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text: public

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text: north america

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text: SUGG.20171103.SCHINDLER.3.DNA-DNA1_CO1BE_4 Taxonomy ID:1711999

characteristic: description

text: freshwater environment

characteristic: environment (biome)

text: area of open water

text: fresh water

text: water

text: USA

characteristic: geographic location (country and/or sea)

text: mimarks-survey

characteristic: investigation type

text: invertebrate

text: invertebrate metagenome

characteristic: organism

text: zooplankton individuals per liter

text: NEON Zooplankton DNA Barcodes - 2017

text: Schindler-Patalas

text: 24 L

text: invertebrate metagenome

text: illumina

characteristic: title

text: water


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: National Ecological Observatory Network

text: public

text: MGRAST

text: north america

text: SUGG.20171103.SCHINDLER.3.DNA-DNA1_CO1BE_3 Taxonomy ID:1711999

text: freshwater environment

text: area of open water

characteristic: environment (feature)

text: fresh water

characteristic: environment (material)

text: water

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text: USA

characteristic: geographic location (depth)

characteristic: geographic location (elevation)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

characteristic: geographic location (region and locality)

text: mimarks-survey

text: invertebrate

characteristic: mgrast id

text: invertebrate metagenome

text: zooplankton individuals per liter

characteristic: organism count

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characteristic: project name

text: Schindler-Patalas

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characteristic: sample name

text: 24 L

characteristic: sample size

text: invertebrate metagenome

text: illumina

characteristic: sequencing method

text: water

characteristic: water environmental package


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: National Ecological Observatory Network

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: MGRAST

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text: north america

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text: SUGG.20171103.SCHINDLER.1.DNA-DNA1_CO1BE_3 Taxonomy ID:1711999

characteristic: description

text: freshwater environment

characteristic: environment (biome)

text: area of open water

text: fresh water

text: water

text: USA

characteristic: geographic location (country and/or sea)

text: mimarks-survey

characteristic: investigation type

text: invertebrate

text: invertebrate metagenome

characteristic: organism

text: zooplankton individuals per liter

text: NEON Zooplankton DNA Barcodes - 2017

text: Schindler-Patalas

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text: invertebrate metagenome

text: illumina

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text: water


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: National Ecological Observatory Network

text: public

text: MGRAST

text: north america

text: BARC.20171031.TOWNET.1.DNA-DNA1_CO1BE_3 Taxonomy ID:1711999

text: freshwater environment

text: area of open water

characteristic: environment (feature)

text: fresh water

characteristic: environment (material)

text: water

characteristic: environmental package

text: USA

characteristic: geographic location (depth)

characteristic: geographic location (elevation)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

characteristic: geographic location (region and locality)

text: mimarks-survey

text: invertebrate

characteristic: mgrast id

text: invertebrate metagenome

text: zooplankton individuals per liter

characteristic: organism count

text: NEON Zooplankton DNA Barcodes - 2017

characteristic: project name

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text: 840.96 L

characteristic: sample size

text: invertebrate metagenome

text: illumina

characteristic: sequencing method

text: water

characteristic: water environmental package


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: National Ecological Observatory Network

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: MGRAST

characteristic: broker name

characteristic: collection date

characteristic: collection time

text: north america

characteristic: continent

text: BARC.20171031.TOWNET.1.DNA-DNA1_CO1F230_4 Taxonomy ID:1711999

characteristic: description

text: freshwater environment

characteristic: environment (biome)

text: area of open water

text: fresh water

text: water

text: USA

characteristic: geographic location (country and/or sea)

text: mimarks-survey

characteristic: investigation type

text: invertebrate

text: invertebrate metagenome

characteristic: organism

text: zooplankton individuals per liter

text: NEON Zooplankton DNA Barcodes - 2017

text: tow net

text: 840.96 L

text: invertebrate metagenome

text: illumina

characteristic: title

text: water


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: CRG

text: public

characteristic: isolate

text: Zygosaccharomyces sapae

text: Zygosaccharomyces sapae


text: CRG

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: Zygosaccharomyces rouxii

text: Zygosaccharomyces rouxii


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


text: MPI-MM

text: public

characteristic: collection date

text: isolate

characteristic: environment (biome)

text: isolate

characteristic: environment (feature)

text: sediment

characteristic: environment (material)

text: USA

characteristic: geographic location (country and/or sea)

characteristic: geographic location (depth)

characteristic: geographic location (elevation)

text: 41° 31' 35.392

characteristic: geographic location (latitude)

text: -70° 40' 23.109

characteristic: geographic location (longitude)

