characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: public

text: ArrayExpress

text: Protocols: Heads were flushed with RNAlater™ (Qiagen) to ensure complete permeation of the head tissue. The samples were transported on ice to the field station and kept overnight at 4 °C to ensure full permeation. Then samples were kept frozen in a -20 °C fridge not more than two weeks. During transport, the samples were kept in an insulated container, cooled on ice, until arrival in the laboratory in Freiburg (Germany). There, samples were kept in a -80 °C freezer until further processing. Total RNA was extracted from the head of single individuals according to a modified version of the peqGOLD TriFast™ protocol: modifications were an incubation time of 10 min instead of 5 min at room temperature after adding 900 μl peqGOLD Tri Fast™ and inverting the tube. After adding chloroform and after incubation, centrifugation was modified to 10 min at 4 °C, 10,800 rpm. After transfer of the aqueous phase into a new Eppendorf tube, we added another centrifugation step for 5 min at 4 °C (10,800 rpm). Then the supernatant was transferred into a new Eppendorf tube and 2 μl nuclease free glycogen (5 mg/ml) was added per sample. After adding isopropanol, the mixture was incubated for 10 min at room temperature and not on ice. After washing the RNA pellet with 75% ethanol and vortexing, the sample was centrifuged for 5 min at 4 °C, 8,500 rpm. This step was repeated three times. After dissolving the pellet in nuclease-free water, samples were kept for at least one hour at 4 °C. DNA digestion was performed using DNase I Amplification Grade Kit (Sigma-Aldrich). The concentration and quality of the isolated RNA was checked with an Agilent Bioanalyzer (Agilent RNA 6000 Nano Kit). Library preparation was done by BGI. Libraries were constructed with the TruSeq RNA Kit following the BGI sample preparation protocol was applied.

text: Macrotermes bellicosus

text: Macrotermes bellicosus

text: head

text: major worker

text: Macrotermes bellicosus


status: PUBLIC

tag: attribute

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

tag: Namespace:University of Freiburg Institute for Biology I (Zoology) Evolutionary Biology & Ecology

characteristic: Submitter Id

unit: month

characteristic: age

text: ArrayExpress

characteristic: broker name

characteristic: description

text: Macrotermes bellicosus

characteristic: organism

text: Macrotermes bellicosus

text: head

characteristic: organism part

text: major worker

characteristic: phenotype

text: Africa, Cote d'Ivoire, Comoe National Park, Coordinates 8.6550568, -3.7823524 +- 1 km, 200m

characteristic: sampling site

text: Macrotermes bellicosus

characteristic: title


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: University of Freiburg Institute for Biology I (Zoology) Evolutionary Biology & Ecology

text: public

text: ArrayExpress

text: Protocols: Heads were flushed with RNAlater™ (Qiagen) to ensure complete permeation of the head tissue. The samples were transported on ice to the field station and kept overnight at 4 °C to ensure full permeation. Then samples were kept frozen in a -20 °C fridge not more than two weeks. During transport, the samples were kept in an insulated container, cooled on ice, until arrival in the laboratory in Freiburg (Germany). There, samples were kept in a -80 °C freezer until further processing. Total RNA was extracted from the head of single individuals according to a modified version of the peqGOLD TriFast™ protocol: modifications were an incubation time of 10 min instead of 5 min at room temperature after adding 900 μl peqGOLD Tri Fast™ and inverting the tube. After adding chloroform and after incubation, centrifugation was modified to 10 min at 4 °C, 10,800 rpm. After transfer of the aqueous phase into a new Eppendorf tube, we added another centrifugation step for 5 min at 4 °C (10,800 rpm). Then the supernatant was transferred into a new Eppendorf tube and 2 μl nuclease free glycogen (5 mg/ml) was added per sample. After adding isopropanol, the mixture was incubated for 10 min at room temperature and not on ice. After washing the RNA pellet with 75% ethanol and vortexing, the sample was centrifuged for 5 min at 4 °C, 8,500 rpm. This step was repeated three times. After dissolving the pellet in nuclease-free water, samples were kept for at least one hour at 4 °C. DNA digestion was performed using DNase I Amplification Grade Kit (Sigma-Aldrich). The concentration and quality of the isolated RNA was checked with an Agilent Bioanalyzer (Agilent RNA 6000 Nano Kit). Library preparation was done by BGI. Libraries were constructed with the Ribo-Zero® rRNA Removal Kit (Human/Mouse/Rat), Illumina (http://www.illumina.com/products/ribo-zero-rrna-removal-human-mouse-rat.html).

text: Macrotermes bellicosus

text: Macrotermes bellicosus

text: head

text: major worker

text: Macrotermes bellicosus


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: public

text: ArrayExpress

text: Protocols: Heads were flushed with RNAlater™ (Qiagen) to ensure complete permeation of the head tissue. The samples were transported on ice to the field station and kept overnight at 4 °C to ensure full permeation. Then samples were kept frozen in a -20 °C fridge not more than two weeks. During transport, the samples were kept in an insulated container, cooled on ice, until arrival in the laboratory in Freiburg (Germany). There, samples were kept in a -80 °C freezer until further processing. Total RNA was extracted from the head of single individuals according to a modified version of the peqGOLD TriFast™ protocol: modifications were an incubation time of 10 min instead of 5 min at room temperature after adding 900 μl peqGOLD Tri Fast™ and inverting the tube. After adding chloroform and after incubation, centrifugation was modified to 10 min at 4 °C, 10,800 rpm. After transfer of the aqueous phase into a new Eppendorf tube, we added another centrifugation step for 5 min at 4 °C (10,800 rpm). Then the supernatant was transferred into a new Eppendorf tube and 2 μl nuclease free glycogen (5 mg/ml) was added per sample. After adding isopropanol, the mixture was incubated for 10 min at room temperature and not on ice. After washing the RNA pellet with 75% ethanol and vortexing, the sample was centrifuged for 5 min at 4 °C, 8,500 rpm. This step was repeated three times. After dissolving the pellet in nuclease-free water, samples were kept for at least one hour at 4 °C. DNA digestion was performed using DNase I Amplification Grade Kit (Sigma-Aldrich). The concentration and quality of the isolated RNA was checked with an Agilent Bioanalyzer (Agilent RNA 6000 Nano Kit). Library preparation was done by BGI. RnaseH treatment was performed additionally to the Ribo-Zero® rRNA Removal Kit (Human/Mouse/Rat), Illumina (http://www.illumina.com/products/ribo-zero-rrna-removal-human-mouse-rat.html).

