MiRNA expression in response to LPS stimulus in macrophages
Ontology highlight
ABSTRACT:
PROVIDER: EGAS00001000691 | EGA |
REPOSITORIES: EGA
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Project description:Our lab is currently using macrophages as a model system for understanding how genetic
variation modulates the response to external environmental stimulus. We want to extend this
beyond regular polyadenylated RNA to small RNAs such as miRNAs. This project would
cover the costs of a pilot to study miRNA response to LPS stimulus, and will be performed as
part of a rotation project in the lab. We will require a small number of miRNA libraries and a
single lane of MiSeq
| EGAD00001002196 | EGA
Project description:This project aims to study the role played by small non-coding RNAs in the response of aquatic organisms to the presence of micropollutants in the environment. MiRNA were purified from Eels (Anguilla anguilla) sampled from two sites along the Gironde aquatic system with contrasted pollution profiles.
2019-04-09 | GSE109689 | GEO
Project description:Cervical cancer is a global public health subject as it affects women in the reproductive ages, and accounts for the second largest burden among cancer patients worldwide with an unforgiving 50% mortality rate. Poor awareness and access to effective diagnosis have led to this enormous disease burden, calling for point-of-care, minimally invasive diagnosis methods. Here, an end-to-end quantitative approach for a new kind of diagnosis has been developed, comprising identification of optimal biomarkers, design of the sensor, and simulation of the diagnostic circuit. Using miRNA expression data in the public domain, we identified circulating miRNA biomarkers specific to cervical cancer using multi-tier screening. Synthetic riboregulators called toehold switches specific for the biomarker panel were then designed. To predict the dynamic range of toehold switches for use in genetic circuits as biosensors, we developed a generic grammar of these switches, and built a multivariate linear regression model using thermodynamic features derived from RNA secondary structure and interaction. The model yielded predictions of toehold efficacy with an adjusted R2 = 0.59. Reaction kinetics modelling was performed to predict the sensitivity of the second-generation toehold switches to the miRNA biomarkers. Simulations showed a linear response between 10nM and 100nM before saturation. Our study demonstrates an end-to-end workflow for the efficient design of genetic circuits geared towards the effective detection of unique genomic signatures that would be increasingly important in today’s world. The approach has the potential to direct experimental efforts and minimise costs. All resources are provided open-source (https://github.com/igem2019) under GNU GPLv3 licence.
2022-05-05 | MODEL2107150001 | BioModels
Project description:modENCODE_submission_2009 This submission comes from a modENCODE project of Eric Lai. For full list of modENCODE projects, see http://www.genome.gov/26524648 Project Goal: We plan to generate a comprehensive catalog of expressed and functional microRNAs, and generate biological evidence for their regulatory activity. We plan also to delineate the primary transcription units of microRNA genes. Finally, we plan to annotate other classes of non-miRNA expressed small RNAs, as least some of which may define novel classes of small RNA genes. For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf Keywords: RNA-seq EXPERIMENT TYPE: RNA-seq. BIOLOGICAL SOURCE: Strain: Y cn bw sp; Developmental Stage: Adult female, eclosion + 1 day; Genotype: y[1] oc[R3.2]; Gr22b[1] Gr22d[1] cn[1] CG33964[R4.2] bw[1] sp[1]; LysC[1] lab[R4.2] MstProx[1] GstD5[1] Rh6[1]; Sex: Female; EXPERIMENTAL FACTORS: Developmental Stage Adult female, eclosion + 1 day; Strain Y cn bw sp
2010-10-18 | E-GEOD-24305 | biostudies-arrayexpress
Project description:modENCODE_submission_2008 This submission comes from a modENCODE project of Eric Lai. For full list of modENCODE projects, see http://www.genome.gov/26524648 Project Goal: We plan to generate a comprehensive catalog of expressed and functional microRNAs, and generate biological evidence for their regulatory activity. We plan also to delineate the primary transcription units of microRNA genes. Finally, we plan to annotate other classes of non-miRNA expressed small RNAs, as least some of which may define novel classes of small RNA genes. For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf Keywords: RNA-seq EXPERIMENT TYPE: RNA-seq. BIOLOGICAL SOURCE: Strain: Y cn bw sp; Developmental Stage: Adult male, eclosion + 1 day; Genotype: y[1] oc[R3.2]; Gr22b[1] Gr22d[1] cn[1] CG33964[R4.2] bw[1] sp[1]; LysC[1] lab[R4.2] MstProx[1] GstD5[1] Rh6[1]; Sex: Male; EXPERIMENTAL FACTORS: Developmental Stage Adult male, eclosion + 1 day; Strain Y cn bw sp
