ABSTRACT
Single-cell RNA sequencing is a method for transcriptome profiling at the single-cell level,and is a hotspot technology in the field of biological research currently.Compared with the common high-throughput RNA sequencing,single-cell RNA sequencing can distinguish the biological differences between single cells,and identify rare cell populations and subpopulations.This review mainly describes the single-cell RNA sequencing method,summarizes current application of this technique in the field of dermatology,and discusses limitations and prospects of this technique.
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Objective To observe the expression dynamics of lens-related transcription factors in human embryonic stem cell (hESC) differentiated into lentoid body(LB).Methods A "three-stage" protocol was used for LB directional differentiation from hESC in vitro.The hESC (D0) and three differentiation stages cells were collected to analyze the expression dynamics of lens development-associated transcription factors by high throughput RNA sequencing technology in hESC-induced LB.Western blot and cell immunofluorescence were used to observe the involved genes at protein level.Results During D0-D6,cells became more round and compact.And during D7-D18,cells morphology gradually changed to spindle.At the end of D35,three-dimensional and transparent structurelentoid body (LB) was obtained.RT-PCR results showed that the stem cell related genes reduced and the lens specific genes increased significantly,and the LB was characterized by the expression of crystallins.According to clustering analysis of high throughput sequencing,a distinct difference in transcription factors gene expression was observed between D0 and D32.Meanwhile,the difference between D6 and D18 was minimum.The expressions of preplacodal genes,including DLX3,DLX5,DLX6,HES1,HES4,OTX2 and EYA1 increased remarkably at the first induction stage and then decreased.Lens-specification gene SOX2 declined gradually and then increased.In addition,the expression of PAX6 increased during all three induction stages.Furthermore,lens-differentiation genes including MAB21L1,CMAF,PROXI and PITX3 had no significant change in the early induction stage,but increased significantly at the third induction stage.Conclusions The expression dynamics of lens development-associated transcription factors in the hESC induced LB corresponded to those in vivo,which indicate that this induction system can recapitulate early lens development well and lay the foundation of studying lens embryonic development andtranscription factor associated congenital lens diseases.
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The spinal origin of cholestatic itch in experimental obstructive jaundice mouse model remains poorly understood.In this study,the jaundice model was established by bile duct ligation (BDL) in mice,and differential gene expression patterns were analyzed in the lower thoracic spinal cord involved in cholestatic pruritus after BDL operation using high-throughput RNA sequencing.At 21st day after BDL,the expression levels of ENSRNOG00000060523,ENSRNOG00000058405 and ENSRNOG00000055193 mRNA were significantly up-regulated,and those of ENSRNOG00000042197,ENSRNOG00000008478,ENSRNOG00000019607,ENSRNOG00000020647,ENSRNOG00000046289,Gemin8,Serpina3n and Trim63 mRNA were significantly down-regulated in BDL group.The RNAseq data of selected mRNAs were validated by RT-qPCR.The expression levels of ENSRNOG00000042197,ENSRNOG00000008478,ENSRNOG00000019607,ENSRNOG00000020647,ENSRNOG00000046289 and Serpina3n mRNA were significantly down-regulated in BDL group.This study suggested that cholestatic pruritus in experimental obstructive jaundice mouse model is related with in the changes of gene expression profiles in spinal cord.
ABSTRACT
The spinal origin of cholestatic itch in experimental obstructive jaundice mouse model remains poorly understood.In this study,the jaundice model was established by bile duct ligation (BDL) in mice,and differential gene expression patterns were analyzed in the lower thoracic spinal cord involved in cholestatic pruritus after BDL operation using high-throughput RNA sequencing.At 21st day after BDL,the expression levels of ENSRNOG00000060523,ENSRNOG00000058405 and ENSRNOG00000055193 mRNA were significantly up-regulated,and those of ENSRNOG00000042197,ENSRNOG00000008478,ENSRNOG00000019607,ENSRNOG00000020647,ENSRNOG00000046289,Gemin8,Serpina3n and Trim63 mRNA were significantly down-regulated in BDL group.The RNAseq data of selected mRNAs were validated by RT-qPCR.The expression levels of ENSRNOG00000042197,ENSRNOG00000008478,ENSRNOG00000019607,ENSRNOG00000020647,ENSRNOG00000046289 and Serpina3n mRNA were significantly down-regulated in BDL group.This study suggested that cholestatic pruritus in experimental obstructive jaundice mouse model is related with in the changes of gene expression profiles in spinal cord.
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RNA is a polymeric molecule implicated in various biological processes, such as the coding, decoding, regulation, and expression of genes. Numerous studies have examined RNA features using whole transcriptome sequencing (RNA-seq) approaches. RNA-seq is a powerful technique for characterizing and quantifying the transcriptome and accelerates the development of bioinformatics software. In this review, we introduce routine RNA-seq workflow together with related software, focusing particularly on transcriptome reconstruction and expression quantification.
Subject(s)
Biological Phenomena , Clinical Coding , Computational Biology , Gene Expression , High-Throughput Nucleotide Sequencing , Polymers , RNA , TranscriptomeABSTRACT
Long intergenic non-coding RNAs (lincRNAs) have historically been ignored in cancer biology. However, thousands of lincRNAs have been identified in mammals using recently developed genomic tools, including microarray and high-throughput RNA sequencing (RNA-seq). Several of the lincRNAs identified have been well characterized for their functions in carcinogenesis. Here we performed RNA-seq experiments comparing gastric cancer with normal tissues to find differentially expressed transcripts in intergenic regions. By analyzing our own RNA-seq and public microarray data, we identified 31 transcripts, including a known expressed sequence tag, BM742401. BM742401 was downregulated in cancer, and its downregulation was associated with poor survival in gastric cancer patients. Ectopic overexpression of BM742401 inhibited metastasis-related phenotypes and decreased the concentration of extracellular MMP9. These results suggest that BM742401 is a potential lincRNA marker and therapeutic target.