BioSample Accession(s)

SAMEA6955067, ERS4664939

assembly software

megahit

environment (material)

water

collection date

2015-08-10

sample derived from

ERS4649311

geographic location (longitude)

25.063055555555557

metagenomic OTU

anoxic_mOTU_0991

binning parameters

min_len:1500,min_bin_size:10000,maxP:93,minS:50

contamination score

3.23

gtdb_taxonomy

d__Bacteria;p__Myxococcota;c__Myxococcia;o__Myxococcales;f__Myxococcaceae;g__FEN-1143

water environmental package

water

sample owner

Leyden Fernandez

ENA-FIRST-PUBLIC

2020-06-15

ENA-LAST-UPDATE

2020-06-18

completeness software

checkm

collection data

metagenome

environment (biome)

lentic water body

environment (feature)

lake

geographic location (country and/or sea)

Finland

ENA-CHECKLIST

ERC000047

binning software

metabat

organism

uncultured Myxococcales bacterium

assembly quality

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

taxonomic identity marker

gtdbtk followed by sourmash-lca, see publication

completeness score

90.75

geographic location (latitude)

61.242222222222225

scientific_name

uncultured Myxococcales bacterium

common name

investigation type

metagenome

metagenomic source

lake water metagenome

project name

microbes in stratified freshwaters

sequencing method

NovaSeq

region

Evo

isolation_source

lake water

site name

Valkea Kotinen

BioSample Accession(s)

SAMEA6939419, ERS4649311

ENA-CHECKLIST

ERC000011

collection_date

2015-08-10

environment (material)

water

organism

lake water metagenome

sample derived from

ERS4600578,ERS4600579,ERS4600580,ERS4600581

geographic location (longitude)

25.063055555555557

Run

R1

geographic location (latitude)

61.242222222222225

scientific_name

lake water metagenome

common name

investigation type

metagenome

water environmental package

water

sample owner

Leyden Fernandez

ENA-FIRST-PUBLIC

2020-06-15

project name

microbes in stratified freshwaters

sequencing method

NovaSeq

ENA-LAST-UPDATE

2020-06-18

collection data

metagenome

environment (biome)

lentic water body

region

Evo

Lake_code

VK

environment (feature)

lake

geographic location (country and/or sea)

Finland

site name

Valkea Kotinen

BioSample Accession(s)

SAMEA6873014, ERS4600578

geographic location (depth)

0.5

environment (material)

water

sulfate

3.87

ferric iron

18

collection date

2015-08-10

ferrous iron

0.7

ammonium

0.332612672542824

geographic location (longitude)

25.063055555555557

nitrate

0.335457359015175

water environmental package

water

sample owner

Leyden Fernandez

ENA-FIRST-PUBLIC

2020-06-15

ENA-LAST-UPDATE

2020-06-18

temperature

19.5

collection data

metagenome

environment (biome)

lentic water body

Lake_code

VK

oxygen

8.47

environment (feature)

lake

geographic location (country and/or sea)

Finland

ENA-CHECKLIST

ERC000024

organism

lake water metagenome

phosphate

0.021058971437717

Run

R1

dissolved carbon dioxide

30.391

geographic location (latitude)

61.242222222222225

scientific_name

lake water metagenome

common name

investigation type

metagenome

project name

microbes in stratified freshwaters

sequencing method

NovaSeq

methane

0.199

iron

18.7

region

Evo

site name

Valkea Kotinen

BioSample Accession(s)

SAMEA6873015, ERS4600579

geographic location (depth)

2.25

environment (material)

water

sulfate

1.36

ferric iron

13.8

collection date

2015-08-10

ferrous iron

11.6

ammonium

0.27717722711902

geographic location (longitude)

25.063055555555557

nitrate

1.41924267275651

water environmental package

water

sample owner

Leyden Fernandez

ENA-FIRST-PUBLIC

2020-06-15

ENA-LAST-UPDATE

2020-06-18

temperature

14

collection data

metagenome

environment (biome)

lentic water body

Lake_code

VK

oxygen

0.38

environment (feature)

lake

geographic location (country and/or sea)

Finland

ENA-CHECKLIST

ERC000024

organism

lake water metagenome

phosphate

0.021058971437717

Run

R1

dissolved carbon dioxide

131.868

geographic location (latitude)

61.242222222222225

scientific_name

lake water metagenome

common name

investigation type

metagenome

project name

microbes in stratified freshwaters

sequencing method

NovaSeq

methane

0.149

iron

25.4

region

Evo

site name

Valkea Kotinen

BioSample Accession(s)

