Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Panicum sumatrense

ABSTRACT: Panicum sumatrense Organism overview

PROVIDER: PRJNA359130 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR15703100_1.fastq.gz	Fastqsanger.gz
	SRR15703100_2.fastq.gz	Fastqsanger.gz
	SRR15703101_1.fastq.gz	Fastqsanger.gz
	SRR15703101_2.fastq.gz	Fastqsanger.gz
	SRR15703102_1.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 132

Similar Datasets

Panicum sumatrense

Project description:Panicum sumatrense Raw sequence reads

| PRJNA718414 | ENA

Panicum sumatrense

Project description:Panicum sumatrense Transcriptome or Gene expression

| PRJNA267462 | ENA

Little Millet (Panicum sumatrense L.)

Project description:Little Millet (Panicum sumatrense L.) Transcriptome

| PRJNA885279 | ENA

Little Millet (Panicum sumatrense L.)

Project description:Little Millet (Panicum sumatrense L.) Transcriptome

| PRJNA880733 | ENA

Panicum sumatrense cultivar:OLM20

Project description:Whole genome sequencing and assembly of Panicum sumatrense

| PRJNA758207 | ENA

Panicum miliaceum

Project description:Panicum miliaceum Organism overview

| PRJNA295443 | ENA

Genic microsatellite marker characterization and development in little millet (Panicum sumatrense) using transcriptome sequencing.

Project description:Little millet is a climate-resilient and high-nutrient value plant. The lack of molecular markers severely limits the adoption of modern genomic approaches in millet breeding studies. Here the transcriptome of three samples were sequenced. A total of 4443 genic-SSR motifs were identified in 30,220 unigene sequences. SSRs were found at a rate of 12.25 percent, with an average of one SSR locus per 10 kb. Among different repeat motifs, tri-nucleotide repeat (66.67) was the most abundant one, followed by di- (27.39P), and tetra- (3.83P) repeats. CDS contained fewer motifs with the majority of tri-nucleotides, while 3' and 5' UTR carry more motifs but have shorter repeats. Functional annotation of unigenes containing microsatellites, revealed that most of them were linked to metabolism, gene expression regulation, and response to environmental stresses. Fifty primers were randomly chosen and validated in five little millet and 20 minor millet genotypes; 48% showed polymorphism, with a high transferability (70%) rate. Identified microsatellites can be a noteworthy resource for future research into QTL-based breeding, genetic resource conservation, MAS selection, and evolutionary genetics.

| S-EPMC8523711 | biostudies-literature

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

High-throughput sequencing of small RNAs in Panicum virgatum

2011-05-10 | GSE28980 | GEO

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

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