text: Macrotermes bellicosus

text: Macrotermes bellicosus

text: head

text: major worker

text: Macrotermes bellicosus


characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: ArrayExpress

text: Macrotermes bellicosus

text: Macrotermes bellicosus

text: head

text: minor worker

text: Macrotermes bellicosus


characteristic: INSDC last update

text: public

characteristic: INSDC status

text: ArrayExpress

text: Macrotermes bellicosus

text: Macrotermes bellicosus

text: head

text: minor worker

text: Macrotermes bellicosus


text: public

characteristic: SRA accession

characteristic: Submitter Id

text: less than 1

unit: year

text: ArrayExpress

text: Macrotermes bellicosus

text: Macrotermes bellicosus

text: head

text: queen

text: Macrotermes bellicosus

text: female

characteristic: sex


text: public

text: less than 6

characteristic: age

text: ArrayExpress

characteristic: broker name

characteristic: description

text: Macrotermes bellicosus

text: Macrotermes bellicosus

text: head

text: queen

text: Macrotermes bellicosus

text: female


text: public

tag: Namespace:SWEDISH UNIVERSITY OF AGRICULTURAL SCIENCES (SLU)

text: spores

characteristic: cell type

text: Germany

characteristic: geographic location (country and/or sea)

text: Lower Saxony

characteristic: geographic location (region and locality)

text: Solanum tuberosum

characteristic: host scientific name

text: potato tuber

characteristic: isolation source

text: Spongospora subterranea

characteristic: organism

text: Spongospora subterranea

text: Draft genome of Spongospora subterranea


text: synthetic construct

characteristic: ArrayExpress-SPECIES

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: SC

text: public

text: synthetic construct

characteristic: common name

text: synthetic construct

text: synthetic construct

characteristic: subject id

characteristic: title


text: INSERM U1170

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

tag: Namespace:INSERM U1170

characteristic: Submitter Id

text: ArrayExpress

text: CD14-positive, CD16-negative classical monocyte

text: human

text: Protocols: Peripheral blood mononucleated cells (PBMC) were obtained from healthy donor buffy coats (Etablissement Français du sang, Rungis, France) and from CMML patients, separated on Pancoll (Pan-Biotech, Dutscher, Brumath, France). Peripheral blood classical monocytes were sorted with magnetic beads and the AutoMacs system (Miltenyi Biotech, Paris), using the monocyte isolation kit II (Miltenyi Biotech, Paris, France). Cells were cross-linked with addition of 1% formaldehyde directly to the culture medium for 10 min at RT with agitation. Fixation was stopped by addition of 125mM glycin during 5 min at RT with agitation and samples were then washed 2 times in ice-cold PBS before addition of SDS lysis buffer (Millipore, 10uL per 1.106 cells) supplemented with 1% protease inhibitor cocktail (Active Motif). Samples were vortexed and incubated 15 min on ice before 10 min sonication at 40W (Covaris S220, Woodingdean, UK). The chromatin immunoprecipitation was carried out using ChIP-it express kit according to manufacturer's instruction (Active Motif) with a polyclonal anti-H3K4me3 antibody (39159, Active Motif). Enriched DNA from ChIP and Input DNA fragments were end-repaired, extended with an 'A' base on the 3′end, ligated with indexed paired-end adaptors (NEXTflex, Bioo Scientific, Proteigene, Saint Marcel, France) using the Bravo Platform (Agilent, Les Ulis, France), size-selected after 4 cycles of PCR with AMPure XP beads (Beckman Coulter, Villepinte, France) and amplified by PCR for 10 cycles more.

text: normal

characteristic: disease

characteristic: individual

text: Homo sapiens

text: Homo sapiens

text: blood

characteristic: organism part

text: Homo sapiens


text: INSERM U1170

text: public

text: ArrayExpress

characteristic: broker name

characteristic: cell type

text: human

characteristic: description

text: chronic myelomonocytic leukemia

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: blood

text: Homo sapiens


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: TRINITY COLLEGE DUBLIN

text: public

tag: Namespace:TRINITY COLLEGE DUBLIN

text: goat

text: Goat from Bronze Age Tilla Bulak, Uzbekistan.

text: Capra hircus

text: Capra hircus

text: Petrous Bone

characteristic: tissue lib


text: TRINITY COLLEGE DUBLIN

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: wild goat

characteristic: common name

text: Bezoar from the Upper/Middle Paleolithic Site Hovk-1 Cave.

text: Capra aegagrus

text: Capra aegagrus

text: Petrous Bone

characteristic: title


text: TRINITY COLLEGE DUBLIN

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: goat

text: Goat from the Neolithic occupation of Monjukli Depe, Turkmenistan.

text: Capra hircus

text: Capra hircus

text: Petrous Bone


text: TRINITY COLLEGE DUBLIN

text: public

text: goat

text: Goat from the Chalcolithic occupation of Monjukli Depe, Turkmenistan.

text: Capra hircus

text: Capra hircus

text: Petrous Bone


text: TRINITY COLLEGE DUBLIN

text: public

text: goat

text: Neolithic goat from Sang-e Chakmaq, Iran.

text: Capra hircus

text: Capra hircus

text: Petrous Bone


text: TRINITY COLLEGE DUBLIN

text: public

text: goat

text: Domestic goat from Bronze Age Tepe Hasanlu, Iranian Azerbaijan, Iran.

text: Capra hircus

text: Capra hircus

text: Petrous Bone


text: TRINITY COLLEGE DUBLIN

text: public

text: goat

text: Goat from medieval Darre-ye Bolaghi, Fars, Iran.

text: Capra hircus

text: Capra hircus

text: Petrous Bone


text: Escherichia coli

characteristic: ArrayExpress-SPECIES

text: SC

text: public

text: Escherichia coli

text: Escherichia coli

text: Escherichia coli

characteristic: subject id


text: Canis lupus familiaris

text: SC

text: public

text: dog

text: Canis lupus familiaris

text: Canis lupus familiaris


status: KILLED

text: Public Health Agency of Sweden

text: killed

text: sam_FOHMtest_6664d072-6f52-4316-b3fd-cf8890b098e6

tag: Namespace:Public Health Agency of Sweden

text: FOHM

text: Sweden

characteristic: geographic location (country and/or sea)