SAMEA6873016, ERS4600580

geographic location (depth)

3.25

environment (material)

water

sulfate

3.65

ferric iron

0

collection date

2015-08-10

ferrous iron

82

ammonium

0.388048117966628

geographic location (longitude)

25.063055555555557

nitrate

0.464479420174857

water environmental package

water

sample owner

Leyden Fernandez

ENA-FIRST-PUBLIC

2020-06-15

ENA-LAST-UPDATE

2020-06-18

temperature

9.8

collection data

metagenome

environment (biome)

lentic water body

Lake_code

VK

oxygen

0.46

environment (feature)

lake

geographic location (country and/or sea)

Finland

ENA-CHECKLIST

ERC000024

organism

lake water metagenome

phosphate

0.042117942875434

Run

R1

dissolved carbon dioxide

248.239

geographic location (latitude)

61.242222222222225

scientific_name

lake water metagenome

common name

investigation type

metagenome

project name

microbes in stratified freshwaters

sequencing method

NovaSeq

methane

2.946

iron

82

region

Evo

site name

Valkea Kotinen

BioSample Accession(s)

SAMEA6873017, ERS4600581

geographic location (depth)

4.5

environment (material)

water

sulfate

2.38

ferric iron

0

collection date

2015-08-10

ferrous iron

89.2

ammonium

4.49027107932812

geographic location (longitude)

25.063055555555557

nitrate

0.330619031721686

water environmental package

water

sample owner

Leyden Fernandez

ENA-FIRST-PUBLIC

2020-06-15

ENA-LAST-UPDATE

2020-06-18

temperature

7.6

collection data

metagenome

environment (biome)

lentic water body

Lake_code

VK

oxygen

0.49

environment (feature)

lake

geographic location (country and/or sea)

Finland

ENA-CHECKLIST

ERC000024

organism

lake water metagenome

phosphate

0.094765371469727

Run

R1

dissolved carbon dioxide

277.652

geographic location (latitude)

