scholarly journals NvERTx: A gene expression database to compare Embryogenesis and Regeneration in the sea anemone Nematostella vectensis

2018 ◽  
Author(s):  
Jacob F. Warner ◽  
Vincent Guerlais ◽  
Aldine R. Amiel ◽  
Hereroa Johnston ◽  
Karine Nedoncelle ◽  
...  
Keyword(s):  
Gene Expression ◽  
High Throughput ◽  
De Novo ◽  
Transcriptome Assembly ◽  
Sea Anemone ◽  
Lessons Learned ◽  
Model Systems ◽  
Nematostella Vectensis ◽  
Gene Clustering ◽  
Gene Expression Database

AbstractFor more than a century researchers have been comparing embryogenesis and regeneration hoping that lessons learned from embryonic development will unlock hidden regenerative potential. This problem has historically been a difficult one to investigate since the best regenerative model systems are poor embryonic models and vice versa. Recently however, the comparison of embryogenesis and regeneration has seen renewed interest as emerging models including the sea anemone Nematostella vectensis have allowed researchers to investigate these processes in the same organism. This interest has been further fueled by the advent of high-throughput transcriptomic analyses that provide virtual mountains of data. Unfortunately much of this data remains in raw unanalyzed formats that are difficult to access or browse. Here we present NematostellavectensisEmbryogenesis and Regeneration Transcriptomics - NvERTx, the first platform for comparing gene expression during embryogenesis and regeneration. NvERTx is comprised of close to 50 RNAseq datasets spanning embryogenesis and regeneration in Nematostella. These data were used to perform a robust de novo transcriptome assembly which users can search, BLAST and plot expression of multiple genes during these two developmental processes. The site is also home to the results of gene clustering analyses, to further mine the data and identify groups of co-expressed genes. The site can be accessed at http://nvertx.kahikai.org.

scholarly journals Analysis of a spatial gene expression database for sea anemone Nematostella vectensis during early development

2015 ◽  
Vol 9 (1) ◽  
Author(s):  
Daniel Botman ◽  
Fredrik Jansson ◽  
Eric Röttinger ◽  
Mark Q. Martindale ◽  
Johann de Jong ◽  
...  
Keyword(s):  
Gene Expression ◽  
Early Development ◽  
Sea Anemone ◽  
Nematostella Vectensis ◽  
Gene Expression Database

scholarly journals The brain transcriptome of the wolf spider, Schizocosa ocreata

2021 ◽  
Vol 14 (1) ◽  
Author(s):  
Daniel Stribling ◽  
Peter L. Chang ◽  
Justin E. Dalton ◽  
Christopher A. Conow ◽  
Malcolm Rosenthal ◽  
...  
Keyword(s):  
Gene Expression ◽  
De Novo ◽  
Transcriptome Assembly ◽  
Model Organisms ◽  
De Novo Transcriptome Assembly ◽  
De Novo Transcriptome ◽  
Wolf Spiders ◽  
Schizocosa Ocreata ◽  
Genomic Studies ◽  
The Brain

Abstract Objectives Arachnids have fascinating and unique biology, particularly for questions on sex differences and behavior, creating the potential for development of powerful emerging models in this group. Recent advances in genomic techniques have paved the way for a significant increase in the breadth of genomic studies in non-model organisms. One growing area of research is comparative transcriptomics. When phylogenetic relationships to model organisms are known, comparative genomic studies provide context for analysis of homologous genes and pathways. The goal of this study was to lay the groundwork for comparative transcriptomics of sex differences in the brain of wolf spiders, a non-model organism of the pyhlum Euarthropoda, by generating transcriptomes and analyzing gene expression. Data description To examine sex-differential gene expression, short read transcript sequencing and de novo transcriptome assembly were performed. Messenger RNA was isolated from brain tissue of male and female subadult and mature wolf spiders (Schizocosa ocreata). The raw data consist of sequences for the two different life stages in each sex. Computational analyses on these data include de novo transcriptome assembly and differential expression analyses. Sample-specific and combined transcriptomes, gene annotations, and differential expression results are described in this data note and are available from publicly-available databases.

scholarly journals De Novo Transcriptome Assembly and Analyses of Gene Expression during Photomorphogenesis in Diploid Wheat Triticum monococcum

PLoS ONE ◽  
2014 ◽  
Vol 9 (5) ◽  
pp. e96855 ◽  
Author(s):  
Samuel E. Fox ◽  
Matthew Geniza ◽  
Mamatha Hanumappa ◽  
Sushma Naithani ◽  
Chris Sullivan ◽  
...  
Keyword(s):  
Gene Expression ◽  
De Novo ◽  
Transcriptome Assembly ◽  
Triticum Monococcum ◽  
Diploid Wheat ◽  
De Novo Transcriptome Assembly ◽  
De Novo Transcriptome

Attacking Oncogene Addiction in B-CLL: Seliciclib First Engages the Mcl-1/Noxa Axis, after Which Gradual Exhaustion of Bcl-2 Protection Leads to Bax Activation.