text: Homo sapiens

characteristic: host scientific name

text: yes

characteristic: isolate

text: Salmonella enterica

text: Salmonella enterica

text: Salmonella enterica


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: public

tag: Namespace:Department of Molecular Microbiology John Innes Centre

text: ArrayExpress

characteristic: broker name

text: Protocols: Using ‘Redirect’ PCR targeting (Gust et al., 2003; Gust et al., 2004), the whiH gene was replaced with a single apramycin resistance (apr) cassette in Streptomyces venezuelae (ATCC10712). An integrating plasmid, encoding a 3xFLAG-tagged version of WhiH, was then conjugated into the whiH mutant (SV8). The resulting strain was used in the subsequent ChIP-seq experiments, with the wild-type (ATCC10712) serving as a negative control. Both strains were grown as described in the growth protocol. Cultures were grown in 4 x 30 ml volumes of MYM-TAP according to Stuttard C. 1982. (Microbiology 128:115121) made with 50% tap water and supplemented with 200 ul of trace element solution (Kieser T et al. 2000. Practical Streptomyces genetics. John Innes Foundation, Norwich, United Kingdom.) per 100 ml. Cultures were incubated at 30 degrees c and 250 RPM until sporulation was at an advanced stage (38 hours, as determined by light microscopy). Formaldehyde was added to cultures at a final concentration of 1% (vol/vol), and incubation was continued for 30 min. Glycine was then added to a final concentration of 125 mM to stop the cross-linking. The samples were left at room temperature for 5 min and washed twice in phosphate-buffered saline (PBS) buffer (pH 7.4). The pellets were resuspended in 0.5 ml of lysis buffer (10 mM Tris-Cl, pH 8.0, 50 mM NaCl), containing 15 mg/ml of lysozyme and 1x protease inhibitor (Roche Applied Science) and incubated at 37 degree C for 25 min or until lysed. Subsequently, 0.5 ml immunoprecipitation (IP) buffer (50 mM Tris-Cl, pH 8.0, 250 mM NaCl, 0.8% [vol/vol] Triton X-100), containing 1x protease inhibitor, was added, and the samples were chilled on ice. The samples were sonicated for six cycles of 20 s each at 10 micrometer to shear chromosomal DNA into fragments ranging from 300 to 1,000 bp on average. The samples were centrifuged twice at 16,000g at 4 degree C for 10 min to clear the cell extracts. Cell lysates were incubated with anti-FLAG M2 Affinity Gel (Sigma A2220) overnight at 4 degree C followed by centrifugation for 30 s at 4 degree C and 5,500g. The pellets were washed twice with 0.5x IP buffer and then twice with 1x IP buffer and transferred to new Eppendorf tubes after the first washing step. The pellets and 50 microlitres of total cell extracts (set aside earlier) were eluted overnight at 65 degree C in 100 microlitres of IP elution buffer (50 mM Tris-Cl, pH 7.6, 10 mM EDTA, 1% SDS) to reverse the cross-links. The samples were centrifuged at 16,000g for 5 min to remove the beads. The pellets were reextracted with 50 microlitres of TE buffer (10 mM Tris-Cl, pH 7.4, 1 mM EDTA) and incubated with 0.2 mg/ml proteinase K (Roche) for 2 h at 55 degree C. The samples were extracted twice with phenol-chloroform and once with chloroform and further purified using QiaQuick columns (Qiagen). DNA was eluted in 50 microlitres EB buffer (10 mM Tris-Cl, pH 8.5) and quantified using a NanoDrop spectrophotometer (Thermo Scientific). Library construction and sequencing were performed by The Genome Analysis Centre (TGAC), Norwich Research Park, Norwich, United Kingdom. The TruSeq ChIP sample preparation kit from Illumina Inc. (part 15023092, revision A, August 2012) was used according to the recommended protocol. In brief, 5 to 10 ng ChIP DNA is blunt ended and phosphorylated, and a single A nucleotide is added to the 3 ends of the fragments in preparation for ligation to an adapter with a single-base T overhang. The ligation products are purified and accurately size selected by agarose gel electrophoresis. Size-selected DNA is then purified and PCR amplified to enrich for fragments that have adapters on both ends. The final purified product is then quantified using a combination of Bioanalyzer DNA HS Chip from Agilent Technology 2100 Bioanalyzer and Qubit 2.0 from Invitrogen. The libraries were normalized to 10 nM and pooled, and quantitative PCR (q-PCR) was performed prior to cluster generation. Each library pool was diluted to 2 nM with NaOH, and 5 microlitres was transferred into 995 microlitres HT-1 to give a final concentration of 10 pM.

characteristic: description

text: FLAG-tagged WhiH expression

characteristic: genotype

text: Streptomyces venezuelae

characteristic: organism

text: Streptomyces venezuelae

text: Streptomyces venezuelae

text: ATCC 10712

characteristic: strain


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Department of Molecular Microbiology John Innes Centre

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: ArrayExpress

text: FLAG-tagged WhiH expression

text: Streptomyces venezuelae

text: Streptomyces venezuelae

text: Streptomyces venezuelae

text: ATCC 10712

characteristic: title


characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: ArrayExpress

text: wild type genotype

text: Streptomyces venezuelae

text: Streptomyces venezuelae

text: Streptomyces venezuelae

text: ATCC 10712


text: Giant Hogweed

characteristic: ArrayExpress-SPECIES

text: SC

text: public

text: Giant Hogweed

characteristic: common name

text: Heracleum mantegazzianum

text: Heracleum mantegazzianum


text: European robin

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: SC

text: public

text: European robin

text: Erithacus rubecula

text: Erithacus rubecula


Papilio machaon 295.1

text: UNIVERSITY OF MONTPELLIER 2

text: public

text: Papilio machaon 295.1

tag: Namespace:UNIVERSITY OF MONTPELLIER 2

characteristic: collection date

text: common yellow swallowtail

text: USA

characteristic: geographic location (country and/or sea)

text: Missouri, Benton county, 2 mi west of Truman State Park

characteristic: geographic location (region and locality)

text: Papilio machaon

text: Papilio machaon

text: Papilio machaon 295.1


text: Univeristy of helsinki

text: public

tag: Namespace:Univeristy of helsinki

text: human

characteristic: environment (biome)

characteristic: environment (feature)

characteristic: environment (material)

text: United Kingdom

unit: DD

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

unit: centuries

characteristic: host age

characteristic: host body mass index

unit: cm

characteristic: host height

characteristic: host subject id

text: human-gut

characteristic: human gut environmental package

text: metagenome

characteristic: investigation type

text: IHMS_SOP 06 V1

characteristic: nucleic acid extraction

text: Homo sapiens

characteristic: organism

text: Bakt_341F (CCTACGGGNGGCWGCAG), Bakt_805R (GACTACHVGGGTATCTAATCC)

characteristic: pcr primers

text: FOG-

characteristic: project name

text: Homo sapiens

text: MiSeq

characteristic: sequencing method

text: A low FODMAP diet is associated with changes in the microbiota and reduction in breath hydrogen but not colonic volume in healthy subjects


