Oryza sativa strain:Taichung 65
Ontology highlight
ABSTRACT:
PROVIDER: PRJDB11157 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| DRR334952_1.fastq.gz | Fastqsanger.gz | |||
| DRR334952_2.fastq.gz | Fastqsanger.gz | |||
| DRR334953_1.fastq.gz | Fastqsanger.gz | |||
| DRR334953_2.fastq.gz | Fastqsanger.gz | |||
| DRR334954_1.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 5 of 16 |
Similar Datasets
Project description:A highly contiguous mitochondrial and plastid genome sequences of a japonica rice cultivar, Taichung 65, were determined by a hybrid approach with long- and short-read sequences. The assembled mitochondrial genome was 465,453 bases in length with an overall GC content of 43.8%. It was predicted to harbor 62 protein-encoding genes, 16 kinds (33 copies) of transfer RNA, and three kinds (six copies) of ribosomal RNA genes. The mitochondrial genome structure in Taichung 65 is largely the same as that of Nipponbare, but the first ∼9.5 kb sequence in Nipponbare (DQ167400) is replaced with a ∼27 kb sequence duplicated from other parts of the mitochondrial genome. Phylogenetic and sequence polymorphism analysis indicated that Taichung 65 is classified as typical japonica. The assembled plastid genome sequence was 134,551 bases in length and completely identical to the previously reported Nipponbare sequence. These near-complete organelle genome sequences will serve as fundamental resources for investigating alloplasmic cytoplasmic male sterile lines and other organelle-controlled phenomena in rice.
| S-EPMC10777130 | biostudies-literature
Project description:Rice tungro disease is caused by the interaction between Rice tungro spherical virus (RTSV) and Rice tungro bacilliform virus. Infection with RTSV alone does not result in any distinctive symptoms in Taichung Native 1 (TN1) that is one of RTSV susceptive indica rice cultivar. To elucidate the basis of asymptomatic response of rice to RTSV at the gene expression level, global gene response in RTSV-infected TN1 was detected by custom microarray. Keywords: time course, virus infection, disease response
2009-12-07 | GSE16141 | GEO
Project description:Phosphate starvation/sufficient rice seedling, root or shoot Pi-starvation or Pi-sufficient stresses responsible rice genes, including previously unannotated genes were identified by Illumina mRNA-seq technology. 53 million reads from Pi-starvation or Pi-sufficient root or shoot tissues were uniquely mapped to the rice genome, and these included 40574 RAP3 transcripts in root and 39748 RAP3 transcripts in shoot. We compared our mRNA-seq expression data with that from Rice 44K oligomicroarray, and about 95.5% (root) and 95.4% (shoot) transcripts supported by the array were confirmed expression both by the array and by mRNA-seq, Moreover, 11888 (root) and 11098 (shoot) RAP genes which were not supported by array, were evidenced expression with mRNA-seq. Furthermore, we discovered 8590 (root) and 8193 (shoot) previously unannotated transcripts upon Pi-starvation and/or Pi-sufficient.
2012-01-06 | E-MTAB-4302 | biostudies-arrayexpress
Project description:Comparative transcriptome analysis of different root types in rice under salinity stress
| PRJNA319757 | ENA
Project description:Rice possesses a fibrous root system with a primary root, lateral roots and crown roots. The cellular origins and early morphologies of the three root types vary greatly, but the adult structures are remarkably similar. Previous studies have highlighted diverse mechanisms involved in rice roots formation However, the gene expression reprograming and the underling epigenetic mechanisms of cell differentiation and initiation of the different roots are not studied. Here, we analyzed spatiotemporally resolved transcriptomes and DNA methylomes during the initiation processes of the three root types using a precise laser microdissection (LM) coupled with RNA-Seq and BS-seq. The analysis reveals distinct gene expression programs during the first stages during the initiation of the three root types. DNA methylome analysis uncovers a dynamic but distinct CHH methylation reprogramming during initiation of the three roots, with a genome-wide decrease of CHH methylation in crown and lateral root initials, but an increase in embryonic root primordium. In addition, a more drastic reprogramming of CHH methylation was observed in lateral root initials. Together, the results provide stage-specific gene expression signatures of the rice roots initiation and show distinct epigenetic and gene expression reprograming during the formation of the three different root types in rice.
2020-02-01 | GSE136767 | GEO
Project description:To transcriptionally characterize lateral root development in rice, we subjected the rice LRIS to genome-wide transcript profiling via RNA-sequencing. Taking into account the appearance of the first (stage I primordium) cell divisions starting from 6 hours after NAA treatment, we sampled at 2 hours and at 5 hours after NAA treatment to capture the primary auxin response and the gene expression related to initiation, respectively. Additionally, we sampled at 8 hours, 14 hours and 20 hours, in which the root was highly enriched for stage I, II and III primordia, respectively. As the spatiotemporal assessment of the primordia in the LRIS showed a highly synchronous induction and development of lateral roots in particular in the region just above the root meristem, root sections between 750 µm and 2000 µm from the root tip were microdissected and used for RNA-extraction. To assess possible artefacts induced by the replacement of the medium, we sampled a control before and 2 hours after replacement with NPA containing medium.
2023-08-24 | E-MTAB-13094 | biostudies-arrayexpress
Project description:Rice tungro disease is caused by the interaction between Rice tungro spherical virus (RTSV) and Rice tungro bacilliform virus. Infection with RTSV alone does not result in any distinctive symptoms in Taichung Native 1 (TN1) that is one of RTSV susceptive indica rice cultivar. To elucidate the basis of asymptomatic response of rice to RTSV at the gene expression level, global gene response in RTSV-infected TN1 was detected by custom microarray. Keywords: time course, virus infection, disease response Comparison between RTSV and mock infected rice. Biological replicates: 3 control (mock), 3 RTSV-infected at each time point, independently grown and harvested at 6 to 15 days after inoculation (DAI). 1 samples prepared with whole plant 5 cm above ground and pooled from 5 plants grown under same conditons.
2010-05-18 | E-GEOD-16141 | biostudies-arrayexpress
Project description:In this study, we used RNA-Seq to understand the mechanisms of Cd toxicity, cellular detoxification and protection pathways in response to Cd in rice roots. To gain additional insight into the rice transcriptomic response to environmental Cd stress, 15-day-old rice seedlings were treated with 10 or 100 μM solutions of Cd2+, or without Cd (control), for 24 h, at which point root samples were harvested and labeled as Cd+, Cd++, and control, respectively. These samples were used for 101 bp paired-end (PE) deep sequencing on an Illumina HiSeq 2500 platform.
2015-06-08 | E-MTAB-4445 | biostudies-arrayexpress
Project description:Whole genome arrays have been used to analyze the transcriptomic response to vanadium stress in rice root. Identify genes and pathways that would respond to vanadium stress
2015-03-23 | GSE36760 | GEO
Project description:Autotoxicity plays an important mechanism in regulating plant productivity. Ferulic acid (FA) is phytotoxic and was identified in extracts and residues of rice plants as a candidate for rice allelochemicals. To help characterize the autotoxicity mechanism of rice, we present the first large-scale, transcriptomic analysis of rice root responses to ferulic acid.
2013-07-22 | GSE34899 | GEO