{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"submitter":["Waritthorn Thanakarn"],"organism":["Halomonas sp."],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-MTAB-15059"],"description":["Whole genome sequencing was performed on Halomonas sp. DSM7328 both original strain and evolved population in low dissolved oxygen (DO) level at 0.5% DO. The evolved Halomonas sp. DSM7328 was analysed and compared to the original strain."],"repository":["biostudies-arrayexpress"],"sample_protocol":["Sequencing - The library pool was denatured and sequenced on the MiSeq instrument (Illumina, San Diego, US) at 12pM, using a V3 600 cycle kit (paired end reads; 2 x 300bp).","Library Construction - The sequencing library was constructed from 300 ng genomic DNA sample using the Illumina DNA Prep kit with Unique Dual Indexes. The library pool concentration was estimated using the Qubit dsDNA HS assay (Life Technologies). The library pool size was confirmed using the Agilent TapeStation 4200 (Agilent HS D1000 assay).","Nucleic Acid Extraction - DNA from Halomonas sp. DSM7328 samples was extracted using DNeasy Blood & Tissue Kit (Qiagen) according to the manufacturer's protocols with pre-treatment of enzymatic lysis buffer.","Sample Collection - Evolved population and original strain of Halomonas sp. DSM7328 were collected after overnight cultivation. Cell numbers around 2 x 10^9 cells were used for extraction."],"figure_sub":["Organization","MINSEQE Score","Assays and Data","Processed Data","MAGE-TAB Files"],"data_protocol":["Data Transformation - Samples were quality and adapter trimmed using fastp. The trimmed reads were run through Kraken using the standard-8 database. Kraken output was processed using Bracken to estimate abundances. Raw reads for the original strain sample were then processed through Bactopia pipeline. Reads were quality trimmed and assembled using Unicycler and annotated with Prokka within the Bactopia framework. The annotated consensus was imported to CLC Genomics Workbench v11.01."],"omics_type":["Unknown","Transcriptomics","Genomics","Proteomics"],"instrument_platform":["Illumina MiSeq"],"study_type":["DNA-seq"],"species":["Halomonas sp."],"pubmed_authors":["Waritthorn Thanakarn"],"additional_accession":[]},"is_claimable":false,"name":"DNA-seq of Halomonas sp. DSM7328 original strain and evolved population in low dissolved oxygen level","description":"Whole genome sequencing was performed on Halomonas sp. DSM7328 both original strain and evolved population in low dissolved oxygen (DO) level at 0.5% DO. The evolved Halomonas sp. DSM7328 was analysed and compared to the original strain.","dates":{"release":"2026-04-15T00:00:00Z","modification":"2026-04-17T01:01:29.347Z","creation":"2025-04-17T15:46:26.189Z"},"accession":"E-MTAB-15059","cross_references":{"ENA":["ERP171781"],"EFO":["EFO_0002944","EFO_0004170","EFO_0002693","EFO_0005518","EFO_0003816","EFO_0004184"]}}