Ontology highlight
ABSTRACT:
PROVIDER: PRJEB23100 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Whole-exome sequencing for the detection of SNPs and indels
| PRJEB44814 | ENA
Project description:Mechanisms by which non-coding genetic variation influences gene expression remain only partially understood but are considered to be major determinants of phenotypic diversity and disease risk. To investigate these mechanisms with respect to signal-dependent gene expression, we evaluated effects of > 50 million SNPs and InDels provided by five inbred strains of mice on the responses of macrophages to the anti-inflammatory cytokine IL-4. Remarkably, of the > 600 genes observed to be induced >2-fold across the five strains after 24 hours of IL-4 treatment, only 26 genes reached this threshold in all strains and more than half of the induced genes were observed in only a single strain. By examining the effects of SNPs and InDels on transcription factor binding and enhancer activity under basal and IL-4 treatment conditions, we identified dominant collaborative roles of the signal-dependent transcription factors (SDTFs) STAT6, PPARg and EGR2 in driving late enhancer activation that were dependent on general macrophage lineage determining factors (LDTFs). As expected, SNPs and InDels that affected the relative affinities of SDTFs primarily influenced the ability of enhancers with similar basal activities to respond to IL-4. In contrast, SNPs and InDels that altered the relative binding affinities of macrophage LDTFs had divergent effects on basal and activated enhancer activity. Variants resulting in strong reductions in LDTF binding affinity were associated with low basal enhancer activity and failure to recruit SDTFs, whereas variants that increased LDTF binding affinities were associated with constitutively high levels of enhancer activity and a blunted response to SDTF recruitment. Together, these studies reveal mechanisms by which noncoding genetic variation influences absolute levels of enhancer activity and their dynamic responses to IL-4, thereby contributing to strain-specific patterns of gene expression and phenotypic diversity.
2021-06-19 | GSE159629 | GEO
Project description:RNA-seq was performed in order to identify qualitative variation of transcripts in clf-29 lhp1-4 compared to WT, including SNPS, indels, splicing fidelity
2022-09-19 | E-MTAB-11263 | biostudies-arrayexpress
Project description:Domesticated animals all show the same patterns regarding phenotypic traits and behaviour, collectively known as the domestic phenotype. All domestic chicken come from the red junglefowl. By keeping three separate populations of junglefowl and selecting for high, low or intermediate fear responses towards humans, the goal is to in the low fear group start to unlock domestic phenotypes.
2016-12-05 | E-MTAB-4113 | biostudies-arrayexpress
Project description:To increase our understanding of the genes involved in flowering in citrus, we performed genome resequencing of an early flowering trifoliate orange mutant (Poncirus trifoliata L. Raf.) and its wild type. At the genome level, 3,932,628 single nucleotide polymorphisms (SNPs), 1,293,383 insertion/deletion polymorphisms (InDels), and 52,135 structural variations (SVs) were identified between the mutant and its wild type based on the citrus reference genome. Based on integrative analysis of resequencing and transcriptome analysis, 233,998 SNPs and 75,836 InDels were also identified between the mutant and its wild type at the transcriptional level. Also, 272 citrus homologous flowering-time transcripts containing genetic variation were also identified. GO and KEGG annotation revealed that the transcripts containing the mutant and the wild-type-specific InDel were involved in diverse biological processes and molecular function. Among these transcripts, there were 131 transcripts that were expressed differently in the two genotypes. When 268 selected InDels were tested on 32 genotypes of the three generas of Rutaceae for the genetic diversity assessment, these InDel-based markers showed high transferability. This work provides important information that will allow a better understanding of the citrus genome and that will be helpful for dissecting the genetic basis of important traits in citrus.
2016-05-05 | GSE78810 | GEO
Project description:Domesticated animals all show the same patterns regarding phenotypic traits and behaviour, collectively known as the domestic phenotype. All domestic chicken come from the red junglefowl. By keeping three separate populations of junglefowl and selecting for high, low or intermediate fear responses towards humans, the goal is to in the low fear group start to unlock domestic phenotypes. For this study, tissue from the cerebral hemisphere was used.
2017-02-28 | E-MTAB-4741 | biostudies-arrayexpress
Project description:Background: This study aimed to explore potential tobramycin-resistant mutagenesis of Escherichia coli (E. coli) strains after spaceflight. Methods: A spaceflight-induced mutagenesis of multi-drug resistant E.coli strain (T1_13) on the outer space for 64 days (ST5), and a ground laboratory with the same conditions (GT5) were conducted. Both whole-genome sequencing and RNA-sequencing were performed. Results: A total of 75 SNPs and 20 InDels were found to be associated with the resistance mechanism. Compared to T1_13, 1242 genes were differentially expressed in more than 20 of 38 tobramycin-resistant E. coli isolates while not in GT5. Function annotation of these SNPs/InDels related genes and differentially expressed genes was performed. Conclusion: This study provided clues for potential tobramycin-resistant spaceflight-induced mutagenesis of E. coli.
2019-12-13 | GSE123795 | GEO
Project description:We performed whole genome re-sequencing to reveal the comprehensive genetic variation of the fruit development between kumquat (Fortunella japonica) and Clementine mandarin. Total 5,865,235 single-nucleotide polymorphisms (SNPs) and 414,447 insertion/deletion (InDels) were identified in the two citrus species. Meanwhile, a total of 640,801 SNPs and 20,733 InDels were identified based on integrative analysis of genome and transcriptome of fruit. The variation feature, genomic distribution, functional effect and other characteristics of these genetic variation were explored. Total 1,090 differentially expressed genes (DEGs) were found during fruit development process of kumquat and Clementine mandarin by RNA-sequencing. Gene Ontology revealed that these genes were involved in various molecular functional and biological processes. Meanwhile, the genetic variation of 939 DEGs and 74 multiple fruit development pathway genes from previous reported were also identified. In addition, a global survey of genes splicing events identified 24,237 specific alternative splicing (AS) events in the two citrus species and showed that intron retention is the most prevalent pattern of alternative splicing.
2018-02-01 | GSE107812 | GEO