Arabidopsis thaliana
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA137341 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:We report the identification of parent-of-origin specific gene expression in Arabidopsis seeds. F1 hybrid seeds were generated by reciprocally crossing Arabidopsis accessions Col-0 and Bur-0. Seeds were harvested at 4 DAP and total RNA was isolated and analyzed by deep sequencing. Overall identification of parent-of-origin-allelic expression by analysis of SNP distribution
2011-04-30 | E-GEOD-27292 | biostudies-arrayexpress
Project description:This SuperSeries is composed of the following subset Series: GSE20005: Parent-of-origin effects in seeds of Arabidopsis thaliana: Affymetrix GSE20006: Parent-of-origin effects in seeds of Arabidopsis thaliana: Agilent Refer to individual Series
2010-08-26 | E-GEOD-20007 | biostudies-arrayexpress
Project description:Parent-of-origin effects in seeds of Arabidopsis thaliana: Affymetrix
| PRJNA129765 | ENA
Project description:Parent-of-origin effects in seeds of Arabidopsis thaliana: Agilent
| PRJNA129767 | ENA
Project description:High resolution NO3 response of Arabidopsis Roots
| PRJNA124307 | ENA
Project description:Desiccation Tolerance of Arabidopsis thaliana seeds
| PRJNA306014 | ENA
Project description:Expression data of germinating Arabidopsis seeds
| PRJNA143719 | ENA
Project description:High throughput Illumina sequencing of poly-A selected RNA from Arabidopsis Col and Ler reciprocal F1 hybrid embryo and endosperm tissue isolated at 6-7 days after pollination to identify imprinted genes. Examination of parent-of-origin specific and total gene expression in seed tissues.
2011-07-18 | E-GEOD-30511 | biostudies-arrayexpress
Project description:Multiple regulatory layers influence allele-specific expression (ASE), particularly through sequence-dependent and parent-of-origin-dependent mechanisms at the transcriptional level. However, little is known about allele-specific gene regulation at the post-transcriptional level. Here, we conduct transcriptome-wide analysis of allele-specific m6A in mice. Using early postnatal cerebellum and cerebrum samples from reciprocal crosses of two divergent mouse strains, we employed quantitative m6A assays to measure allelic differences in m6A at single-base resolution. Our study reveals widespread sequence-dependent allelic imbalance in m6A methylation, identifying thousands of allele-specific m6A (ASm6A) sites with statistically significant and reproducible allelic methylation differences across diverse samples. We find evidence of potential cis-regulatory variants within 50-nt flanking regions of these ASm6A sites, with the highest enrichment at the motif positions. Intriguingly, we detect parental effects on allelic methylation across m6A sites exhibiting parent-of-origin-dependent ASE. For both sequence- and parent-of-origin-dependent allelic m6A methylation, we observe opposing allelic preferences between methylation and expression, suggesting a potential role of ASm6A in regulating ASE through negative effects on gene expression. Overall, our findings reveal that both cis-acting and parent-of-origin effects influence ASm6A, offering new insights into post-transcriptional mechanisms of ASE regulation.
2024-04-26 | GSE265978 | GEO
Project description:Multiple regulatory layers influence allele-specific expression (ASE), particularly through sequence-dependent and parent-of-origin-dependent mechanisms at the transcriptional level. However, little is known about allele-specific gene regulation at the post-transcriptional level. Here, we conduct transcriptome-wide analysis of allele-specific m6A in mice. Using early postnatal cerebellum and cerebrum samples from reciprocal crosses of two divergent mouse strains, we employed quantitative m6A assays to measure allelic differences in m6A at single-base resolution. Our study reveals widespread sequence-dependent allelic imbalance in m6A methylation, identifying thousands of allele-specific m6A (ASm6A) sites with statistically significant and reproducible allelic methylation differences across diverse samples. We find evidence of potential cis-regulatory variants within 50-nt flanking regions of these ASm6A sites, with the highest enrichment at the motif positions. Intriguingly, we detect parental effects on allelic methylation across m6A sites exhibiting parent-of-origin-dependent ASE. For both sequence- and parent-of-origin-dependent allelic m6A methylation, we observe opposing allelic preferences between methylation and expression, suggesting a potential role of ASm6A in regulating ASE through negative effects on gene expression. Overall, our findings reveal that both cis-acting and parent-of-origin effects influence ASm6A, offering new insights into post-transcriptional mechanisms of ASE regulation.
2024-04-26 | GSE265977 | GEO