MicroRNA expression profile in Newcastle disease virus-infected HeLa cells
Ontology highlight
ABSTRACT:
INSTRUMENT(S): Illumina HiSeq 2500
ORGANISM(S): Homo sapiens
SUBMITTER: Yu Chen
PROVIDER: E-MTAB-9690 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
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Project description:MicroRNAs (miRNAs) and small interfering RNAs (siRNAs) are short (19â25 nucleotides) non-coding RNA molecules that have large-scale regulatory effects on development and on stress responses in plants.The objective of this study is to investigate the transcriptional profile of miRNAs and other small non-coding RNAs in Verticilliumâinoculated cotton roots. Four small RNA libraries were constructed from mocked and infected roots of two cotton cultured species which are with different Verticillium tolerance (âHai-7124â, Gossypium barbadense L., a Verticillium-tolerant cultivar, and âYi-11â, Gossypium hirsutum L. a Verticillium-sensitive cultivar). The length distribution of obtained small RNA pools was significantly different among libraries. A total of 215 conserved miRNA families were identified in the two cotton species, of them 14 are novel. There were >65 families with different expression between two libraries. We also identified two ta-siRNAs and thousands of endogenous siRNA candidates, and hundred of them exhibited altered expression after inoculation of Verticillium. The profiling of these miRNAs and other small non-coding RNAs lay the foundation for further understanding of small RNAs function in the regulation of Verticillium defence responses in cotton roots. Examination of 2 different traetments in 2 cotton types.
2011-04-29 | E-GEOD-28236 | biostudies-arrayexpress
Project description:To identify potential miRNAs involved in fiber development and elucidate their expression differences between G. barbadense and G. hirsutum, we constructed two small RNA libraries, Gb10 and Gh10, prepared from fibers of 3-79 (G. barbadense) and TM-1 (G. hirsutum) collected at 10 days post-anthesis (DPA). We identified 28 conserved miRNA families, including 24 that exactly match known plant miRNA families in miRBase. With MIREAP and newly developed software miRsearcher, 7 candidate-novel miRNAs were found. 5 candidate-novel miRNAs were expressed in both species, 2 candidate-novel miRNAs were expressed only in one species. Moreover, 4 miRNA families showed significant expression differences between sea-island cotton and upland cotton in 10 DPA fibers. two examples including 3-79 and TM-1 10 DPA fibers
2010-12-03 | E-GEOD-25773 | biostudies-arrayexpress
Project description:Using microRNA-Seq, we examined the alteration of microRNA expression profiles in the nucleus accumbens of methamphetamine-sensitized and saline-control mice. Nucleus accumbens lysate from eight mice of each group were pooled as one sample. Two RNA samples from each group were prepared and were then processed to generate small RNA libraries, which were sequenced on the Illumina Hiseq 2000. The aberrant expression of microRNAs identified in this study may involve in METH-induced locomotor sensitization and addiction.
2022-07-13 | E-MTAB-2901 | biostudies-arrayexpress
Project description:MicroRNAs (miRNAs) are involved in nearly every biological process examined to date. Mounting evidence show that some spermatozoa specific miRNAs play important roles in the regulation of spermatogenesis and germ cells development, but little is known of the exact identity and function of miRNA in sperm cells or their potential involvement in spermatogenesis and germ cells development. Here, we investigated the spermatozoa miRNA profiles using illumina deep sequencing combined with bioinformatic analysis using zebrafish as a model system. Deep sequencing of small RNAs yielded 12 million raw reads from zebrafish spermatozoa. Analysis showed that the noncoding RNA of the spermatozoa included tRNA, rRNA, snRNA, snoRNA and miRNA. By mapping to the zebrafish genome, we identified 400 novel and 204 conserved miRNAs which could be grouped into 104 families, including zebrafish specific families, such as mir-731, mir-724, mir-725, mir-729 and mir-2185. We report the first characterization of the miRNAs profiling in zebrafish spermatozoa. The obtained spermatozoa miRNAs profiling will serve as valuable resources to systematically study spermatogenesis in fish and vertebrate. Examination of small RNA populations in zebrafish spermatozoa
2015-04-01 | E-GEOD-61984 | biostudies-arrayexpress
Project description:Background: WitchesM-bM-^@M-^Y broom disease of Mexican lime (Citrus aurantifolia L.), which is caused by the phytoplasma M-bM-^@M-^\Candidatus Phytoplasma aurantifoliaM-bM-^@M-^], is a devastating disease that results in significant economic losses. Plants adapt to abiotic stresses by regulating gene expression at the transcriptional and post-transcriptional levels. MicroRNAs (miRNAs) are a recently identified family of molecules that regulate plant responses to environmental stresses through post-transcriptional gene silencing. Methods: Using a high-throughput approach to sequence small RNAs, we compared the expression profiles of miRNAs in healthy Mexican lime trees and in plants infected with M-bM-^@M-^\Ca. Phytoplasma aurantifoliaM-bM-^@M-^]. Results: Our results demonstrated the involvement of different miRNAs in the response of Mexican lime trees to infection by M-bM-^@M-^\Ca. Phytoplasma aurantifoliaM-bM-^@M-^]. We identified miRNA families that are expressed differentially upon infection with phytoplasmas. Most of the miRNAs had variants with small sequence variations (isomiRs), which are expressed differentially in response to pathogen infection. Conclusions: It is likely that the miRNAs that are expressed differentially in healthy and phytoplasma-infected Mexican lime trees are involved in coordinating the regulation of hormonal, nutritional, and stress signalling pathways, and the complex interactions between them. Future research to elucidate the roles of these miRNAs should improve our understanding of the level of diversity of specific plant responses to phytoplasmas. Small mRNA profiles of healthy (H) and Phytoplasma-infected Mexican lime trees were generated by deep sequencing, six replicate, using Illumina Hiseq2000
2013-03-09 | E-GEOD-44279 | biostudies-arrayexpress
Project description:Two small RNA libraries were generated from micropropagated â??Muscat Hamburgâ?? (Vitis vinifera) plantlets under normal and low temperatures (4 °C). A total of 163 known miRNAs and 299 putative novel miRNAs were detected from two small RNA libraries by Solexa sequencing. Forty-four cold-inducible miRNAs were identified through differentially expressed miRNAs (DEMs) analysis; among which, 13 belonged to upregulated DEMs while 31 belonged downregulated DEMs. This study indicated that a diverse set of miRNAs in V. vinifera are cold-inducible and may play an important role in cold stress response. Examination of small RNA populations in grapevine under cold treatment and none cold treatment.
