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: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
Project description:Background: Ependymomas encompass multiple, clinically relevant tumor types based on localization and molecular profiles. Although tumors of the methylation class “spinal ependymoma” (SP-EPN) represent the most common intramedullary neoplasms in children and adults, their developmental origin is ill-defined, molecular data are scarce, and the potential heterogeneity within SP-EPN remains unexplored. The only known recurrent genetic events in SP-EPN are loss of chromosome 22q and NF2 mutations, but neither types and frequency of these alterations nor their clinical meaning have been described in a large, epigenetically defined series. Methods: We mapped SP-EPN transcriptomes (n=76) to developmental atlases of the developing and adult spinal cord to uncover potential developmental origins of these tumors. In addition, transcriptomic, epigenetic (n=234), genetic (n=140), and clinical analyses (n=115) were integrated for a detailed overview on this entity. Results: Integration of transcriptomic ependymoma data with single-cell atlases of the spinal cord identified mature adult ependymal cells to display highest similarities to SP-EPN. Unsupervised hierarchical clustering of tumor data together with integrated analysis of methylation profiles identified two molecular SP-EPN subtypes. Subtype 1 predominantly contained NF2 wild type sequences with regular NF2 expression but revealed more extensive copy number alterations. Subtype 2 harbored previously known germline or sporadic NF2 mutations and was NF2-deficient in most cases, more often showed multilocular disease, and demonstrated a significantly reduced progression-free survival. Conclusion: Based on integrated molecular profiling of a large tumor series we identify two distinct SP-EPN subtypes with important implications for genetic counseling, patient surveillance, and drug development priorities.