{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"submitter":["Keiichi Mochida"],"organism":["Euglena agilis"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-MTAB-6349"],"description":["We predicted genes and their exon-intron structure for the E. agilis genome based on a transcriptome alignment with RNA-seq reads from E. agilis cells cultured under various conditions."],"repository":["biostudies-arrayexpress"],"sample_protocol":["Nucleic Acid Extraction - Total RNA was extracted from cells using NucleoSpin RNA (Macherey-Nagel, USA).","Library Construction - A sequencing library was constructed using a TruSeq Stranded mRNA LT Sample Preparation Kit (Illumina, Inc.) according to the manufacturer’s instructions (TruSeq Stranded mRNA Sample Preparation Guide Rev. E; Illumina, Inc.).","Growth Protocol - Each culture was maintained in 100 mL volume test tubes for more than 3 days using 50 mL of either culture media type at 29°C with aeration (50 mL/min) and constant illumination (100 μmol photon/m2s).","Sample Collection - We cultured E. agilis in mAC, AF-6, and C media for mRNA preparation. E","Sequencing - Clonal clusters of each library were generated using cBot with a TruSeq PE Cluster Kit v3 – cBot – HS (Illumina, Inc.) and sequenced using a Hiseq 2000 sequencer with a TruSeq SBS Kit v2 – HS (Illumina, Inc.) by the paired-end sequencing method for sequences 100 bp in length. The sequence data were analysed using HCS v2.0.12, RTA v1.17.21.3 and CASAVA v1.8.2 (Illumina, Inc.)."],"figure_sub":["Organization","MINSEQE Score","Assays and Data","Processed Data","MAGE-TAB Files"],"data_protocol":["Data Transformation - Using the mapping result with reads of MQ ≥ 1, exon-intron structures of transcribed regions were predicted using StringTie (ver. 1.3.0) with the parameter settings of -p = 30, -f = 0.5, -g = 20, and -c = 5.","Sequence Alignment - The quality-checked RNA-seq reads of E. agiliswere mapped to each of the genome sequences, respectively, using HISAT2 (ver. 2.0.5) with the parameter setting of --pen-noncansplice = 0 -no-softclip."],"omics_type":["Metabolomics","Unknown","Transcriptomics","Genomics","Proteomics"],"instrument_platform":["Illumina HiSeq 2000"],"study_type":["RNA-seq of coding RNA"],"species":["Euglena agilis"],"pubmed_authors":["Keiichi Mochida"],"additional_accession":[]},"is_claimable":false,"name":"Strand-specific RNA-seq in Euglena agilis","description":"We predicted genes and their exon-intron structure for the E. agilis genome based on a transcriptome alignment with RNA-seq reads from E. agilis cells cultured under various conditions.","dates":{"release":"2025-09-01T00:00:00Z","modification":"2025-09-01T01:02:25.27Z","creation":"2022-03-14T16:25:06.841Z"},"accession":"E-MTAB-6349","cross_references":{"ENA":["ERP106156"],"EFO":["EFO_0002944","EFO_0004170","EFO_0003789","EFO_0004917","EFO_0003816","EFO_0005518","EFO_0003738","EFO_0004184"]}}