Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Sorghum bicolor and Setaria viridis PARE-seq

ABSTRACT: Sorghum bicolor and Setaria viridis PARE-seq

PROVIDER: PRJNA633605 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR11819449.fastq.gz	Fastqsanger.gz
	SRR11819450.fastq.gz	Fastqsanger.gz
	SRR11819451.fastq.gz	Fastqsanger.gz
	SRR11819452.fastq.gz	Fastqsanger.gz
	SRR11808773.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 8

Similar Datasets

Sorghum bicolor and Setaria viridis PARE-seq

Project description:Parallel Analysis of RNA Ends (PARE) sequencing reads were generated to validate putative microRNAs and identify cleavage sites in Sorghum bicolor and Setaria viridis.

2020-05-19 | GSE150798 | GEO

Leaf transcriptome analysis of Setaria viridis MPA1 RNAi plants

Project description:This experiment was conducted to investigate the effect of RNAi of MPA1 on the global leaf transcriptome of Setaria viridis.

2022-01-01 | E-MTAB-8907 | biostudies-arrayexpress

Setaria viridis (A10.1) circadian expression after light or temperature entrainment

Project description:Setaria viridis (A10.1) circadian expression after light or temperature entrainment

2017-07-01 | GSE97739 | GEO

RNA-Seq and BS-Seq of Sorghum bicolor tissues

Project description:This study utilized next generation sequencing technology (RNA-Seq and BS-Seq) to examine the transcriptome and methylome of various tissues within sorghum plants with the ultimate goal of improving the Sorghum bicolor annotation We examined the mRNA of various Sorghum bicolor (BTx623) tissues (flowers, vegitative and floral meristems, embryos, roots and shoots) and bisulfite treated DNA from two root samples

2014-08-29 | E-GEOD-50464 | biostudies-arrayexpress

RNA-Seq and BS-Seq of Sorghum bicolor tissues

2014-08-29 | GSE50464 | GEO

Tissue specific expression data in Sorghum bicolor BTx623

Project description:This study used with RNA-Seq to examine the tissue specific expression data within sorghum plants for improving the Sorghum bicolor gene annotation. We examined the RNA from tissues (spikelet, seed and stem) in Sorghum bicolor (BTx623).Total RNAs form each tissues were extracted using SDS/phenol method followed by LiCl purification

2015-03-11 | E-MTAB-4273 | biostudies-arrayexpress

RNA-Seq and BS-Seq of Sorghum bicolor tissues

Project description:This experiment contains the subset of data corresponding to sorghum RNA-Seq data from experiment E-GEOD-50464 (http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-50464/), which goal is to examine the transcriptome of various Sorghum bicolor (BTx623) tissues: flowers, vegetative and floral meristems, embryos, roots and shoots. Thus, we expanded the existing transcriptome atlas for sorghum by conducting RNA-Seq analysis on meristematic tissues, florets, and embryos, and these data sets have been used to improve on the existing community structural annotations.

2014-08-29 | E-MTAB-3839 | biostudies-arrayexpress

A dynamic co-expression map of early inflorescence development in Setaria viridis provides a resource for gene discovery and comparative genomics

Project description:Setaria viridis is a small, rapidly growing grass species in the subfamily Panicoideae, a group that includes economically important cereal crops such as maize and sorghum. The S. viridis inflorescence displays complex branching patterns, but its early development is similar to that of other panicoid grasses, and thus is an ideal model for studying inflorescence architecture. Here we report detailed transcriptional resource that captures dynamic transitions across six sequential stages of S. viridis inflorescence development, from reproductive onset to floral organ differentiation. Co-expression analyses identified stage-specific signatures of development, which include homologs of previously known developmental genes from maize and rice, suites of transcription factors and gene family members, and genes of unknown function. This spatiotemporal co-expression map and associated analyses provide a foundation for gene discovery in S. viridis inflorescence development, and a comparative model for exploring related architectural features in agronomically important cereals.

2018-08-17 | GSE118673 | GEO

Setaria viridis small RNAs from panicle tissues

Project description:A total of 18 libraries from Setaria viridis were constructed using the Illumina TruSeq sample preparation method. We used two biological replicate libraries from the leaf, whole panicles (inside leaf sheath), whole panicles (coming out of leaf sheath), whole panicles (completely out of leaf sheath), whole panicles (completely out of leaf sheath, after pollination), spikelet (inside leaf sheath), spikelet (coming out of leaf sheath), and spikelet (completely out of leaf sheath).

2018-07-28 | GSE111490 | GEO

DNase-SEQ analysis of whole leaf and bundle sheath tissues in Zea mays, Sorghum bicolor, Setaria italica and Brachypodium distachyon.

Project description:Photosynthesis supports life on Earth but the regulatory architecture associated with photosynthesis gene expression is poorly understood. Most crops use either C3 or C4 photosynthesis with the latter allowing significantly higher efficiencies as well as improved water and nitrogen use. Here we use DNAse-SEQ to define >1 million transcription factor binding sites in leaves of grasses that either operate C3 or C4 photosynthesis and that are consistent with significant differences in the modes of gene regulation between the kingdoms of life. Leaf samples were collected from seedlings to allow for comparison of regulatory interactions between species from the same (Zea mays and Sorghum bicolor) and different (Setaria italica) C4 lineages, as well as a C3 grass (Brachypodium distachyon) in order to investigate evolution of C4 photosynthetic gene expression. Additionally bundle sheath tissues were mechanically isolated from C4 species and analysed by DNAse-SEQ to identify DNA regulatory elements controlling cell-specific gene expression patterns.

2017-07-24 | GSE97369 | 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