Keywords: GSC:MIxS;MIGS:6.0

strain

PSNIH6

collection_date

2015

isol_growth_condt

missing

ref_biomaterial

missing

env_feature

not collected

type-material

type strain of Pantoea alvi

INSDC secondary accession

SRS2916983

organism

Pantoea alvi

NCBI submission package

MIGS.ba.6.0

env_material

not collected

num_replicons

missing

geo_loc_name

USA

env_biome

human-associated habitat

lat_lon

38.984652 N 77.094709 W

BioSampleModel

MIGS.ba

ENA-FIRST-PUBLIC

2015-11-23

ENA-LAST-UPDATE

2023-11-27

Metadata as EBI XML

<EXPERIMENT_SET>
<EXPERIMENT accession="SRX3652526" alias="MISEQ_PSNIH6_L11324044" center_name="NISC" broker_name="NCBI">
  <IDENTIFIERS>
    <PRIMARY_ID>SRX3652526</PRIMARY_ID>
    <SUBMITTER_ID namespace="NISC">MISEQ_PSNIH6_L11324044</SUBMITTER_ID>
  </IDENTIFIERS>
  <TITLE>Illumina MiSeq Sequencing of Pantoea sp. PSNIH6 Genomic Paired-end Library</TITLE>
  <STUDY_REF accession="SRP131199" refcenter="NISC">
    <IDENTIFIERS>
      <PRIMARY_ID>SRP131199</PRIMARY_ID>
      <EXTERNAL_ID namespace="BioProject">PRJNA430813</EXTERNAL_ID>
    </IDENTIFIERS>
  </STUDY_REF>
  <DESIGN>
    <DESIGN_DESCRIPTION>Illumina MiSeq 2x300 sequencing of Pantoea sp. PSNIH6 whole genome paired-end library</DESIGN_DESCRIPTION>
    <SAMPLE_DESCRIPTOR accession="SRS2916983">
      <IDENTIFIERS>
        <PRIMARY_ID>SRS2916983</PRIMARY_ID>
        <EXTERNAL_ID namespace="BioSample">SAMN04287067</EXTERNAL_ID>
      </IDENTIFIERS>
    </SAMPLE_DESCRIPTOR>
    <LIBRARY_DESCRIPTOR>
      <LIBRARY_NAME>PSNIH6_L11324044</LIBRARY_NAME>
      <LIBRARY_STRATEGY>WGS</LIBRARY_STRATEGY>
      <LIBRARY_SOURCE>GENOMIC</LIBRARY_SOURCE>
      <LIBRARY_SELECTION>RANDOM</LIBRARY_SELECTION>
      <LIBRARY_LAYOUT>
        <PAIRED NOMINAL_LENGTH="500" NOMINAL_SDEV="50"/>
      </LIBRARY_LAYOUT>
      <LIBRARY_CONSTRUCTION_PROTOCOL>Nextera DNA Sample Preparation Kit</LIBRARY_CONSTRUCTION_PROTOCOL>
    </LIBRARY_DESCRIPTOR>
    <SPOT_DESCRIPTOR>
      <SPOT_DECODE_SPEC>
        <SPOT_LENGTH>600</SPOT_LENGTH>
        <READ_SPEC>
          <READ_INDEX>0</READ_INDEX>
          <READ_CLASS>Application Read</READ_CLASS>
          <READ_TYPE>Forward</READ_TYPE>
          <BASE_COORD>1</BASE_COORD>
        </READ_SPEC>
        <READ_SPEC>
          <READ_INDEX>1</READ_INDEX>
          <READ_CLASS>Application Read</READ_CLASS>
          <READ_TYPE>Reverse</READ_TYPE>
          <BASE_COORD>301</BASE_COORD>
        </READ_SPEC>
      </SPOT_DECODE_SPEC>
    </SPOT_DESCRIPTOR>
  </DESIGN>
  <PLATFORM>
    <ILLUMINA>
      <INSTRUMENT_MODEL>Illumina MiSeq</INSTRUMENT_MODEL>
    </ILLUMINA>
  </PLATFORM>
  <PROCESSING>
    <PIPELINE>
      <PIPE_SECTION>
        <STEP_INDEX>1</STEP_INDEX>
        <PREV_STEP_INDEX>NIL</PREV_STEP_INDEX>
        <PROGRAM>RTA</PROGRAM>
        <VERSION>1.18.54</VERSION>
      </PIPE_SECTION>
    </PIPELINE>
  </PROCESSING>
  <EXPERIMENT_LINKS>
    <EXPERIMENT_LINK>
      <XREF_LINK>
        <DB>ENA-SAMPLE</DB>
        <ID>SRS2916983</ID>
      </XREF_LINK>
    </EXPERIMENT_LINK>
    <EXPERIMENT_LINK>
      <XREF_LINK>
        <DB>ENA-SUBMISSION</DB>
        <ID>SRA656343</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=SRX3652526&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=SRX3652526&result=read_run&fields=run_accession,submitted_ftp,submitted_md5,submitted_bytes,submitted_format]]></ID>
      </XREF_LINK>
    </EXPERIMENT_LINK>
  </EXPERIMENT_LINKS>
</EXPERIMENT>
</EXPERIMENT_SET>