gap_accession

phs001237

submitter_handle

WHI_SHARe

biospecimen_repository

WHI_SHARe

study_name

NHLBI TOPMed: Women's Health Initiative (WHI)

study_design

Prospective Longitudinal Cohort

biospecimen_repository_sample_id

NWD421994

submitted_sample_id

NWD421994

submitted_subject_id

718066

gap_sample_id

2203445

gap_subject_id

1440960

sex

female

tissue

Blood

analyte_type

DNA

is_tumor

No

molecular_data_type

SNP/CNV Genotypes (NGS)

gap_consent_code

1

gap_consent_short_name

HMB-IRB

ncbi_package

Generic.1.0

Cattle rumen microbiome bin 10674_0011_idba_bin.59

assembly software

IDBA-UD; v1.1.3; --num_threads 16 --pre_correction --min_contig 300

environment (material)

bodily fluid

collection date

not collected

sample derived from

ERS3190171

geographic location (longitude)

-3.206493

binning parameters

tetra-nucleotide frequencies and abundance

contamination score

0

ENA-FIRST-PUBLIC

2019-08-01

ENA-LAST-UPDATE

2019-07-31

completeness software

checkm

environment (biome)

Bos taurus

environment (feature)

stomach

geographic location (country and/or sea)

United Kingdom

ENA-CHECKLIST

ERC000050

binning software

MetaBAT2

organism

uncultured bacterium

assembly quality

Many fragments with little to no review of assembly other than reporting of standard assembly statistics

taxonomic identity marker

multi-marker approach (checkm)

completeness score

92.7

geographic location (latitude)

55.861398

scientific_name

uncultured bacterium

investigation type

metagenome

metagenomic source

bovine gut metagenome

project name

Metagenomic sequencing of the rumen of 240 cattle from Scotland

sequencing method

Illumina HiSeq 4000

isolation_source

cattle rumen

Cattle rumen microbiome. breed:LIMx; sex:M; age:582

ENA-CHECKLIST

ERC000013

environment (material)

bodily fluid

organism

bovine gut metagenome

collection date

not collected

geographic location (longitude)

-3.206493

host taxid

9913

geographic location (latitude)

55.861398

scientific_name

bovine gut metagenome

investigation type

metagenome

host body habitat

gut

host common name

cow

host body product

rumen fluid

host body site

rumen

host sex

male

subspecific genetic lineage

LIMx

host-associated environmental package

host-associated

ENA-FIRST-PUBLIC

2019-03-11

project name

Metagenomic sequencing of the rumen of 240 cattle from Scotland

sequencing method

Illumina HiSeq 4000

ENA-LAST-UPDATE

2019-05-31

host age

582 days

environment (biome)

Bos taurus

environment (feature)

stomach

geographic location (country and/or sea)

United Kingdom

Metadata as EBI XML

<EXPERIMENT_SET>
<EXPERIMENT accession="ERX3238976" alias="ena-EXPERIMENT-THE ROSLIN INSTITUTE-11-03-2019-14:17:01:487-11" center_name="THE ROSLIN INSTITUTE">
  <IDENTIFIERS>
    <PRIMARY_ID>ERX3238976</PRIMARY_ID>
    <SUBMITTER_ID namespace="THE ROSLIN INSTITUTE">ena-EXPERIMENT-THE ROSLIN INSTITUTE-11-03-2019-14:17:01:487-11</SUBMITTER_ID>
  </IDENTIFIERS>
  <TITLE>Illumina HiSeq 4000 paired end sequencing</TITLE>
  <STUDY_REF accession="ERP113798">
    <IDENTIFIERS>
      <PRIMARY_ID>ERP113798</PRIMARY_ID>
      <SECONDARY_ID>PRJEB31266</SECONDARY_ID>
    </IDENTIFIERS>
  </STUDY_REF>
  <DESIGN>
    <DESIGN_DESCRIPTION>Whole metagenomic sequencing</DESIGN_DESCRIPTION>
    <SAMPLE_DESCRIPTOR accession="ERS3190171">
      <IDENTIFIERS>
        <PRIMARY_ID>ERS3190171</PRIMARY_ID>
        <EXTERNAL_ID namespace="BioSample">SAMEA5383799</EXTERNAL_ID>
      </IDENTIFIERS>
    </SAMPLE_DESCRIPTOR>
    <LIBRARY_DESCRIPTOR>
      <LIBRARY_NAME>10674_0011</LIBRARY_NAME>
      <LIBRARY_STRATEGY>WGS</LIBRARY_STRATEGY>
      <LIBRARY_SOURCE>METAGENOMIC</LIBRARY_SOURCE>
      <LIBRARY_SELECTION>RANDOM</LIBRARY_SELECTION>
      <LIBRARY_LAYOUT>
        <PAIRED NOMINAL_LENGTH="500"/>
      </LIBRARY_LAYOUT>
      <LIBRARY_CONSTRUCTION_PROTOCOL>TruSeq Nano</LIBRARY_CONSTRUCTION_PROTOCOL>
    </LIBRARY_DESCRIPTOR>
  </DESIGN>
  <PLATFORM>
    <ILLUMINA>
      <INSTRUMENT_MODEL>Illumina HiSeq 4000</INSTRUMENT_MODEL>
    </ILLUMINA>
  </PLATFORM>
  <EXPERIMENT_LINKS>
    <EXPERIMENT_LINK>
      <XREF_LINK>
        <DB>ENA-SAMPLE</DB>
        <ID>ERS3190171</ID>
      </XREF_LINK>
    </EXPERIMENT_LINK>
    <EXPERIMENT_LINK>
      <XREF_LINK>
        <DB>ENA-SUBMISSION</DB>
        <ID>ERA1761269</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=ERX3238976&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=ERX3238976&result=read_run&fields=run_accession,submitted_ftp,submitted_md5,submitted_bytes,submitted_format]]></ID>
      </XREF_LINK>
    </EXPERIMENT_LINK>
  </EXPERIMENT_LINKS>
</EXPERIMENT>
</EXPERIMENT_SET>