Ontology highlight
ABSTRACT:
PROVIDER: PRJNA270761 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR2103540.fastq.gz | Fastqsanger.gz | |||
| SRR2102701.fastq.gz | Fastqsanger.gz | |||
| SRR2103561.fastq.gz | Fastqsanger.gz | |||
| SRR2102472.fastq.gz | Fastqsanger.gz | |||
| SRR2102702.fastq.gz | Fastqsanger.gz |
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Project description:Transposable elements (TEs) are ubiquitous in genomes. Many of these TEs remain active and are an important fraction of the transcriptomes with potential effects on the host genomes. The functional impact of TEs is well known for model organisms, however, in transcriptomes analysis of non-model organisms, this information is ignored due to the difficulty in identifying and quantifying TEs. Here we develop ExplorATE, a pipeline that allows the identification and quantification of active TEs in non-model organisms that can be easily implemented within the R environment. Based on simulated data, we show that our pipeline accurately identifies and quantifies TEs, over-performing the commonly used tools in model organisms. We show the implementation of ExplorATE using real data for RNA-seq samples from different tissues (liver, ovary, and brain) of Liolaemus parthenos, the only parthenogenetic lizard known to date in the entire clade Iguanidae (pleurodonta). Our results show that a significant fraction of the transcriptome contains repeats, however many of these are co-expressed with genes. The implementation of our pipeline in real data allowed the identification of the most abundant transposon families in each tissue. The ERV2, CR1, and SINE3 families were particularly abundant in the liver. A test data set is provided in the ExplorATE package.
2021-07-30 | GSE173261 | GEO
Project description:Studies in model organisms suggest that aged cells can be functionally rejuvenated, but whether this concept applies to human skin is unclear. Here we apply deep sequencing of RNA 3' ends ("3-seq") to discover the gene expression program associated with human photoaging and intrinsic skin aging (collectively termed "skin aging") and the impact of broadband light (BBL) treatment. We find that skin aging was associated with the significantly altered expression level of 2,265 coding and noncoding RNAs, of which 1,293 became "rejuvenated" after BBL treatment, i.e. more similar in expression level of youthful skin. Rejuvenated genes (RGs) included several known key regulators of organismal longevity and their proximal long non-coding RNAs. Skin aging is not associated with systematic changes in 3' end mRNA processing. Hence, BBL treatment can restore the gene expression pattern of photoaged and intrinsically aged human skin to resemble young skin. In addition, our data reveals a novel set of targets that may lead to new insights into the human skin aging process. Examination of broadband light treated and untreated human skin transcriptomes of 5 women aged 50 years or more. They were compared to the skin transcriptomes of 5 young women aged 30 years or less.
2012-07-30 | E-GEOD-39170 | biostudies-arrayexpress
Project description:Sensing and responding to light provides organisms an adaptive advantage, in part by altering gene expression. The complement of light-activated genes in model organisms is largely known, and some of the mechanisms by which proteins modulate the light response are likewise well defined. However, how light alters post translation modifications to chromatin and how changes in chromatin facilitates and/or inhibit changes in gene expression has not been examined in depth. Nor is know how specific chromatin-modifiers assist in modulating the light response or the extent of the defects in strains lacking certain chromatin modifications. Using a combination of RNA-seq and ChIP-seq we examines H3K4 methylation and H3K9 methylation and found paradigm changing properties beyond the consensus that H3K4me3 is a solely a mark for activation and H3K9me3 marks silent heterochromatin domains.
2018-11-30 | GSE121333 | GEO
Project description:Despite the large amounts of transcriptome data generated for many non-model organisms, there has been a much lesser uptake of individual genomic sequencing for detecting SNPs and determining haplotypes in these species. Transcriptome data represents a source of variant information, specifically for coding DNA, however there is little information on the accuracy, coverage and limitations of using transcriptomic data for the identification of single nucleotide polymorphisms (SNPs) in non-model organisms. To investigate this, we generated the first whole exome design for bovine using the Roche Nimblegen Developer system (Roche, USA) and used it to sequence and call SNPs from a lactating dairy cow model with genetically divergent fertility phenotypes (Fert+, n=8; Fert-, n=8). We compared these results to SNPs called from liver and muscle transcriptomes from the same animals. Our exome demonstrated 99.1% coverage of the target design of 56.7MB, whereas the transcriptomes only covered 60 and 54.5% of 44.2 and 42.8MB in liver and muscle respectively. We found that specificity of SNP detection in the transcriptome data is ~75% following basic hard-filtering, but could be increased marginally to ~80% by increasing the minimum threshold of reads covering a SNP, and number of samples in which it was found. Functional annotation of non-synonymous SNPs specific to both the high and low fertility phenotype identified immune response-related genes, supporting previous work that identified this process as key to the phenotype.
