biostudies-arrayexpressKeiichi MochidaEuglena agilishttps://www.ebi.ac.uk/biostudies/studies/E-MTAB-6349We 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.biostudies-arrayexpressNucleic 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. ESequencing - 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.).OrganizationMINSEQE ScoreAssays and DataProcessed DataMAGE-TAB FilesData 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.MetabolomicsUnknownTranscriptomicsGenomicsProteomicsIllumina HiSeq 2000RNA-seq of coding RNAEuglena agilisKeiichi MochidafalseStrand-specific RNA-seq in Euglena agilisWe 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.2025-09-01T00:00:00Z2025-09-01T01:02:25.27Z2022-03-14T16:25:06.841ZE-MTAB-6349ERP106156EFO_0002944EFO_0004170EFO_0003789EFO_0004917EFO_0003816EFO_0005518EFO_0003738EFO_0004184