{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"submitter":["Matteo Buti"],"organism":["Cicer arietinum"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-MTAB-13970"],"description":["The primary objective of this study is to investigate the molecular differences between chickpea varieties with early and late flowering, focusing on gene expression in response to heat stress. Through the analysis of differentially expressed genes under high-temperature conditions, we aim to gain a deeper understanding of the molecular mechanisms underlying early flowering in chickpea. This approach will not only help bridge the current gaps in our scientific knowledge but may also provide valuable insights for the development of targeted genetic improvement strategies to enhance the thermal resilience of chickpea crops."],"repository":["biostudies-arrayexpress"],"sample_protocol":["Nucleic Acid Extraction - Frozen leaves (100mg) have been ground to a fine powder with a previously sterilized mortar and pestle using liquid nitrogen to prevent RNA degradation. RNA extraction was performed using 100 mg of ground material using Zymo Quick RNA miniprep (Zymo Research) with DNAse treatment, following the protocol.","Sample Collection - Leaf tissues of five selected chickpea lines (309E, 309L, 224E, 224L, 4958) were collected before heat stress, after heat stress, and during the recovery, immediately frozen in liquid nitrogen and stored at −80 °C. Three biological replicates were carried out for each genotype and treatment. Frozen leaves were ground to a fine powder with a previously sterilized mortar and pestle using liquid nitrogen to prevent RNA degradation.","Growth Protocol - Seeds were sowed in 4L pots (one plant/pot) containing a mixture of tuff, coarse vermiculite and coarse peat (1:1:1, v/v/v), on 26.1.2022. The pots were supplemented with 10gr of slow-release fertilizer (Osmocote, ICL, Israel) and drip irrigated with tap water. The plants were grown in Beersheva, Israel, in two chambers within a controlled greenhouse under a temperature of 28/18oC (day/night).","Sequencing - Libraries were sequenced on the Illumina Novaseq6000 platform. Sequencing was performed using Novaseq 6000 S1 Reagent Kit (2 x 100 + 10 + 10 bp parameters) using XP mode. Samples were run in a single flow cell lane.","Sample Treatment - Heat stress treatment was achieved in one of the chambers by applying a regime of 38/28oC (day/night) for 4 days during the pod set (from 29.5.2022 to 2.6.2022).","Library Construction - RNA libraries were prepared using Illumina mRNA Prep kit, following the manufacturer instructions and a unique dual index combinations were used for each sample for barcoding. The concentration of each of the libraries was determined using Qubit™ 4 Fluorometer (dsDNA High Sensitivity Kit - Invitrogen)."],"figure_sub":["Organization","MINSEQE Score","Assays and Data","Processed Data","MAGE-TAB Files"],"data_protocol":["Data Transformation - EdgeR package was used to filter out unexpressed or poorly expressed transcript (a transcript was considered to be ‘active’ if the reads per million mapping to that gene were >1 in at least two libraries), and to normalize the RNA libraries depending on their dimension and assigning a CPM value for each active transcript and for each RNA library.","Sequence Alignment - After the adaptor sequences, low-quality bases and sequence shorter than 40 bases were removed using Trimmomatic v0.39, the clea RNA reads were mapped to the ASM33114v1 reference assembly (cultivar CDC Frontier) retrieved from NCBI RefSeq using HiSat2 v2.2.1 with default parameters. Read counts were generated from alignment files using the featureCounts v2.0.3 software with default parameters, according to the transcripts predicted on the reference genome."],"omics_type":["Unknown","Transcriptomics","Genomics","Proteomics"],"instrument_platform":["Illumina NovaSeq 6000"],"study_type":["RNA-seq of coding RNA"],"species":["Cicer arietinum"],"pubmed_authors":["Matteo Buti"],"additional_accession":[]},"is_claimable":false,"name":"Gene expression responses to heat stress in early- and late-flowering chickpea cultivars","description":"The primary objective of this study is to investigate the molecular differences between chickpea varieties with early and late flowering, focusing on gene expression in response to heat stress. Through the analysis of differentially expressed genes under high-temperature conditions, we aim to gain a deeper understanding of the molecular mechanisms underlying early flowering in chickpea. This approach will not only help bridge the current gaps in our scientific knowledge but may also provide valuable insights for the development of targeted genetic improvement strategies to enhance the thermal resilience of chickpea crops.","dates":{"release":"2025-10-20T00:00:00Z","modification":"2025-10-20T10:08:06.157Z","creation":"2024-04-02T14:11:33.716Z"},"accession":"E-MTAB-13970","cross_references":{"ENA":["ERP159124"],"EFO":["EFO_0002944","EFO_0004170","EFO_0003789","EFO_0004917","EFO_0005518","EFO_0003816","EFO_0003738","EFO_0004184","EFO_0003969"]}}