Similar Datasets
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:SmallRNA-SEQ of mutants B cell for IgH 3'RR and Emu
2017-06-13 | GSE90759 | 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
Project description:To analyse smallRNA expression differences between A375 and A375-BIR during the treatment with dabrafenib (DAB)
2024-05-03 | GSE165335 | GEO
Project description:We aim to elucidate regulatory miRNA and target networks contributing to Placenta accreta spectrum development using smallRNA-Seq.
2022-11-01 | GSE216742 | 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.
2012-07-01 | GSE37770 | GEO
Project description:In this study, we employed a 44K microarray approach to analyse the hepatic transcriptomic response of post smolt Atlantic salmon subjected to control conditions (12°C, ~100% air saturation), an incremental increase in temperature (12°C to 20°C; 1°C per week) under normoxia (~100% air saturation) or moderate hypoxia (~70% air saturation). Significance Analysis of Microarrays (FDR < 5%) identified 1900 and 2105 differentially expressed probes (DEPs) in salmon exposed to either Warm&Normoxic (WN) or Warm&Hypoxic (WH) conditions as compared with those maintained under control conditions (CT). Further, we found that heat stress alone or in combination with hypoxia caused most similar transcriptional responses and 1,111 (38%) DEPs were shared between WN and WH treatment groups. Consequently, in this study a unique set of 2,894 DEPs was determined.
2021-02-16 | GSE146471 | GEO