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Oryza sativa

ABSTRACT: Rice RNA secondary structurome under heat stress

PROVIDER: PRJNA392817 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR5796930.fastq.gz	Fastqsanger.gz
	SRR5796931.fastq.gz	Fastqsanger.gz
	SRR5796932.fastq.gz	Fastqsanger.gz
	SRR5796933.fastq.gz	Fastqsanger.gz
	SRR5796934.fastq.gz	Fastqsanger.gz

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Nucleosome free chromatin measured by ATAC-seq in Rice leaves (Oryza sativa)

Project description:Nucleosome free measurement of 14 day old rice leaves (2nd leaf) in heat stress and recovery and dehydration stress and recovery

2016-01-01 | GSE75794 | GEO

Identification of Genes and miRNAs Affecting Pre-harvest Sprouting in Rice (Oryza sativa L.) by Transcriptome and Small RNAome Analyses

Project description:Purpose: The goal of our study is to compare two different ecotypes of Oryza sativa L., PHS-susceptible rice trait and PHS-resistant rice trait under three different maturation stages in rice seed embryo with profile of miRNA-seq. Methods: Oryza sativa. L miRNA profiles of two different ecotypes with 3 different maturation stages of rice seed embryo were generated by NGS, in duplicate, following Illumina NGS workflow. Results: We found the differentially expressed microRNAs between PHS-susceptible rice trait and PHS-resistant rice trait according to the three different seed maturation stages. Target transcripts of differentially expressed microRNAs have been predicted via psRNATarget web server, and a part of those target genes are likely to be regulated by microRNAs, affecting overall responses to heat stress and the regulation of seed dormancy during maturation. Conclusions: Our study represents the analysis of rice seed small RNAs, specifically microRNAs, under two different ecotypes, three different seed maturation stages in rice seed embryo. Our results show that microRNAs are involved in response to heat stress and the regulation of seed dormancy. This study will provide a foundation for understanding dynamics of seed dormancy during the seed development and overcoming pre-harvest sprouting.

2021-07-04 | GSE175561 | GEO

Nucleosome free chromatin measured by ATAC-seq in Rice leaves (Oryza sativa)

Project description:Nucleosome free measurement of 14 day old rice leaves (2nd leaf) in heat stress and recovery and dehydration stress and recovery 5 conditions: control (30C, liquid media; at 0.5h, 2h, 4h); Heat (transferred from 30C to 40C; at 0.5h, 2h, 4h); Heat recovery (transferred back to 30C after 2h at 40C; after 2h); Dehydration (roots exposed to air; at 2h); Dehydration recovery (roots returned to liquid media after 1.5h in air; after 2h) Samples: 2 biological replicates.

2016-07-03 | E-GEOD-75794 | biostudies-arrayexpress

Rice RNA secondary structurome under heat stress

Project description:We used the Structure-seq2 protocol and applied it to 14-day-old rice (Oryza sativa) shoot tissue for genome-wide RNA structure probing to investigate the effect of heat stress on the RNA structurome.

2018-11-12 | GSE100714 | GEO

Small RNAs from 4-week old seedling of Oryza sativa

2008-12-08 | GSE12317 | GEO

Identification of Genes and miRNAs Affecting Pre-harvest Sprouting in Rice (Oryza sativa L.) by Transcriptome and Small RNAome Analyses

Project description:Purpose: The goal of our study is to compare two different ecotypes of Oryza sativa L., PHS-susceptible rice trait and PHS-resistant rice trait under three different maturation stages and two different tissues, embryo and endosperm of rice seeds with profile of RNA-seq. Methods: Oryza sativa. L mRNA profiles of two different ecotypes with 3 different maturation stages and 2 different tissues were generated by NGS, in duplicate, following Illumina NGS workflow. qRT–PCR validation was performed using SYBR Green assays. Results: We found the differentially expressed genes (DEGs) between PHS-susceptible rice trait and PHS-resistant rice trait according to the three different seed maturation stages. In DEGs, gene ontology (GO) analysis and Mapman analysis were performed, and we discovered genes related to plant hormones and heat stress, which are not yet reported. These genes were validated through qRT-PCR, and it is likely to be highly related to seed dormancy. Conclusions: Our study represents the analysis of rice seed transcriptomes under two different ecotypes, three different seed maturation stages and two different tissues (Embryo and endosperm). Our results show that seed dormancy is affected and regulated by a plant hormones and heat stress. This study might provide a foundation for understanding dynamics of seed dormancy during the seed development and overcoming pre-harvest sprouting.

2021-05-07 | GSE174017 | GEO

Oryza sativa Raw sequence reads

Project description:Using the HiSeqTM 2000 sequencing platform, the anther transcriptome of photo thermo sensitive genic male sterile lines (PTGMS) rice Y58S and P64S (Peiâai 64S) were analyzed at the fertility sensitive stage under cold stress.These datas would be most beneficial for further studies investigating the molecular mechanisms of rice responses to cold stress.

2015-04-22 | E-MTAB-4312 | biostudies-arrayexpress

Small RNAs from 4-week old seedling of Oryza sativa

Project description:In order to identify new miRNAs, NAT-siRNAs and possibly abiotic-stress regulated small RNAs in rice, three small RNA libraries were constructed from control rice seedlings and seedlings exposed to drought or salt stress, and then subjected to pyrosequencing. Totally three sets of small RNAs, which were obtained under normal condition as well as salt and drought stress conditions

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Oryza sativa

Project description:Expression data from panicle in heat tolerant and heat susceptible rice under high temperature stress

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Preliminary exploration of Oryza sativa small RNAs - Run 1 and 2

Project description:The small RNAs presented here were produced as a preliminary exploration of small RNAs in rice, and as such, various tissues and stress conditions were sampled. Small RNAs present in these samples were all mapped to the rice genome TIGR version 5. The total number of distinct mapped sequences are 12879 for Run 1 and 88508 for Run 2. The total number of sequence reads were respectively 70406 and 191682. The datasets contain Oryza sativa var Nipponbar endogenous small RNA sequences in the size range 18 to 34 nt. Plants were grown in a Conviron Environmental Chamber at high light intensity using both high pressure sodium and metal halide lamps for 10.5 hr at 28 degrees C and for 13.5 hr at 26 degrees C in the dark. RNA was extracted from rice tissues at various stages of development and under different abiotic and biotic stresses. The small RNAs presented here were all mapped to the rice genome TIGR version 5. The total number of distinct mapped sequences are 12879 for Run 1 and 88508 for Run 2. The total number of sequence reads were respectively 70406 and 191682.

2009-06-08 | GSE16248 | GEO

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