61.242222222222225

scientific_name

lake water metagenome

common name

investigation type

metagenome

project name

microbes in stratified freshwaters

sequencing method

NovaSeq

methane

7.82

iron

89.2

region

Evo

site name

Valkea Kotinen

Metadata as EBI XML

<EXPERIMENT_SET>
<EXPERIMENT accession="ERX4155763" alias="webin-reads-microbes_in_stratified_freshwaters_-_lake_Valkea_Kotinen_sample_VK1" center_name="Department of Aquatic Sciences and Assessment">
  <IDENTIFIERS>
    <PRIMARY_ID>ERX4155763</PRIMARY_ID>
    <SUBMITTER_ID namespace="Department of Aquatic Sciences and Assessment">webin-reads-microbes_in_stratified_freshwaters_-_lake_Valkea_Kotinen_sample_VK1</SUBMITTER_ID>
  </IDENTIFIERS>
  <TITLE>Raw reads: microbes_in_stratified_freshwaters_-_lake_Valkea_Kotinen_sample_VK1</TITLE>
  <STUDY_REF accession="ERP122124">
    <IDENTIFIERS>
      <PRIMARY_ID>ERP122124</PRIMARY_ID>
      <SECONDARY_ID>PRJEB38681</SECONDARY_ID>
    </IDENTIFIERS>
  </STUDY_REF>
  <DESIGN>
    <DESIGN_DESCRIPTION>unspecified</DESIGN_DESCRIPTION>
    <SAMPLE_DESCRIPTOR accession="ERS4600578">
      <IDENTIFIERS>
        <PRIMARY_ID>ERS4600578</PRIMARY_ID>
        <EXTERNAL_ID namespace="BioSample">SAMEA6873014</EXTERNAL_ID>
      </IDENTIFIERS>
    </SAMPLE_DESCRIPTOR>
    <LIBRARY_DESCRIPTOR>
      <LIBRARY_NAME>lake Valkea Kotinen sample VK1</LIBRARY_NAME>
      <LIBRARY_STRATEGY>WGS</LIBRARY_STRATEGY>
      <LIBRARY_SOURCE>METAGENOMIC</LIBRARY_SOURCE>
      <LIBRARY_SELECTION>RANDOM</LIBRARY_SELECTION>
      <LIBRARY_LAYOUT>
        <PAIRED/>
      </LIBRARY_LAYOUT>
    </LIBRARY_DESCRIPTOR>
  </DESIGN>
  <PLATFORM>
    <ILLUMINA>
      <INSTRUMENT_MODEL>Illumina NovaSeq 6000</INSTRUMENT_MODEL>
    </ILLUMINA>
  </PLATFORM>
  <EXPERIMENT_LINKS>
    <EXPERIMENT_LINK>
      <XREF_LINK>
        <DB>ENA-SAMPLE</DB>
        <ID>ERS4600578</ID>
      </XREF_LINK>
    </EXPERIMENT_LINK>
    <EXPERIMENT_LINK>
      <XREF_LINK>
        <DB>ENA-SUBMISSION</DB>
        <ID>ERA2668116</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=ERX4155763&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=ERX4155763&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="ERX4155764" alias="webin-reads-microbes_in_stratified_freshwaters_-_lake_Valkea_Kotinen_sample_VK2" center_name="Department of Aquatic Sciences and Assessment">
  <IDENTIFIERS>
    <PRIMARY_ID>ERX4155764</PRIMARY_ID>
    <SUBMITTER_ID namespace="Department of Aquatic Sciences and Assessment">webin-reads-microbes_in_stratified_freshwaters_-_lake_Valkea_Kotinen_sample_VK2</SUBMITTER_ID>
  </IDENTIFIERS>
  <TITLE>Raw reads: microbes_in_stratified_freshwaters_-_lake_Valkea_Kotinen_sample_VK2</TITLE>
  <STUDY_REF accession="ERP122124">
    <IDENTIFIERS>
      <PRIMARY_ID>ERP122124</PRIMARY_ID>
      <SECONDARY_ID>PRJEB38681</SECONDARY_ID>
    </IDENTIFIERS>
  </STUDY_REF>
  <DESIGN>
    <DESIGN_DESCRIPTION>unspecified</DESIGN_DESCRIPTION>
    <SAMPLE_DESCRIPTOR accession="ERS4600579">
      <IDENTIFIERS>
        <PRIMARY_ID>ERS4600579</PRIMARY_ID>
        <EXTERNAL_ID namespace="BioSample">SAMEA6873015</EXTERNAL_ID>
      </IDENTIFIERS>
    </SAMPLE_DESCRIPTOR>
    <LIBRARY_DESCRIPTOR>
      <LIBRARY_NAME>lake Valkea Kotinen sample VK2</LIBRARY_NAME>
      <LIBRARY_STRATEGY>WGS</LIBRARY_STRATEGY>
      <LIBRARY_SOURCE>METAGENOMIC</LIBRARY_SOURCE>
      <LIBRARY_SELECTION>RANDOM</LIBRARY_SELECTION>
      <LIBRARY_LAYOUT>
        <PAIRED/>
      </LIBRARY_LAYOUT>
    </LIBRARY_DESCRIPTOR>
  </DESIGN>
  <PLATFORM>
    <ILLUMINA>
      <INSTRUMENT_MODEL>Illumina NovaSeq 6000</INSTRUMENT_MODEL>
    </ILLUMINA>
  </PLATFORM>
  <EXPERIMENT_LINKS>
    <EXPERIMENT_LINK>
      <XREF_LINK>
        <DB>ENA-SAMPLE</DB>
        <ID>ERS4600579</ID>
      </XREF_LINK>
    </EXPERIMENT_LINK>
    <EXPERIMENT_LINK>
      <XREF_LINK>
        <DB>ENA-SUBMISSION</DB>
