title: Genome-wide gene expression analysis reveals major chickpea and lentil genes associated with branching
design: Genome-wide gene expression analysis reveals major chickpea and lentil genes associated with branching
library_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).