scholarly journals Oak Root Response to Ectomycorrhizal Symbiosis Establishment: RNA-Seq Derived Transcript Identification and Expression Profiling

PLoS ONE ◽  
2014 ◽  
Vol 9 (5) ◽  
pp. e98376 ◽  
Author(s):  
Mónica Sebastiana ◽  
Bruno Vieira ◽  
Teresa Lino-Neto ◽  
Filipa Monteiro ◽  
Andreia Figueiredo ◽  
...  
Keyword(s):  
Expression Profiling ◽  
Rna Seq ◽  
Ectomycorrhizal Symbiosis ◽  
Root Response ◽  
Transcript Identification

scholarly journals NKL Homeobox Gene VENTX Is Part of a Regulatory Network in Human Conventional Dendritic Cells

2021 ◽  
Vol 22 (11) ◽  
pp. 5902
Author(s):  
Stefan Nagel ◽  
Claudia Pommerenke ◽  
Corinna Meyer ◽  
Hans G. Drexler
Keyword(s):  
Dendritic Cells ◽  
Transcription Factors ◽  
Cell Lines ◽  
Expression Profiling ◽  
Regulatory Network ◽  
Homeobox Gene ◽  
Leukemia Cell Line ◽  
Specific Gene ◽  
Rna Seq ◽  
And Function

Recently, we documented a hematopoietic NKL-code mapping physiological expression patterns of NKL homeobox genes in human myelopoiesis including monocytes and their derived dendritic cells (DCs). Here, we enlarge this map to include normal NKL homeobox gene expressions in progenitor-derived DCs. Analysis of public gene expression profiling and RNA-seq datasets containing plasmacytoid and conventional dendritic cells (pDC and cDC) demonstrated HHEX activity in both entities while cDCs additionally expressed VENTX. The consequent aim of our study was to examine regulation and function of VENTX in DCs. We compared profiling data of VENTX-positive cDC and monocytes with VENTX-negative pDC and common myeloid progenitor entities and revealed several differentially expressed genes encoding transcription factors and pathway components, representing potential VENTX regulators. Screening of RNA-seq data for 100 leukemia/lymphoma cell lines identified prominent VENTX expression in an acute myelomonocytic leukemia cell line, MUTZ-3 containing inv(3)(q21q26) and t(12;22)(p13;q11) and representing a model for DC differentiation studies. Furthermore, extended gene analyses indicated that MUTZ-3 is associated with the subtype cDC2. In addition to analysis of public chromatin immune-precipitation data, subsequent knockdown experiments and modulations of signaling pathways in MUTZ-3 and control cell lines confirmed identified candidate transcription factors CEBPB, ETV6, EVI1, GATA2, IRF2, MN1, SPIB, and SPI1 and the CSF-, NOTCH-, and TNFa-pathways as VENTX regulators. Live-cell imaging analyses of MUTZ-3 cells treated for VENTX knockdown excluded impacts on apoptosis or induced alteration of differentiation-associated cell morphology. In contrast, target gene analysis performed by expression profiling of knockdown-treated MUTZ-3 cells revealed VENTX-mediated activation of several cDC-specific genes including CSFR1, EGR2, and MIR10A and inhibition of pDC-specific genes like RUNX2. Taken together, we added NKL homeobox gene activities for progenitor-derived DCs to the NKL-code, showing that VENTX is expressed in cDCs but not in pDCs and forms part of a cDC-specific gene regulatory network operating in DC differentiation and function.

scholarly journals RNA-Seq investigations of human post-mortem trigeminal ganglia

Cephalalgia ◽  
2017 ◽  
Vol 38 (5) ◽  
pp. 912-932 ◽  
Author(s):  
Danielle M LaPaglia ◽  
Matthew R Sapio ◽  
Peter D Burbelo ◽  
Jean Thierry-Mieg ◽  
Danielle Thierry-Mieg ◽  
...  
Keyword(s):  
Genetic Association ◽  
Expression Profiling ◽  
Association Studies ◽  
Susceptibility Genes ◽  
Blood Levels ◽  
Trigeminal Ganglia ◽  
Molecular Heterogeneity ◽  
Post Mortem ◽  
Rna Seq ◽  
Hsv 1