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Univeristy of helsinki

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

characteristic: collection date

text: human

characteristic: common name

text: United Kingdom

characteristic: geographic location (country and/or sea)

text: human-gut

text: metagenome

text: IHMS_SOP 06 V2

text: Homo sapiens

text: FOG-

text: Homo sapiens

text: MiSeq

characteristic: title


text: Univeristy of helsinki

text: public

text: human

characteristic: environment (biome)

characteristic: environment (feature)

characteristic: environment (material)

text: United Kingdom

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

characteristic: host age

characteristic: host body mass index

characteristic: host height

characteristic: host subject id

text: human-gut

characteristic: human gut environmental package

text: metagenome

characteristic: investigation type

text: IHMS_SOP 06 V3

characteristic: nucleic acid extraction

text: Homo sapiens

characteristic: organism

characteristic: pcr primers

text: FOG-

text: Homo sapiens

text: MiSeq


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Univeristy of helsinki

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

characteristic: collection date

text: human

characteristic: common name

text: United Kingdom

text: human-gut

text: metagenome

text: IHMS_SOP 06 V4

text: Homo sapiens

text: FOG-

characteristic: project name

text: Homo sapiens

text: MiSeq

characteristic: sequencing method


text: Univeristy of helsinki

text: public

text: human

characteristic: environment (biome)

characteristic: environment (feature)

characteristic: environment (material)

text: United Kingdom

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

characteristic: host age

characteristic: host body mass index

characteristic: host height

characteristic: host subject id

text: human-gut

characteristic: human gut environmental package

text: metagenome

characteristic: investigation type

text: IHMS_SOP 06 V5

characteristic: nucleic acid extraction

text: Homo sapiens

text: FOG-

text: Homo sapiens

text: MiSeq

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Univeristy of helsinki

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

characteristic: collection date

text: human

characteristic: common name

text: United Kingdom

text: human-gut

text: metagenome

text: IHMS_SOP 06 V6

text: Homo sapiens

characteristic: organism

characteristic: pcr primers

text: FOG-

text: Homo sapiens

text: MiSeq


text: Univeristy of helsinki

text: public

text: human

characteristic: environment (biome)

characteristic: environment (feature)

characteristic: environment (material)

text: United Kingdom

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

characteristic: host age

characteristic: host body mass index

characteristic: host height

characteristic: host subject id

text: human-gut

characteristic: human gut environmental package

text: metagenome

characteristic: investigation type

text: IHMS_SOP 06 V7

text: Homo sapiens

text: FOG-

characteristic: project name

text: Homo sapiens

text: MiSeq

characteristic: sequencing method


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Univeristy of helsinki

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

characteristic: collection date

text: human

characteristic: common name

text: United Kingdom

text: human-gut

text: metagenome

text: IHMS_SOP 06 V8

characteristic: nucleic acid extraction

text: Homo sapiens

text: FOG-

text: Homo sapiens

text: MiSeq

characteristic: title


text: Univeristy of helsinki

text: public

text: human

characteristic: environment (biome)

characteristic: environment (feature)

characteristic: environment (material)

text: United Kingdom

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

characteristic: host age

characteristic: host body mass index

characteristic: host height

characteristic: host subject id

text: human-gut

characteristic: human gut environmental package

text: metagenome

characteristic: investigation type

text: IHMS_SOP 06 V9

text: Homo sapiens

characteristic: organism

characteristic: pcr primers

text: FOG-

text: Homo sapiens

text: MiSeq


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Univeristy of helsinki

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

characteristic: collection date

text: human

characteristic: common name

text: United Kingdom

text: human-gut

text: metagenome

text: IHMS_SOP 06 V10

text: Homo sapiens

text: FOG-

characteristic: project name

text: Homo sapiens

text: MiSeq

characteristic: sequencing method


text: Univeristy of helsinki

text: public

text: human

characteristic: environment (biome)

characteristic: environment (feature)

characteristic: environment (material)

text: United Kingdom

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

characteristic: host age

characteristic: host body mass index

characteristic: host height

characteristic: host subject id

text: human-gut

characteristic: human gut environmental package

text: metagenome

characteristic: investigation type

text: IHMS_SOP 06 V11

characteristic: nucleic acid extraction

text: Homo sapiens

text: FOG-

text: Homo sapiens

text: MiSeq

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Univeristy of helsinki

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

characteristic: collection date

text: human

characteristic: common name

text: United Kingdom

text: human-gut

text: metagenome

text: IHMS_SOP 06 V12

text: Homo sapiens

characteristic: organism

characteristic: pcr primers

text: FOG-

text: Homo sapiens

text: MiSeq


text: Univeristy of helsinki

text: public

text: human

characteristic: environment (biome)

characteristic: environment (feature)

characteristic: environment (material)

text: United Kingdom

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characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

characteristic: collection date

text: human

characteristic: common name

text: United Kingdom

text: human-gut

text: metagenome

text: IHMS_SOP 06 V52

text: Homo sapiens

text: FOG-

characteristic: project name

text: Homo sapiens

text: MiSeq

characteristic: sequencing method


text: Univeristy of helsinki

text: public

text: human

characteristic: environment (biome)

characteristic: environment (feature)

characteristic: environment (material)

text: United Kingdom

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

characteristic: host age

characteristic: host body mass index

characteristic: host height

characteristic: host subject id

text: human-gut

characteristic: human gut environmental package

text: metagenome

characteristic: investigation type

text: IHMS_SOP 06 V53

characteristic: nucleic acid extraction

text: Homo sapiens

text: FOG-

text: Homo sapiens

text: MiSeq

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Univeristy of helsinki

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

characteristic: collection date

text: human

characteristic: common name

text: United Kingdom

text: human-gut

text: metagenome

text: IHMS_SOP 06 V54

text: Homo sapiens

characteristic: organism

characteristic: pcr primers

text: FOG-

text: Homo sapiens

text: MiSeq


text: Univeristy of helsinki

text: public

text: human

characteristic: environment (biome)

characteristic: environment (feature)

characteristic: environment (material)

text: United Kingdom

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

characteristic: host age

characteristic: host body mass index

characteristic: host height

characteristic: host subject id

text: human-gut

characteristic: human gut environmental package

text: metagenome

characteristic: investigation type

text: IHMS_SOP 06 V55

text: Homo sapiens

text: FOG-

characteristic: project name

text: Homo sapiens

text: MiSeq

characteristic: sequencing method


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Univeristy of helsinki

characteristic: INSDC center name

characteristic: INSDC first public

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text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

characteristic: collection date

text: human

characteristic: common name

text: United Kingdom

text: human-gut

text: metagenome

text: IHMS_SOP 06 V56

characteristic: nucleic acid extraction

text: Homo sapiens

text: FOG-

text: Homo sapiens

text: MiSeq

characteristic: title


text: Univeristy of helsinki

text: public

text: human

characteristic: environment (biome)

characteristic: environment (feature)

characteristic: environment (material)

text: United Kingdom

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

characteristic: host age

characteristic: host body mass index

characteristic: host height

characteristic: host subject id

text: human-gut

characteristic: human gut environmental package

text: metagenome

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text: IHMS_SOP 06 V57

text: Homo sapiens

characteristic: organism

characteristic: pcr primers

text: FOG-

text: Homo sapiens

text: MiSeq


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

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text: Univeristy of helsinki

