Drosophila melanogaster
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA380942 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR5388800.fastq.gz | Fastqsanger.gz | |||
| SRR5388801.fastq.gz | Fastqsanger.gz | |||
| SRR5388802.fastq.gz | Fastqsanger.gz | |||
| SRR5388803.fastq.gz | Fastqsanger.gz | |||
| SRR5388794.fastq.gz | Fastqsanger.gz |
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Project description:F2 progeny of AKHR mutant and obese parents and controls, 10-11 days old adults
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Project description:Transgenerational effects of parental metabolic state have been shown, but the mechanism is still unclear. Here we present transcriptome sequencing data from AKHR heterozygous F1 progeny, either from obese maternal or paternal parents, compared to genetically matched heterozygous controls or to wild-type controls
2017-06-01 | GSE97201 | GEO
Project description:<p><strong>INTRODUCTION:</strong> Larvae of the invasive emerald ash borer [EAB, <em>Agrilus planipennis</em> Fairmaire (Coleoptera: Buprestidae)], kill over 99% of green ash (<em>Fraxinus pennsylvanica</em> Marshall) trees they infest, yet a small percentage of green ash (“lingering ash”) survive years of heavy EAB attack. In the face of an ongoing invasion that threatens multiple North American <em>Fraxinus</em> species with extinction, any evidence for reproducible defensive responses in the native species merits investigation.</p><p><strong>METHODS: </strong>We evaluated the capacity of 3 families of green ash F1 progeny to kill EAB larvae when challenged in greenhouse studies by infestation with a uniform density of EAB eggs followed by dissection 8 weeks post-infestation and comparison of the host metabolomic profiles.</p><p><strong>RESULTS:</strong> The mean proportions of host-killed larvae in the 2 families of F1 progeny from lingering ash parents were significantly higher than that of host-killed larvae in the family of F1 progeny from susceptible ash parents (<em>p</em> < 0.001). Untargeted metabolomics comparing F1 progeny in the quartile with the highest percent host-killed larvae (HHK) to F1 progeny in the quartile with the lowest percent host-killed larvae (LHK) and to the uninfested F1 progeny within each family revealed evidence for induced biochemical responses to EAB. Infested trees produced significantly higher levels of select secoiridoids than uninfested trees, and LHK progeny produced significantly higher levels of select secoiridoids than the HHK progeny. HHK progeny produced significantly higher abundances of 3 metabolites annotated as aromatic alkaloids than the LHK and uninfested individuals.</p><p><strong>DISCUSSION: </strong>Based on these results, we hypothesize that green ash responds to EAB infestation. However, only certain trees have the genetic capacity to tailor a response that kills enough EAB larvae to prevent lethal damage to the vascular system. Rigorous tests of this hypothesis will require 15–20 years of additional crossing, phenotyping, and omics analyses. The results of this investigation will encourage the establishment and continuation of breeding programs that, in concert with biocontrol and management, could provide trees that slow, if not halt, the decimation of the <em>Fraxinus</em> gene pool. At the same time, ongoing work on host-insect interaction will contribute to our understanding of how forest trees recognize and defend themselves against phloem-feeding insects.</p>
2024-02-08 | MTBLS7999 | MetaboLights
Project description:Heterosis occurs where F1 offspring display superior characteristics to the parents. Heterosis is usually considered to result from crosses of genetically distinct (e.g. homozygous inbred) parents producing heterozygous F1 offspring. Most mechanistic models for heterosis require genetically heterozygous F1 hybrid offspring harbouring allelic diversity. Epigenetic or dosage models for heterosis could allow for heterosis effects in F1 offspring that display no allelic diversity with their parents. Reciprocal inter-ploidy crosses between diploid (2x) and tetraploid (4x) lines in the same genetic background generates genetically identical F1 triploids (3x). Such reciprocal F1 triploids differ according to whether the additional chromosome set is either maternally (maternal excess) or paternally inherited (paternal excess). Biomass accumulation and abiotic stress tolerance between the parental (2x and 4x) and reciprocal F1 triploid (3x) offspring of Arabidopsis thaliana accession C24 reveals a strong parental genome-dosage induced heterosis in the paternal-excess triploid F1 plants. In these F1 triploids, the circadian clock related genes CCA1 and TOC1, and the growth factors PIF4 and PIF5, display different expression levels compared to the non-heterotic maternal excess F1 triploid siblings. Whole transcriptome profiling reveals a paternal genome dosage effect on gene expression levels with strong enrichment for dysregulated abiotic stress-related genes in the paternal excess F1 triploids. This study demonstrates that heterosis can be triggered without allelic diversity in F1 triploid plants. Heterosis without heterozygosity in plants can be induced via an epigenetic “chromosome imprinting” like parental genome dosage effect requiring paternal transmission of an additional chromosome set 4 or 5 biological replicates per ploidy level, each replicate being a single two weeks old seedling
