Characterize the transcriptional response to INO2 and INO4 expression level (INO-level) and efficient factor
Integrated analysis, transcriptome-lipidome, reveals the effects of INO-level (INO2 and INO4) on lipid metabolism in yeast.
No sample metadata fields
View SamplesCharacterize the transcriptional response to inositol-choline and snf1
Integrated analysis of transcriptome and lipid profiling reveals the co-influences of inositol-choline and Snf1 in controlling lipid biosynthesis in yeast.
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View SamplesSnf1 and TORC1 are two global regulators that sense the nutrient availability and regulate the cell growth in yeast Saccharomyces cerevisiae. Here we undertook a systems biology approach to study the effect of deletion of these genes and investigate the interaction between Snf1 and TORC1 in regulation of gene expression and cell metabolism.
Mapping the interaction of Snf1 with TORC1 in Saccharomyces cerevisiae.
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View SamplesWe undertook an inter-laboratory effort to generate high-quality quantitative data for a very large number of cellular components in yeast using transcriptome and metabolome analysis. We ensured the high-quality of the experimental data by evaluating a wide range of sampling and measurement techniques. The data were generated for two different yeast strains, each growing under two different growth conditions and based on integrated analysis of the high-throughput data we hypothesize that differences in growth rates and yields on glucose between the two strains are due to differences in protein metabolism.
Integrated multilaboratory systems biology reveals differences in protein metabolism between two reference yeast strains.
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View SamplesTrans-splicing is a post-transcriptional event that joins exons from separate pre-mRNAs. Detection of trans-splicing is usually severely hampered by experimental artifacts and genetic rearrangements. Here, we develop a new computational pipeline, TSscan, which integrates different types of high-throughput long-/short-read transcriptome sequencing of different human embryonic stem cell (hESC) lines to effectively minimize false positives while detecting trans-splicing. Combining TSscan screening with multiple experimental validation steps revealed that most chimeric RNA products were platform-dependent experimental artifacts of RNA sequencing. We successfully identified and confirmed four trans-spliced RNAs, including the first reported trans-spliced large intergenic noncoding RNA ("tsRMST"). We showed that these trans-spliced RNAs were all highly expressed in human pluripotent stem cells and differentially expressed during hESC differentiation. Our results further indicated that tsRMST can contribute to pluripotency maintenance of hESCs by suppressing lineage-specific gene expression through the recruitment of NANOG and the PRC2 complex factor, SUZ12. Taken together, our findings provide important insights into the role of trans-splicing in pluripotency maintenance of hESCs and help to facilitate future studies into trans-splicing, opening up this important but understudied class of post-transcriptional events for comprehensive characterization
Integrative transcriptome sequencing identifies trans-splicing events with important roles in human embryonic stem cell pluripotency.
Specimen part
View SamplesGene expression profiling of primary mouse articular chondrocyte infected with recombinant adenovirus expressing the zinc transporter ZIP8 (SLC39A8) protein.
Pleiotropic roles of metallothioneins as regulators of chondrocyte apoptosis and catabolic and anabolic pathways during osteoarthritis pathogenesis.
Age, Specimen part, Treatment
View SamplesWe report global gene expression profilies of Brassinosteroid related Arabidopsis mutants in response to dehydration and fixed-carbon starvation stresses by RNA-seq Overall design: Arabidopsis plants of listed genotypes were grown for 4 weeks under long day (16 hour light) conditions before being subjected to control, 4 hour dehydration, or 5 day fixed carbon starvation treatments.
Arabidopsis WRKY46, WRKY54, and WRKY70 Transcription Factors Are Involved in Brassinosteroid-Regulated Plant Growth and Drought Responses.
Specimen part, Treatment, Subject
View SamplesThe underlying change of gene network expression of Guillain-Barre syndrome (GBS) remains elusive. We sought to identify GBS-associated gene networks and signalling pathways by analyzing the transcriptional profile of leukocytes in the patients with GBS.
Identification of gene networks and pathways associated with Guillain-Barré syndrome.
Sex, Age, Specimen part, Race
View SamplesHuman cell line HCT116 incubated with Myxothiazol for 5 or 17 hours
A sustained deficiency of mitochondrial respiratory complex III induces an apoptotic cell death through the p53-mediated inhibition of pro-survival activities of the activating transcription factor 4.
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View SamplesHere we show that MIWI is a small RNA-guided ribonuclease (Slicer) that requires extensive complementarity for target cleavage in vitro. Disruption of its catalytic activity in mice by a single point mutation results in male infertility and displays increased accumulation of LINE1 transposon transcripts. Overall design: MIWI-associated piRNAs from different genotypes were sequenced. Total RNA from purified round spermatids were subjected to Ribozero purification and strand-specific RNAseq lib prepared. Global 5'' RACE library was prepare from indicated genotypes.
Miwi catalysis is required for piRNA amplification-independent LINE1 transposon silencing.
Specimen part, Cell line, Subject
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