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characteristic: SRA accession

characteristic: Submitter Id

characteristic: collection date

text: human

characteristic: common name

text: United Kingdom

text: human-gut

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text: IHMS_SOP 06 V58

text: Homo sapiens

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characteristic: project name

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characteristic: sequencing method


text: Univeristy of helsinki

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characteristic: environment (biome)

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text: United Kingdom

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characteristic: host body mass index

characteristic: host height

characteristic: host subject id

text: human-gut

characteristic: human gut environmental package

text: metagenome

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text: IHMS_SOP 06 V59

characteristic: nucleic acid extraction

text: Homo sapiens

text: FOG-

text: Homo sapiens

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characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

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text: Univeristy of helsinki

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characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

characteristic: collection date

text: human

characteristic: common name

text: United Kingdom

text: human-gut

text: metagenome

text: IHMS_SOP 06 V60

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characteristic: organism

characteristic: pcr primers

text: FOG-

text: Homo sapiens

text: MiSeq


text: Univeristy of helsinki

text: public

text: human

characteristic: environment (biome)

characteristic: environment (feature)

characteristic: environment (material)

text: United Kingdom

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

characteristic: host age

characteristic: host body mass index

characteristic: host height

characteristic: host subject id

text: human-gut

characteristic: human gut environmental package

text: metagenome

characteristic: investigation type

text: IHMS_SOP 06 V61

text: Homo sapiens

text: FOG-

characteristic: project name

text: Homo sapiens

text: MiSeq

characteristic: sequencing method


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

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characteristic: External Id

text: Univeristy of helsinki

characteristic: INSDC center name

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text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

characteristic: collection date

text: human

characteristic: common name

text: United Kingdom

text: human-gut

text: metagenome

text: IHMS_SOP 06 V62

characteristic: nucleic acid extraction

text: Homo sapiens

text: FOG-

text: Homo sapiens

text: MiSeq

characteristic: title


text: Univeristy of helsinki

text: public

text: human

characteristic: environment (biome)

characteristic: environment (feature)

characteristic: environment (material)

text: United Kingdom

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

characteristic: host age

characteristic: host body mass index

characteristic: host height

characteristic: host subject id

text: human-gut

characteristic: human gut environmental package

text: metagenome

characteristic: investigation type

text: IHMS_SOP 06 V63

text: Homo sapiens

characteristic: organism

characteristic: pcr primers

text: FOG-

text: Homo sapiens

text: MiSeq


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

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text: Univeristy of helsinki

characteristic: INSDC center name

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text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

characteristic: collection date

text: human

characteristic: common name

text: United Kingdom

text: human-gut

text: metagenome

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text: Homo sapiens

text: FOG-

characteristic: project name

text: Homo sapiens

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characteristic: sequencing method


text: Univeristy of helsinki

text: public

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characteristic: environment (biome)

characteristic: environment (feature)

characteristic: environment (material)

text: United Kingdom

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

characteristic: host age

characteristic: host body mass index

characteristic: host height

characteristic: host subject id

text: human-gut

characteristic: human gut environmental package

text: metagenome

characteristic: investigation type

text: IHMS_SOP 06 V65

characteristic: nucleic acid extraction

text: Homo sapiens

text: FOG-

text: Homo sapiens

text: MiSeq

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Univeristy of helsinki

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text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

characteristic: collection date

text: human

characteristic: common name

text: United Kingdom

text: human-gut

text: metagenome

text: IHMS_SOP 06 V66

text: Homo sapiens

characteristic: organism

characteristic: pcr primers

text: FOG-

text: Homo sapiens

text: MiSeq


text: Univeristy of helsinki

text: public

text: human

characteristic: environment (biome)

characteristic: environment (feature)

characteristic: environment (material)

text: United Kingdom

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

characteristic: host age

characteristic: host body mass index

characteristic: host height

characteristic: host subject id

text: human-gut

characteristic: human gut environmental package

text: metagenome

characteristic: investigation type

text: IHMS_SOP 06 V67

text: Homo sapiens

text: FOG-

characteristic: project name

text: Homo sapiens

text: MiSeq

characteristic: sequencing method


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Univeristy of helsinki

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

characteristic: collection date

text: human

characteristic: common name

text: United Kingdom

text: human-gut

text: metagenome

text: IHMS_SOP 06 V68

characteristic: nucleic acid extraction

text: Homo sapiens

text: FOG-

text: Homo sapiens

text: MiSeq

characteristic: title


text: Univeristy of helsinki

text: public

text: human

characteristic: environment (biome)

characteristic: environment (feature)

characteristic: environment (material)

text: United Kingdom

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

characteristic: host age

characteristic: host body mass index

characteristic: host height

characteristic: host subject id

text: human-gut

characteristic: human gut environmental package

text: metagenome

characteristic: investigation type

text: IHMS_SOP 06 V69

text: Homo sapiens

characteristic: organism

characteristic: pcr primers

text: FOG-

text: Homo sapiens

text: MiSeq


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Univeristy of helsinki

characteristic: INSDC center name

characteristic: INSDC first public

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text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

characteristic: collection date

text: human

characteristic: common name

text: United Kingdom

text: human-gut

text: metagenome

text: IHMS_SOP 06 V70

text: Homo sapiens

text: FOG-

characteristic: project name

text: Homo sapiens

text: MiSeq

characteristic: sequencing method


text: Univeristy of helsinki

text: public

text: human

characteristic: environment (biome)

characteristic: environment (feature)

characteristic: environment (material)

text: United Kingdom

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

characteristic: host age

characteristic: host body mass index

characteristic: host height

characteristic: host subject id

text: human-gut

characteristic: human gut environmental package

text: metagenome

characteristic: investigation type

text: IHMS_SOP 06 V71

characteristic: nucleic acid extraction

text: Homo sapiens

text: FOG-

text: Homo sapiens

text: MiSeq

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Univeristy of helsinki

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

characteristic: collection date

text: human

characteristic: common name

text: United Kingdom

text: human-gut

text: metagenome

text: IHMS_SOP 06 V72

text: Homo sapiens

characteristic: organism

characteristic: pcr primers

text: FOG-

text: Homo sapiens

text: MiSeq


text: Univeristy of helsinki

text: public

text: human

characteristic: environment (biome)

characteristic: environment (feature)

characteristic: environment (material)

