Mapping and modeling the genomic basis of differential RNA isoform expression at single-cell resolution with LR-Split-seq
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ABSTRACT:
PROVIDER: PRJNA713904 | ENA |
REPOSITORIES: ENA
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Project description:The rise in throughput and quality of long-read sequencing should allow unambiguous identification of full-length transcript isoforms. However, its application to single-cell RNA-seq has been limited by throughput and expense. Here we develop and characterize long-read Split-seq (LR-Split-seq), which uses combinatorial barcoding to sequence single cells with long reads. Applied to the C2C12 myogenic system, LR-split-seq associates isoforms to cell types with relative economy and design flexibility. We find widespread evidence of changing isoform expression during differentiation including alternative transcription start sites (TSS) and/or alternative internal exon usage. LR-Split-seq provides an affordable method for identifying cluster-specific isoforms in single cells.
2021-03-12 | GSE168776 | GEO
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| S-EPMC8495978 | biostudies-literature
Project description:To explore the molecular mechanisms involved in the toxicity in the livers exposed to MC-LR at the environmental level, the hepatic transcriptome was performed. A total of 210 genes were differentially expressed (P<0.05, |fold change|≥2) in response to MC-LR exposure; among them, 143 genes were significantly upregulated, and 67 genes were downregulated. Pathway enrichment analysis identified the top biological functions associated with the genes differentially expressed in response to MC-LR exposure, which were circadian regulation of gene expression, negative regulation of glucocorticoid receptor signaling pathway, the epoxygenase P450 pathway, regulation of insulin secretion, lipid metabolic process, and cell cycle pathway.
2020-03-25 | GSE145459 | GEO
Project description:The expressions of piRNA in mouse sperm were altered by MC-LR-exposure or Hsp90aa1 shRNA. MC-LR could induce intergenerational toxicity.
2020-12-31 | GSE129849 | GEO
Project description:Microcystin-LR (MC-LR), the most toxic member of microcystin family, inhibits protein phosphatase PP2A, triggers oxidative stress and induces hepatotoxicity. Gene expression profiling of MC-LR treated larvae using DNA microarray analysis revealed effects in the retinal visual cycle and pigmentation synthesis pathways that have not been previously associated with MC-LR. Liver-related genes were also differentially expressed. The microarray data were confirmed by quantitative real-time PCR. Our findings provide new evidence that microcystin-LR exposure of zebrafish larvae modulates the retinal visual cycle and pigmentation synthesis pathways and ultimately alter larval zebrafish behavior
2017-02-16 | GSE73739 | GEO
Project description:We have builded a network including mRNA, miRNA, piRNA, lncRNA and circRNA after exposure to MC-LR for 6 months in testicular tissue. And we find MC-LR could induce testicular toxicity and apoptosis by disturbing the netwok.
2020-08-31 | GSE119044 | GEO
Project description:Intoshia linei isolate:LR Genome sequencing
| PRJNA414163 | ENA
Project description:Arable soils are extremely heterogeneous in spatial nutrient distribution. It is well documented that lateral roots (LRs) proliferate in nitrate-rich patch. Yet less information is available as to which genes are involved in this process, in particular in cereals. To understand the molecular mechanism for local nitrate induced LR growth in maize (Zea mays L.), we analyzed the gene expression profiling in maize root in early response (1 hour) to local nitrate stimulation by using Maize Oligonucleotide Array (http://www.maizearray.org) and a split-root system. Selected differentially expressed genes were further confirmed by semi-quantitative RT-PCR. The results showed that reception and/or transduction of local NO3- signal involve some important protein kinases and protein phosphatases (histidine kinases, serine/threonine kinases, protein phosphatase 2A etc.) and transcription factors (F-box, Zinc finger, Myb and bZIP transcription factors and response regulator). Increasing expression of genes encoding auxin response factor 7b, ethylene receptor, and cytokinin oxidase suggests strong interaction among hormonal pathways and local NO3- signaling pathways. Genes involving NO3- uptake and assimilation (NRT2.1, NR, etc.), sugar transport (a sugar transporter) and utilization (a sucrose synthase) were enhanced in the N-fed root. Furthermore, local NO3- induces rapid expression of genes related to cell division and expansion such as alpha-expansin, celluose synthase, kinesin, plasma membrane and tonoplast aquaporins. Based on the differentially expressed genes, a putative model which combines both the 'NO3- signal' and 'metabolic sink' theories is proposed to explain the molecular mechanism controlling local nitrate induced LR elongation in maize. plants were pre-cultured in solution containing 0.5 mmol L-1 NO3- for 6 days and then transferred to N-free solution to grow for another 2 days. Then these plants were transferred to a two-compartment split-root system with only half root supplied with 1.0 mmol L-1 NO3-. Supply of Ca2+ in the N-free half was compensated by adding 1.0 mmol L-1 CaCl2. One hour after the local nitrate treatment, root segments (15cm from root tip to lateral root elongation zone) were sampled for RNA extraction. Two biological replicates were performed for each treatment.
