Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Panicum virgatum cultivar:WBC3

ABSTRACT: Panicum virgatum WBC3 Standard Draft genome sequencing

PROVIDER: PRJNA442788 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR12137156_subreads.fastq.gz	Fastqsanger.gz
	SRR12137157_subreads.fastq.gz	Fastqsanger.gz
	SRR12137158_1.fastq.gz	Fastqsanger.gz
	SRR12137158_2.fastq.gz	Fastqsanger.gz
	SRR6996329_1.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 6

Similar Datasets

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

Panicum virgatum cultivar:WBC3

Project description:Panicum virgatum WBC3 Gene Expression Profiling - WBC3-1XX D1 transcriptome

| PRJNA677318 | ENA

Panicum virgatum cultivar:WBC3

Project description:Panicum virgatum WBC3 Gene Expression Profiling - WBC3-1XX D3 transcriptome

| PRJNA677319 | ENA

Panicum virgatum cultivar:WBC3

Project description:Panicum virgatum WBC3 Gene Expression Profiling - WBC3-2XX D1 transcriptome

| PRJNA677322 | ENA

Panicum virgatum cultivar:WBC3

Project description:Panicum virgatum WBC3 Gene Expression Profiling - WBC3-2XX D3 transcriptome

| PRJNA677323 | ENA

Panicum virgatum cultivar:WBC3

Project description:Panicum virgatum WBC3 Gene Expression Profiling - WBC3-3AS D1 transcriptome

| PRJNA677324 | ENA

Panicum virgatum cultivar:WBC3

Project description:Panicum virgatum WBC3 Gene Expression Profiling - WBC3-3AS D3 transcriptome

| PRJNA677325 | ENA

Panicum virgatum cultivar:WBC3

Project description:Panicum virgatum WBC3 Gene Expression Profiling - WBC3-3XX D1 transcriptome

| PRJNA677326 | ENA

Panicum virgatum cultivar:WBC3

Project description:Panicum virgatum WBC3 Gene Expression Profiling - WBC3-3XX D3 transcriptome

| PRJNA677327 | ENA

Panicum virgatum cultivar:WBC3

Project description:Panicum virgatum WBC3 Gene Expression Profiling - WBC3-4AS D1 transcriptome

| PRJNA677328 | ENA

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