text: United Kingdom

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

characteristic: host age

characteristic: host body mass index

characteristic: host height

characteristic: host subject id

text: human-gut

characteristic: human gut environmental package

text: metagenome

characteristic: investigation type

text: IHMS_SOP 06 V73

text: Homo sapiens

text: FOG-

characteristic: project name

text: Homo sapiens

text: MiSeq

characteristic: sequencing method


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Univeristy of helsinki

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

characteristic: collection date

text: human

characteristic: common name

text: United Kingdom

text: human-gut

text: metagenome

text: IHMS_SOP 06 V74

characteristic: nucleic acid extraction

text: Homo sapiens

text: FOG-

text: Homo sapiens

text: MiSeq

characteristic: title


text: public

tag: Namespace:BRIC - Biotech Research and Innovation Centre

text: ArrayExpress

characteristic: broker name

characteristic: cell line

text: glial cell

characteristic: cell type

text: human

text: Protocols: CRISPR mediated KO of CIC: sgRNAs (Target sequence: mESCs: GCCTTCATGATCTTCAGCAAG; G144: GGGCGAGTGGTGGTATGCCC) were cloned into pSpCas9(BB)-2A-GFP (Addgene 48138) and transfected into mESCs (Lipofectamine 2000) or G144 cells (Amaxa Nucleofector II, Program A033). GFP-positive cells were single cell sorted 48h post-transfection, expanded and screened by immunoblotting for CIC deletion. Inhibitor treatment with 1 μM MEK inhibitor (PD0325901) was performed in 80% confluent cultures for 4 and 24 h respectively. DMSO was used as mock control. Cells were washed once with PBS, lysed directly in RLT buffer (Qiagen). Total RNA was extracted using the RNAeasy kit (Qiagen). 500 ng of total RNA was used for library preparation using TruSeq RNA Library Prep Kit v2 (Illumina) according to manufacturer recommendations.

characteristic: description

text: glioblastoma multiforme

characteristic: disease

text: CRISPR/Cas9 mediated knockout of CIC

characteristic: genotype

text: clonal line #8

characteristic: individual

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: brain

characteristic: organism part

text: Homo sapiens


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: BRIC - Biotech Research and Innovation Centre

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: ArrayExpress

text: glial cell

text: human

text: glioblastoma multiforme

text: CRISPR/Cas9 mediated knockout of CIC

text: clonal line #8

text: Homo sapiens

text: Homo sapiens

text: brain

text: Homo sapiens


text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: ArrayExpress

text: glial cell

text: human

characteristic: common name

text: glioblastoma multiforme

text: CRISPR/Cas9 mediated knockout of CIC

text: clonal line #9

text: Homo sapiens

text: Homo sapiens

text: brain

text: Homo sapiens

characteristic: title


text: public

text: ArrayExpress

characteristic: broker name

characteristic: cell line

text: glial cell

characteristic: cell type

text: human

characteristic: description

text: glioblastoma multiforme

characteristic: disease

text: wild type genotype

text: Homo sapiens

text: Homo sapiens

text: brain

text: Homo sapiens


characteristic: ENA-CHECKLIST

text: public

text: ArrayExpress

text: glial cell

text: human

text: Protocols: CRISPR mediated KO of CIC: sgRNAs (Target sequence: mESCs: GCCTTCATGATCTTCAGCAAG; G144: GGGCGAGTGGTGGTATGCCC) were cloned into pSpCas9(BB)-2A-GFP (Addgene 48138) and transfected into mESCs (Lipofectamine 2000) or G144 cells (Amaxa Nucleofector II, Program A033). GFP-positive cells were single cell sorted 48h post-transfection, expanded and screened by immunoblotting for CIC deletion. MEK inhibition: Inhibitor treatment with 1 μM MEK inhibitor (PD0325901) was performed in 80% confluent cultures for 4 and 24 h respectively. DMSO was used as mock control. Cells were cross-linked (1% formaldehyde, 10 minutes), quenched with 125 mM glycine, washed twice with PBS and harvested in SDS buffer (50 mM Tris at pH 8.1, 0.5 % SDS, 100 mM NaCl, 5 mM EDTA). Cells were pelleted, resuspended in Triton-X IP buffer (100 mM Tris at pH 8.6, 0.3% SDS, 1.7% Triton X-100, and 5 mM EDTA) and chromatin was sonicated (fragment size 200-500bp). 25 µg chromatin (measured by Bradford) was pre-cleared with protein-A Sepharose beads (GE healthcare) for 1 hour and incubated with primary antibody overnight at 4oC. Protein-A Sepharose beads were blocked with 10 µg/ml BSA overnight at 4°C. Next day, beads and antibody/chromatin-mixture were incubated for 3 hours at 4oC. Beads were washed 3x with low salt buffer (1% Triton X-100, 0.1% SDS, 150 mM NaCl, 2 mM EDTA, pH 8.0, 20 mM Tris-HCl, pH 8.0) and twice with high salt buffer (1% Triton X-100, 0.1% SDS, 500mM NaCl, 2 mM EDTA, pH8.0, 20 mM Tris-HCl, pH8.0). DNA was eluted with elution-buffer (1% SDS, 0.1 M sodium bicarbonate) at 65oC overnight and purified using QIAquick PCR Purification Kit (Quiagen). For ChIP-seq 1-2 ng of ChIP DNA was used for library preparation, using the NEBNext Ultra II DNA library prep kit (E7370; NEB).

