Ontology highlight
ABSTRACT:
PROVIDER: PRJNA662041 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Iron-rich pelagic aggregates (iron snow) were collected directly onto silicate glass filters using an electronic water pump installed below the redoxcline. RNA was extracted and library preparation was done using the NEBNext Ultra II directional RNA library prep kit for Illumina. Data was demultiplied by GATC sequencing company and adaptor was trimmed by Trimgalore. After trimming, data was processed quality control by sickle and mRNA/rRNA sequences were sorted by SortmeRNA. mRNA sequences were blast against NCBI-non redundant protein database and the outputs were meganized in MEGAN to do functional analysis. rRNA sequences were further sorted against bacterial/archeal 16S rRNA, eukaryotic 18S rRNA and 10,000 rRNA sequences of bacterial 16S rRNA, eukaryotic 18S rRNA were subset to do taxonomy analysis.
2021-10-15 | E-MTAB-9686 | biostudies-arrayexpress
Project description:Sequencing the metatranscriptome can provide information about the response of organisms to varying environmental conditions. We present a methodology for obtaining random whole-community mRNA from a complex microbial assemblage using Pyrosequencing. The metatranscriptome had, with minimum contamination by ribosomal RNA, significant coverage of abundant transcripts, and included significantly more potentially novel proteins than in the metagenome. Keywords: metatranscriptome, mesocosm, ocean acidification
2008-02-08 | GSE10119 | GEO
Project description:16S+18S nanopore
| PRJEB68077 | ENA
Project description:The drought stress is one of key adverse environmental factors limiting plant growth and development, even threating global crop productivity in many arid and semi-arid regions. Drought stress usually causes huge economic losses for tobacco industries. Understanding how plants respond and adapt to the drought stress helps generate engineered plants with enhanced drought resistance. In this study, integrative analyses of multiple time point-related transcriptome and metabolome generated from K326 and its derived mutant 28 (M28) with contrasting drought tolerance. We found that dramatic changes of gene expression profiles between M28 and K326 before and after drought treatment.
2022-09-26 | GSE214048 | GEO
Project description:Chromatin remodeling and histone modifications are important for development and floral phase transition in plants. However, it is largely unknown whether and how these two epigenetic regulators coordinately regulate the important biological processes. Here, we identified three types of ISWI chromatin remodeling complexes in Arabidopsis thaliana. We found that ARID5, a subunit of a plant-specific ISWI complex, can regulate development and floral phase transition. The ARID-PHD dual domain cassette of ARID5 recognizes both the H3K4me3 histone mark and AT-rich DNA. We determined the ternary complex structure of the ARID5 ARID-PHD cassette with an H3K4me3 peptide and an AT-containing DNA. The H3K4me3 peptide is combinatorially recognized by the PHD and ARID domains, while the DNA is specifically recognized by the ARID domain. Both PHD and ARID domains are necessary for the association of ARID5 with chromatin. The results suggest that the dual recognition of AT-rich DNA and H3K4me3 by the ARID5 ARID-PHD cassette may facilitate the association of the ISWI complex with specific chromatin regions to regulate development and floral phase transition
2019-11-01 | GSE139636 | GEO
Project description:Here we report 16s rRNA data from environmental samples that include metal working fluid and air from a machine facility and lung tissue samples. Microbiota composition of environmental and lung tissue samples showed greater similarity between case samples than between control samples.
2020-09-18 | GSE87406 | GEO
Project description:Abstract - 18S nonfunctional rRNA decay (NRD) detects and eliminates translationally nonfunctional 18S rRNA. While this process is critical for ribosome quality control, the mechanisms underlying nonfunctional 18S rRNA turnover remain elusive, particularly in mammals. Here, we show that mammalian 18S NRD initiates through the integrated stress response (ISR) via GCN2. Nonfunctional 18S rRNA induces translational arrest at start sites. Biochemical analyses demonstrate that ISR activation limits translation initiation and attenuates collisions between scanning 43S preinitiation complexes and stalled nonfunctional ribosomes. The ISR promotes 18S NRD and 40S ribosomal protein turnover by RNF10-mediated ubiquitination. Ultimately, RIOK3 binds the resulting ubiquitinated 40S subunits and facilitates 18S rRNA decay. Overall, mammalian 18S NRD acts through GCN2, followed by ubiquitin-dependent 18S rRNA degradation involving the ubiquitin E3 ligase RNF10 and the atypical protein kinase RIOK3. These findings establish a dynamic feedback mechanism by which the GCN2-RNF10-RIOK3 axis surveils ribosome functionality at the translation initiation step.
2024-12-09 | MSV000096620 | MassIVE