C-Jun promotes cell migration and drives expression of the motility factor ENPP2 in soft tissue sarcomas [RNA-Seq]
ABSTRACT: We assayed the effect of c-Jun overexpression on gene expression in the three DDLPS cell lines using RNA-Seq (Illumina). 141, LPS12 and 510 has been overexpressed with c-Jun or control c-DNA and results were analyzed in high-througput sequencing metadata.
Project description:Background: Microorganisms are the major cause of food spoilage during storage, processing and distribution. Pseudomonas fluorescens is a typical spoilage bacterium that contributes to a large extent to the spoilage process of proteinaceous food. RpoS is considered an important global regulator involved in stress survival and virulence in many pathogens. Our previous work revealed that RpoS contributed to the spoilage activities of P. fluorescens by regulating resistance to different stress conditions, extracellular acylated homoserine lactone (AHL) levels, extracellular protease and total volatile basic nitrogen (TVB-N) production. However, RpoS-dependent genes in P. fluorescens remained undefined. Results: RNA-seq transcriptomics analysis combined with quantitative proteomics analysis basing on multiplexed isobaric tandem mass tag (TMT) labeling was performed for the P. fluorescens wild-type strain UK4 and its derivative carrying a rpoS mutation. A total of 375 differentially expressed genes (DEGs) and 212 differentially expressed proteins (DEPs) were identified in these two backgrounds. The DGEs were further verified by qRT-PCR tests, and the genes directly regulated by RpoS were confirmed by 5’-RACE-PCR sequencing. The combining transcriptome and proteome analysis revealed a role of this regulator in several cellular processes, including polysaccharide metabolism, intracellular secretion and extracellular structures, cell well biogenesis, stress responses, ammonia and biogenic amine production, which may contribute to biofilm formation, stress resistance and spoilage activities of P. fluorescens. Moreover, in this work we indeed observed that RpoS contributed to the production of the macrocolony biofilm’s matrix.
Project description:The cells with the impaired Hsp40/Hsp70 chaperone complex Mas5/Ssa2 exhibit a transriptional response that is simillar to that of cells with the elevated levels of the heat-shock factor 1 (Hsf1) or heat-stressed wild type fission yeast cells A total of 6 experimental conditions has been analyzed including control samples, no replicates were made
Project description:We report the application of next-generation sequencing technology for high-throughput profiling of H3K27ac and transcriptome analysis in pancreatic islets derived from C57Bl/6 mice fed a high-fat diet. We find genomic regions showing change in acetylation of histone H3K27 in response to long-term HFD feeding, which was significantly associated with differential gene expression. Furthermore, increased H3K27ac showed a distinctive genomic distribution surrounding proximal-promoter regions. This study provides a framework for the application of comprehensive chromatin profiling towards characterization of diverse mammalian cells under various environments.
Project description:Overall, the study aims at obtaining a comprehensive picture of the African malaria mosquito, Anopheles gambiae, transcriptome using high-coverage RNA-seq of sexed whole-insect samples collected at different developmental time points. This experiment focuses on transcriptomes of 10h, 20h, 28h and 36h male and female embryos.
Project description:Overall, the study aims at obtaining a comprehensive picture of the African malaria mosquito, Anopheles gambiae, transcriptome using high-coverage RNA-seq of sexed whole-insect samples collected at different developmental time points. This experiment focuses on transcriptomes of 4 h, 10 h and 20 h old male and female pupae.
Project description:Overall, the study aims at obtaining a comprehensive picture of the African malaria mosquito, Anopheles gambiae, transcriptome using high-coverage RNA-seq of sexed whole-insect samples collected at different developmental time points. This experiment focuses on male and female transcriptomes from 4th instar larvae at 12 and 36 hours, and 10 day and 20 day adult mosquitoes. Three biological replicates per sex are included for the 4th instar 12 hour transcriptomes. A single female embryonic 20 hour transcriptome is also included, which is paired with a male transcriptome from the same 20h embryonic timepoint within accession number E-MTAB-2583.
Project description:Overall, the study aims at obtaining a comprehensive picture of the African malaria mosquito, Anopheles gambiae, transcriptome using high-coverage RNA-seq of sexed whole-insect samples collected at different developmental time points. This experiment focuses on transcriptomes of 1st, 2nd, 3rd and 4th instar male and female larvae, and 2 day old male and female adults.
Project description:Affymetrix exon arrays to identify genes that were differentially expressed after c-Jun inhibition in LPS cell line with and with no Jun amplification. We compared the consequences of c-Jun inhibition in LP6 (genomically c-Jun amplified) and LPS141 (non-amplified) DDLPS cells after Lentivrus modulation. We used lentivirus to deliver 2 control (shGFP, shNT) and 2 Jun (shJun1, shJun3) shRNAs and harvested total RNA on days 4 and 7 after infection, timepoints at which we observed maximum c-Jun inhibition by qRT-PCR and immunoblotting
Project description:Mouse embryo fibroblasts (MEFs) closely resemble mouse embryos and are convenient sources for biochemical studies when cell number may be limiting from mouse embryos. To derive the imprinting signature of MEFs and potentially detect novel imprinted genes we characterized them using strand- and allele-specific RNA deep sequencing. We used Sequenom allelotyping in embryo and adult organs to verify parental allele-specific expression patterns. We found correct parental allele-specific transcription of 32 known ubiquitously imprinted genes in MEFs. Our analysis did not reveal any novel imprinted genes in MEFs, but detected extended parental allele-specific transcription in several known imprinted domains: maternal allele-specific transcription downstream of Grb10 and downstream of Meg3, Rtl1as and Rian in the Dlk1-Dio3 cluster, an imprinted domain implicated in development. We detected paternal allele-specific transcription downstream of Nespas, Peg3, Peg12 and Snurf/Snrpn. These imprinted transcript extensions were not unique to MEFs, but were also present in other somatic cells. Their 5’ end points did not carry opposing chromatin marks or parental allele-specific DNA methylation, suggesting that their parental allele-specific transcription is under the control of the extended genes. Based on the imprinting signature of MEFs, they provide valid models for understanding the biochemical aspects of genomic imprinting. Strand-specific and parental allele-specific RNA-seq was done in female mouse embryo fibroblasts.
Project description:Knockdowns of c-JUN and JUND had opposite effects on PC3 prostate cell migration. We predicted that c-JUN and JUND control the same set of cell migration genes, but in opposite directions. To test this hypothesis, mRNA with expression changes in c-JUN and JUND knockdown PC3 cell lines were compared to mRNA levels in control (luciferase knockdown) PC3 cells by RNA-seq. mRNA profiles of luciferase knockdown (WT), c-Jun knockdown, and Jun-D knockdown in PC3 cells were generated using deep sequencing, in triplicate, using Illumina HiSeq. Knockdowns were stable shRNA expression from a lentiviral construct selected with puromycin.