text: adult

characteristic: developmental stage

text: glioblastoma multiforme

text: CRISPR/Cas9 mediated knockout of CIC

characteristic: genotype

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: brain

characteristic: organism part

text: Homo sapiens


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: ArrayExpress

text: glial cell

text: human

text: adult

text: glioblastoma multiforme

text: wild type genotype

text: Homo sapiens

text: Homo sapiens

text: brain

text: Homo sapiens


characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

unit: week

characteristic: age

text: ArrayExpress

text: neural stem cell

text: human

characteristic: common name

text: late embryo

text: normal

text: wild type genotype

text: Homo sapiens

text: Homo sapiens

text: brain

text: Homo sapiens


text: public

text: ArrayExpress

characteristic: broker name

characteristic: cell line

text: embryonic stem cell

characteristic: cell type

text: house mouse

characteristic: description

text: early embryo

text: normal

characteristic: disease

text: CRISPR/Cas9 mediated knockout of CIC

text: Mus musculus

text: Mus musculus

text: inner cell mass

text: Mus musculus

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: public

text: ArrayExpress

text: embryonic stem cell

text: house mouse

text: early embryo

characteristic: developmental stage

text: normal

text: wild type genotype

characteristic: genotype

text: Mus musculus

characteristic: organism

text: Mus musculus

text: inner cell mass

characteristic: organism part

text: Mus musculus


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: UNIVERSITY OF BERN

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

tag: Namespace:UNIVERSITY OF BERN

text: sheep

text: Ovis aries

text: Ovis aries

text: f

characteristic: sex


text: UNIVERSITY OF BERN

text: public

characteristic: SRA accession

characteristic: Submitter Id

text: sheep

characteristic: common name

text: Ovis aries

text: Ovis aries

text: m


text: SC

text: public

characteristic: anonymized name

characteristic: collection date

text: Enterococcus faecium

text: United Kingdom

characteristic: country

text: carriage

characteristic: host status

text: faecal

characteristic: isolation source

text: Enterococcus faecium

text: Bacterial Genome

characteristic: sample description

text: Enterococcus faecium

text: human

characteristic: specific host

characteristic: strain

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: SC

characteristic: INSDC center name

text: public

text: Enterococcus faecalis

text: United Kingdom

text: carriage

text: faecal

text: Enterococcus faecalis

characteristic: organism

text: Bacterial Genome

text: Enterococcus faecalis

text: human


text: SC

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: Klebsiella pneumoniae

text: United Kingdom

text: carriage

text: faecal

text: Klebsiella pneumoniae

text: Bacterial Genome

text: Klebsiella pneumoniae

text: human


text: SC

text: public

characteristic: anonymized name

characteristic: collection date

text: Escherichia coli

characteristic: common name

text: United Kingdom

characteristic: country

text: carriage

characteristic: host status

text: faecal

text: Escherichia coli

text: Bacterial Genome

text: Escherichia coli

text: human


text: SC

text: public

text: Klebsiella oxytoca

text: United Kingdom

text: carriage

text: faecal

characteristic: isolation source

text: Klebsiella oxytoca

text: Bacterial Genome

characteristic: sample description

text: Klebsiella oxytoca

text: human

characteristic: specific host

characteristic: strain

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: SC

characteristic: INSDC center name

text: public

text: Enterobacter cloacae

text: United Kingdom

text: carriage

text: faecal

text: Enterobacter cloacae

text: Bacterial Genome

text: Enterobacter cloacae

text: human


text: SC

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: Enterococcus casseliflavus

text: United Kingdom

text: carriage

text: faecal

text: Enterococcus casseliflavus

characteristic: organism

text: Bacterial Genome

text: Enterococcus casseliflavus

text: human


text: Plasmodium falciparum

characteristic: ArrayExpress-SPECIES

text: SC

text: public

characteristic: Submitter Id

text: malaria parasite P. falciparum

characteristic: common name

text: Plasmodium falciparum

text: Plasmodium falciparum

characteristic: subject id


unit: mg/L

characteristic: Chl

text: public

text: 7939:4db9f576-9f58-4baa-a3b9-fd016c274b3d

tag: Namespace:Leibniz Centre for Tropical Marine Research

text: GFBIO

characteristic: broker name

characteristic: collection date

text: particle-attached bacterial community in the water column, filtered on 3um pore size, from intensive pond T3 at day 70

characteristic: description

text: tropical marginal sea biome [ENVO:01001230]

characteristic: environment (biome)

text: coastal shrimp pond [ENVO:01001256]

characteristic: environment (feature)

text: saline shrimp pond water [ENVO:01001257]

characteristic: environment (material)

text: water

characteristic: environmental package

characteristic: estimated latitude of seawater source

characteristic: estimated longitude of seawater source

unit: cells/ml

characteristic: free-living cell count

text: Indonesia

characteristic: geographic location (country and/or sea)

unit: m

characteristic: geographic location (depth)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: Java Sea

characteristic: geographic location (region and locality)

text: Rembang Regency

text: mimarks-survey

characteristic: investigation type

text: marine metagenome

characteristic: particle-attached cell count

characteristic: ph

text: ZMT project with RISET-Pro scholarship

characteristic: project name

unit: practical salinity unit

characteristic: salinity

text: marine metagenome

text: Illumina MiSeq

characteristic: sequencing method

text: intensive

text: Tireman

characteristic: site name

text: true

characteristic: submitted to INSDC

unit: ºC

characteristic: temperature

characteristic: turbidity ntu

text: water

characteristic: water environmental package


characteristic: Chl

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Leibniz Centre for Tropical Marine Research

characteristic: INSDC center name

characteristic: INSDC first public

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text: public

characteristic: INSDC status

characteristic: SRA accession

text: 7938:4db9f576-9f58-4baa-a3b9-fd016c274b3d

characteristic: Submitter Id

text: GFBIO

characteristic: broker name

characteristic: collection date

text: particle-attached bacterial community in the water column, filtered on 3um pore size, from intensive pond T2 at day 70

characteristic: description

characteristic: environment (biome)

text: coastal shrimp pond [ENVO:01001256]

characteristic: environment (feature)

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text: water

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characteristic: estimated longitude of seawater source

characteristic: free-living cell count

text: Indonesia

text: Java Sea

text: Rembang Regency

text: mimarks-survey

text: marine metagenome

characteristic: organism

text: ZMT project with RISET-Pro scholarship

text: marine metagenome

text: Illumina MiSeq

text: intensive

text: Tireman

text: true

characteristic: title

text: water


characteristic: Chl

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text: public

text: 7937:4db9f576-9f58-4baa-a3b9-fd016c274b3d

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text: particle-attached bacterial community in the water column, filtered on 3um pore size, from intensive pond T1 at day 70

text: coastal shrimp pond [ENVO:01001256]

text: water

text: Indonesia

characteristic: geographic location (country and/or sea)

characteristic: geographic location (depth)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: Java Sea

characteristic: geographic location (region and locality)

text: Rembang Regency

text: mimarks-survey

characteristic: investigation type

text: marine metagenome

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characteristic: project name

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text: intensive

text: Tireman

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text: true

characteristic: submitted to INSDC

characteristic: temperature

characteristic: turbidity ntu

text: water

characteristic: water environmental package


characteristic: Chl

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC center name

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characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: 7936:4db9f576-9f58-4baa-a3b9-fd016c274b3d

characteristic: Submitter Id

text: GFBIO

characteristic: broker name

characteristic: collection date

text: particle-attached bacterial community in the water column, filtered on 3um pore size, from semi-intensive pond S3 at day 70

characteristic: description

characteristic: environment (biome)

text: coastal shrimp pond [ENVO:01001256]

characteristic: environment (feature)

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characteristic: estimated longitude of seawater source

characteristic: free-living cell count

text: Indonesia

text: Java Sea

text: Rembang Regency

text: mimarks-survey

text: marine metagenome

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text: marine metagenome

text: Illumina MiSeq

text: semi intensive

text: Sluke

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characteristic: title

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characteristic: Chl

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characteristic: ENA-LAST-UPDATE