text: metatranscriptome

characteristic: investigation type

text: Sulfurimonas denitrificans

characteristic: project name

text: Sulfurimonas denitrificans

text: sediment

characteristic: sediment environmental package

text: Illumina HiSeq

characteristic: sequencing method

text: Sulfurimonas denitrificans cyclooctasulfur utilization


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: MPI-MM

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: isolate

text: isolate

text: sediment

text: USA

text: 41° 31' 35.392

text: -70° 40' 23.109

text: metatranscriptome

text: Sulfurimonas denitrificans

characteristic: organism

text: Sulfurimonas denitrificans

text: sediment

text: Illumina HiSeq

text: Sulfurimonas denitrificans thiosulfate utilization

characteristic: title


text: Homo sapiens

characteristic: ArrayExpress-SPECIES

text: SC

text: public

characteristic: Submitter Id

text: human

characteristic: common name

text: Homo sapiens

text: Homo sapiens

characteristic: subject id


text: URMITE

text: public

text: vagina

characteristic: isolation source

text: Lactobacillus raoultii

text: Lactobacillus raoultii

characteristic: strain

text: Lactobacillus raoultii genome


characteristic: ENA-CHECKLIST

text: public

tag: Namespace:CENTRE FOR GEOGENETICS, NATURAL HISTORY MUSEUM OF

text: human

text: Homo sapiens

text: Homo sapiens

text: Low depth genome sequence for IK002


characteristic: ENA-FIRST-PUBLIC

text: CENTRE FOR GEOGENETICS, NATURAL HISTORY MUSEUM OF

text: public

text: human

text: Homo sapiens

text: Homo sapiens

text: Low depth genome sequence for In661


characteristic: ENA-LAST-UPDATE

text: public

text: human

text: Homo sapiens

text: Homo sapiens

text: Low depth genome sequence for In662


characteristic: External Id

text: public

text: human

text: Homo sapiens

text: Homo sapiens

text: Low depth genome sequence for La364


characteristic: INSDC center name

text: public

text: human

text: Homo sapiens

text: Homo sapiens

text: Low depth genome sequence for La368


characteristic: INSDC first public

text: public

text: human

text: Homo sapiens

text: Homo sapiens

text: Low depth genome sequence for La727


characteristic: INSDC last update

text: public

text: human

text: Homo sapiens

text: Homo sapiens

text: Low depth genome sequence for La898


text: public

characteristic: INSDC status

text: human

text: Homo sapiens

text: Homo sapiens

text: Low depth genome sequence for Ma554


text: public

characteristic: SRA accession

text: human

text: Homo sapiens

text: Homo sapiens

text: Low depth genome sequence for Ma555


text: public

text: human

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: Low depth genome sequence for Ma911


text: public

text: human

text: Homo sapiens

text: Homo sapiens

text: Low depth genome sequence for Ma912

characteristic: title


text: public

text: human

text: Homo sapiens

text: Homo sapiens

text: Low depth genome sequence for Phl534


text: public

text: human

text: Homo sapiens

text: Homo sapiens

text: Low depth genome sequence for Th519


text: public

text: human

text: Homo sapiens

text: Homo sapiens

text: Low depth genome sequence for Th521


text: public

text: human

text: Homo sapiens

text: Homo sapiens

text: Low depth genome sequence for Th530


text: public

text: human

text: Homo sapiens

text: Homo sapiens

text: Low depth genome sequence for Th531


text: public

text: human

text: Homo sapiens

text: Homo sapiens

text: Low depth genome sequence for Th703


text: public

text: human

text: Homo sapiens

text: Homo sapiens

text: Low depth genome sequence for Vt719


text: public

text: human

text: Homo sapiens

text: Homo sapiens

text: Low depth genome sequence for Vt777


text: public

text: human

text: Homo sapiens

text: Homo sapiens

text: Low depth genome sequence for Vt778


text: public

text: human

text: Homo sapiens

text: Homo sapiens

text: Low depth genome sequence for Vt779


text: public

text: human

text: Homo sapiens

text: Homo sapiens

text: Low depth genome sequence for Vt781


text: public

text: human

text: Homo sapiens

text: Homo sapiens

text: Low depth genome sequence for Vt796


text: public

text: human

text: Homo sapiens

text: Homo sapiens

text: Low depth genome sequence for Vt808


text: public

text: human

text: Homo sapiens

text: Homo sapiens

text: Low depth genome sequence for Vt833


text: public

text: human

text: Homo sapiens

text: Homo sapiens

text: Low depth genome sequence for Vt880


text: inki

text: public

text: Vestre Viken Hospital

characteristic: collected by

characteristic: collection date

text: Norway

characteristic: geographic location (country and/or sea)

text: Homo Sapiens

characteristic: host scientific name

characteristic: isolate

text: Streptococcus mitis

text: Streptococcus mitis


text: TAULI

text: public

characteristic: Submitter Id

text: human

characteristic: common name

text: 16S sequences from BIOMEPOC cohort

characteristic: description

text: terrestrial biome

characteristic: environment (biome)

text: organic feature

characteristic: environment (feature)

text: biological product

characteristic: environment (material)