2014-08-01 | E-GEOD-52885 | biostudies-arrayexpress
Project description:Heterosis occurs where F1 offspring display superior characteristics to the parents. Heterosis is usually considered to result from crosses of genetically distinct (e.g. homozygous inbred) parents producing heterozygous F1 offspring. Most mechanistic models for heterosis require genetically heterozygous F1 hybrid offspring harbouring allelic diversity. Epigenetic or dosage models for heterosis could allow for heterosis effects in F1 offspring that display no allelic diversity with their parents. Reciprocal inter-ploidy crosses between diploid (2x) and tetraploid (4x) lines in the same genetic background generates genetically identical F1 triploids (3x). Such reciprocal F1 triploids differ according to whether the additional chromosome set is either maternally (maternal excess) or paternally inherited (paternal excess). Biomass accumulation and abiotic stress tolerance between the parental (2x and 4x) and reciprocal F1 triploid (3x) offspring of Arabidopsis thaliana accession C24 reveals a strong parental genome-dosage induced heterosis in the paternal-excess triploid F1 plants. In these F1 triploids, the circadian clock related genes CCA1 and TOC1, and the growth factors PIF4 and PIF5, display different expression levels compared to the non-heterotic maternal excess F1 triploid siblings. Whole transcriptome profiling reveals a paternal genome dosage effect on gene expression levels with strong enrichment for dysregulated abiotic stress-related genes in the paternal excess F1 triploids. This study demonstrates that heterosis can be triggered without allelic diversity in F1 triploid plants. Heterosis without heterozygosity in plants can be induced via an epigenetic “chromosome imprinting” like parental genome dosage effect requiring paternal transmission of an additional chromosome set
2014-08-01 | GSE52885 | GEO
Project description:Purpose: To investigate the effects of DCHP expoure on F1 male hepatic metabolic disorders Methods: 8 week male WT mice were exposed to DCHP by oral gavage for 4 weeks, 3 week old F1 male mice were fed with HFD for 9 weeks, glucose and insulin tolerant tests were performed at 10-11 week old, liver RNA was isolated for further transcriptome analysis Results: Mice from DCHP exposure sires displayed glucose/insulin resistant phenotype, together with upregulation in inflammatoy related genes in the liver
2023-05-24 | GSE215806 | GEO
Project description:In order to investigate transcriptomic mechanisms underlying radiation exposure, we exposed zebrafish (~6 month old) to 8.7 mGy/h of g-radiation (5.2 Gy total dose) during gametogenesis for 27 days. F1 offspring from exposed parents were sampled at 5.5 hpf (late blastula/early gastrula) one year after parental exposure, for small RNA sequence analysis to determine changes in the sncRNA expression profile. Pairwise comparison between F1 generation from exposed (F1-γ), and control (F1-C) parents, revealed several classes of sncRNAs and one class of lncRNA differentially expressed. Overall, 22 miRNAs, 11 piRNA clusters, 19 snRNAs, and 21 lincRNA were found differentially expressed. When linking the DEmiRs to our previously published mRNA data, a total of 672 differentially expressed mRNAs could be linked to the DEmiRs, of which 380 followed the canonical inverse relation in miRNA-mRNA interaction. Pathway analysis revealed these 380 mRNAs involved in insulin receptor, NFkB and PTEN signaling, linking to apoptosis and cancers. The 84.2% of differentially expressed snRNAs were down-regulated in the F1-γ group, 68.8% of which were U1 and U2 snRNAs. In addition, 45% of differentially expressed DEpiRNA clusters were found associated to 9 TEs (LTR, LINE, and TIR) (p=0.0024). DEpiRNA clusters were expressed from the opposite strand of the associated TEs, indicating expression of DEpiRNAs in response to activation of TEs. Finally, 66.7% and 33.3% of lincRNAs in F1-γ were down- and up-regulated respectively. The cancer and development related lincRNAs malat-1 was found among the most down-regulated genes, denoting a link between lincRNAs expression and altered phenotypes reported previously in our parallel studies.
