Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR12215316_1.fastq.gz | Fastqsanger.gz | |||
| SRR12215316_2.fastq.gz | Fastqsanger.gz |
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Project description:The goal of this study is to compare the transcriptome stability of DN1wt versus DN1gl/gl and DN1CD2-Ostm1gl/glTR Methods: DN1 thymocytes mRNA profiles of 19-day-old wild-type (WT), osteopetrotic grey-lethal (gl/gl) and transgenic CD2-Ostm1 gl/gl mice were generated by deep sequencing,DN1 cells from 2-3 mice per genotype were pooled, no technical replicates, using Illumina HiSeq 2000. The sequence reads that passed quality filters were analyzed at the transcript isoform level with two methods: TopHat and Cufflinks. qRT–PCR validation was performed using SYBR Green assays Results: DN1 gl/gl showed a distinctive transcriptome signature in comparison to DN1 wt and DN1 gl/glTR with respectivelly 146 and 205 differentially expressed genes and 205. Migration genes were significantly affected in DN1 gl/gl samples and RAC1 and S1PR1 gene expressions were confirmed using RT-qPCR. Conclusions: RNA seq allowed us to identify the enhanced expression of migration genes (RAC1 and S1PR1) in DN1gl/gl, that were both normalized in the DN1 cells from transgenic gl/glTR mice, which suggests defective T cell migration associated to the osteopetrotic thymus phenotype.
2016-09-01 | GSE72184 | GEO
Project description:Background: Prevention of hyperlipidemia and associated diseases is a health priority. Complementary medicine based on scientific evidence has recently recognized the potential of natural products for modulating lipid metabolism, such as the medicinal mushroom Ganoderma lucidum (Gl), which possesses hypocholesterolemic, prebiotic and antidiabetic properties. Methods: Whole-transcriptomic changes in liver and kidney from a mouse model (C57BL/6), under a high-cholesterol diet and standardized Gl extracts (Gl-1, Gl-2) or simvastatin administration, were analyzed to determine Gl hypocholesterolemic activity. Further effects of Gl extracts on lipid metabolism were evaluated using an in vitro hepatic-like macrophage model. Additionally, correlations among hepatic gene expression, microbiota and serum lipid profiles in vivo established by Gl extracts were evaluated. Results: Based on the hepatic and renal mRNA profiles of mice treated with Gl extracts and high-cholesterol diet, we identified relevant metabolic pathways modulated by Gl involving the restriction of lipid biosynthesis and the enrichment of lipid degradation and secretion. We further showed that Gl extracts induce a significant decrease of macrophage lipid storage and cholesterol biosynthesis, which occurs concomitantly by the down-modulation of Fasn and Elovl6. We also determined that prebiotic effects of Gl extracts modulating gut microbiota are correlated with the gene expression portraits. Conclusions: Our high-throughput analysis allowed to identify key transcriptomic nodes established by Gl extracts and their interaction with microbiome composition related to lipid catabolic signaling. Our results indicated that our Gl extracts have a robust potential to be used as transcriptome modulators and prebiotic agents to prevent metabolic disorders associated to hypercholesterolemia.
2020-12-15 | GSE159656 | GEO
Project description:The goal of this study is to compare the transcriptome stability of DN1wt versus DN1gl/gl and DN1CD2-Ostm1gl/glTR Methods: DN1 thymocytes mRNA profiles of 19-day-old wild-type (WT), osteopetrotic grey-lethal (gl/gl) and transgenic CD2-Ostm1 gl/gl mice were generated by deep sequencing,DN1 cells from 2-3 mice per genotype were pooled, no technical replicates, using Illumina HiSeq 2000. The sequence reads that passed quality filters were analyzed at the transcript isoform level with two methods: TopHat and Cufflinks. qRTâ??PCR validation was performed using SYBR Green assays Results: DN1 gl/gl showed a distinctive transcriptome signature in comparison to DN1 wt and DN1 gl/glTR with respectivelly 146 and 205 differentially expressed genes and 205. Migration genes were significantly affected in DN1 gl/gl samples and RAC1 and S1PR1 gene expressions were confirmed using RT-qPCR. Conclusions: RNA seq allowed us to identify the enhanced expression of migration genes (RAC1 and S1PR1) in DN1gl/gl, that were both normalized in the DN1 cells from transgenic gl/glTR mice, which suggests defective T cell migration associated to the osteopetrotic thymus phenotype. DN1 thymocytes mRNA profiles of 19-day-old wild-type (WT), osteopetrotic grey-lethal (gl/gl) and transgenic CD2-Ostm1 gl/gl mice were compared by deep sequencing,DN1 cells from 2-3 mice per genotype were pooled, no technical replicates, using Illumina HiSeq 2000.
