BioSample Accession(s)

SAMN51516533, SRS26763954

collection_date

2016-05

geo_loc_name

Canada: Saint-douard-de-Lotbinire

host

Acer

isolation_source

Commercially collected maple sap

sample_type

Bacterial genome

strain

LF135

Metadata as EBI XML

<EXPERIMENT_SET>
<EXPERIMENT accession="SRX30748060" alias="MSP_LF135" center_name="SUB15675063" broker_name="NCBI">
  <IDENTIFIERS>
    <PRIMARY_ID>SRX30748060</PRIMARY_ID>
    <SUBMITTER_ID namespace="SUB15675063">MSP_LF135</SUBMITTER_ID>
  </IDENTIFIERS>
  <TITLE>Pseudomonas strains isolated from maple sap</TITLE>
  <STUDY_REF accession="SRP630254">
    <IDENTIFIERS>
      <PRIMARY_ID>SRP630254</PRIMARY_ID>
      <EXTERNAL_ID namespace="BioProject">PRJNA1330368</EXTERNAL_ID>
    </IDENTIFIERS>
  </STUDY_REF>
  <DESIGN>
    <DESIGN_DESCRIPTION>Genomic DNA was extracted from Pseudomonas isolates using the Qiagen Blood and Tissue Kit according to the manufacturers instructions. DNA quality was verified by agarose gel electrophoresis and quantified using a NanoDrop spectrophotometer. Sequencing libraries were prepared following standard Illumina protocols with random fragmentation of genomic DNA and paired-end adapter ligation. Libraries were sequenced on an Illumina MiSeq platform. Raw reads were quality-checked with FastQC and trimmed using Trimmomatic to remove low-quality bases. De novo assembly was performed with SPAdes (v3.15.5), and resulting scaffolds were filtered for length (>1000 bp). Assembly quality and completeness were evaluated using QUAST and BUSCO, and contamination was assessed with CheckM.</DESIGN_DESCRIPTION>
    <SAMPLE_DESCRIPTOR accession="SRS26763954">
      <IDENTIFIERS>
        <PRIMARY_ID>SRS26763954</PRIMARY_ID>
        <EXTERNAL_ID namespace="BioSample">SAMN51516533</EXTERNAL_ID>
      </IDENTIFIERS>
    </SAMPLE_DESCRIPTOR>
    <LIBRARY_DESCRIPTOR>
      <LIBRARY_NAME>MSP_LF135</LIBRARY_NAME>
      <LIBRARY_STRATEGY>WGS</LIBRARY_STRATEGY>
      <LIBRARY_SOURCE>GENOMIC</LIBRARY_SOURCE>
      <LIBRARY_SELECTION>RANDOM</LIBRARY_SELECTION>
      <LIBRARY_LAYOUT>
        <PAIRED/>
      </LIBRARY_LAYOUT>
    </LIBRARY_DESCRIPTOR>
  </DESIGN>
  <PLATFORM>
    <ILLUMINA>
      <INSTRUMENT_MODEL>Illumina MiSeq</INSTRUMENT_MODEL>
    </ILLUMINA>
  </PLATFORM>
  <EXPERIMENT_LINKS>
    <EXPERIMENT_LINK>
      <XREF_LINK>
        <DB>ENA-SAMPLE</DB>
        <ID>SRS26763954</ID>
      </XREF_LINK>
    </EXPERIMENT_LINK>
    <EXPERIMENT_LINK>
      <XREF_LINK>
        <DB>ENA-SUBMISSION</DB>
        <ID>SRA2241360</ID>
      </XREF_LINK>
    </EXPERIMENT_LINK>
    <EXPERIMENT_LINK>
      <XREF_LINK>
        <DB>ENA-FASTQ-FILES</DB>
        <ID><![CDATA[https://www.ebi.ac.uk/ena/portal/api/filereport?accession=SRX30748060&result=read_run&fields=run_accession,fastq_ftp,fastq_md5,fastq_bytes]]></ID>
      </XREF_LINK>
    </EXPERIMENT_LINK>
    <EXPERIMENT_LINK>
      <XREF_LINK>
        <DB>ENA-SUBMITTED-FILES</DB>
        <ID><![CDATA[https://www.ebi.ac.uk/ena/portal/api/filereport?accession=SRX30748060&result=read_run&fields=run_accession,submitted_ftp,submitted_md5,submitted_bytes,submitted_format]]></ID>
      </XREF_LINK>
    </EXPERIMENT_LINK>
  </EXPERIMENT_LINKS>
  <EXPERIMENT_ATTRIBUTES>
    <EXPERIMENT_ATTRIBUTE>
      <TAG>ENA-STATUS-ID</TAG>
      <VALUE>4</VALUE>
    </EXPERIMENT_ATTRIBUTE>
  </EXPERIMENT_ATTRIBUTES>
</EXPERIMENT>
</EXPERIMENT_SET>