Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR21551917_1.fastq.gz | Fastqsanger.gz | |||
| SRR21551917_2.fastq.gz | Fastqsanger.gz | |||
| SRR21551918_1.fastq.gz | Fastqsanger.gz | |||
| SRR21551918_2.fastq.gz | Fastqsanger.gz | |||
| SRR21551919_1.fastq.gz | Fastqsanger.gz |
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Similar Datasets
Project description:We report the application of CHIP-seq technology for high-throughput profiling of histone modifications in HY(Hwayong) and chd1(chr729). By obtaining about 12 million reads of sequence from chromatin immunoprecipitated DNA, we generated genome-wide H3K4me3 and H3k27me3 maps of HY(Hwayong) and chd1(chr729). We find that lysine 4 and lysine 27 trimethylation marked genes effectively losed in chd1 compared to HY. Examination of two histone modifications in two rice species.
2012-03-10 | E-GEOD-30490 | biostudies-arrayexpress
Project description:We report the application of CHIP-seq technology for high-throughput profiling of histone modifications in HY(Hwayong) and chd1(chr729). By obtaining about 12 million reads of sequence from chromatin immunoprecipitated DNA, we generated genome-wide H3K4me3 and H3k27me3 maps of HY(Hwayong) and chd1(chr729). We find that lysine 4 and lysine 27 trimethylation marked genes effectively losed in chd1 compared to HY.
2012-03-10 | GSE30490 | GEO
Project description:RNA-Seq data of human colorectal cancer cell line SW837 transfected with siRNA against STAT3 (siSTAT3) or control RNA (siCtrl), untreated or treated with Hyper-IL-6 (Hy-IL-6)
2021-01-25 | GSE139455 | GEO
Project description:To determine whether lymphangiogenesis is required for cardiac regeneration, vegfc(hy-/-);vegfd(-/-) double mutants and control hearts were collected and analyzed at 180 days after cryoinjury, this corresponds to a time point when the regenerative response is normally completed in wild-type zebrafish. Surprisingly, the vast majority (~70%) of vegfc(hy-/-);vegfd(-/-) mutants, which completely lack cardiac lymphatics, were able to mount a complete regenerative response without any signs of fibrosis. We found that the cardiac regenerative response was impaired only in a subset (3/8) of vegfc(hy-/-);vegfd(-/-) mutants, which were characterized by large deposits of fibrotic scar tissue present at the injury site. To profile vegfc/d-dependent genetic pathways contributing to lymphangiogenesis in cardiac regeneration, we performed RNA-seq on cryosections from control and mutant ventricles at 180 days following cryoinjury. Overall, vegfc(hy-/-);vegfd(-/-) mutant ventricles were characterized by an up-regulation of pathways related to metabolism, inflammation, hemostasis, negative regulation of FGFR signaling, translation, protein maturation and nonsense mediated decay compared to control hearts. These findings are consistent with the cardiac hypertrophy phenotype in vegfc(hy-/-);vegfd(-/-) mutants. To determine the molecular basis of the regenerative capacity within the mutant fish population, we next compared the transcriptional profiles of vegfc(hy-/-);vegfd(-/-) mutant hearts that did not regenerate (n=3) with the profiles of mutant hearts which recovered completely (n=5) at 180 days post cryoinjury. The subset of vegfc(hy-/-);vegfd(-/-) mutant hearts that failed to regenerate were characterized by an enrichment of inflammatory pathways, in particular TRAF6-mediated IRF7 activation, interferon alpha beta signaling and regulation of IFNA signaling. These findings suggest that loss of the vegfc/d signaling axis causes a sustained and pronounced inflammatory response following injury. This change in the cardiac micro-environment seems to favor adverse conditions which impair the regenerative process.
2019-09-03 | GSE133129 | GEO
Project description:To identify genes and metabolic pathways involved in the heat-stress response, digital gene expression analysis was performed on the midgut of thermotolerant silkworm variety ‘932’ and thermosensitive variety ‘HY’ after exposure to high temperature (932T and HYT). Deep sequencing yielded 6,211,484, 5,898,028, 5,870,395, and 6,088,303 reads for the 932, 932T, HY, and HYT samples, respectively. After filtering adaptor sequences and removing low-quality tags, 6,139,297, 5,828,615, 5,799,074, and 6,005,746 clean tags remained, respectively. The annotated genes associated with these tags numbered 4357, 4378, 4296, and 4658 for the 932, 932T, HY, and HYT samples, respectively. In HY-vs-932, 932-vs-932T, and HY-vs-HYT comparisons, 561, 316, and 281 differentially expressed genes were identified, which could be assigned to 179, 140, and 123 biological pathways, respectively.
