Browse
Submit Data
Databases
API
Help

Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

PacBio Iso-seq of Lupinus angustifolius L. leaf and stem transcriptomes

ABSTRACT: The aim of this experiment was to obtain full length transcript sequences of genes expressed in leaves and stems of narrow-leafed lupin (Lupinus angustifolius L.) using PacBio Iso-Seq. Total RNA was isolated from leaves and stems of five narrow-leafed lupin (Lupinus angustifolius L.) genotypes with contrasting alkaloid regulation, including an iucundus low-alkaloid line (83A:476), a bitter Iucundus line (P27255) and three Bryansk low-alkaloid lines carrying the Iucundus-type RAP2-7 allele: 95826 (Bryanskij-35), 95927 (Bryanskij-123) and 95928 (Bryanskij-237/83). Plants, in five replicates per genotype, were grown under controlled conditions optimal for growth, and leaf and stem samples were collected at flowering stage. For each genotype and organ, total RNA from five biological replicates was pooled in equal amounts and used for PacBio Iso-Seq library preparation and sequencing.

INSTRUMENT(S): Sequel II

ORGANISM(S): Lupinus angustifolius

SUBMITTER: Magdalena Kroc

PROVIDER: E-MTAB-16429 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

Illumina RNA-seq of Lupinus angustifolius L. leaf and stem transcriptomes

Project description:The aim of this experiment was to compare gene expression in leaves and stems of narrow-leafed lupin (Lupinus angustifolius L.) using Illumina RNA sequencing. Total RNA was isolated from leaves and stems of five narrow-leafed lupin (Lupinus angustifolius L.) genotypes with contrasting alkaloid regulation, including an iucundus low-alkaloid line (83A:476), a bitter Iucundus line (P27255) and three Bryansk low-alkaloid lines carrying the Iucundus-type RAP2-7 allele: 95826 (Bryanskij-35), 95927 (Bryanskij-123) and 95928 (Bryanskij-237/83). Plants, in five replication per genotype, were grown under controlled conditions optimal for growth, and leaf and stem samples were collected at flowering stage.

2026-06-30 | E-MTAB-16431 | biostudies-arrayexpress

RAP2-7 DAP-seq (Lupinus angustifolius L.)

Project description:In this study we used DNA affinity purification sequencing (DAP-seq) to identify genome-wide binding of allele-specific RAP2-7 transcription factor variants in five narrow-leafed lupin (Lupinus angustifolius L.) genotypes with contrasting alkaloid regulation, including low-alkaloid iucundus line (83A:476), high-alkaloid Iucundus line (P27255) and three Bryansk low-alkaloid lines (95826 (Bryanskij-35), 95927 (Bryanskij-123) and 95928 (Bryanskij-237/83)).

2026-06-30 | E-MTAB-16430 | biostudies-arrayexpress

Iso-Seq analysis of Miscanthus sinensis plants

Project description:Iso-Seq (PacBio) sequencing was performed to generate a reference transcriptome library of M. sinensis.

2025-11-21 | E-MTAB-15228 | biostudies-arrayexpress

Iso-Seq analysis of cell suspension culture and plantlets of Hypericum perforatum

Project description:Iso-Seq (PacBio) sequencing was performed to generate a reference library of H. perforatum. We generated genome-wide transcriptome data from in vitro cell suspensions and shoot cultures of H. perforatum.

2022-12-31 | E-MTAB-11423 | biostudies-arrayexpress

PacBio Iso-Seq transcriptome sequencing data of multiplexed maize cDNA

Project description:Full-Length cDNA transcriptome (Iso-Seq) data sequenced on the PacBio Sequel system using 2.1 chemistry. Multiplexed cDNA library of 12 samples (3 tissues x 4 strains). Tissues: root, embryo, endosperm. Strains: B73, Ki11, B73xKi11, Ki11xB73.

2020-02-25 | E-MTAB-7837 | biostudies-arrayexpress

A modular system regulates specialized metabolite pathway branch choice in the medicinal plant Catharanthus roseus

Project description:This dataset belongs to a set of three RNA-Seq experiments that were carried out to study the regulation of monoterpenoid indole alkaloid production in the medicinal plant Catharanthus roseus. For this dataset, C. roseus stems were dissected to separate the epidermis from the lower tissues. Leaves were dissected to obtain veins and veinless leaves. As controls, undissected leaves and stems were used. Three biological replicates were analyzed per sample.

2020-09-07 | E-MTAB-9516 | biostudies-arrayexpress

The temperature quickly modulates protein expression by Codon Usage in wheat filling grain

Project description:The protein content determines the cell state. The variation in protein abundance is crucial when organisms are in the early stages of heat stress, but the reasons affecting their changes are largely unknown. We quantified 47,535 mRNAs and 3,742 proteins in filling grain of wheat under two thermal environments. The impact of mRNA abundance and sequence features which implicated in protein translation and degradation on protein expression was evaluated by regression analysis. Transcription, codon usage and amino acid frequency mainly drive the changes in protein expression under heat stress, and their combined contribution explains 58.2% and 66.4% of protein variation in 30 and 40 °C, respectively. Of which, transcription contributes more to the alteration in protein content under 40 °C (31%) than to 30 °C (6%). Codon usage plays a stable and powerful role in protein expression under heat stress, even surpassing transcription. What’s more, the usage of AAG is a key factor regulating rapid protein expression under heat stress.

2021-03-24 | PXD021460 | Pride

Protein solution method for direct identification of Arabidopsis stem proteins

Project description:Identifying the intracellular and cell wall-ionically bound glycoside hydrolases (GHs) carbohydrate esterases (CEs) at the late growth stage of Arabidopsis stems is important for understanding the mechanisms regulating the cell wall integrity. The fact that whole plant stems are used as biomass feedstocks and the mixing of intracellular proteins with the cell wall proteome caused by an increasing proportion of broken cells of stems at the late growth stage pose a challenge in identifying these GHs and CEs. Here, we used a CaCl2-extraction procedure to isolate non-structural proteins from Arabidopsis whole stems, followed by protein solution method for direct identification of stem proteins, and by SDS-PAGE separation and protein gel band method for improving the identification of stem proteins, using Nano-LC-MS/MS analysis. Totally, 75 and 236 stem proteins were identified by using these two methods, respectively, confirming the later method (i.e. protein gel method) identified three time more stem proteins. Among these proteins, based on cell wall protein databases and data mining analyses, 6 and 22 proteins were identified as cell wall proteins from the late growth stage Arabidopsis stems, by using these two methods respectively.

2015-05-11 | PXD001851 | Pride

PacBio Iso-seq of Lupinus angustifolius L. leaf and stem transcriptomes

Project description:PacBio Iso-seq of Lupinus angustifolius L. leaf and stem transcriptomes

| PRJEB105680 | ENA

Alfalfa (Medicago sativa L.) pho2 mutant plants hyperaccumulate phosphate [Iso-seq]

Project description:RNA-seq and Iso-seq reads used used for gene charaterization. Pacbio amplicon sequencing reads used for mutant characterization

2022-03-31 | GSE197480 | 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