Background The trigeminal ganglion contains neurons that relay sensations of pain, touch, pressure, and many other somatosensory modalities to the central nervous system. The ganglion is also a reservoir for latent herpes virus 1 infection. To gain a better understanding of molecular factors contributing to migraine and headache, transcriptome analyses were performed on postmortem human trigeminal ganglia. Methods RNA-Seq measurements of gene expression were conducted on small sub-regions of 16 human trigeminal ganglia. The samples were also characterized for transcripts derived from viral and microbial genomes. Herpes simplex virus 1 (HSV-1) antibodies in blood were measured using the luciferase immunoprecipitation assay. Results Observed molecular heterogeneity could be explained by sampling of anatomically distinct sub-regions of the excised ganglia consistent with neurally-enriched and non-neural, i.e. Schwann cell, enriched subregions. The levels of HSV-1 transcripts detected in trigeminal ganglia correlated with blood levels of HSV-1 antibodies. Multiple migraine susceptibility genes were strongly expressed in neurally-enriched trigeminal samples, while others were expressed in blood vessels. Conclusions These data provide a comprehensive human trigeminal transcriptome and a framework for evaluation of inhomogeneous post-mortem tissues through extensive quality control and refined downstream analyses for RNA-Seq methodologies. Expression profiling of migraine susceptibility genes identified by genetic association appears to emphasize the blood vessel component of the trigeminovascular system. Other genes displayed enriched expression in the trigeminal compared to dorsal root ganglion, and in-depth transcriptomic analysis of the KCNK18 gene underlying familial migraine shows selective neural expression within two specific populations of ganglionic neurons. These data suggest that expression profiling of migraine-associated genes can extend and amplify the underlying neurobiological insights obtained from genetic association studies.

scholarly journals Characterization and improvement of RNA-Seq precision in quantitative transcript expression profiling

2011 ◽  
Vol 27 (13) ◽  
pp. i383-i391 ◽  
Author(s):  
Paweł P. Łabaj ◽  
Germán G. Leparc ◽  
Bryan E. Linggi ◽  
Lye Meng Markillie ◽  
H. Steven Wiley ◽  
...  
Keyword(s):  
Expression Profiling ◽  
Transcript Expression ◽  
Rna Seq

scholarly journals Strigolactones And Auxin Cooperate To Regulate Maize Root Development and Response to Nitrate

2021 ◽  
Author(s):  
Laura Ravazzolo ◽  
Stéphanie Boutet-Mercey ◽  
François Perreau ◽  
Cristian Forestan ◽  
Serena Varotto ◽  
...  
Keyword(s):  
Root Development ◽  
Lateral Root ◽  
Root Density ◽  
Maize Root ◽  
Rna Seq ◽  
Acid Biosynthesis ◽  
Transcriptional Signature ◽  
Downstream Target ◽  
Nitrate Supply ◽  
Root Response

Abstract In maize, nitrate regulates root development thanks to the coordinated action of many players. In this study, the involvement of SLs and auxin as putative components of the nitrate regulation of lateral root was investigated. To this aim, the endogenous SL content of maize root in response to nitrate was assessed by LC-MS/MS and measurements of lateral root density in the presence of analogues or inhibitors of auxin and strigolactones were performed. Furthermore, an untargeted RNA-seq based approach was used to better characterize the participation of auxin and strigolactones to the transcriptional signature of maize root response to nitrate. Our results suggested that N deprivation induces zealactone and carlactonoic acid biosynthesis in root, to a higher extent if compared to P-deprived roots. Moreover, data on lateral root density led to hypothesise that the induction of LR development early occurring upon nitrate supply involves the inhibition of SL biosynthesis, but that the downstream target of SL shutdown, beside auxin, includes also additional unknown players. Furthermore, RNA-seq results provided a set of putative markers for the auxin- or SL-dependent action of nitrate, meanwhile allowing to identify also novel components of the molecular regulation of maize root response to nitrate. Globally the existence of at least four different pathways was hypothesised, one dependent on auxin, a second one mediated by SLs, a third deriving from the SL-auxin interplay and one last attributable to nitrate itself through further downstream signals. Further work will be necessary to better assess the reliability of the model proposed.

scholarly journals Integrating single-cell RNA-seq and imaging with SCOPE-seq2

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Zhouzerui Liu ◽  
Jinzhou Yuan ◽  
Anna Lasorella ◽  
Antonio Iavarone ◽  
Jeffrey N. Bruce ◽  
...  
Keyword(s):  
Single Cell ◽  
Expression Profiling ◽  
Live Cell Imaging ◽  
Cell Imaging ◽  
Imaging Features ◽  
Primary Cells ◽  
Rna Seq ◽  
Single Cell Imaging ◽  
Cellular Identity ◽  
Surgical Sample

Abstract Live cell imaging allows direct observation and monitoring of phenotypes that are difficult to infer from transcriptomics. However, existing methods for linking microscopy and single-cell RNA-seq (scRNA-seq) have limited scalability. Here, we describe an upgraded version of Single Cell Optical Phenotyping and Expression (SCOPE-seq2) for combining single-cell imaging and expression profiling, with substantial improvements in throughput, molecular capture efficiency, linking accuracy, and compatibility with standard microscopy instrumentation. We introduce improved optically decodable mRNA capture beads and implement a more scalable and simplified optical decoding process. We demonstrate the utility of SCOPE-seq2 for fluorescence, morphological, and expression profiling of individual primary cells from a human glioblastoma (GBM) surgical sample, revealing relationships between simple imaging features and cellular identity, particularly among malignantly transformed tumor cells.

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