2016-09-01 | E-GEOD-72184 | biostudies-arrayexpress
Project description:Galiellalactone (GL) is a fungal metabolite that presents antitumor and anti-inflammatory activities in vitro and in vivo. Previous studies have shown that GL targets NF-KB and STAT3 pathways and induces G2/M cell cycle arrest in androgen-insensitive prostate cancer cells. In this study, we show that GL-induced cell cycle arrest is independent of the NF-KB and STAT3 pathways in DU145 and PC-3 cells, and also that GL did not affect cell cycling in androgen-sensitive prostate cancer cell such as LNCaP and 22Rv1 cells. In addition, we showed confluence resistance to GL in DU145 cells. Using a SWATH proteomic approach we identified the down-regulation of Nucleolar and spindle associated protein 1 (NUSAP1) under DU145 confluence and in LNCaP cells. Also, the inhibition of NUSAP1 by siRNAs induced resistance to GL in DU145 cells, suggesting that NUSAP1 may be a target for GL and could be useful as biomarker for responsiveness of the antitumor activity of GL.
2019-01-14 | PXD010993 | Pride
Project description:Proteome analysis of Lung tissue of mice bearing B16-F10-luc-G5 melanoma tumor with sleep fragmentation and with or with out the asdmistration of GL-pp. The mice were randomly divided into 4 groups: control group in general condition with no further treatment (CON group), tumor group with the burden of B16-F10-luc-G5 cells (Tumor group), T+SF group with SF and the burden of B16-F10-luc-G5 cells (T+SF group), and GL-pp group with SF, tumor cells burden, and the administration of 80 mg/kg GL-pp (GL-pp group). B16-F10-luc-G5 cells (5 × 1000000 cells/100 µL per mouse) were injected into the mice through the tail vein. The lung tissue of T+SF group and GL-pp group were analyzed by the proteome.
2021-09-10 | PXD025171 | Pride
Project description:Endothelization of the luminal surface of vascular grafts is required for their long-term functioning. In order to select the best surface we have cultivated HUVEC on different 3D matrices and assessed the efficacy of cell proliferation and the changes in the gene expression profiles. 3D matrices were produced by electrospinning from solutions of poly(D,L-lactide-co-glycolide) (PLGA), polycaprolactone (PCL) and blends of PCL with gelatin (PCL-Gl) and glutaraldehyde-treated PCL-GL (PCL-Gl-glu) in hexafluoroisopropanol. Gene expression profiling was executed using Illumina HiSeq2500 platform.
2018-11-29 | GSE123045 | GEO
Project description:DZ (B220+ IgDlo GL-7+ CD95+CXCR4+CD86lo) or LZ (B220+ IgDlo GL-7+ CD95+CXCR4loCD86+) GC B cells were sorted from male Sle1.yaa lupus mice at 2,4,6 months of age. RNA-seq was employed to assess transcriptional changes in the different GC B cell subsets throughout course of disease.
2024-11-08 | GSE250607 | GEO
Project description:Next generation sequencing analysis of DN1 transcriptomes from Wild type, gl/gl and transgenic CD2-Ostm1 gl/gl mice
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Project description:Using whole-genome bisulfite sequencing (WGBS), we profiled 18 DNA methylomes of cattle sperms that were collected from 18 representative age-matched Holstein bulls with high reliable phenotypes on many complex traits, including sire-conception rate (SCR), gestation length (GL), sire calving ease (SCE), cow conception rate (CCR) and body depth (BDE). Through comparison with human sperm methylome, we observed that genomic regions with differetial DNA methylation levels were enriched for GWAS signals and had important evolutionary impact. By comparing animals with extreme SCR, we showed that differentially methylated regions (DMR) associated with SCR and aging were significantly and selectively enriched for GWAS signals of male fertility traits in cattle. In addition, we detected ans compared DMRs assocaited with GL, CCR, SCE and BDE. We integrated GWAS signals of 37 complex traits with DMRs associated with GL to provide insights into genetic basis of GL.
2019-03-20 | GSE119263 | GEO
Project description:In this study we want to map the gene expression profile of liver infected with Adenovirus, either transgene-encoding Ad-CMV-GL or a non-coding control virus Ad-ctrl, to uninfected (healthy) livers. This comparison will reveal transcriptional signature of Ad-CMV-GL infected liver responsible for virus-mediated sensitization of hepatocytes towards TNF-induced apoptosis.
2020-06-16 | GSE131335 | GEO