        <ID>ERA2668117</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=ERX4155764&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=ERX4155764&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="ERX4156114" alias="webin-reads-microbes_in_stratified_freshwaters_-_lake_Valkea_Kotinen_sample_VK3" center_name="Department of Aquatic Sciences and Assessment">
  <IDENTIFIERS>
    <PRIMARY_ID>ERX4156114</PRIMARY_ID>
    <SUBMITTER_ID namespace="Department of Aquatic Sciences and Assessment">webin-reads-microbes_in_stratified_freshwaters_-_lake_Valkea_Kotinen_sample_VK3</SUBMITTER_ID>
  </IDENTIFIERS>
  <TITLE>Raw reads: microbes_in_stratified_freshwaters_-_lake_Valkea_Kotinen_sample_VK3</TITLE>
  <STUDY_REF accession="ERP122124">
    <IDENTIFIERS>
      <PRIMARY_ID>ERP122124</PRIMARY_ID>
      <SECONDARY_ID>PRJEB38681</SECONDARY_ID>
    </IDENTIFIERS>
  </STUDY_REF>
  <DESIGN>
    <DESIGN_DESCRIPTION>unspecified</DESIGN_DESCRIPTION>
    <SAMPLE_DESCRIPTOR accession="ERS4600580">
      <IDENTIFIERS>
        <PRIMARY_ID>ERS4600580</PRIMARY_ID>
        <EXTERNAL_ID namespace="BioSample">SAMEA6873016</EXTERNAL_ID>
      </IDENTIFIERS>
    </SAMPLE_DESCRIPTOR>
    <LIBRARY_DESCRIPTOR>
      <LIBRARY_NAME>lake Valkea Kotinen sample VK3</LIBRARY_NAME>
      <LIBRARY_STRATEGY>WGS</LIBRARY_STRATEGY>
      <LIBRARY_SOURCE>METAGENOMIC</LIBRARY_SOURCE>
      <LIBRARY_SELECTION>RANDOM</LIBRARY_SELECTION>
      <LIBRARY_LAYOUT>
        <PAIRED/>
      </LIBRARY_LAYOUT>
    </LIBRARY_DESCRIPTOR>
  </DESIGN>
  <PLATFORM>
    <ILLUMINA>
      <INSTRUMENT_MODEL>Illumina NovaSeq 6000</INSTRUMENT_MODEL>
    </ILLUMINA>
  </PLATFORM>
  <EXPERIMENT_LINKS>
    <EXPERIMENT_LINK>
      <XREF_LINK>
        <DB>ENA-SAMPLE</DB>
        <ID>ERS4600580</ID>
      </XREF_LINK>
    </EXPERIMENT_LINK>
    <EXPERIMENT_LINK>
      <XREF_LINK>
        <DB>ENA-SUBMISSION</DB>
        <ID>ERA2668185</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=ERX4156114&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=ERX4156114&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="ERX4156245" alias="webin-reads-microbes_in_stratified_freshwaters_-_lake_Valkea_Kotinen_sample_VK4" center_name="Department of Aquatic Sciences and Assessment">
  <IDENTIFIERS>
    <PRIMARY_ID>ERX4156245</PRIMARY_ID>
    <SUBMITTER_ID namespace="Department of Aquatic Sciences and Assessment">webin-reads-microbes_in_stratified_freshwaters_-_lake_Valkea_Kotinen_sample_VK4</SUBMITTER_ID>
  </IDENTIFIERS>
  <TITLE>Raw reads: microbes_in_stratified_freshwaters_-_lake_Valkea_Kotinen_sample_VK4</TITLE>
  <STUDY_REF accession="ERP122124">
    <IDENTIFIERS>
      <PRIMARY_ID>ERP122124</PRIMARY_ID>
      <SECONDARY_ID>PRJEB38681</SECONDARY_ID>
    </IDENTIFIERS>
  </STUDY_REF>
  <DESIGN>
    <DESIGN_DESCRIPTION>unspecified</DESIGN_DESCRIPTION>
    <SAMPLE_DESCRIPTOR accession="ERS4600581">
      <IDENTIFIERS>
        <PRIMARY_ID>ERS4600581</PRIMARY_ID>
        <EXTERNAL_ID namespace="BioSample">SAMEA6873017</EXTERNAL_ID>
      </IDENTIFIERS>
    </SAMPLE_DESCRIPTOR>
    <LIBRARY_DESCRIPTOR>
      <LIBRARY_NAME>lake Valkea Kotinen sample VK4</LIBRARY_NAME>
      <LIBRARY_STRATEGY>WGS</LIBRARY_STRATEGY>
      <LIBRARY_SOURCE>METAGENOMIC</LIBRARY_SOURCE>
      <LIBRARY_SELECTION>RANDOM</LIBRARY_SELECTION>
      <LIBRARY_LAYOUT>
        <PAIRED/>
      </LIBRARY_LAYOUT>
    </LIBRARY_DESCRIPTOR>
  </DESIGN>
  <PLATFORM>
    <ILLUMINA>
      <INSTRUMENT_MODEL>Illumina NovaSeq 6000</INSTRUMENT_MODEL>
    </ILLUMINA>
  </PLATFORM>
  <EXPERIMENT_LINKS>
    <EXPERIMENT_LINK>
      <XREF_LINK>
        <DB>ENA-SAMPLE</DB>
        <ID>ERS4600581</ID>
      </XREF_LINK>
    </EXPERIMENT_LINK>
    <EXPERIMENT_LINK>
      <XREF_LINK>
        <DB>ENA-SUBMISSION</DB>
        <ID>ERA2668247</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=ERX4156245&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=ERX4156245&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>