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27 results for “Physcomitrella patens”
The loss of SMG1 causes defects in quality control pathways in Physcomitrella patens
<p>Nonsense-mediated mRNA decay (NMD) is important for both RNA quality control and gene regulation. NMD targets aberrant mRNA transcripts for decay and also directly influences the abundance of specific, non-aberrant transcripts in a wide range of eukaryotes. In animals, the PIK kinase, SMG1, plays an essential role in NMD, by phosphorylating the core NMD effector, UPF1. Despite being absent from the genome of the model plant, <em>Arabidopsis thaliana</em>, SMG1 is ubiquitous throughout the plant kingdom. Here we utilize RNA-seq to reveal the full range of processes involving <em>SMG1</em> in plants. In NMD-compromised, <em>smg1</em> mutant moss, 30% of multi-isoform genes produce NMD targeted transcript isoforms. Taking a machine learning approach, we show that an exon-exon junction downstream of a stop codon acts as the major feature to target transcripts to NMD and that retained intron isoforms are underrepresented among NMD targets. Furthermore, we show that <em>SMG1</em> is involved in other quality control pathways, affecting DNA repair and the unfolded protein response, in addition to its role in mRNA quality control. <em>smg1</em> plants have increased susceptibility to DNA damage, but increased tolerance to unfolded protein inducing agents. The involvement of SMG1 in RNA, DNA and protein quality control has major implications for the study of these processes in plants.</p>
Fig. 3 in Lipoxygenase pathway in model bryophytes: 12-oxo-9(13),15-phytodienoic acid is a predominant oxylipin in Physcomitrella patens
Fig. 3. The proposed pathways of biosynthesis of major cyclopentenones in P. patens and M. polymorpha. β oxn, β oxidation.
Fig. 2 in Lipoxygenase pathway in model bryophytes: 12-oxo-9(13),15-phytodienoic acid is a predominant oxylipin in Physcomitrella patens
Fig. 2. The electron impact mass spectra and fragmentation schemes (insets) for products 1 (A), 2 (B), and 3 (C).
Fig. 1 in Lipoxygenase pathway in model bryophytes: 12-oxo-9(13),15-phytodienoic acid is a predominant oxylipin in Physcomitrella patens
Fig. 1. The GC-MS oxylipin profiles of P. patens (A, B) and M. polymorpha (C, D). A and C, the profiles of endogenous oxylipins (Me/TMSi), the mixed ion current chromatograms (m/z 149, 177, 210, 225, 238, 278, 306, 308, 311). B and D, profiles of oxylipins (Me/TMSi) biosynthesized upon the in vitro preincubations of P. patens and M. polymorpha with α linolenic acid. The experimental details are described under "Experimental".
Mutating DDM1 in Physcomitrella patens disrupts DNA methylation with a minute effect on transposon regulation and development
GEO Series GSE198693. Physcomitrium patens. 8 samples. Type: Methylation profiling by high throughput sequencing; Expression profiling by high throughput sequencing.
Genome-wide transcriptomic analysis of the sporophyte of the moss Physcomitrella patens
GEO Series GSE32928. Physcomitrium patens. 8 samples. Type: Expression profiling by array.
Small RNA genes of Physcomitrella patens
GEO Series GSE44900. Physcomitrium patens. 10 samples. Type: Non-coding RNA profiling by high throughput sequencing.
small RNA-seq of Physcomitrella patens small RNA mutants
GEO Series GSE51419. Physcomitrium patens. 30 samples. Type: Non-coding RNA profiling by high throughput sequencing.
Transcriptome of Protoplasts Reprogrammed into Stem Cells in Physcomitrella patens
GEO Series GSE36117. Physcomitrium patens. 4 samples. Type: Expression profiling by high throughput sequencing.
Dynamics of the transcriptome response to heat in the moss, Physcomitrella Patens
GEO Series GSE138467. Physcomitrium patens. 24 samples. Type: Expression profiling by high throughput sequencing.
Mutating DDM1 in Physcomitrella patens disrupts DNA methylation with a minute effect on transposon regulation and development [Bisulfite-seq]
GEO Series GSE197592. Physcomitrium patens. 2 samples. Type: Methylation profiling by high throughput sequencing.
Mutating DDM1 in Physcomitrella patens disrupts DNA methylation with a minute effect on transposon regulation and development [RNA-seq]
GEO Series GSE198691. Physcomitrium patens. 6 samples. Type: Expression profiling by high throughput sequencing.
Transcriptome data (mRNA-seq) for Physcomitrella patens (Physcomitrium patens) wild type.
GEO Series GSE266910. Physcomitrium patens. 4 samples. Type: Expression profiling by high throughput sequencing.
Genome-wide transcriptome analysis of gametophyte development in Physcomitrella patens
GEO Series GSE33279. Physcomitrium patens. 6 samples. Type: Expression profiling by high throughput sequencing.
ChIP-seq of H3K4me1, H3K4me2, H3K4me3, H3K36me1, H3K36me2, and H3K36me3 for Physcomitrella patens (Physcomitrium patens).
GEO Series GSE266903. Physcomitrium patens. 14 samples. Type: Genome binding/occupancy profiling by high throughput sequencing.
Small RNAs from the moss Physcomitrella patens
GEO Series GSE5103. Physcomitrium patens. 3 samples. Type: Non-coding RNA profiling by high throughput sequencing.
The DNA damage response transcriptome of the moss Physcomitrella patens
GEO Series GSE25237. Physcomitrium patens. 2 samples. Type: Expression profiling by high throughput sequencing.
High throughput sequencing data for Oryza sativa, Chlamydomonas reinhardtii, and Physcomitrella patens
GEO Series GSE266911. Physcomitrium patens; Chlamydomonas reinhardtii; Oryza sativa. 196 samples. Type: Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing.
Genome-wide transcriptome analysis during dehydration and recovery in gametophores of Physcomitrella patens
GEO Series GSE66467. Physcomitrium patens. 15 samples. Type: Expression profiling by high throughput sequencing.
Genome-wide small RNAtranscriptome analysis during dehydration and recovery in gametophores of Physcomitrella patens
GEO Series GSE66589. Physcomitrium patens. 10 samples. Type: Non-coding RNA profiling by high throughput sequencing.
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Allen Brain Atlas
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DANDI Archive for NWB datasets
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International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.