Ontology highlight
ABSTRACT:
PROVIDER: PRJEB39754 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| ERR4467700_1.fastq.gz | Fastqsanger.gz | |||
| ERR4467700_2.fastq.gz | Fastqsanger.gz | |||
| ERR4467710_1.fastq.gz | Fastqsanger.gz | |||
| ERR4467710_2.fastq.gz | Fastqsanger.gz | |||
| ERR4467701_1.fastq.gz | Fastqsanger.gz |
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Project description:DNA methylomes of ovaries during pubertal transition in gilts
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Project description:We sequenced mRNA from mouse E14.5 embryonic cortex to compare gene expression level and alternative splicing events between 2 control (WT) and 2 Qk cKO. A set of tissue specific splicing factors are thought to govern alternative splicing events during neural progenitors (NPC) to neuron transition by regulating neuron specific exons. Here we proposed one such a factor, RNA-binding protein Qki5, which is specifically expressed in neural stem cells. We performed mRNAseq analysis by using mRNAs obtained from developing cerebral cortices in Qk conditional knockout (cKO) mice. Expectedly, we found huge numbers of alternative splicing changes between control and conditional knock-out relative to that of transcripts level changes. Furthermore, DAVID and Meta-scape analysis revealed that affected spliced genes are involved in axon-development and microtubule-based process. Among these, Ninein protein coding mRNA is listed as a Qk protein dependent alternative splicing targets. Interestingly, this exon encodes very long poly-peptides (2,121 nt) and is known as a previously defined dynamic RNA switch during NPC-to-neuron transition. In addition, we validated that the regulation of this large exon is consistent with Qki5 dependent alternative exon inclusion mode obtained from our previous Qki5 HITS-CLIP analysis. Together Qki5 will add to a list factor of alternative splicing in NPC-to-neuron transition.
2019-04-17 | GSE123927 | GEO
Project description:Objective: Despite organoid formation and characterization from different tissues have been extensively studied, pancreas remains one among the least investigated organs. Here we proposed a multifaced characterization of cell types present in human pancreatic organoids (hPO) and starting from their progenitor we described their maturation and their lineage relationships. Design: We performed unbiased transcriptome-wide scRNA-seq analysis on 3187 cells of human pancreatic organoids obtained from 3 healthy islet-depleted tissue. To support our results, we strengthened these findings with proteomic and qRT-PCR analyses performed during the long-term culture of hPO. Results: First, we described hPO focusing on their morphology and long-term culture molecular aspects and showing a well-defined epithelial organization supported by a genetic stability through all cell passages. Successively, based on single-cell RNA sequencing technology, we defined all cell types present in hPO confirming that our pancreatic organoid methodology is highly reproducible. Moreover, exploiting the latest bioinformatic tools and comparing our data with recently published ones we reshaped the conventional theory of univocal ductal nature of hPO. Finally, we defined a new strategy to sort a refined multipotent progenitor from hPO and we gave a new definition of pancreatic progenitor demonstrating its capacity to renew the hPO stem population while maintaining its heterogeneity. Conclusions: Taken together, our results give a new definition of human pancreatic organoids, which reveals the complex nature of these structures and provides a strong basis to pave the way for future study in the pancreatic field.
2024-10-30 | GSE158035 | GEO
Project description:RNA secondary structures have been increasingly reported to serve critical regulatory roles in post-transcriptional gene regulation. RNA G-quadruplex secondary structures can serve as cis-elements to recruit splicing factors and regulate alternative RNA splicing. We recently showed that RNA G-quadruplexes play a critical regulatory role in regulating alternative splicing during the epithelial mesenchymal transition. Due to the critical role alternative splicing plays in human health and disease, an unmet need exists to identify small molecule modulators of alternative splicing. In this study, we performed high-throughput screening using a dual-output splicing reporter to identify small molecules capable of regulating alternative splicing by interacting with RNA secondary structure G-quadruplexes. We identify emetine and its analog cephaeline as small molecules that denature RNA G-quadruplexes in a sequence and location independent manner to modify alternative splicing. Transcriptome analysis reveals that treatment with emetine globally regulates alternative splicing, including events associated with exon-proximal G-quadruplexes. These data suggest a critical role for emetine and cephealine as splicing regulators with the selective ability to disrupt RNA G-quadruplex-associated alternative splicing in vivo.