2008-12-30 | E-GEOD-11145 | biostudies-arrayexpress
Project description:Microcystins (MCs) are cyclic hepatotoxins produced worldwide by various species of cyanobacteria. Their structure includes two variable amino acids (AAs) and most of the studies focused on the most toxic variant: the microcystin LR (MC-LR). However, more than 80 MC variants have been described to date. Despite ingestion being the major pathway of human exposure, few in vivo studies have demonstrated macroscopic effects on the gastro-intestinal tract, but no data are available on the affected pathways by several variants on intestinal cells. Here, using a non-selective method, we investigated for the first time the effect of MC-RR and MC-LR on the human intestinal cell line Caco-2 and compared their response at the pangenomic scale. The cells were incubated for 4 hrs or 24 hrs with the same range of sub-lethal concentrations of MC-RR or MC-LR. Low effects were observed for both variants after a short-term exposure. On the contrary, dose-dependent modulations of the genes transcription levels were noticed with MC-RR and MC-LR after 24 hrs. Furthermore, the genomic profiles induced by both variants were similar suggesting a common toxicity mechanism but with higher modulation following MC-LR than MC-RR exposure. However, the functional annotation revealed major differences between the variants effects. Indeed, the well-known MC-LR affected mainly two pathways, the oxidative stress response and the cell cycle regulation, which did not elicit significant alteration following MC-RR exposure. This work is the first comparative description of the MC-LR and MC-RR effects on a human intestinal cell model. It allowed us to suggest differences in the mechanism of toxicity for MC-RR and MC-LR. These results illustrate that the toxicity of MC variants remains a key point for risk assessment. Differentiated Caco-2 cells were exposed to microcystins in free FCS culture medium for either 4 or 24 hours. Sub-lethal concentrations of 10, 50 and 100 M-BM-5M of MC-LR or MC-RR were chosen for 4 hours, while 1, 5 and 10 M-BM-5M were selected for 24 hours. For each condition (including the controls), the solvent concentration was fixed to 2% EtOH for MC-LR and 1.5% of 80% MeOH for MC-RR. Four to five culture replicates per condition were done.
2012-12-31 | E-GEOD-29861 | biostudies-arrayexpress
Project description:Microcystins (MCs) are cyclic hepatotoxins produced worldwide by various species of cyanobacteria. Their structure includes two variable amino acids (AAs) and most of the studies focused on the most toxic variant: the microcystin LR (MC-LR). However, more than 80 MC variants have been described to date. Despite ingestion being the major pathway of human exposure, few in vivo studies have demonstrated macroscopic effects on the gastro-intestinal tract, but no data are available on the affected pathways by several variants on intestinal cells. Here, using a non-selective method, we investigated for the first time the effect of MC-RR and MC-LR on the human intestinal cell line Caco-2 and compared their response at the pangenomic scale. The cells were incubated for 4 hrs or 24 hrs with the same range of sub-lethal concentrations of MC-RR or MC-LR. Low effects were observed for both variants after a short-term exposure. On the contrary, dose-dependent modulations of the genes transcription levels were noticed with MC-RR and MC-LR after 24 hrs. Furthermore, the genomic profiles induced by both variants were similar suggesting a common toxicity mechanism but with higher modulation following MC-LR than MC-RR exposure. However, the functional annotation revealed major differences between the variants effects. Indeed, the well-known MC-LR affected mainly two pathways, the oxidative stress response and the cell cycle regulation, which did not elicit significant alteration following MC-RR exposure. This work is the first comparative description of the MC-LR and MC-RR effects on a human intestinal cell model. It allowed us to suggest differences in the mechanism of toxicity for MC-RR and MC-LR. These results illustrate that the toxicity of MC variants remains a key point for risk assessment.
2012-12-31 | GSE29861 | GEO