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Chủ đề : Single-cell RNA-seq

Có 11+ tài liệu thuộc chủ đề "Single-cell RNA-seq"

Blinatumomab-induced T cell activation at single cell transcriptome resolution

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Here, blinatumomab-induced transcriptional changes reflected the functional immune activity of the blinatumomab-activated T cells, including the upregulation of pathways such as the immune system, glycolysis, IFNA signaling, gap junctions, and IFNG signaling. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material....

#BMC Genomics #Bi-specific T-cell engager antibody #Acute B cell lymphoblastic leukemia #T cell activation #Single-cell RNA-seq

The effect of methanol fixation on singlecell RNA sequencing data

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The effect of methanol fixation on single- cell RNA sequencing data. Results: We adapted an existing methanol fixation protocol and performed scRNA-seq on both live and methanol fixed cells. In this study, we comprehensively evalu- ated the effect of methanol fixation on single-cell RNA- seq results. We performed the analysis at gene and tran- script levels and observed both similarities...

#BMC Genomics #Single-cell RNA-seq #Methanol fixation #Smarts-seq2 #Drop-seq

Systematic comparison of high-throughput single-cell RNA-seq methods for immune cell profiling

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Systematic comparison of high-throughput single-cell RNA-seq methods for immune cell profiling. Background: Elucidation of immune populations with single-cell RNA-seq has greatly benefited the field of immunology by deepening the characterization of immune heterogeneity and leading to the discovery of new subtypes. However, single-cell methods inherently suffer from limitations in the recovery of complete. Results: Here, we systematically benchmarked seven high-throughput...

#BMC Genomics #Single cell #Single-cell RNA-seq #High-throughput sequencing #Immune-cell profiling #Immune heterogeneity

Cloud accelerated alignment and assembly of full-length single-cell RNA-seq data using Falco

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#BMC Genomics #Single-cell RNA-seq #cloud computing #Transcript assembly #Read alignment #Transcript isoform discovery

Exploring the changing landscape of cellto-cell variation after CTCF knockdown via single cell RNA-seq

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#BMC Genomics #Single-cell RNA-seq #Cell-to-cell variation #Change of cellular variation #CTCF knockdown

Single-cell RNA-seq of esophageal squamous cell carcinoma cell line with fractionated irradiation reveals radioresistant gene expression patterns

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A total of 218 scRNA-seq libraries were obtained from 88 cells exposed to 12 Gy (KYSE-180-12 Gy), 89 exposed to 30 Gy (KYSE-180- 30 Gy), and 41 parental KYSE-180 cells not exposed to FIR. Biological experiments showed that KYSE-180 cells became radioresistant after FIR. PCA analysis of scRNA-seq data showed KYSE-180, KYSE-180-12 Gy and KYSE-180-30 Gy cells were discrete away...

#BMC Genomics #Single-cell RNA-seq #Esophageal squamous cell carcinoma #Gene expression #Easily develop radioresistance #Heterogeneous behaviors

Single cell RNA-seq data clustering using TF-IDF based methods

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Single cell RNA-seq data clustering using TF-IDF based methods. Conclusions: Empirical experimental results show that TF-IDF methods consistently outperform commonly used scRNA-Seq clustering approaches.. Keywords: Single cell RNA-Seq, Clustering, TF-IDF. Empirical evaluation on simulated and real cell mix- tures of FACS sorted cells with different levels of com- plexity suggests that the TF-IDF methods consistently outperform existing scRNA-Seq clustering methods....

#BMC Genomics #Single-cell RNA-seq #Single cell transcriptomics #Novel cell types #Term Frequency - Inverse Document Frequency

Long non-coding RNAs potentially function synergistically in the cellular reprogramming of SCNT embryos

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Long non-coding RNAs potentially function synergistically in the cellular. A total of 7009 mouse polyadenylation lncRNAs (including 5204 novel lncRNAs) were obtained, and a comprehensive analysis of in vivo and SCNT mouse pre-implantation embryo lncRNAs was further performed based on our single-cell RNA sequencing data. Expression profile analysis revealed that lncRNAs were expressed in a developmental stage-specific manner during mouse...

#BMC Genomics #Single-cell RNA-seq #Somatic cell nuclear transfer #Cell reprogramming #Mouse embryo

Identification and characterization of functional modules reflecting transcriptome transition during human neuron maturation

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functional modules reflecting transcriptome transition during human neuron maturation. Background: Neuron maturation is a critical process in neurogenesis, during which neurons gain their morphological, electrophysiological and molecular characteristics for their functions as the central components of the nervous system.. Results: To better understand the molecular changes during this process, we combined the protein-protein interaction network and public single cell RNA-seq...

#BMC Genomics #Neuron maturation #Single-cell RNA-seq #Protein-protein interaction network #Critical process

Single-cell RNA-Seq analysis reveals dynamic trajectories during mouse liver development

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Single-cell RNA-Seq analysis reveals. Background: The differentiation and maturation trajectories of fetal liver stem/progenitor cells (LSPCs) are not fully understood at single-cell resolution, and a priori knowledge of limited biomarkers could restrict trajectory tracking.. Results: We employed marker-free single-cell RNA-Seq to characterize comprehensive transcriptional profiles of 507 cells randomly selected from seven stages between embryonic day 11.5 and postnatal day...

#BMC Genomics #Progenitor cells #Single-cell RNA-seq #Developmental trajectory #Liver stem

Characteristics of allelic gene expression in human brain cells from single-cell RNA-seq data analysis

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However, there are exceptions where only one of the two alleles is expressed. Arguably, many of the previous studies actually investigated allele-biased expression rather than monoallelic expression, including our published work [14], as pointed out by recent reports [15, 16].. Full list of author information is available at the end of the article. Finally, an RNA-seq study using human prenatal...

#BMC Genomics #Allelic gene expression #Single-cell RNA-seq #Human brain #Autosomal genes