{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"submitter":["Nicolas Negre"],"organism":["Spodoptera frugiperda"],"software":["nf-core/rnaseq v3.10.1"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-MTAB-14826"],"description":["Spodoptera frugiperda is a major crop pest worldwide. In its native are - the american continent- two mitochondrial strains have been described with different host-plant preferences: the corn strain (or SfC) and the rice strain (SfR). We have previously showed that constitutive differences existed between the strains at the transcriptomic level and were associated to mitochondrial differential expression. To determine whether maternal inheritance was impacting overall expression variations between the strains and eventually their physiological differences, we performed again RNA-seq experiment on the two strains and their F1 reciprocal hybrids (CR and RC) in triplicate, in laboratory conditions when fed on artificial diet and not on plant diet as to avoid the induced challenge by the plant diet on gene expression and focus only on the intrinsic differences."],"repository":["biostudies-arrayexpress"],"sample_protocol":["Sequencing - Quantified libraries will be pooled and sequenced on Illumina platforms, according to effective library concentration and data amount.","Growth Protocol - Larvae were reared on individual cups with artificial diet. 3à larvae per genotype, in triplicate have been reared in parallel in the same conditions within an incubator of the DGIMI quarantine facility for insects (PIQ).","Library Construction - Libraries have been performed on total RNA by Novogene. Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers followed by the second strand cDNA synthesis. The library was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification. The library was checked with Qubit and real-time PCR for quantification and bioanalyzer for size distribution detection.","Sample Treatment - No treatment has been performed. The experimental design consists of parralel rearing of four different genotypes. Two parental strains CC and RR, and their reciprocal hybrids CR and RC (first letter is the mother type).","Nucleic Acid Extraction - Homogenate was then processed with the AllPrep DNA/RNA kit (Qiagen # 80204) according to manufacturer's protocol to purify bot DNA and RNA from the same sample. DNA contaminants from RNA sample was removed by TURBO-DNA-free kit (Invitrogen # AM1907). Amount and purity of DNA was measured by Nanodrop to match the requirements of the sequencing company (Novogene).","Sample Collection - Rearing of 30 larvae per genotype has been performed in individual cups filled with artificial diet. 1 day after molting of 4th instar larvae (L4), individual caterpillars were placed in a 2 mL Eppendorf tube with RLT Plus buffer from AllPrepr DNA/RNA kit  (Qiagen). Larvae were then immediately disrupted and homogenized with a TissueLyser II (Qiagen #85300) with the aid of a 5mm metal bead."],"figure_sub":["Organization","MINSEQE Score","Assays and Data","Processed Data","MAGE-TAB Files"],"data_protocol":["Data Transformation - In the nf-core/rnaseq pipeline, DESeq2 is used to normalize the data.","Sequence Alignment - The fastq files from sequencing were processed by the nf-core/rnaseq workflo (v 3.10.1) on the Genouest cluster. In this pipeline the alignment is performed by STAR on the reference genome v7.0 (BIPAA).  The counting was performed by feature counts using the gff file of our OGSv7.1 annotation of the genome."],"omics_type":["Metabolomics","Unknown","Transcriptomics","Genomics","Proteomics"],"instrument_platform":["Illumina HiSeq 2000"],"study_type":["RNA-seq of coding RNA"],"species":["Spodoptera frugiperda"],"pubmed_authors":["Nicolas Negre"],"additional_accession":[]},"is_claimable":false,"name":"RNA-seq of Spodoptera frugiperda larvae strains (SfC and SfR) and hybrids (CR and RC)","description":"Spodoptera frugiperda is a major crop pest worldwide. In its native are - the american continent- two mitochondrial strains have been described with different host-plant preferences: the corn strain (or SfC) and the rice strain (SfR). We have previously showed that constitutive differences existed between the strains at the transcriptomic level and were associated to mitochondrial differential expression. To determine whether maternal inheritance was impacting overall expression variations between the strains and eventually their physiological differences, we performed again RNA-seq experiment on the two strains and their F1 reciprocal hybrids (CR and RC) in triplicate, in laboratory conditions when fed on artificial diet and not on plant diet as to avoid the induced challenge by the plant diet on gene expression and focus only on the intrinsic differences.","dates":{"release":"2025-06-30T00:00:00Z","modification":"2025-02-11T17:56:03.634Z","creation":"2025-02-11T17:44:58.965Z"},"accession":"E-MTAB-14826","cross_references":{"ENA":["ERP169145"],"Biostudies":["E-MTAB-6540"],"EFO":["EFO_0002944","EFO_0004170","EFO_0003789","EFO_0004917","EFO_0005518","EFO_0003816","EFO_0003738","EFO_0004184","EFO_0003969"]}}