Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

ABSTRACT: rice cold treatment RNA-seq

PROVIDER: PRJNA1102144 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR28741178_1.fastq.gz	Fastqsanger.gz
	SRR28741178_2.fastq.gz	Fastqsanger.gz
	SRR28741179_1.fastq.gz	Fastqsanger.gz
	SRR28741179_2.fastq.gz	Fastqsanger.gz
	SRR28741180_1.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 12

Similar Datasets

R-loops act as a master regulatory switch modulating transcription of cold-responsive genes in rice

Project description:Cold is a major naturally occurring stress that usually causes complex symptoms and severe yield loss in plants. R-loops can function in a series of biological processes, including normal development and stress responses, in plants. However, how R-loops function in cold responses is still largely unknown in plants, especially in cold sensitive rice. Herein, we conducted DRIP-seq in combination with other newly generated omics data (RNA-seq, DNase-seq, ChIP-seq and MNase-seq) in rice with or without cold treatment. We found that cold treatment caused R-loop dynamics across the genome, indicating that R-loops are cold sensitive non-B DNA structures. Moreover, cold biased R-loops had high GC content and novel motifs the binding of distinct TFs as compared to CK biased R-loops, indicative of occurrence of differential biological implications of R-loop dynamics in response to cold stress. More importantly, we for the first time to provide evidence showing that, in addition to the direct involvement of R-loops in the regulation of cold-responsive gene transcription, R-loops can indirectly modulate transcription of subsets of cold-responsive genes through R-loop overlapping TF-centered or cis-regulatory element related regulatory networks and lncRNAs in rice. Thus, our study for the first time provides evidence showing functions of R-loop dynamics in rice cold responses. It also provides some potential R-loop loci for genetic and epigenetic manipulation towards breeding of enhanced cold tolerance rice varieties.

2023-09-26 | GSE217841 | GEO

A global profiling of gene expression in chilling stress in rice

Project description:RNA-Seq was performed to study the change of gene expression before and after chilling treatment in rice. Different change patterns were identified. We have provided a complete view of transcriptome under cold stress condition, which will deepen our understanding of gene expression regulation in cold stress response as well as cold stress response mechanism for monocot plants. The mRNA profiles of 15-day-old rice seedlings with and without chilling treatment (4 Â°C for 33 h) were generated by deep sequencing using Illumina Hiseq 2000 platform.

2016-04-13 | E-GEOD-67373 | biostudies-arrayexpress

A global profiling of gene expression in chilling stress in rice

2016-04-13 | GSE67373 | GEO

Transcriptome sequencing of 36 rice samples was used to identify the cold tolerance mechanism of rice

Project description:Purpose: In this study, RNA-seq was used to analyzed the molecular mechanism of cold tolerance in rice Methods: Rice 9311 (cold intolerant) and DC907 (cold tolerant) were used as experimental materials for transcriptome sequencing on Illumina HIseq platform. Fastq is used to evaluate the quality of the original data, and NGS QC Toolkit is used to filter the original data to obtain clean reads. Clean reads were compared to the rice 9311 reference genome using HISAT2 software. Put the genome mapping results of all sequenced reads data together, assemble them with cufflinks, and then compare them with known gene models with cuffcompare. The gene expression level of each sample was analyzed by HTSeq software. All treatments were analyzed for differential expression using DEseq. Results: A total of 36 samples were used for RNA sequencing analysis, with three biological replicates per treatment. Each sample generates at least 2G data. The genes regulated by cold stress treatment (1,3 days) and recovery treatment (1,3 days) were determined by comparative analysis.

2022-04-06 | GSE182563 | GEO

Transcriptional profiling of shoots and roots in japonica and indica rice seedlings under cold stress and recovery stage

Project description:Rice seedlings at 3-leaf stage were used for expression analysis in control and cold stressed (incloudling cold treatment for 3, 24hrs and recovery from cold stress for 24hrs) samples. Samples of shoots and roots from biological replicates of both genotypes were generated and the expression profiles were determined using Phalanx Rice OneArray＠ v1.

2014-10-15 | GSE57895 | GEO

Project description:RNA-seq of glutinous rice 89-1 and indica rice R07 under cold treatment experiment

| PRJNA894465 | ENA

Acidianus filamentous virus 2

Project description:Cold stress greatly affects plant growth and crop yield. To identify novel genes and possible mechanisms involved in chilling tolerance responses in rice seedlings, RNA sequencing (RNA-seq) technology was used for genome-wide gene expression profiling analysis to compare three cold-tolerant genotypes and one cold-sensitive genotype under both normal temperature and cold stress treatments.

2013-07-11 | E-MTAB-4407 | biostudies-arrayexpress

The rice anther transcriptomes responded to low temperature [RNA-seq]

Project description:The booting stage of rice shows the most sensitivity to cold stress, and low-temperature stress causes irreversible pollen sterility. We performed transcriptome analysis using RNA-seq to investigate the response of rice anthers to low-temperature stress. In this RNA-seq analysis, to validate the results of transcriptome analysis of anthers from 13 rice lines using microarrays, four cultivars were selected for analysis from the 13 tested for microarrays.

2024-11-29 | GSE270782 | GEO

Transcriptional profiling of shoots and roots in japonica and indica rice seedlings under cold stress and recovery stage

2014-10-15 | E-GEOD-57895 | biostudies-arrayexpress

Genome-wide profiling of small RNAs in rice under abiotic stresses

Project description:To identify novel miRNA and NAT-siRNAs that are associated with abiotic stresses in rice, we generated small RNA sequences from inflorescences from rice under control and under dought, salt, and cold stress treatments. Over 30 million reads were generated.

2012-03-12 | GSE26357 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data