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ERX11781233: Genome-wide gene expression analysis reveals major chickpea and lentil genes associated with branching
1 ILLUMINA (Illumina NovaSeq 6000) run: 9.3M spots, 1.9G bases, 641.2Mb downloads

Design: Genome-wide gene expression analysis reveals major chickpea and lentil genes associated with branching
Submitted by: EBI (European Bioinformatics Institute)
Study: Genome-wide gene expression analysis reveals major chickpea and lentil genes associated with branching
show Abstracthide Abstract
Chickpea and lentil are two important pulse crops used for human consumption as sources of vegetable protein, rich in amino acids and bioactive compounds. The search for elite cultivars with better architecture has been a demand by farmers of these two crops, which aims to systematize their mechanized planting and harvesting on a large scale. Therefore, the identification of genes associated with the regulation of the branching and architecture of these plants has currently gained great importance. This work aimed to gain insight into transcriptomic changes of two contrasting chickpea and lentil cultivars in terms of branching pattern (little versus highly branched cultivars). In addition, we aimed to identify candidate genes involved in the regulation of shoot branching that could be used as future targets for molecular breeding. The axillary and apical buds of chickpea cultivars Blanco lechoso and FLIP07-318C, and lentil cultivars Castellana and Campisi, considered as little and highly branched, respectively, were harvested.
Sample: BX1
SAMEA115078241 • ERS17691980 • All experiments • All runs
Organism: Cicer arietinum
Library:
Name: BX1_p
Instrument: Illumina NovaSeq 6000
Strategy: RNA-Seq
Source: TRANSCRIPTOMIC
Selection: RANDOM
Layout: PAIRED
Construction protocol: Axillary and apical buds were collected separately from at least 15 plants randomized per biological replicate after 20 days of transplanting and the samples were kept in liquid nitrogen. Seeds of the chickpea and lentil cultivars were superficially sterilized with 1.5% sodium hypochlorite solution for 1 minute, washed abundantly with distilled water, soaked for 3 minutes in distilled water, and germinated in Petri plates containing humid filter paper during three days at room temperature. The germinated seeds with a 1-2 cm radicle were transferred to pots containing commercial substrate and kept well-watered and fertilized under greenhouse conditions. Frozen tissues (50-100 mg) were ground to a fine powder with a mortar and pestle using liquid nitrogen. The total RNA was purified with GenUP™ Total RNA Kit (Biotechrabbit, Volmerstraße, Berlin, Germany). The RNA integrity was checked in through agarose electrophoresis, while the concentration of total RNA was measured using a Qubit 4 Fluorometer and appropriate Qubit kit (Invitrogen, Waltham, Massachusetts, USA). The purity and integrity of RNA were confirmed by the Agilent Bioanalyser 2100 system (RNA 6000 Nano Kit, Agilent Technologies, Santa Clara, CA, USA). Twenty-four sequencing libraries were prepared using Truseq Stranded mRNA Library Prep and Truseq RNA Single Indexes (Illumina, San Diego, CA, USA) following the manufacturer's instructions. A unique dual index combination was used for each sample/library for barcoding. The concentration of each of the 24 libraries was determined using the Qubit 4 Fluorometer and the dsDNA High Sensitivity Kit (Invitrogen).
Runs: 1 run, 9.3M spots, 1.9G bases, 641.2Mb
Run# of Spots# of BasesSizePublished
ERR124051709,290,5031.9G641.2Mb2024-07-20

ID:
33933346

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