2016-06-14 | E-GEOD-68970 | biostudies-arrayexpress
Project description:Purpose: The miRNA profiles were compared among groups of chronic stress exposure and control in two different breeds to identify the differentially expressed miRNAs related to response to chronic stress in the pituitary-adrenal axis. Methods: 6 male adult CFD and 6 Beagles were chosen at random with the similarities in good health, weight and other aspects. Separately, 3 of these two breeds were freely selected for the stress exposure via intermittent electrical stimulation and restraint stress, while the other 3 of these two breeds were non-disposed for normal control.The details for the disposal of dogs were: every morning dogs were restrained and electrical stimulations were exerted with a stable current of 10 mA for 6 s and then with a 6 s interval, lasting for 20 min every day. The duration of disposal was ten days.ll 12 dogs were killed by air embolism in the 11th day. Subsequently, pituitary and adrenal cortex tissues were fast collected and isolated for further high-sequencing. Results: 8 small miRNA libraries were constructed for miRNA-seq. A number of reads ranging from 15,926,611 to 81,028,035 was obtained in those 8 groups.a total of 29 (7 up, 22 down), 37 (16 up, 21 down), 30 (22 up, 8 down), 23 (16 up, 7 down), 21 (15 up, 6 down), 50 (11 up, 39 down), 28 (6 up, 22 down) and 40 (29 up, 11 down) DE-miRNAs (P-value < 0.001, log2(Fold_change) >1) were detected in the comparisons of BAC1_vs_BAC2, BAC1_vs_CFDAC1, BAC2_vs_CFDAC2, CFDAC1_vs_CFDAC2, BP1_vs_BP2, BP1_vs_CFDP1, BP2_vs_CFDP2 and CFDP1_vs_CFDP2, respectively Conclusions: Our results shed light on the miRNA profiles with and within chronic stress exposure in adrenal cortex and pituitary. Adrenal cortex and pituitary miRNA profiles of adult Chinese Field Dog and Beagle under chronic stress exposure and normal control, including BAC1 (Beagle adrenal cortex with disposal), BAC2 (Beagle adrenal cortex with non-disposal), BP1 (Beagle pituitary with disposal), BP2 (Beagle pituitary with non-disposal), CFDAC1 (Chinese Field Dog adrenal cortex with disposal), CFDAC2 (Chinese Field Dog adrenal cortex with non-disposal), CFDP1 (Chinese Field Dog pituitary with disposal), CFDP2 (Chinese Field Dog pituitary with non-disposal), were generated by deep sequencing, using Illumina Hiseq 2000.
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Project description:To compare MicroRNA expression in 16HBE infected with EV71 and CA16 we defined the following experimental groups: EV71-0h, EV71-6h, EV71-12h, CA16-0h, CA16-6h and CA16-12h
2016-08-20 | E-GEOD-85829 | biostudies-arrayexpress
Project description:The dendritic cell (DC) is a master regulator of immune responses. Pathogenic viruses subvert normal immune function in DCs through the expression of immune antagonists. Understanding how these antagonists interact with the host immune system requires knowledge of the underlying genetic regulatory network that operates during an uninhibited antiviral response. In order to isolate and identify this network, we studied DCs infected with Newcastle Disease Virus (NDV), which is able to stimulate innate immunity and DC maturation through activation of RIG-I signaling, but lacks the ability to evade the human interferon response. To analyze this experimental model, we developed a new approach integrating genome-wide expression kinetics and time-dependent promoter analysis. We found that the genetic program underlying the antiviral cell state transition during the first 18-hours post-infection could be explained by a single regulatory network. Gene expression changes were driven by a step-wise multi-factor cascading control mechanism, where the specific transcription factors controlling expression changed over time. Within this network, most individual genes are regulated by multiple factors, indicating robustness against virus-encoded immune evasion genes. In addition to effectively recapitulating current biological knowledge, we predicted, and validated experimentally, antiviral roles for several novel transcription factors. More generally, our results show how a genetic program can be temporally controlled through a single regulatory network to achieve the large-scale genetic reprogramming characteristic of cell state transitions. Total RNA from Monocyte-derived conventional DCs of 2 different donors were infected with Newcastle disease virus (NDV) or as control with allantoic fluid (AF) alon. DC were then harvested at : 0, 1, 2, 6, 10 and 18 hour for control and 1, 2, 4, 6, 8, 10, 12, 14, 16 and 18 hours for NDV infection. Replicates were performed for each of the donors at all timepoints.
2010-03-08 | E-GEOD-18791 | biostudies-arrayexpress
Project description:High-throughput small RNA sequencing were performed to identify a large number of miRNAs and their targets in mature G. biloba ovules. Our study is the first to provide useful information for uncovering the regulatory networks of miRNAs in basal gymnosperm G. biloba ovules. small RNAÂ sequencing in ovules of G. biloba
2016-02-12 | E-GEOD-74024 | biostudies-arrayexpress