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text: public

text: 7935:4db9f576-9f58-4baa-a3b9-fd016c274b3d

text: GFBIO

text: particle-attached bacterial community in the water column, filtered on 3um pore size, from semi-intensive pond S2 at day 70

text: coastal shrimp pond [ENVO:01001256]

text: water

text: Indonesia

characteristic: geographic location (country and/or sea)

characteristic: geographic location (depth)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: Java Sea

characteristic: geographic location (region and locality)

text: Rembang Regency

text: mimarks-survey

characteristic: investigation type

text: marine metagenome

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text: Illumina MiSeq

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characteristic: site name

text: true

characteristic: submitted to INSDC

characteristic: temperature

characteristic: turbidity ntu

text: water

characteristic: water environmental package


characteristic: Chl

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC center name

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characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: 7934:4db9f576-9f58-4baa-a3b9-fd016c274b3d

characteristic: Submitter Id

text: GFBIO

characteristic: broker name

characteristic: collection date

text: particle-attached bacterial community in the water column, filtered on 3um pore size, from semi-intensive pond S1 at day 70

characteristic: description

characteristic: environment (biome)

text: coastal shrimp pond [ENVO:01001256]

characteristic: environment (feature)

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characteristic: environmental package

characteristic: estimated latitude of seawater source

characteristic: estimated longitude of seawater source

characteristic: free-living cell count

text: Indonesia

text: Java Sea

text: Rembang Regency

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text: Sluke

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characteristic: title

text: water


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text: public

text: 7933:4db9f576-9f58-4baa-a3b9-fd016c274b3d

text: GFBIO

text: particle-attached bacterial community in the water column, filtered on 3um pore size, from intensive pond T3 at day 60

text: coastal shrimp pond [ENVO:01001256]

text: water

text: Indonesia

characteristic: geographic location (country and/or sea)

characteristic: geographic location (depth)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: Java Sea

characteristic: geographic location (region and locality)

text: Rembang Regency

text: mimarks-survey

characteristic: investigation type

text: marine metagenome

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text: intensive

text: Tireman

characteristic: site name

text: true

characteristic: submitted to INSDC

characteristic: temperature

characteristic: turbidity ntu

text: water

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characteristic: Chl

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: 7932:4db9f576-9f58-4baa-a3b9-fd016c274b3d

characteristic: Submitter Id

text: GFBIO

characteristic: broker name

characteristic: collection date

text: particle-attached bacterial community in the water column, filtered on 3um pore size, from intensive pond T2 at day 60

characteristic: description

characteristic: environment (biome)

text: coastal shrimp pond [ENVO:01001256]

characteristic: environment (feature)

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text: water

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characteristic: estimated latitude of seawater source

characteristic: estimated longitude of seawater source

characteristic: free-living cell count

text: Indonesia

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text: mimarks-survey

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characteristic: organism

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characteristic: Chl

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text: public

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text: GFBIO

text: particle-attached bacterial community in the water column, filtered on 3um pore size, from intensive pond T1 at day 60

text: tropical marginal sea biome [ENVO:01001230]

text: coastal shrimp pond [ENVO:01001256]

text: water

text: Indonesia

characteristic: geographic location (country and/or sea)

characteristic: geographic location (depth)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: Java Sea

characteristic: geographic location (region and locality)

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text: mimarks-survey

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characteristic: project name

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text: intensive

text: Tireman

characteristic: site name

text: true

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characteristic: temperature

characteristic: turbidity ntu

text: water

characteristic: water environmental package


characteristic: Chl

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Leibniz Centre for Tropical Marine Research

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: 7930:4db9f576-9f58-4baa-a3b9-fd016c274b3d

characteristic: Submitter Id

text: GFBIO

characteristic: broker name

characteristic: collection date

text: particle-attached bacterial community in the water column, filtered on 3um pore size, from semi-intensive pond S3 at day 60

characteristic: description

characteristic: environment (biome)

text: coastal shrimp pond [ENVO:01001256]

characteristic: environment (feature)

text: saline shrimp pond water [ENVO:01001257]

characteristic: environment (material)

text: water

characteristic: environmental package

characteristic: estimated latitude of seawater source

characteristic: estimated longitude of seawater source

characteristic: free-living cell count

text: Indonesia

text: Java Sea

text: Rembang Regency

text: mimarks-survey

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characteristic: organism

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text: marine metagenome

text: Illumina MiSeq

text: semi intensive

text: Sluke

text: true

characteristic: title

text: water


characteristic: Chl

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text: public

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text: particle-attached bacterial community in the water column, filtered on 3um pore size, from semi-intensive pond S2 at day 60

text: coastal shrimp pond [ENVO:01001256]

text: water

text: Indonesia

characteristic: geographic location (country and/or sea)

characteristic: geographic location (depth)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: Java Sea

characteristic: geographic location (region and locality)

text: Rembang Regency

text: mimarks-survey

characteristic: investigation type

text: marine metagenome

characteristic: particle-attached cell count

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text: ZMT project with RISET-Pro scholarship

characteristic: project name

characteristic: salinity

text: marine metagenome

text: Illumina MiSeq

characteristic: sequencing method

text: semi intensive

text: Sluke

characteristic: site name

text: true

characteristic: submitted to INSDC

characteristic: temperature

characteristic: turbidity ntu

text: water

characteristic: water environmental package


characteristic: Chl

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: 7928:4db9f576-9f58-4baa-a3b9-fd016c274b3d

characteristic: Submitter Id

text: GFBIO

characteristic: broker name

characteristic: collection date

text: particle-attached bacterial community in the water column, filtered on 3um pore size, from semi-intensive pond S1 at day 60

characteristic: description

characteristic: environment (biome)

text: coastal shrimp pond [ENVO:01001256]

characteristic: environment (feature)

characteristic: environment (material)

text: water

characteristic: environmental package

characteristic: estimated latitude of seawater source

characteristic: estimated longitude of seawater source

characteristic: free-living cell count

text: Indonesia

text: Java Sea

text: Rembang Regency

text: mimarks-survey

text: marine metagenome

characteristic: organism

text: ZMT project with RISET-Pro scholarship

text: marine metagenome

text: Illumina MiSeq

text: semi intensive

text: Sluke

text: true

characteristic: title

text: water


characteristic: Chl

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

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characteristic: INSDC first public

text: public

text: 7927:4db9f576-9f58-4baa-a3b9-fd016c274b3d

text: GFBIO

text: particle-attached bacterial community in the water column, filtered on 3um pore size, from intensive pond T3 at day 50

text: coastal shrimp pond [ENVO:01001256]

text: water

text: Indonesia

characteristic: geographic location (country and/or sea)

characteristic: geographic location (depth)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: Java Sea

characteristic: geographic location (region and locality)

text: Rembang Regency

text: mimarks-survey

characteristic: investigation type

text: marine metagenome

characteristic: particle-attached cell count

characteristic: ph

text: ZMT project with RISET-Pro scholarship

characteristic: project name

characteristic: salinity

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text: Illumina MiSeq

characteristic: sequencing method

text: intensive

text: Tireman

characteristic: site name

text: true

characteristic: submitted to INSDC

characteristic: temperature

characteristic: turbidity ntu

text: water

characteristic: water environmental package