Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Panicum virgatum cultivar:J001.B.1.6

ABSTRACT: Panicum virgatum J001.B.1.6 Resequencing

PROVIDER: PRJNA463272 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR7665576_1.fastq.gz	Fastqsanger.gz
	SRR7665576_2.fastq.gz	Fastqsanger.gz

Items per page:

1 - 2 of 2

Similar Datasets

Panicum virgatum cultivar:J001.B.1.4

Project description:Panicum virgatum J001.B.1.4 Resequencing

| PRJNA463270 | ENA

Panicum virgatum cultivar:J001.B.1.5

Project description:Panicum virgatum J001.B.1.5 Resequencing

| PRJNA463271 | ENA

Panicum virgatum cultivar:J001.B.1.2

Project description:Panicum virgatum J001.B.1.2 Resequencing

| PRJNA463268 | ENA

Panicum virgatum cultivar:J001.B.1.1

Project description:Panicum virgatum J001.B.1.1 Resequencing

| PRJNA463267 | ENA

Panicum virgatum cultivar:J001.B.1.3

Project description:Panicum virgatum J001.B.1.3 Resequencing

| PRJNA463269 | ENA

High-throughput sequencing of small RNAs in Panicum virgatum

Project description:Small RNAs (21-24 nt) are pivotal regulators of gene expression that guide both transcriptional and post-transcriptional silencing mechanisms in diverse eukaryotes, including most if not all plants. MicroRNAs (miRNAs) and short interfering RNAs (siRNAs) are the two major types, both of which have a demonstrated and important role in plant development, stress responses and pathogen resistance. In this work, we used a deep sequencing approach (Sequencing-By-Synthesis, or SBS) to develop sequence resources of small RNAs from Panicum virgatum tissues (including leaves, drought-treated leaves and flowers). The high depth of the resulting datasets enabled us to examine in detail critical small RNA features as size distribution, tissue-specific regulation and sequence conservation between different organs in this species. We also developed database resources and a dedicated website (http://smallrna.udel.edu/) with computational tools for allowing other users to identify new miRNAs or siRNAs involved in specific regulatory pathways, verify the degree of conservation of these sequences in other plant species and map small RNAs on genes or larger regions of the maize genome under study. Small RNA libraries were derived from leaves, drought-treated leaves and flowers of Panicum virgatum. Total RNA was isolated using the Plant RNA Purification Reagent (Invitrogen), and submitted to Illumina (Hayward, CA, http://www.illumina.com) for small RNA library construction using approaches described in (Lu et al., 2007) with minor modifications. The small RNA libraries were sequenced with the Sequencing-By-Synthesis (SBS) technology by Illumina. PERL scripts were designed to remove the adapter sequences and determine the abundance of each distinct small RNA. We thank Pamela Green for providing the plant material as well as Kan Nobuta and Gayathri Mahalingam for assistance with the computational methods.

2011-05-09 | E-GEOD-28980 | biostudies-arrayexpress

Greenbug (Schizaphis graminum) Herbivory Effect on Switchgrass (Panicum virgatum) PhosphoProteomeGreenbug (Schizaphis graminum) Herbivory Effect on Switchgrass (Panicum virgatum) PhosphoProteome

Project description:Cereal aphids can successfully colonize and damage switchgrass (Panicum virgatum) plants. Among the aphids tested, greenbugs (Schizaphis graminum, GB) caused significant plant damage likely through a combination of aphid-salivary proteins that are injected into plants during feeding and a strong host response elicited by herbivory. In this study, changes in protein phosphorylation present in GB-infested and uninfested control plants was determined. These data were compared against transcriptome changes recently published for this system.

2022-02-04 | PXD018546 | Pride

High-throughput sequencing of small RNAs in Panicum virgatum

2011-05-10 | GSE28980 | GEO

Greenbug (Schizaphis graminum) Herbivory Effect on Switchgrass (Panicum virgatum) Proteome

Project description:Cereal aphids can successfully colonize and damage switchgrass (Panicum virgatum) plants. Among the aphids tested, greenbugs (Schizaphis graminum, GB) caused significant plant damage likely through a combination of aphid-salivary proteins that are injected into plants during feeding and a strong host response elicited by herbivory. In this study, shotgun label-free proteomics has been used to document changes to the switchgrass proteome as a result of GB infestation. These proteomic data were compared against transcriptome changes recently published for this system.

2022-02-04 | PXD018547 | Pride

Transcriptional, Metabolic, Physiological and Developmental Responses to Nitrogen Limitation in Switchgrass (Panicum virgatum)

Project description:Sustainable production of switchgrass (Panicum virgatum) as a bioenergy crop hinges in part on efficient use of soil macronutrients, especially nitrogen (N). This study investigated the physiological, metabolic and transcriptomic responses of switchgrass to N limitation. Moderate N limitation marked a tipping point for large changes in plant growth, root-to-shoot ratio, root system architecture and total nitrogen content. Integration of transcriptomic and metabolic data revealed that N limitation reduced switchgrass photosynthetic capacity and carbon(C)-fixation activities. Switchgrass balanced C-fixation with N-assimilation, transport and recycling of N compounds by rerouting C-flux from glycolysis, the oxidative branch of the pentose phosphate pathway (OPPP) and from the tricarboxylic acid (TCA) cycle in an organ specific manner. The energy and reduction power so generated, and C-skeletons appear to be directed towards N uptake, biosynthesis of energy storage compounds with high C/N ratio such as sucrose, non-N-containing lipids, and various branches of secondary metabolism.

2023-12-31 | GSE237286 | 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