2021-02-09 | GSE152189 | GEO
Project description:We analyzed samples from two affected brothers (Affected 3 and 4) and their two affected female cousins (Affected 7 and 9) homozygous for the MLASA ? associated C656T mutation in the PUS1 gene; four parents ? heterozygous carriers of the C656T mutation (Parents 1, 2, 5, 6), and an unaffected female carrying wild-type genotype at the PUS1 gene (Control 8). In addition, two females and one male with normal hearing from Arab-Israeli family with nonsyndromic deafness carrying wild-type PUS1 sequence were used as controls (Controls 10, 11, 12). Keywords: Comparison of genome-wide expression in cell lines of patients and controls
2006-11-29 | GSE6374 | GEO
Project description:In Hymenoptera, sex is determined by a single-locus complementary sex determining system (sl-CSD). Males are normally haploid (hemizygous at the sl-CSD locus) but if the genotype of the sl-CSD locus is homozygous, they develop into diploid males. Here, we study the effects of ploidy and the sl-CSD-locus genotype by comparing gene expression differences between haploid males, diploid males and virgin queens at three developmental stages, pupae, 1 day and 11 days after eclosion. Keywords: diploid males, sl-CSD, ploidy-spcific gene, sex-specific gene, doublesex, sex-biased gene Six-condition experiment: haploid male pupae, diploid male pupae, queen pupae, 1-day-old haploid male adults, 1-day-old diploid male adults, 1-day-old queen adults (accession number GSM1031732 - GSM1031734, GSM1031737 - GSM1031738, GSM1031740 - GSM1031742, GSM1031745 - GSM1031746; reprocessed for this study), 11-day-old haploid male adults, 11-day-old diploid male adults, 11-day-old queen adults (accession number GSM1031748 - GSM1031750, GSM1031753 - GSM1031754, GSM1031756 - GSM1031758, GSM1031761 - GSM1031762; reprocessed for this study). Biological replicates: 5 colonies (x 2 genotypes for each colony). Samples were labeled with Cy3 and were compared to the same common reference RNA labeled with Cy5.
2012-12-06 | E-GEOD-42494 | biostudies-arrayexpress
Project description:In Hymenoptera, sex is determined by a single-locus complementary sex determining system (sl-CSD). Males are normally haploid (hemizygous at the sl-CSD locus) but if the genotype of the sl-CSD locus is homozygous, they develop into diploid males. Here, we study the effects of ploidy and the sl-CSD-locus genotype by comparing gene expression differences between haploid males, diploid males and virgin queens at three developmental stages, pupae, 1 day and 11 days after eclosion. Keywords: diploid males, sl-CSD, ploidy-spcific gene, sex-specific gene, doublesex, sex-biased gene Six-condition experiment: haploid male pupae, diploid male pupae, queen pupae, 1-day-old haploid male adults, 1-day-old diploid male adults, 1-day-old queen adults (accession number GSM1031732 - GSM1031734, GSM1031737 - GSM1031738, GSM1031740 - GSM1031742, GSM1031745 - GSM1031746; reprocessed for this study), 11-day-old haploid male adults, 11-day-old diploid male adults, 11-day-old queen adults (accession number GSM1031748 - GSM1031750, GSM1031753 - GSM1031754, GSM1031756 - GSM1031758, GSM1031761 - GSM1031762; reprocessed for this study). Biological replicates: 5 colonies (x 2 genotypes for each colony). Samples were labeled with Cy3 and were compared to the same common reference RNA labeled with Cy5.
2012-12-06 | E-GEOD-42785 | biostudies-arrayexpress