Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| ERR2283630.fastq.gz | Fastqsanger.gz | |||
| ERR2283631.fastq.gz | Fastqsanger.gz | |||
| ERR2283632.fastq.gz | Fastqsanger.gz | |||
| ERR2283633.fastq.gz | Fastqsanger.gz | |||
| ERR2283634.fastq.gz | Fastqsanger.gz |
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Project description:P granules are germ-cell-specific cytoplasmic structures containing RNA and protein and required for proper germ cell development in C. elegans. A new P-granule-associated protein, DEPS-1, whose loss disrupts P granule structure and function was analysed in this study. Genome wide analysis of gene expression in deps-1 mutant germ lines identified additional targets of DEPS-1 regulation, many of which are also regulated by the RNAi factor RDE-3. Our studies suggest that DEPS-1 is a key component of the P granule assembly pathway and that its roles include promoting accumulation of some mRNAs, such as glh-1 and rde-4, and reducing accumulation of other mRNAs, perhaps by collaborating with RDE-3 to generate endogenous short interfering RNAs (endo-siRNAs). We isolated dissected gonads from deps-1 mutant adults and compared each to wild type dissected gonads. RNA was linearly amplified prior to labeling for all genotypes. The comparisons were done in quadruplicate on independently grown and isolated animals.
2010-05-26 | E-GEOD-9993 | biostudies-arrayexpress
Project description:P granules are germ-cell-specific cytoplasmic structures containing RNA and protein and required for proper germ cell development in C. elegans. A new P-granule-associated protein, DEPS-1, whose loss disrupts P granule structure and function was analysed in this study. Genome wide analysis of gene expression in deps-1 mutant germ lines identified additional targets of DEPS-1 regulation, many of which are also regulated by the RNAi factor RDE-3. Our studies suggest that DEPS-1 is a key component of the P granule assembly pathway and that its roles include promoting accumulation of some mRNAs, such as glh-1 and rde-4, and reducing accumulation of other mRNAs, perhaps by collaborating with RDE-3 to generate endogenous short interfering RNAs (endo-siRNAs). Keywords: Mutant analysis of deps-1 dissected C. elegans gonads
2008-02-01 | GSE9993 | GEO
Project description:Background: Schizophrenia (SZ) is a debilitating mental illness with uncertain etiology and challenges in early diagnosis and treatment outcomes. For the first time, we applied a multiomics techniques to explore plasma exosomal markers of SZ and underlying molecular mechanisms. Methods: Exosomes were separated and identified from ten drug-naive first-episode SZ patients and ten healthy controls. Then small RNA-seq and high-performance liquid chromatography-tandem mass spectrometry technology were used to detect the profiles of microRNAs (miRNAs) and proteomics, respectively. The integrative multiomics analysis was further performed. Results: A total of 167 differentially expressed miRNAs (DE miRNAs) were identified in plasma exosomes from drug-naive first-episode SZ patients. The potential target genes of DE miRNAs were predicted, and GO and KEGG enrichment analysis showed that they were associated with RNA catabolic process, proteasome-mediated ubiquitin-dependent protein catabolic process, etc. Proteomic analysis identified 274 differentially expressed proteins (DEPs), and DEPs were mainly enriched in immune response and some signaling pathways. The combination of Top 10 DE miRNAs/ DEPs both had good values to diagnose SZ. Importantly, miRNA-protein ceRNA networks were constructed by integrating multiomics, one consisting of 21 downregulated DE miRNAs and 21 upregulated DEPs and the other consisting of 64 upregulated DE miRNAs and 86 downregulated DEPs in SZ patients. Conclusions: Our study for the first time describes the multiomics landscape of plasma exosomes in first-episode drug-naïve of SZ, and provides novel insights into the molecular alterations of SZ. These findings hold promise for advancing diagnostic and therapeutic strategies in SZ management.
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Project description:SmallRNA-SEQ of mutants B cell for IgH 3'RR and Emu
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Project description:To analyse smallRNA expression differences between A375 and A375-BIR during the treatment with dabrafenib (DAB)
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Project description:We aim to elucidate regulatory miRNA and target networks contributing to Placenta accreta spectrum development using smallRNA-Seq.
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Project description:Analysis of smallRNA in THP1 (human monocytic leukemia) cell line in order to correlate miRNA activity with target abundance.
2012-07-01 | GSE37770 | GEO
Project description:For the first time, we report differentially expressed genes (DEGs) and differentially expressed proteins (DEPs) in potato (Solanum tuberosum L.) tubers characterized by light and dark chip color after cold storage. Two potato diploid progenies derived from reciprocal crosses of parental clones possessing the T- and D-type cytoplasm were used. We recognized 48 and 15 DEGs as compared to RNA-seq data of contrasting segregants. We identified DEPs in potato tuber amyloplast and mitochondrial fractions. Seven and five DEPs were identified in the amyloplast fractions of the T – and D – type cytoplasm, respectively. Higher number of DEPs were selected from the mitochondrial fraction. The corresponding values were 97 and 105, including 39 common DEPs in the T – and D – type cytoplasm. These findings suggest that mitochondria may play a more important role than amyloplasts in response of potato tubers to cold treatment and that this influence can be different for the T – and D – type cytoplasm. However, we showed that the mt/nucDNA and pt/nucDNA ratios tend to increase for tubers characterized by dark chip color when compared with light chip color samples. Therefore, a protective effect of reducing sugars on both amyloplasts and mitochondria during low temperature treatment should be considered.
2021-09-17 | GSE184141 | GEO
Project description:Lepeophtheirus salmonis (sea lice) and bacterial co-infection threatens wild and farmed Atlantic salmon performance and welfare. The present microarray-based study examined the dorsal skin transcriptome response to formalin-killed Aeromonas salmonicida bacterin (ASAL) in pre-adult sea lice-infected and non-infected Atlantic salmon to fill the existing knowledge gap and aid in developing anti-co-infection strategies. To this aim, sea lice-infected and non-infected salmon were intraperitoneally injected with either phosphate-buffered saline (PBS) or ASAL (i.e., 4 injection/infection groups: PBS/no lice, PBS/lice, ASAL/no lice, and ASAL/lice). The analysis of the dorsal skin transcriptome data [Significance Analysis of Microarrays (5% FDR)] identified 345 up-regulated and 2,189 down-regulated DEPs in the comparison PBS/lice vs. PBS/no lice, and 82 up-regulated and 3 down-regulated DEPs in the comparison ASAL/lice vs. ASAL/no lice. The comparison ASAL/lice vs. PBS/lice identified 272 up-regulated and 11 down-regulated DEPs, whereas ASAL/no lice vs. PBS/no lice revealed 27 up-regulated DEPs. The skin transcriptome differences between the co-stimulated salmon (i.e., ASAL/lice) and PBS/no lice salmon accounted for 1,878 up-regulated and 3,120 down-regulated DEPs.
2022-02-28 | GSE186292 | GEO
Project description:Analysis of smallRNA in THP1 (human monocytic leukemia) cell line in order to correlate miRNA activity with target abundance. THP1 smallRNA profiles were generated in triplicates by deep-sequencing in Illumina HiSeq2000.
2012-06-30 | E-GEOD-37770 | biostudies-arrayexpress