor cortex was further analyzed to illuminatethe biological implications of differentially methylated genes and cell communication changes.Analysis of peripheral immune cells revealed extensive RNA hypermethylation, highlighting candidate genesSerum proteome analysis demonstrated the role of dysregulated immune cell migration in ALS.

Keywords： amyotrophic lateral sclerosis     N6-methyladenosine     epi-transcriptome     proteome     single cellRNA sequencing analysis     CX3CR1    

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Title Author Date Type Operation

Distinct immune escape and microenvironment between RG-like and pri-OPC-like glioma revealed by single-cellRNA-seq analysis

Journal Article

Single-cell RNA-seq reveals the transcriptional program underlying tumor progression and metastasis in

Journal Article

Effects of vitrification and cryostorage duration on single-cell RNA-Seq profiling of vitrified-thawed

Ying Huo, Peng Yuan, Qingyuan Qin, Zhiqiang Yan, Liying Yan, Ping Liu, Rong Li, Jie Yan, Jie Qiao

Journal Article

Single-cell RNA-seq data analysis on the receptor ACE2 expression reveals the potential risk of different

Xin Zou, Ke Chen, Jiawei Zou, Peiyi Han, Jie Hao, Zeguang Han

Journal Article

PathogenTrack and Yeskit: tools for identifying intracellular pathogens from single-cell RNA-sequencing

Journal Article

Distinct mononuclear diploid cardiac subpopulation with minimal cell–cell communications persists in

Journal Article

Microfluidic Barcode Biochips for High-Throughput Real-Time Biomolecule and Single-Cell Screening

Jiaoyan Qiu,Yanbo Liang,Chao Wang,Yang Yu,Yu Zhang,Hong Liu,Lin Han,

Journal Article

Global transcriptome analysis for identification of interactions between coding and noncoding RNAs during human erythroid differentiation

Nan Ding,Jiafei Xi,Yanming Li,Xiaoyan Xie,Jian Shi,Zhaojun Zhang,Yanhua Li,Fang Fang,Sihan Wang,Wen Yue,Xuetao Pei,Xiangdong Fang

Journal Article

Identification of transporter proteins for PQQ-secretion pathways by transcriptomics and proteomics analysis in

Hui Wan,Yu Xia,Jianghua Li,Zhen Kang,Jingwen Zhou

Journal Article

A cytoprotective graphene oxide-polyelectrolytes nanoshell for single-cell encapsulation

Luanying He, Yulin Chang, Junhao Zhu, Ying Bi, Wenlin An, Yiyang Dong, Jia-Hui Liu, Shihui Wang

Journal Article

BULKED SEGREGANT RNA SEQUENCING (BSR-SEQ) IDENTIFIES A NOVEL ALLELE ASSOCIATED WITH WEEPING TRAITS IN

Journal Article

Emerging Trends for Microbiome Analysis: From Single-Cell Functional Imaging to Microbiome Big Data

Jian Xu, Bo Ma, Xiaoquan Su, Shi Huang, Xin Xu, Xuedong Zhou, Wei Huang, Rob Knight

Journal Article

A Single-Cell Landscape of Human Liver Transplantation Reveals a Pathogenic Immune Niche Associated with

Xin Shao,Zheng Wang,Kai Wang,Xiaoyan Lu,Ping Zhang,Rongfang Guo,Jie Liao,Penghui Yang,Xiao Xu,Xiaohui Fan

Journal Article

BULKED SEGREGANT RNA SEQUENCING (BSR-SEQ) IDENTIFIES A NOVEL ALLELE ASSOCIATED WITH WEEPING TRAITS IN

Xiaokang ZHUO, Tangchun ZHENG, Zhiyong ZHANG, Suzhen LI, Yichi ZHANG, Lidan SUN, Weiru YANG, Jia WANG, Tangren CHENG, Qixiang ZHANG

Journal Article

Dysregulated N-methyladenosine modification in peripheral immune cells contributes to the pathogenesis of amyotrophic lateral sclerosis

Journal Article