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Single-cell rna-sequencing combined with bulk rna-sequencing analysis of peripheral blood reveals the characteristics and key immune cell genes of ulcerative colitis

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World Journal of Clinical Cases 2022年第33期10卷 12116-12135页

作者： Yan-Cheng Dai Dan Qiao Chen-Ye Fang Qiu-Qin Chen Ren-Ye Que Tie-Gang Xiao Lie Zheng Li-Juan Wang Ya-Li Zhang Department of Gastroenterology Shanghai Traditional Chinese Medicine-Integrated HospitalShanghai University of Traditional Chinese MedicineShanghai 200082China Department of Gastroenterology Traditional Chinese Medicine Hospital of NingboNingbo 315000Zhejiang ProvinceChina Department of Pathology Shanghai Traditional Chinese Medicine-Integrated HospitalShanghai University of Traditional Chinese MedicineShanghai 200082China Department of Gastroenterology Traditional Chinese Medicine Hospital of Xi’an 730000Shaanxi ProvinceChina Experimental Education Center Shanghai University of Traditional Chinese MedicineShanghai 201203China Institute of Digestive Diseases LongHua Hospital Shanghai University of Traditional Chinese MedicineShanghai 200032China

BACKGROUND Ulcerative colitis(UC)is a complicated disease caused by the interaction between genetic and environmental factors that affects mucosal homeostasis and triggers an inappropriate immune ***-cell rna sequencing(scrna-seq)can be used to rapidly obtain the precise gene expression patterns of thousands of cells in the intestine,analyze the characteristics of cells with the same phenotype,and provide new insights into the growth and development of intestinal organs,the clonal evolution of cells,and immune cell *** findings can provide new ideas for the diagnosis and treatment of intestinal *** identify clinical phenotypes and biomarkers that can predict the response of UC patients to specific therapeutic drugs and thus aid the diagnosis and treatment of *** Using the Gene Expression Omnibus(GEO)database,we analyzed peripheral blood cell subtypes of patients with UC by scrna-seq combined with bulk rna sequencing(rna-seq)to reveal the core genes of *** then combined weighted gene correlation network analysis(WGCNA)and least absolute shrinkage and selection operator(LASSO)analysis to reveal diagnostic markers of *** After processing the scrna-seq data,we obtained data from approximately 24340 cells and identified 17 cell *** intercellular communication analysis,we selected monocyte marker genes as the candidate gene set for the prediction *** of a WGCNA coexpression network identified RhoB,cathepsin D(CTSD)and zyxin(ZYX)as core *** infiltration analysis showed that these three core genes were strongly correlated with immune *** enrichment analysis showed that the differentially expressed genes were closely related to immune and inflammatory responses,which are associated with many challenges in the diagnosis and treatment of *** Through scrna-seq analysis,LASSO diagnostic model building and WGCNA,we identified RhoB,CTSD and ZYX as core genes of UC that are closel

关键词： Ulcerative colitis Single-cell rna-seq bulk rna-seq Peripheral blood Key genes

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A reproducible and sensitive method for generating high-quality transcriptomes from single whitefly salivary glands and other low-input tissues

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Insect Science 2022年第5期29卷 1318-1328页

作者： Marco Gebiola Brandon H.Le Kerry EMauck Department of Entomology University of California RiversideRiversideCalifornia Department of Botany and Plant Sciences University of California RiversideRiversideCalifornia Institute of Integrative Genome Biology University of California RiversideRiversideCaliforniaUSA

Transcriptomic studies are an important tool for understanding the molecular pathways underlying host plant use by agricultural pests,including vectors of damaging plant *** far,bulk rna-seq has been the main approach for non-model *** method relies on pooling large numbers of whole organisms or hundreds of individually dissected *** latter approach is logistically challenging,may introduce artifacts of handling and storage,and is not compatible with biological ***,we tested an approach to generate transcriptomes of individual salivary glands and other low-input body tissues from whiteflies(Bemisia tabaci MEAM1),which are major vectors of plant *** comparing our outputs to published bulk rna-seq datasets for whole whitefly bodies and pools of salivary glands,we demonstrate that this approach recovers similar numbers of transcripts relative to bulk rna-seq in a tissue-specific manner,and for some metrics,exceeds performance of bulk tissue *** generated from individual salivary glands also yielded additional novel transcripts not identified in pooled salivary gland datasets,and had hundreds of enriched transcripts when compared with whole head ***,our study demonstrates that it is feasible to produce high quality,replicated transcriptomes of whitefly salivary glands and other low-input *** anticipate that our approach will expand hypothesis-driven research on salivary glands of whiteflies and other Hemiptera,thus enabling novel control strategies to disrupt feeding and virus transmission.

关键词： Aleyrodidae Bemisia tabaci bulk rna-seq insect vectors low-input rna-seq plant pathogens

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Direct Comparative Analyses of 10X Genomics Chromium and Smart-seq2

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Genomics, Proteomics & Bioinformatics 2021年第2期19卷 253-266页

作者： Xiliang Wang Yao He Qiming Zhang Xianwen Ren Zemin Zhang BIOPIC Beijing Advanced Innovation Center for Genomicsand School of Life SciencesPeking UniversityBeijing 100871China Peking-Tsinghua Center for Life Sciences Academy for Advanced Interdisciplinary StudiesPeking UniversityBeijing 100871China

Single-cell rna sequencing(scrna-seq)is generally used for profiling transcriptome of individual *** droplet-based 10X Genomics Chromium(10X)approach and the plate-based Smart-seq2 full-length method are two frequently used scrna-seq platforms,yet there are only a few thorough and systematic comparisons of their advantages and ***,by directly comparing the scrna-seq data generated by these two platforms from the same samples of CD45cells,we systematically evaluated their features using a wide spectrum of ***-seq2 detected more genes in a cell,especially low abundance transcripts as well as alternatively spliced transcripts,but captured higher proportion of mitochondrial *** composite of Smart-seq2 data also resembled bulk rna-seq data *** 10X-based data,we observed higher noise for mrnas with low expression *** 10%30%of all detected transcripts by both platforms were from non-coding genes,with long non-coding rnas(lncrnas)accounting for a higher proportion in 10X.10X-based data displayed more severe dropout problem,especially for genes with lower expression ***,10X-data can detect rare cell types given its ability to cover a large number of *** addition,each platform detected distinct groups of differentially expressed genes between cell clusters,indicating the different characteristics of these *** study promotes better understanding of these two platforms and offers the basis for an informed choice of these widely used technologies.

关键词： Single-cell rna sequencing 10X Smart-seq2 bulk rna-seq Comparison

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