Search results for "transcriptome"

Response: platelet transcriptome and proteome—relation rather than correlation

2013

We have demonstrated by a detailed statistical analysis of proteome and transcriptome data of human platelets and human cell lines that protein and transcript abundance in platelets, if at all, are only weakly correlated.[1][1] This analysis appears to be in contradiction to previous claims made

Early life stress programming of NG2+ glia transcriptome alters functional properties of voltage gated sodium (Nav) channels and cognitive performance

2020

AbstractThe precise mechanisms underlying the detrimental effects of early life stress (ELS) on adult mental health remain still elusive. To date, most studies have exclusively targeted neuronal populations and not considered neuron-glia crosstalk as a crucially important element for the integrity of stress-related brain function. Here, we have investigated the impact of ELS on a glial subpopulation with unique properties in brain homeostasis, the NG2+ cells. ELS shifted the NG2+ transcriptome towards more mature stages, and these transcriptional effects were dependent on stress-induced glucocorticoids. The functional relevance of one candidate gene, Scn7a, could be confirmed by an increase…

Single Cell RT-PCR on Mouse Embryos: A General Approach for Developmental Biology

2010

Preimplantation development is a complicated process, which involves many genes. We have investigated the expression patterns of 17 developmentally important genes and isoforms in early mouse embryos as well as in single cells of the mouse embryo. The comparison is an excellent example for showing the importance of studying heterogeneity among cell populations on the RNA level, which is being increasingly addressed in basic research and medical sciences, particularly with a link to diagnostics (e.g. the analysis of circulating tumor cells and their progenitors). The ubiquitously expressed histone variant H3f3a and the transcription factor Pou5f1 generated mRNA-derived products in all analyz…

Messenger RNA Sequencing of Rare Cell Populations in the Lung and Lung-Draining Lymph Nodes

2017

Next-generation sequencing (NGS) techniques provide unique prospects for in-depth transcriptome analyses. Nevertheless, the emerging and still growing knowledge about the large diversity and heterogeneity of cells that participate in immunological responses in a tissue- and micromilieu-specific manner calls for advanced isolation and sequencing methods for the accurate quantification of gene expression in small cell populations and even individual cells from any organ or tissue. One of the major limitations in performing transcriptome analyses of rare cell populations was and still is quality and quantity of RNA that often limits analyses of complex mixtures of immune cell populations. Here…

In Silico HLA Typing Using Standard RNA-Seq Sequence Reads

2015

Next-generation sequencing (NGS) enables high-throughput transcriptome profi ling using the RNA-Seq assay, resulting in billions of short sequence reads. Worldwide adoption has been rapid: many laboratories worldwide generate transcriptome sequence reads daily. Here, we describe methods for obtaining a sample’s human leukocyte antigen (HLA) class I and II types and HLA expression using standard NGS RNA- Seq sequence reads. We demonstrate the application using our algorithm, seq2HLA, and a publicly available RNA-Seq dataset from the Burkitt lymphoma cell line Raji.

Heterogeneity in the response of different subtypes of Drosophila melanogaster enteroendocrine cells to viral infections

2020

SummarySingle cell RNA sequencing (scRNA-seq) offers the possibility to monitor both host and pathogens transcriptomes at the cellular level. Here, public scRNA-seq data from Drosophila melanogaster have been used to compare the differences in replication strategy and cellular response between two viruses, Thika virus (TV) and D. melanogaster Nora virus (DMelNV) in enteroendocrine cells (EEs). TV and DMelNV exhibited different patterns of replication and for TV, accumulation varied according to cell subtype. Cells infected with TV underwent down-regulation of genes that represent bottlenecks in the fruit fly interactome, while cells infected with DMelNV went through a down-expression of tra…

Evidence for PTGER4, PSCA and MBOAT7 as risk genes for gastric cancer on the genome and transcriptome level

2017

1432P Characterizing diversity in the immune profile by a transcriptomic customized gene signature to potentially personalize treatment in advanced g…

2021

Deciphering the Early Mouse Embryo Transcriptome by Low-Input RNA-Seq

2020

Early preimplantation embryos are precious and scarce samples that contain limited numbers of cells, which can be problematic for quantitative gene expression analyses. Nonetheless, low-input genome-wide techniques coupled with cDNA amplification steps have become a gold standard for RNA profiling of as minimal as a single blastomere. Here, we describe a single-cell/single-embryo RNA sequencing (RNA-seq) method, from embryo collection to sample validation steps prior to DNA library preparation and sequencing. Key quality controls and external Spike-In normalization approaches are also detailed.

Comparative transcriptomics of albino and warningly coloured caterpillars

2018

AbstractColouration is perhaps one of the most prominent adaptations for survival and reproduction of most taxa. Colouration is of particular importance for aposematic species, which rely on their colouring and patterning to act as a warning signal against predators. Most research has focused on the evolution of warning colouration by natural selection. However, little information is available for colour mutants of aposematic species, particularly at the genomic level. Here I compare the transcriptomes of albino mutant caterpillars of the wood tiger moth (Arctia plantaginis) to those of their full-sibs having their distinctive orange-black warning colouration. The results showed >300 dif…