2010-10-18 | E-GEOD-24304 | biostudies-arrayexpress
Project description:modENCODE_submission_2742 This submission comes from a modENCODE project of Eric Lai. For full list of modENCODE projects, see http://www.genome.gov/26524648 Project Goal: We plan to generate a comprehensive catalog of expressed and functional microRNAs, and generate biological evidence for their regulatory activity. We plan also to delineate the primary transcription units of microRNA genes. Finally, we plan to annotate other classes of non-miRNA expressed small RNAs, as least some of which may define novel classes of small RNA genes. For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf Keywords: RNA-seq EXPERIMENT TYPE: RNA-seq. BIOLOGICAL SOURCE: Strain: Y cn bw sp; Developmental Stage: Embryo 14-16h; Genotype: y[1] oc[R3.2]; Gr22b[1] Gr22d[1] cn[1] CG33964[R4.2] bw[1] sp[1]; LysC[1] lab[R4.2] MstProx[1] GstD5[1] Rh6[1]; EXPERIMENTAL FACTORS: Developmental Stage Embryo 14-16h; Strain Y cn bw sp
2010-10-18 | E-GEOD-24309 | biostudies-arrayexpress
Project description:modENCODE_submission_2743 This submission comes from a modENCODE project of Eric Lai. For full list of modENCODE projects, see http://www.genome.gov/26524648 Project Goal: We plan to generate a comprehensive catalog of expressed and functional microRNAs, and generate biological evidence for their regulatory activity. We plan also to delineate the primary transcription units of microRNA genes. Finally, we plan to annotate other classes of non-miRNA expressed small RNAs, as least some of which may define novel classes of small RNA genes. For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf Keywords: RNA-seq EXPERIMENT TYPE: RNA-seq. BIOLOGICAL SOURCE: Strain: Y cn bw sp; Developmental Stage: Embryo 2-4h; Genotype: y[1] oc[R3.2]; Gr22b[1] Gr22d[1] cn[1] CG33964[R4.2] bw[1] sp[1]; LysC[1] lab[R4.2] MstProx[1] GstD5[1] Rh6[1]; EXPERIMENTAL FACTORS: Developmental Stage Embryo 2-4h; Strain Y cn bw sp
2010-10-18 | E-GEOD-24539 | biostudies-arrayexpress
Project description:MicroRNAs (miRNAs) are small regulatory RNAs that control plant and animal development by regulating post-transcriptional gene expression. Primary transcripts of miRNAs contain small ORFs that can be translated into small peptides (miPEPs). MiPEPs specifically enhance the expression of their cognate miRNA in a positive feedback loop. Here, by addressing the molecular bases of miPEP specificity, we identified an unanticipated mechanism modulating coding gene expression. We found that the miORF itself constitutes a prerequisite for the miPEP to specifically control the expression of its miRNA. We extended this property to any coding gene through the design of artificial peptides. We called these peptides « complementary peptides » (cPEPs) as their external application modulates the translation of their corresponding protein. We discovered here a yet undescribed mechanism of post-transcriptional regulation, opening new promising avenues in fundamental research and applied biology. Quantitative proteomics using LC-MS/MS after co-immunoprecipitation with a HA-tagged cPEP or scrambled peptide was performed to identify interactors of the cPEP or scrambled peptide in co-eluates of plants.
2023-01-09 | PXD017404 | Pride
Project description:The aim of this project was to evaluate the ploidy of a S. cerevisiae *S. kudriavzevii hybrid in comparison to the lab strain S288C. Other wine yeast have been icluded in the project for the global analysis.
2012-02-09 | GSE31703 | GEO
Project description:This group is studying the role of glycoproteins in embryo implantation and development of the maternal-fetal interface. The Aplin lab is developing an embryo implantation model in which blastocysts attach to human endometrial cells. The project aims to investigate the molecular interactions mediating attachment and subsequent events including trophoblast invasion and displacement of maternal cells. In the present phase of the project, the lab is using the Ishikawa (human endometrial) cell line with mouse embryos.
2011-04-29 | GSE28925 | GEO