{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"omics_type":["Metabolomics","Unknown","Transcriptomics","Genomics","Proteomics"],"submitter":["Raya Faigenbaum-Romm"],"instrument_platform":["ILMN DNA LP (M) Tagmentation (24 Samples, IPB) 20060060","DNeasy Blood & Tissue Kit (Qiagen)","NextSeq 550"],"study_type":["DNA-seq"],"organism":["Escherichia coli"],"species":["Escherichia coli"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-MTAB-13428"],"description":["Bacteria from anaerobic Microcolony-seq condition that were kept at the -80C were regrown in liquid LB at 37C for 5 hours. DNA was extracted from 1 mL of bacteria using the DNeasy Blood & Tissue Kit (Qiagen). Library preparation and sequencing was carried out by the Genomics Applications Laboratory, Core Research Facility, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel. DNA libraries for sequencing were prepared using the kit (ILMN DNA LP (M) Tagmentation (24 Samples, IPB) 20060060) (Illumina, Inc., USA) according to manufacturing instructions. At least 100X sequencing depth for each nucleotide in each sample was targeted. Samples were deep-sequenced with the Nextseq500 machine using the 150-cycle mid output kit (Illumina, Inc., USA) from the forward read direction."],"repository":["biostudies-arrayexpress"],"sample_protocol":["Sequencing - At least 100X sequencing depth for each nucleotide in each sample was targeted. Samples were deep-sequenced with the Nextseq500 machine using the 150-cycle mid output kit (Illumina, Inc., USA) from the forward read direction.","Sample Collection - Microcolonies were selected from an anaerobic LB plate are kept at -80C. Bacteria were regrown in LB at 37C with shaking for 5h.","Nucleic Acid Extraction - DNA was extracted from 1 mL of bacteria using the DNeasy Blood & Tissue Kit (Qiagen).","Library Construction - Library preparation and sequencing was carried out by the Genomics Applications Laboratory, Core Research Facility, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel. DNA libraries for sequencing were prepared using the kit (ILMN DNA LP (M) Tagmentation (24 Samples, IPB) 20060060) (Illumina, Inc., USA) according to manufacturing instructions."],"figure_sub":["Organization","MINSEQE Score","Assays and Data","MAGE-TAB Files"],"pubmed_authors":["Raya Faigenbaum-Romm"],"additional_accession":[]},"is_claimable":false,"name":"Whole genome sequencing of EPEC microcolonies from anaerobic conditions","description":"Bacteria from anaerobic Microcolony-seq condition that were kept at the -80C were regrown in liquid LB at 37C for 5 hours. DNA was extracted from 1 mL of bacteria using the DNeasy Blood & Tissue Kit (Qiagen). Library preparation and sequencing was carried out by the Genomics Applications Laboratory, Core Research Facility, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel. DNA libraries for sequencing were prepared using the kit (ILMN DNA LP (M) Tagmentation (24 Samples, IPB) 20060060) (Illumina, Inc., USA) according to manufacturing instructions. At least 100X sequencing depth for each nucleotide in each sample was targeted. Samples were deep-sequenced with the Nextseq500 machine using the 150-cycle mid output kit (Illumina, Inc., USA) from the forward read direction.","dates":{"release":"2025-08-04T00:00:00Z","modification":"2025-08-05T00:01:32.034Z","creation":"2023-10-14T14:53:38.578Z"},"accession":"E-MTAB-13428","cross_references":{"ENA":["ERP152494"],"EFO":["EFO_0002944","EFO_0004170","EFO_0002693","EFO_0005518","EFO_0004184"]}}