Blood ◽  
2006 ◽  
Vol 108 (11) ◽  
pp. 2103-2103 ◽  
Author(s):  
Delfine Y.H. Hallaert ◽  
Rene Spijker ◽  
Margot Jak ◽  
Annelieke Jaspers ◽  
Ingrid A.M. Derks ◽  
...  
Keyword(s):  
Gene Expression ◽  
Kinase Inhibitor ◽  
De Novo ◽  
Gene Expression Pattern ◽  
Retroviral Vectors ◽  
Lymphocytic Leukemia ◽  
Model Systems ◽  
Oncogene Addiction ◽  
Neutralizing Capacity ◽  
Apoptosis Gene

Abstract Background : Seliciclib (R-roscovitine) is a cyclin-dependent kinase inhibitor in clinical development. It triggers apoptosis by inhibiting de novo transcription of the short-lived anti-apoptotic Mcl-1 protein, but it is unclear if and how this leads to Bax or Bak activation that is required for most forms of cell death. Aim: To study the effects of seliciclib on apoptosis gene expression and Mcl-1 and Bcl-2 protein interactions in B cell chronic lymphocytic leukemia (B-CLL), a malignancy with known aberrant apoptosis regulation. Methods: Purified B-CLL cells (PBMC consisting of >90% B-CLL cells; n=20) and Ramos cell lines overexpressing different apoptosis regulators were used in this study. The effect of seliciclib on viability, apoptosis gene expression pattern, and protein associations was investigated via RT-Multiplex-Ligation-dependent Probe Amplification (RT-MLPA), Western blotting and co-immunoprecipitation assays. Ramos cells were transduced with retroviral vectors expressing either Noxa siRNA, Bim siRNA or control-GFP virus, and tested for different apoptosis stimuli. Results: We found that although seliciclib resulted in proteasome-dependent Mcl-1 degradation within 4 hrs in B-CLL cells, Bax and Bak activation and apoptosis occurred with a considerable delay, i.e. at 16 hrs. During this period, there was no evidence of transcriptional changes in p53-responsive or apoptosis-related genes. In freshly isolated, viable B-CLL cells, pro-survival Mcl-1 was engaged by the pro-apoptotic proteins Noxa and Bim but not by Bak. The contribution of Noxa [Figure1] and Bim (liberated from McL-1 within 4 hours) as specific mediators of seliciclib-induced apoptosis was demonstrated via RNAi in two model systems. Interestingly, 16 hrs after seliciclib treatment, there was a clear accumulation of Bcl-2, Bim, and Bax in the detergent insoluble (mitochondria containing) fraction of B-CLL cells. This suggests that after Mcl-1 degradation, the remaining apoptosis neutralizing capacity of Bcl-2 is gradually overwhelmed, probably resulting in Bax multimerisation and pore formation in the mitochondria. Conclusions: These data support the ’oncogene-addiction’ model in which malignant cells depend on increased Bcl-2 levels, and extend it to include Mcl-1. Furthermore, since Noxa is elevated in B-CLL, its involvement in p53-independent apoptosis suggests this BH3-only protein may be a therapeutic target. Figure Figure

scholarly journals Transcriptional signatures of somatic neoblasts and germline cells in Macrostomum lignano

eLife ◽  
2016 ◽  
Vol 5 ◽  
Author(s):  
Magda Grudniewska ◽  
Stijn Mouton ◽  
Daniil Simanov ◽  
Frank Beltman ◽  
Margriet Grelling ◽  
...  
Keyword(s):  
Gene Expression ◽  
Stem Cells ◽  
De Novo ◽  
Transcriptome Assembly ◽  
Model Organism ◽  
Proliferating Cells ◽  
Macrostomum Lignano ◽  
Germline Cells

The regeneration-capable flatworm Macrostomum lignano is a powerful model organism to study the biology of stem cells in vivo. As a flatworm amenable to transgenesis, it complements the historically used planarian flatworm models, such as Schmidtea mediterranea. However, information on the transcriptome and markers of stem cells in M. lignano is limited. We generated a de novo transcriptome assembly and performed the first comprehensive characterization of gene expression in the proliferating cells of M. lignano, represented by somatic stem cells, called neoblasts, and germline cells. Knockdown of a selected set of neoblast genes, including Mlig-ddx39, Mlig-rrm1, Mlig-rpa3, Mlig-cdk1, and Mlig-h2a, confirmed their crucial role for the functionality of somatic neoblasts during homeostasis and regeneration. The generated M. lignano transcriptome assembly and gene expression signatures of somatic neoblasts and germline cells will be a valuable resource for future molecular studies in M. lignano.

scholarly journals Development of a relevant strategy using de novo transcriptome assembly method for transcriptome comparisons between Muscovy and common duck species and their reciprocal inter-specific Mule and Hinny hybrids fed ad libitum and overfed

2020 ◽  
Author(s):  
Xi Liu ◽  
Frédéric Hérault ◽  
Christian Diot ◽  
Erwan Corre
Keyword(s):  
Gene Expression ◽  
De Novo ◽  
Transcriptome Assembly ◽  
Genetic Type ◽  
Rna Seq ◽  
Genetic Types ◽  
Assembly Method ◽  
Muscovy Ducks ◽  
Ad Libitum ◽  
Different Response

Abstract Background: Common Pekin and Muscovy ducks and their intergeneric hinny and mule hybrids have different abilities for fatty liver production. RNA-Seq analyses from the liver of these different genetic types fed ad libitum or overfed would help to identify genes with different response to overfeeding between them. However RNA-seq analyses from different species and comparison is challenging. The goal of this study was develop a relevant strategy for transcriptome analysis and comparison between different species.Results: Transcriptomes were first assembled with a reference-based approach. Important mapping biases were observed when heterologous mapping were conducted on common duck reference genome, suggesting that this reference-based strategy was not suited to compare the four different genetic types. De novo transcriptome assemblies were then performed using Trinity and Oases. Assemblies of transcriptomes were not relevant when more than a single genetic type was considered. Finally, single genetic type transcriptomes were assembled with DRAP in a mega-transcriptome. No bias was observed when reads from the different genetic types were mapped on this mega-transcriptome and differences in gene expression between the four genetic types could be identified.Conclusions: Analyses using both reference-based and de novo transcriptome assemblies point out a good performance of the de novo approach for the analysis of gene expression in different species. It also allowed the identification of differences in responses to overfeeding between Pekin and Muscovy ducks and hinny and mule hybrids.

Sign in / Sign up

Export Citation Format

Share Document