2015-12-31 | GSE55990 | GEO
Project description:(1) Transcriptional profiling of mouse CD4 T cells comparing naïve HY-specific TCR transgenic T cells with the same cells recovered after adoptive transfer into WT female C57BL/6 mice on day 5 following treatment with HY peptide (100microgrammes intranasally days 1,2 and 3) and comparing naïve HY-specific TCR transgenic T cells with the same cells recovered after adoptive transfer into WT female C57BL/6 mice on day 5 following treatment with HY peptide plus LPS (100microgrammes peptide and 20microgrammes LPS intranasally day 1) (2)Transcriptional profiling of mouse CD8 T cells comparing naïve CD8 T cells with HY-tetramer positive cells recovered from tolerant peptide treated (see above) WT female C57BL/6 mice on day 22 after male skin graft or 10-15 days after treatment with male spleen cells and comparing naïve CD8 T cells with HY-tetramer positive cells recovered from untreated (rejecting) WT female C57BL/6 mice on day 22 after male skin graft or 10-15 days after treatment with male spleen cells.
2011-03-28 | GSE26908 | GEO
Project description:Recent studies have suggested that promoting lymphangiogenesis enhances cardiac repair following injury, but it is unknown whether lymphangiogenesis is required for cardiac regeneration. Here, we describe the anatomical distribution, regulation and function of the cardiac lymphatic network in a highly regenerative zebrafish model system using transgenic reporter lines and loss-of-function approaches.To understand the transcriptional profile of the model, we performed RNA-seq on cardiac ventricles from control and mutant (vegfc(hy-/-);vegfd(-/-)) ventricles. Overall, vegfc(hy-/-;vegfd-/-) mutant ventricles were characterized by an up-regulation of pathways related to sphingolipid and phospholipid metabolism, translation, protein maturation and nonsense mediated decay compared to control hearts. Our findings suggest that lymphatics vasculature play a role in lipid transport and when lymphatic function is compromised in vegfch(y-/-;vegfd-/-) mutant, there are consequences to sphingolipid and phospholipid metabolism. Vegfc(hy-/-;vegfd-/-) mutant ventricles were not characterized by an enrichment of genes pathways implicated in pathological hypertrophy. This finding suggests that the absence of cardiac lymphatics induced a physiological rather than pathological cardiac hypertrophy.
2019-09-03 | GSE133130 | GEO
Project description:Accurate and comprehensive de novo transcriptome profiling in heart is a central issue to better understand cardiac physiology and diseases. Although significant progress has been made in genome-wide profiling for quantitative changes in cardiac gene expression, current knowledge offers limited insights to the total complexity in cardiac transcriptome at individual exon level. To develop more robust bioinformatic approaches to analyze high-throughput RNA sequencing (RNA-Seq) data, with the focus on the investigation of transcriptome complexity at individual exon and transcript levels. In addition to overall gene expression analysis, the methods developed in this study were used to analyze RNA-Seq data with respect to individual transcript isoforms, novel spliced exons, novel alternative terminal exons, novel transcript clusters (i.e., novel genes) and long non-coding RNA genes. We applied these approaches to RNA-Seq data obtained from mouse hearts following pressure-overload induced by trans-aortic constriction. Based on experimental validations, analyses of the features of the identified exons/transcripts, and expression analyses including previously published RNA-Seq data, we demonstrate that the methods are highly effective in detecting and quantifying individual exons and transcripts. Novel insights inferred from the examined aspects of the cardiac transcriptome open ways to further experimental investigations. Our work provided a comprehensive set of methods to analyze mouse cardiac transcriptome complexity at individual exon and transcript levels. Applications of the methods may infer important new insights to gene regulation in normal and disease hearts in terms of exon utilization and potential involvement of novel components of cardiac transcriptome. Left ventricular tissues were collected from C57BL/6 mice after 1 week (hypertrophy stage, HY) and 8 weeks post trans-aortic constriction (TAC) procedure (heart failure stage, HF), respectively, and their corresponding Sham controls (Sham-HY, Sham-HF). To conduct RNA-Seq analysis, total RNAs from six TAC and Sham-operated mice at the HY stage and four TAC and corresponding Sham mice at the HF stage were obtained.
2011-10-18 | E-GEOD-29446 | biostudies-arrayexpress