Rice ssRNA-seq
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REPOSITORIES: ENA
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Project description:We took advantage of ssRNA-seq technology to deeply sequence mRNAs of the model plant species Oryza sativa ssp.japonica cv Nipponbare with clear transcriptional orientations for assessing rice cis-NATs at the best possible resolution. We also deeply sequenced rice small RNAs from the same tissues as that for preparing mRNAs to investigate rice cis-NAT pairs that potentially give rise to endogenous short interfering RNAs from their overlapping regions under normal and stress conditions.
2011-12-28 | E-MTAB-721 | biostudies-arrayexpress
Project description:unclassified ssRNA positive-strand viruses
| PRJNA16928 | ENA
Project description:The transcriptome profile after antisense L1 ASO treatment [ssRNA-Seq]
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Project description:We have performed a Proteogenomics meta-analysis of data sets deposited in ProteomeXchange: PXD000265, PXD000313, PXD000923, PXD001030, PXD001058, PXD002291, PXD002739, PXD002740 and PXD003156 and using 29 RNA-Seq data sets on rice (Oryza sativa). We created a search database comprising translated reads that had been mapped onto the rice genome, as well as officially annotated rice proteins sequences. The RNA Seq database was pre-processed to identify “novel transcripts” for those not mapping fully to an existing exon, and “novel junctions” for those reads mapped with a gap, implying a potential novel splice site that was not annotated in the official gene set. Confidentially identified “novel peptides” i.e. those mapping to a novel junction or novel transcript were post-processed to ensure that there were no other better explanations for the corresponding spectra e.g. peptide from a canonical gene with a modification or amino acid substitution. Data were exported from the pipeline in PSI mzIdentML 1.2 format, containing chromosomal coordinates, and further converted to PSI proBed format for genome visualisation. Novel peptides were searched against other plant databases using BLAST to see if they had predicted in genes from other species. A total of 1584 novel peptides were identified, mapping to ~700 genomic loci in which either new genes have been predicted (~100) or updates to existing gene models have been predicted (~600).
2018-10-30 | PXD008960 | Pride
Project description:The translational landscape of phenylephrine-treated neonatal rat cardiomyocytes [ssRNA-seq]
| PRJNA713923 | ENA
Project description:The molecular mechanism for ssRNA+dsDNA triple helix structure formation on chromatin are unclear. We analyzed the triplex-nucleosomes complex fomration in vitro and in vivo, and show that triplexes are stabilized by the nucleosomes. We developed a method to monitor nucleosome bound RNA triplexes in vivo, revealing that RNA binding maintained the nucleosomes on an accessible structure supporting a gene activating role of nucleosome-triplex complexes in cells.
2019-02-18 | GSE114900 | GEO
Project description:In order to systematically identify the possible regulatory roles of (long nocoding RNAs) lncRNAs and (circular RNAs) cirRNAs in the rice photo-thermosensitive genic male sterile (PTGMS) line that were involved in fertility transition, 18 RNA libraries from rice young panicles of the Wuxiang S sterile line rice (WXS (S)) and its fertile line rice (WXS (F)) at the pollen mother cell (PMC) formation stage (P2), the meiosis stage (P3), and the microspore formation stage (P4) were constructed, with three biological replicates for each condition. These libraries were sequenced using an Illumina Hiseq 2500 platform, and approximately 214.54 Gb clean reads were generated. we performed genome-wide identification and characterization of lncRNAs circRNAs using high-throughput strand-specific RNA sequencing (ssRNA-seq) technology and bioinformatics tools to investigate the expression profiles of circRNAs in the PTGMS rice line WXS and their potential roles in the fertility transition.A total of 3948 lncRNAs and 9994 circRNAs were indentifiled in WXS rice, and our findings clearly revealed that lnRNAs and circRNAs might be endogenous noncoding regulators of flower and pollen development in the PTGMS rice line.
2021-05-30 | GSE125608 | GEO
Project description:chip-seq for MoIug4 in rice, putative transcription factor MoIug4 was secrected from M. oryzae to the nucleus of rice. Here, we performed of MoAtf1 chip-seq assays to uncovered the regulation network
2021-11-17 | GSE188802 | GEO
Project description:In this study, using a novel dual RNA-seq approach we monitored the global transcriptional changes in real time of Xanthomonas oryzae pv. oryzicola and rice during infection. Our transcriptome maps of Xoc strains infecting rice provide mechanistic insights into the bacterias adaptive responses to the host niche, with modulation of central metabolism being an important signature. The study also uncovers that infected rice responds by substantial alteration of the cell wall, stress and structural proteins.
2019-03-29 | GSE126994 | GEO