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Project description:We conducted a genome wide survey of mosquito gene expression profiles during 8 different time periods of the Anopheles gambiae lifecycle. The timeperiods included embryos, E, collected 12-14 hours post oviposition (hpo), five larval samples, La-Le, with La collected approximately 48h hpo and the rest, Lb-Le, collected at 48 intervals thereafter, irrespective of larval size and instar, pupae, P, collected at the same time as Le samples (240 hpo) and freshly emerged adult females, F and males, M, collected 312 hpo. To investigate mosquito expression during development, we performed competitive two-dye hybridizations of experimental and standard reference RNA samples to MMC1 microarrays. MMC1 microarrays contain approximately 20,000 EST clones. Standard reference RNA was produced in vitro from the spotted ESTs and was utilized to provide consistent, non-zero reference values for almost all probes of the array. For the experiment, three biological replicates, corresponding to three successive mosquito generations and one technical (dye-swap) replicate was conducted.
2007-07-19 | E-TABM-186 | biostudies-arrayexpress
Project description:Alternative splicing produces multiple, distinct mRNA transcripts from the same gene locus. To explore tissue-type specific gene expression and alternative splicing, we generated mRNA-Seq data from pupal tissues dissected from Drosophila. This allowed us to compare expression between dissected, highly enriched brain and indirect flight muscle (IFM) samples as well as whole legs. Bioinformatic analysis allowed us to characterize tissue-specific differences in gene expression as well as alternative splicing among the three tissues, as well as to identify a multitude of novel splicing events that are not currently contained in the Drosophila annotation. This suggests that tissue or cell-type specific sequencing at multiple timepoints during the fly life cycle will help extend existing annotations, and novel splice junction discovery is an important consideration in mRNA-Seq data analysis.
2022-01-25 | GSE194199 | GEO
Project description:We carried out the first analysis of alternative splicing complexity in human tissues using mRNA-Seq data. New splice junctions were detected in 20% of multiexon genes, many of which are tissue specific. By combining mRNA-Seq and EST-cDNA sequence data, we estimate that transcripts from 95% of multiexon genes undergo alternative splicing and that there are 100,000 intermediate- to high-abundance alternative splicing events in major human tissues. From a comparison with quantitative alternative splicing microarray profiling data, we also show that mRNA-Seq data provide reliable measurements for exon inclusion levels. Keywords: mRNA expression 32-nucleotide sequence reads from six human tissues including brain, cerebral cortex, heart, liver, lung and skeletal muscle.
2008-11-19 | E-GEOD-13652 | biostudies-arrayexpress
Project description:Background: There are significant sex differences in human physiology and disease; the genomic sources of these differences, however, are not well understood. During puberty, a drastic neuroendocrine shift signals physical changes resulting in robust sex differences in human physiology. Here, we explore how shifting patterns of DNA methylation may inform these pathways of biological plasticity during the pubertal transition. Methods: In this study we analyzed DNA methylation (DNAm) in saliva at two time points across the pubertal transition within the same individuals. We targeted two domains of DNAm patterns that may inform processes of sexual differentiation 1) sex related sites, which demonstrated differences between males from females and 2) time related sites in which DNAm shifted significantly between timepoints. We further explored the correlated network structure sex and time related DNAm networks and linked these patterns to pubertal stage, assays of salivary testosterone, a reliable diagnostic of free, unbound hormone that is available to act on target tissues, and overlap with androgen response elements. Results: Sites that differed by biological sex were largely independent of sites that underwent change across puberty. Time-related DNAm sites, but not sex-related sites, formed correlated networks that were associated with pubertal stage. Both time and sex DNAm networks reflected salivary testosterone levels that were enriched for androgen response elements, with sex-related DNAm networks being informative of testosterone levels above and beyond biological sex later in the pubertal transition. Conclusions: These results inform our understanding of the distinction between sex- and time-related differences in DNAm during the critical period of puberty and highlight a novel linkage between correlated patterns of sex-related DNAm and levels of salivary testosterone.
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Project description:To find the lipolysis-related function of Hpo, RNA-sequencing analysis was processed using Hpo-induced larval fat tissue.
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