Project description:We report the transcriptomic response of a moderately growing subisolate from the culture of Botryococcus sp. CCALA-779 upon nitrogen deprivation (ND). Examination of transcriptomes upon nitrogen deprivation (ND). B.braunii_non_redundant_transcriptome_assembly_61220.fasta: non-redundant assembly (with 61220 in number) of B.braunii 779 transcriptome in this study B.braunii_annotated_12292.fasta: investigated ESTs (with 12292 in number, which perfectly matches with our processed RNA expression profiling) in this study
Project description:The cnidarian freshwater polyp Hydra sp. exhibits an unparalleled regeneration capacity in the animal kingdom. Using an integrative transcriptomic and stable isotope labeling by amino acids in cell culture proteomic/phosphoproteomic approach, we studied stem cell-based regeneration in Hydra polyps.
Project description:The cnidarian freshwater polyp Hydra sp. exhibits an unparalleled regeneration capacity in the animal kingdom. Using an integrative transcriptomic and stable isotope labeling by amino acids in cell culture proteomic/phosphoproteomic approach, we studied stem cell-based regeneration in Hydra polyps.
Project description:By comparing the gene expression profiling in Anoxybacillus sp. SK 3-4 with and without aluminum exposure, the sets of gene up-regulated and down-regulated by aluminum were identified. The function of genes or proteins induced under these conditions can a reflection of the mechanism of resistance. Transcriptome profiling of Anoxybacillus sp. SK 3-4 treated by aluminum would allow a better understanding of the gene involving in tolerance and removal of aluminum. Global transcriptomic response of Anoxybacillus sp. SK 3-4 to aluminum exposure
Project description:Acute kidney injury frequently occurs in patients with severe pneumonia and contributes to poor clinical outcomes. In this study, we established a mouse model of severe pneumonia–associated acute kidney injury (SP-AKI) and performed RNA sequencing to investigate transcriptomic alterations in both lung and kidney tissues. Lung and kidney samples were collected from control mice and SP-AKI mice, followed by high-throughput RNA sequencing. Differential gene expression and pathway analyses were performed to identify molecular mechanisms involved in organ injury and inter-organ communication during SP-AKI. This dataset provides a comprehensive transcriptomic resource for understanding the molecular mechanisms underlying SP-AKI.
Project description:In this study transcriptomic data of three life history stages of Orciraptor agilis was generated: 1) Gliding cells in absence of food ('gliding'), 2) Cells attached to the cell wall of its algal prey during perforation ('fattacking'), 3) Cells after acquisition of the algal plastid material ('digesting'). Furthermore, RNA-seq of the algal prey Mougeotia sp. was also performed. A de novo transcriptome assembly of the algal reads was performed in order to identify and substract algal reads of the Orciraptor samples by mapping the Orciraptor reads to the algal transcriptome. After this filtering step the remaining Orciraptor reads from all libraries were pooled for a de novo transcriptome assembly of Orciraptor agilis. This transcriptome was the basis for a comparative transcriptomic study in which transcript expression was compared between the three life history stages.
Project description:iErLJJL01 is the first genome-scale metabolic model (GEM) of Erwinia sp. str. LJJL01, a non-model Gammaproteobacterium developed as a chassis for upcycling organic waste materials and plastic-derived compounds into value-added products. The model links 3,100 reactions, 1,962 metabolites, and 1,520 genes, and is provided in SBML Level 3 Version 1 with the Flux Balance Constraints (FBC v2) package.
The reconstruction was generated with CarveMe from the strain proteome, manually curated for plastic-monomer catabolism, strain-specific biomass, and product pathways, and integrated with transcriptomic data across eight growth conditions. It reproduces 88% of experimental carbon-source growth phenotypes with zero false negatives, and scores 75.9% on MEMOTE with 100% SBO-term coverage and 99.96% of reactions mass-balanced.
The source genome is NCBI GenBank CP178576.1 (RefSeq assembly GCF_047300805.1). This archive contains the SBML model, a JSON copy for browser-based exploration in Escher-FBA, the full MEMOTE quality report, a COBRApy usage script, a user guide, and the technical development report.
Released under CC-BY-4.0. Developed by Dushmantha Madushanka and Lahiru N. Jayakody, Southern Illinois University Carbondale, with support from the NSF-funded plastic-upcycling project.
Project description:We report the transcriptomic response of a moderately growing subisolate from the culture of Botryococcus sp. CCALA-779 upon nitrogen deprivation (ND).
Project description:Purpose: analyze the transcriptomic changes occurring in spleen (SP) and lymph node (LN) stromal cells in a murine model of DLBCL. Purpose: analyze the transcriptomic changes occurring in FRCs in DLBCL
Project description:This study examines genome-wide expression of the phenanthrene-degrading Sphingomonas sp. LH128 as a response to short-term starvation stress. For this purpose, the strain was subjected to complete nutrient starvation for 4h after growth on a rich medium. Survival was monitored by plating and transcriptomic response was determined by whole-genome microarray analysis. The data showed no major differences were obsrved in gene expression and the viability of the cells were not affected during short-term incubation time Transcriptomic response of phenanthrene degrading Sphingomonas sp. LH128 starved for 4h in isotonic solution of 0.01 mM MgS04 was studied using genome-wide gene expression analysis. For this purpose, the strain was pregrown in minimal medium to an OD600 of 0.5, washed twice with 0.01 mM MgS04 and resuspended in the same solution to an OD of 0.5. RNA was extracted both from starved cells and from the initial culture (non-starved cells) and cDNA was synthesized and labeled with Cy3. Transcriptomic response of three replicates were analyzed and compared with the initial inoculum