2015-10-08 | GSE62160 | GEO
Project description:Genomes and transcriptomes of non-model organisms can be analyzed using next-generation sequencing technologies, but de-novo sequencing and annotating a full eukaryotic genome is still challenging. So, -omics experimentation with non-model organisms requires a suite of technologies to obtain reliable results in a cost-effective manner. Here, a novel method for microarray-based genome analysis is presented which is especially suitable for non-model organisms. We show that it is useful for complementing regular aCGH analyses and for evaluating transcriptome next-generation sequencing reads. The principle of the method is straightforward: feature intensities obtained after hybridizing the test genome are compared with the feature intensities of a control hybridization. The control hybridization is performed with negative control probes (no targets in the control sample), and with positive control probes (with targets in the control sample). The method has in principle a resolution of a single probe and it does not depend on the structural information of a reference genome: the genomic ordering of probe targets is irrelevant. In a test, analyzing the genome content of a sequenced bacterial strain: Staphylococcus aureus MRSA252, this approach proved to be successful demonstrated by receiver operating characteristic area under the curve values larger than 0.9995.
2014-05-19 | GSE52121 | GEO
Project description:Genomes and transcriptomes of non-model organisms can be analyzed using next-generation sequencing technologies, but de-novo sequencing and annotating a full eukaryotic genome is still challenging. So, -omics experimentation with non-model organisms requires a suite of technologies to obtain reliable results in a cost-effective manner. Here, a novel method for microarray-based genome analysis is presented which is especially suitable for non-model organisms. We show that it is useful for complementing regular aCGH analyses and for evaluating transcriptome next-generation sequencing reads. The principle of the method is straightforward: feature intensities obtained after hybridizing the test genome are compared with the feature intensities of a control hybridization. The control hybridization is performed with negative control probes (no targets in the control sample), and with positive control probes (with targets in the control sample). The method has in principle a resolution of a single probe and it does not depend on the structural information of a reference genome: the genomic ordering of probe targets is irrelevant. In a test, analyzing the genome content of a sequenced bacterial strain: Staphylococcus aureus MRSA252, this approach proved to be successful demonstrated by receiver operating characteristic area under the curve values larger than 0.9995.
2014-05-19 | GSE51148 | GEO
Project description:Disruption of the circadian clock, which directs rhythmic expression of numerous genes, accelerates aging. To inquire how the circadian system protects organisms during aging, we compared circadian transcriptomes in heads of young and old Drosophila melanogaster. These data revealed a class of genes that adopt de novo rhythmicity during aging, termed "late life cyclers" (LLCs). We show that application of exogenous oxidative stress in young flies mimics aging by inducing robust, rhythmic LLC upregulation in a light- and CLOCK-dependent fashion. Additionally, we identified age-onset rhythmicity in some primary piRNA transcripts that overlap antisense transposable elements. To share our data, we developed a database for public viewing of graphical RNA-seq results for coding and non-coding RNAs in young and old flies. Taken together, our results suggest that aging organisms recruit the circadian system to launch a temporally coordinated defense to cope with their increasingly stressful cellular environments.
2017-01-14 | GSE81100 | GEO
Project description:MicroRNAs (miRNAs) are non-coding small RNAs that regulate gene expression at the post-transcriptional level. Several miRNAs are exclusively expressed in skeletal muscle and participate in the regulation of muscle differentiation by interacting with myogenic factors. These miRNAs can be found at high levels in the serum of patients and animal models for Duchenne muscular dystrophy, and which is expected to be useful as biomarkers for their clinical conditions. By miRNA microarray analysis, we identified miR-188 as a novel miRNA that is elevated in the serum of the muscular dystrophy dog model, CXMDJ. miR-188 was not muscle-specific miRNA, but its expression was up-regulated in skeletal muscles associated with muscle regeneration induced by cardiotoxin-injection in normal dogs and mice. Manipulation of miR-188 expression using antisense oligo and mimic oligo RNAs alters the mRNA expression of the myogenic regulatory factors, MRF4 and MEF2C. Searching for the direct target of miR-188 suggested that it could be MEF2-interacting transcription repressor (MITR). Our results suggest that miR-188 regulates myogenic factors targeting MITR during muscle differentiation and that it may serve as a serum biomarker reflecting skeletal muscle regeneration.
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Project description:Sensing and responding to light provides organisms an adaptive advantage, in part by altering gene expression. The complement of light-activated genes in model organisms is largely known, and some of the mechanisms by which proteins modulate the light response are likewise well defined. However, how light alters post translation modifications to chromatin and how changes in chromatin facilitates and/or inhibit changes in gene expression has not been examined in depth. Nor is know how specific chromatin-modifiers assist in modulating the light response or the extent of the defects in strains lacking certain chromatin modifications. Using a combination of RNA-seq and ChIP-seq we examines H3K4 methylation and H3K9 methylation and found paradigm changing properties beyond the consensus that H3K4me3 is a solely a mark for activation and H3K9me3 marks silent heterochromatin domains.
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Project description:Multiplexed ISSR genotyping by sequence (MIG-seq) with non-model organisms
| PRJDB3910 | ENA