{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"omics_type":["Unknown","Transcriptomics","Genomics","Proteomics"],"submitter":["Jean-Francois Rami"],"instrument_platform":["Illumina HiSeq 4000"],"study_type":["RNA-seq of total RNA"],"organism":["Arachis hypogaea"],"species":["Arachis hypogaea"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-MTAB-15520"],"description":["In this study, we conducted RNA-Seq during pod development at 20 and 40 days after flowering (DAF20 and DAF40, respectively) to identify differentially expressed genes (DEGs) within a fine-mapped region of 168.37 kb associated with pod and seed size variation during peanut domestication."],"repository":["biostudies-arrayexpress"],"sample_protocol":["Nucleic Acid Extraction - Total RNA was extracted using RNeasy Lipid Tissue Mini kit (Qiagen), following the manufacturer’s procedure. RNA quality and quantity were assessed using a TapeStation 4200 System (Aligent Technologies).","Growth Protocol - The four genotypes were grown at the Centre d’Étude Régional pour l’Amélioration de l’Adaptation à la Sécheresse (CERAAS) under screenhouse conditions.","Sequencing - The quality of each pool (fragments size and libraries quantity at 20 nM) was assessed using the TapeStation 4200 System and cDNA fragments of approximately 299 bp were sequenced on an Illumina HiSeq4000 sequencer (Genewiz, Germany). The sequencing generated paired-end reads of 150 nucleotides.","Library Construction - cDNA libraries were constructed for each sample using 1 µg of total RNA. Different index codes were added to each sample for identification. Briefly, cDNA libraries construction was carried out as following: first, mRNA was isolated using oligo-dT attached magnetic beads. Then, mRNA was fragmented, using divalent cations under elevated temperature (65°C for 5 min), before double strand cDNA synthesis. After these steps, adenylation and adaptor ligation were performed. Subsequently, an enrichment of cDNA fragments, consisting of PCR amplification, was carried out to constitute the libraries. Finally, two equimolar pools (pool 1: all samples at DAF20 and pool 2: all samples at DAF40) of cDNA libraries were formed according to the indexes used.","Sample Collection - Fresh pods were harvested at two time points: 20 days after flowering (DAF20) and 40 days after flowering (DAF40). These stages correspond to early and middle pod development, respectively, as reported in previous studies. For each genotype and at each developmental stage, pods were collected from three independent plants that exhibited similar size and appearance. The pods were rapidly pooled together and immediately frozen in liquid nitrogen for total RNA extraction."],"figure_sub":["Organization","MINSEQE Score","Assays and Data","MAGE-TAB Files"],"pubmed_authors":["Jean-Francois Rami"],"additional_accession":[]},"is_claimable":false,"name":"Structural variations, gene polymorphism and expression reveal major candidate genes associated with pod and seed size variation during peanut (Arachis hypogaea L.) domestication","description":"In this study, we conducted RNA-Seq during pod development at 20 and 40 days after flowering (DAF20 and DAF40, respectively) to identify differentially expressed genes (DEGs) within a fine-mapped region of 168.37 kb associated with pod and seed size variation during peanut domestication.","dates":{"release":"2025-09-26T00:00:00Z","modification":"2025-09-26T01:04:50.922Z","creation":"2025-09-02T10:35:28.58Z"},"accession":"E-MTAB-15520","cross_references":{"ENA":["ERP179473"],"EFO":["EFO_0002944","EFO_0004170","EFO_0009653","EFO_0003789","EFO_0005518","EFO_0004184"]}}