Strain isolated from a diseased onion bulb. Strain is HiVir+ (pathogenic on onions) and Alt+.

BioSample Accession(s)

SAMN22046685

biomaterial provider

Steven Beer, Cornell University

collected by

grower

collection date

2015

env_broad_scale

area of cropland [ENVO:01000892]

geo loc name

USA: Oregon

host

Allium cepa

host_tissue_sampled

bulb [BTO:0000159]

identified by

Jean Bonasera

sample type

cell culture

strain

AR5

Metadata as EBI XML

<EXPERIMENT_SET>
<EXPERIMENT accession="SRX21767590" alias="AR5_nanopore" center_name="SUB13838429" broker_name="NCBI">
  <IDENTIFIERS>
    <PRIMARY_ID>SRX21767590</PRIMARY_ID>
    <SUBMITTER_ID namespace="SUB13838429">AR5_nanopore</SUBMITTER_ID>
  </IDENTIFIERS>
  <TITLE>Genomic sequence of Pantoea agglomerans AR5: Nanopore reads</TITLE>
  <STUDY_REF accession="SRP270336">
    <IDENTIFIERS>
      <PRIMARY_ID>SRP270336</PRIMARY_ID>
      <EXTERNAL_ID namespace="BioProject">PRJNA642846</EXTERNAL_ID>
    </IDENTIFIERS>
  </STUDY_REF>
  <DESIGN>
    <DESIGN_DESCRIPTION>High molecular weight genomic DNA was extracted (Miller et al. 1988) with the following modifications: the pre-lysozyme lysis buffer was 1M Tris pH 7.5, 0.5M EDTA pH 8.0, 5M NaCl, lysozyme digestion was performed at 48C for 1h, DNA resuspension was in 10 mM Tris pH 7.5, RNAse treatment was followed by two additional washes. DNA quantity was assessed using a Qubit 3.0 fluorometer (Thermo Fisher Scientific, U.S.A.). DNA integrity was assessed by agarose gel electrophoresis. The isolated DNA was used to prepare a Nanopore sequencing library using the ONT Rapid Barcoding Sequencing kit (SQK-RBK004). The sequencing reaction was run in a MinION flow cell. Base calling was performed using Guppy v. 4.4.1 and de-multiplexed with QCAT.</DESIGN_DESCRIPTION>
    <SAMPLE_DESCRIPTOR accession="SRS18873874">
      <IDENTIFIERS>
        <PRIMARY_ID>SRS18873874</PRIMARY_ID>
        <EXTERNAL_ID namespace="BioSample">SAMN22046685</EXTERNAL_ID>
      </IDENTIFIERS>
    </SAMPLE_DESCRIPTOR>
    <LIBRARY_DESCRIPTOR>
      <LIBRARY_NAME>AR5_nanopore</LIBRARY_NAME>
      <LIBRARY_STRATEGY>WGS</LIBRARY_STRATEGY>
      <LIBRARY_SOURCE>GENOMIC</LIBRARY_SOURCE>
      <LIBRARY_SELECTION>RANDOM</LIBRARY_SELECTION>
      <LIBRARY_LAYOUT>
        <SINGLE/>
      </LIBRARY_LAYOUT>
    </LIBRARY_DESCRIPTOR>
  </DESIGN>
  <PLATFORM>
    <OXFORD_NANOPORE>
      <INSTRUMENT_MODEL>MinION</INSTRUMENT_MODEL>
    </OXFORD_NANOPORE>
  </PLATFORM>
  <EXPERIMENT_LINKS>
    <EXPERIMENT_LINK>
      <XREF_LINK>
        <DB>ENA-SAMPLE</DB>
        <ID>SRS18873874</ID>
      </XREF_LINK>
    </EXPERIMENT_LINK>
    <EXPERIMENT_LINK>
      <XREF_LINK>
        <DB>ENA-SUBMISSION</DB>
        <ID>SRA1711286</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=SRX21767590&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=SRX21767590&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>

Metadata as EBI XML

<EXPERIMENT_SET>
<EXPERIMENT accession="SRX21767591" alias="AR5_illumina" center_name="SUB13838429" broker_name="NCBI">
  <IDENTIFIERS>
    <PRIMARY_ID>SRX21767591</PRIMARY_ID>
    <SUBMITTER_ID namespace="SUB13838429">AR5_illumina</SUBMITTER_ID>
  </IDENTIFIERS>
  <TITLE>Genomic sequence of Pantoea agglomerans AR5: Illumina reads</TITLE>
  <STUDY_REF accession="SRP270336">
    <IDENTIFIERS>
      <PRIMARY_ID>SRP270336</PRIMARY_ID>
      <EXTERNAL_ID namespace="BioProject">PRJNA642846</EXTERNAL_ID>
    </IDENTIFIERS>
  </STUDY_REF>
  <DESIGN>
    <DESIGN_DESCRIPTION>High molecular weight genomic DNA was extracted (Miller et al. 1988) with the following modifications: the pre-lysozyme lysis buffer was 1M Tris pH 7.5, 0.5M EDTA pH 8.0, 5M NaCl, lysozyme digestion was performed at 48C for 1h, DNA resuspension was in 10 mM Tris pH 7.5, RNAse treatment was followed by two additional washes. DNA quantity was assessed using a Qubit 3.0 fluorometer (Thermo Fisher Scientific, U.S.A.). DNA integrity was assessed by agarose gel electrophoresis. For short-read sequencing, was prepared by the Cornell Genomics Facility, part of the Biotechnology Resource Center using the the DNA library Nextera DNA Flex Library Prep Kit (Illumina). The DNA library was sequenced on a MiSeq platform (Illumina, USA).</DESIGN_DESCRIPTION>
    <SAMPLE_DESCRIPTOR accession="SRS18873874">
      <IDENTIFIERS>
        <PRIMARY_ID>SRS18873874</PRIMARY_ID>
        <EXTERNAL_ID namespace="BioSample">SAMN22046685</EXTERNAL_ID>
      </IDENTIFIERS>
    </SAMPLE_DESCRIPTOR>
    <LIBRARY_DESCRIPTOR>
      <LIBRARY_NAME>AR5_illumina</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>SRS18873874</ID>
      </XREF_LINK>
    </EXPERIMENT_LINK>
    <EXPERIMENT_LINK>
      <XREF_LINK>
        <DB>ENA-SUBMISSION</DB>
        <ID>SRA1711286</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=SRX21767591&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=SRX21767591&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>