Ontology highlight
ABSTRACT:
PROVIDER: PRJNA875077 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR21350419_1.fastq.gz | Fastqsanger.gz | |||
| SRR21350419_2.fastq.gz | Fastqsanger.gz | |||
| SRR21350420_1.fastq.gz | Fastqsanger.gz | |||
| SRR21350420_2.fastq.gz | Fastqsanger.gz | |||
| SRR21350421_1.fastq.gz | Fastqsanger.gz |
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Project description:An in vivo and in vitro potato tuber development gene expression study. Keywords: Developmental stage analysis, time course
2007-07-18 | GSE5360 | GEO
Project description:The periderm is a protective barrier crucial for land plants survival, but genetic factors involved in its regulation are fairly unknown. In a previous transcriptomic approach in the cork oak periderm (Quercus suber) we identified a RS2-INTERACTING KH PROTEIN (RIK) homolog, of unknown function and with a K homology (KH)-domain RNA-binding protein, as a regulatory candidate gene in the periderm. To gain insight into the function of RIK in periderm, the potato (Solanum tuberosum) tuber periderm was used as a model. The StRIK transcript profile showed ubiquitous accumulation in all vegetative tissues analyzed, including periderm and other suberized tissues such as root and wound-healing tissues. Downregulation of StRIK in potato by RNA interference (StRIK-RNAi) did not show evident effects in tuber periderm anatomy but unexpectedly unlike Wild type, the transgenic plants flowered. Nevertheless, the periderm of StRIK-RNAi lines did show altered expression of genes associated with RNA metabolism, stress and signaling, mirroring the biological processes found enriched within the in silico co-expression network of the Arabidopsis ortholog. Altogether those findings suggest that the potato StRIK might play roles in RNA maturation and stress response throughout diverse plant developmental processes such as flowering and periderm formation.
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Project description:Wound healing process after TBI in zebrafish: time course (zebrafish)
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Project description:To delineate the role of microRNAs in the site-specific injury response, we compared the microRNAome of skin and oral mucosa both at baseline and throughout the time course of wound healing.
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Project description:The mechanism of cardiomyocyte prliferation and migration after ventricular resection is a complex and dynamic process. To resolve this, we chose the zebrafish model organism for studying post-injury heart regeneration and wound healing progress via systems biology approach. Transcriptome microarray data and histological analysis of injured fish were sampled at different time points during recovery process. Time-course microarray data following wound healing of zebrafish were obatined. From this set of data, we constructed two intracellular protein–protein interaction (PPI) networks to provide insights into the ventricular resection wound healing mechanism.
2018-04-02 | GSE72348 | GEO
Project description:For many potato cultivars, tuber yield is optimal at average day time temperatures in the range of 14-22 ⁰C. Further rises in ambient temperature can reduce or completely inhibit potato tuber production, with damaging consequences for both producer and consumer. In our previous work we observed that the steady-state expression level of the core circadian clock gene, TIMING OF CAB EXPRESSION 1 (TOC1), in potato tubers increased at moderately elevated temperature, whereas expression of the tuberisation signal gene StSP6A decreased along with tuber yield. In this study we investigated the potential roles of StTOC1 in linking environmental signalling and potato tuberisation. We show that transgenic lines with decreased expression of StTOC1 exhibit enhanced StSP6A transcript levels in tuberising stolons, and show changes in gene expression consistent with elevated tuber sink strength.
2019-09-02 | E-MTAB-7443 | biostudies-arrayexpress
Project description:Wound healing process after ventricular resection in zebrafish: time course (zebrafish)
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Project description:The interaction between neurogenesis and angiogenesis after traumatic brain injury is a complex and dynamic process. To resolve this, we chose the zebrafish model organism for studying brain wound healing via systems biology approach. Transcriptome microarray data and histological analysis of injured fish were sampled at different time points during recovery process. Time-course microarray data following wound healing of zebrafish were obtained. From this set of data, we constructed two intracellular protein–protein interaction (PPI) networks for the traumatic brain injury healing mechanism.
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Project description:We analyzed the transcriptome change during photoperiodic regulation of potato tuber formation
2014-03-20 | GSE45008 | GEO
Project description:Purpose: MicroRNAs (miRNAs) are ubiquitous components of endogenous plant transcriptome. miRNAs are small, single-stranded and ~21 nt long RNAs which regulate gene expression at the post-transcriptional level and are known to play essential roles in various aspects of plant development and growth. Previously, a number of miRNAs have been identified in potato through in silico analysis and deep sequencing approach. However, identification of miRNAs through deep sequencing approach was limited to a few tissue types and developmental stages. This study reports the identification and characterization of potato miRNAs in three different vegetative tissues and four stages of tuber development by high throughput sequencing. Results: Small RNA libraries were constructed from leaf, stem, root and four early developmental stages of tuberization and subjected to deep sequencing, followed by bioinformatics analysis. A total of 89 conserved miRNAs (belonging to 33 families), 147 potato-specific miRNAs (with star sequence) and 112 candidate potato-specific miRNAs (without star sequence) were identified. The digital expression profiling based on TPM (Transcripts Per Million) and qRT-PCR analysis of conserved and potato-specific miRNAs revealed that some of the miRNAs showed tissue specific expression (leaf, stem and root) while a few demonstrated tuberization stage-specific expressions. Targets were predicted for identified conserved and potato-specific miRNAs, and predicted targets of four conserved miRNAs, miR160, miR164, miR172 and miR171, which are ARF16 (Auxin Response Factor 16), NAM (NO APICAL MERISTEM), RAP1 (Relative to APETALA2 1) and HAIRY MERISTEM (HAM) respectively, were experimentally validated using 5M-bM-^@M-2RLM-RACE (RNA ligase mediated rapid amplification of cDNA ends). Gene ontology (GO) analysis for potato-specific miRNAs was also performed to predict their potential biological functions. Conclusions: We report a comprehensive study of potato miRNAs at genome-wide level by high-throughput sequencing and demonstrate that these miRNAs have tissue and/or developmental stage specific expression profile. Also, predicted targets of conserved miRNAs were experimentally confirmed for the first time in potato. Our findings indicate the existence of extensive and complex small RNA population in this crop and suggest their important role in pathways involved in diverse biological processes, including tuber developmental process. Total seven (Leaf, Root, Stem, Potato Tuber stage 0(PT0),Potato Tuber stage 1(PT1),Potato Tuber stage 2(PT2),Potato Tuber stage 3(PT3) ) small RNA libraries were consctructed and sequenced by deep sequencing using Illumina GAIIx.
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