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Frontiers of Medicine 2022, Volume 16, Issue 2, Pages 251-262 doi: 10.1007/s11684-021-0915-9
Keywords: scRNA-seq intracellular pathogen microbe COVID-19 SARS-CoV-2
Frontiers of Medicine doi: 10.1007/s11684-023-1017-7
Keywords: single-cell RNA-seq glioma radial glia primitive oligodendrocyte precursor cell immune escape
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
Keywords: human metaphase II oocyte vitrification cryostorage duration single-cell RNA-Seq lncRNA
Characterization of chromatin accessibility in psoriasis
Frontiers of Medicine 2022, Volume 16, Issue 3, Pages 483-495 doi: 10.1007/s11684-021-0872-3
Keywords: psoriasis ATAC-seq epigenetics transcription factor
Frontiers of Agricultural Science and Engineering 2021, Volume 8, Issue 2,
Weeping species are used both as ornamental plants and for breeding dwarf plant types. However, exploration of casual genes controlling weeping traits is rather limited. Here, we identified individuals with contrasting phenotypes from an F1 bi-parental mapping population of Prunus mume which was developed from a cross between the upright cultivar ‘Liuban’ and the weeping cultivar ‘Fentai Chuizhi’. Bulked segregant RNA sequencing was used and five QTLs on Chromosome 7 were identified. The Pm024074(PmUGT72B3) allele, belonging to the UDP-glycosyltransferase superfamily containing the coniferyl-alcohol glucosyltransferase domain, was identified in a genomic region overlapping with a previously identified QTL, and had a synonymous transition of T66(upright) to C (weeping) in the coding sequence and a 470-bp deletion in the promoter region. Pm024074 had exceptionally high expression in buds and stems of weeping P. mume. Weighted correlation network analysis indicates that genes neighboring Pm024074 were significantly associated with plant architecture. In addition, a reliable single nucleotide polymorphism marker was developed based on the variation in the Pm024074 gene, providing precise marker-assisted breeding for weeping traits. This study provides insights into the genetic mechanism governing the weeping trait in P. mume, and indicates potential applications for the manipulation of tree architecture.
Keywords: BSR-seq / PmUGT72B3 / Prunus mume / UDP-glycosyltransferase / weeping shoots / WGCNA
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
Keywords: BSR-seq PmUGT72B3 Prunus mume UDP-glycosyltransferase weeping shoots WGCNA
Xin Zou, Ke Chen, Jiawei Zou, Peiyi Han, Jie Hao, Zeguang Han
Frontiers of Medicine Pages 185-192 doi: 10.1007/s11684-020-0754-0
Keywords: 2019-nCoV ACE2 single-cell RNA-seq
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
Keywords: 2D-DIGE pqqB pyrroloquinoline quinone RNA-Seq Vitamin C
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
Studies on coding genes, miRNAs, and lncRNAs during erythroid development have been performed in recent years. However, analysis focusing on the integration of the three RNA types has yet to be done. In the present study, we compared the dynamics of coding genes, miRNA, and lncRNA expression profiles. To explore dynamic changes in erythropoiesis and potential mechanisms that control these changes in the transcriptome level, we took advantage of high throughput sequencing technologies to obtain transcriptome data from cord blood hematopoietic stem cells and the following four erythroid differentiation stages, as well as from mature red blood cells. Results indicated that lncRNAs were promising cell marker candidates for erythroid differentiation. Clustering analysis classified the differentially expressed genes into four subtypes that corresponded to dynamic changes during stemness maintenance, mid-differentiation, and maturation. Integrated analysis revealed that noncoding RNAs potentially participated in controlling blood cell maturation, and especially associated with heme metabolism and responses to oxygen species and DNA damage. These regulatory interactions were displayed in a comprehensive network, thereby inferring correlations between RNAs and their associated functions. These data provided a substantial resource for the study of normal erythropoiesis, which will permit further investigation and understanding of erythroid development and acquired erythroid disorders.
Keywords: erythroid differentiation hematopoietic stem cell RNA-seq miRNA lncRNA
Title Author Date Type Operation
PathogenTrack and Yeskit: tools for identifying intracellular pathogens from single-cell RNA-sequencing datasets as illustrated by application to COVID-19
Journal Article
immune escape and microenvironment between RG-like and pri-OPC-like glioma revealed by single-cell RNA-seq
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
BULKED SEGREGANT RNA SEQUENCING (BSR-SEQ) IDENTIFIES A NOVEL ALLELE ASSOCIATED WITH WEEPING TRAITS IN
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
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
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