title: 7S
organism: metagenome
description: Protocols: Samples of bed sediment where collected using a standard 1m drop corer with an internal plastic sleeve, or where recovered from commercial dredging operations. All samples where stored at 4C prior to analysis. 0.25 g of samples of the sediment and the corrosion blisters were extracted using the optimised Power Soil DNA Isolation kit (MoBio Laboratories) methods. Prior to the microbiome analysis, raw reads were de-barcoded based on the unique forward and reverse inline-barcode sequences. To preserve only high-quality reads, sequencing errors in the inline-barcodes and primer sequences were not tolerated. Additionally, reads with ambiguous bases (N) were removed. Inline-barcodes as well as primer sequences were clipped from the reads. The remaining set of high-quality reads was processed using minimum entropy decomposition (Eren AM, 2013 and 2015).To assign taxonomic information to each OTU, BLAST alignments of cluster representative sequences to the NCBI sequence database were performed. A most specific taxonomic assignment for each OTU was then transferred from the set of best-matching reference sequences. Hereby, a sequence identity of 80% across at least 80% of the representative sequence was a minimal requirement for considering reference sequences.Further processing of OTUs and taxonomic assignments was performed using the QIIME software package (version1.8.0, http://qiime.org/).
attributes.tag: ENA-FIRST-PUBLIC
attributes.value: 2019-10-06T04:03:27Z
attributes.tag: ENA-LAST-UPDATE
attributes.value: 2019-09-26T11:36:23Z
attributes.tag: External Id
attributes.value: SAMEA5976175
attributes.tag: INSDC center name
attributes.value: School of Environment and Technology, University of Brighton.
attributes.tag: INSDC first public
attributes.value: 2019-10-06T04:03:27Z
attributes.tag: INSDC last update
attributes.value: 2019-09-26T11:36:23Z
attributes.tag: INSDC status
attributes.value: public
attributes.tag: Submitter Id
attributes.value: E-MTAB-8373:7S
attributes.tag: broker name
attributes.value: ArrayExpress
attributes.tag: geographical location
attributes.value: Shoreham Harbour, Dredger Berth
attributes.tag: sample name
attributes.value: E-MTAB-8373:7S
attributes.tag: sampling site
attributes.value: sediment sample 0cm
attributes.tag: scientific_name
attributes.value: metagenome