text: Spain

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: human-associated

characteristic: human associated environmental package

text: metagenome

characteristic: investigation type

text: COPD

characteristic: lung/pulmonary disorder

text: Homo sapiens

text: BIOMEPOC

characteristic: project name

text: Homo sapiens

text: 16S sequencing ILLUMINA

characteristic: sequencing method

text: BIOMEPOC


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: EMBL

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: ArrayExpress

characteristic: broker name

characteristic: cell line

text: embryonic stem cell

characteristic: cell type

text: house mouse

text: Protocols: Mouse embryonic stem cells (129B-13) were cultured in ESC media containing Knockout-DMEM (Thermo Fisher) with 15% EmbryoMax FBS (Millipore) and 20 ng/ml leukemia inhibitory factor (LIF, produced by Protein Expression Facility at EMBL Heidelberg), 1% non-essential amino acids, 1% Glutamax, 1% Pen/Strep, 1% of 55mM beta-Mercaptoethanol solution. Cells were maintained at 37C with 5% CO2. Fresh cell pellets of 20 Mio. cells were resuspended in 20 ml of 1% fresh paraformaldeyde (PFA) diluted in PBS and rotated for 10 min at room temperature. Unreacted PFA was quenched with glycine. Cells were washed twice to remove PFA, snap-frozen and stored at -80C. Frozen cell pellet of 10 Mio. cells was resuspended in digestion buffer, 100 U MNase (Worthington) were added and samples were incubated at 37C for 5 minutes while shaking at 500 rpm. Samples were immediately moved to ice and MNase was quenched by addition of EDTA. Lysates were sonicated using Bioruptor Pico (Diagenode) and dialyzed against RIPA buffer for 3 hours at 4C. Insoluble material was pelleted at 10.000rpm for 10 min, 4C and supernatant was used as input for ChIP. To check that mostly mono-nucleosomes and di-nucleosomes were obtained, DNA fragment sizes of inputs were analyzed by agarose gel electrophoresis. For native ChIP of histone modifications, Protein-G-Dynabeads (Invitrogen) were precoated with antibodies for 4 hours at 4C while rotating. We used the following antibodies: H3K4me1 (39297, active motif), H3K4me3 (39915, Active Motif), H3K27ac (39685, Active Motif). Beads were added to lysates and rotated over night at 4C. On the next day, beads were washed with 3x RIPA, 2xRIPA+NaCl, 2x LiCl Buffer and finally rinsed 1x with TE+50mM NaCl Buffer. Samples were eluted from ProteinG Dynabeads using SDS-elution buffer (50 mM Tris-HCl ph8.0, 10 mM EDTA, 1% SDS) at 65C for 30 minutes, shaking at 1500 rpm. Proteinase K was added (0.2 mg/ml final) to eluted samples and digestion was carried out for 2 hours at 55C followed by PCR purification (Qiagen). Samples were eluted from ProteinG Dynabeads using SDS-elution buffer (50 mM Tris-HCl ph8.0, 10 mM EDTA, 1% SDS) at 65C for 30 minutes, shaking at 1500 rpm. Proteinase K was added (0.2 mg/ml final) to eluted samples and digestion was carried out for 2 hours at 55C followed by PCR purification (Qiagen). For Inputs (MNase-Seq) 300 ng of prepared MNase-digested DNA was used for library preparation. For ChIP, entire IP-eluate was used for library preparation. Sequencing libraries were prepared using DNA Ultra II library preparation kit (NEB) according to the manufacturer???s instructions. Number of Amplification cycles was adjusted depending on ChIP: H3K27ac 10x cycles, H3K4me3 10x cycles, H3K4me1 11x cycles, H3.3 12x cycles, H3K36me3 12x cycles, Inputs 10x cycles. Samples were barcoded, pooled and sequenced on Illumina???s HiSeq2000 Sequencer (50 bp single-end mode) or NextSeq 500 Sequencer (75 bp single-end mode).

text: gene knock out

characteristic: genetic modification

text: H3f3a -/-

characteristic: genotype

text: Mus musculus

characteristic: organism

text: Mus musculus

text: Mus musculus

unit: day

characteristic: time

characteristic: title


characteristic: ENA-CHECKLIST

text: EMBL

text: public

characteristic: Submitter Id

text: ArrayExpress

text: embryonic stem cell

text: house mouse

characteristic: common name

text: Protocols: Mouse embryonic stem cells (129B-13) were cultured in ESC media containing Knockout-DMEM (Thermo Fisher) with 15% EmbryoMax FBS (Millipore) and 20 ng/ml leukemia inhibitory factor (LIF, produced by Protein Expression Facility at EMBL Heidelberg), 1% non-essential amino acids, 1% Glutamax, 1% Pen/Strep, 1% of 55mM beta-Mercaptoethanol solution. Cells were maintained at 37C with 5% CO2. Lysates were prepared by resuspending crosslinked cells in hypotonic buffer (15 mM HEPES pH8, 5 mM MgCl2, 10 mM KCl, 0.5mM EDTA, 2x Protease Inhibitors) followed by douncing to release intact nuclei. Nuclei were pelleted and resuspended in digestion buffer (15 mM HEPES pH8, 5 mM MgCl2, 30 mM KCl, 3mM CaCl2, 2x Protease Inhibitors) by douncing. In-nuclei MNase digestion was started by addition of 150U MNase (Worthington). Samples were then quickly vortexed and incubated at 37C for 5 min while shaking at 500rpm. Reaction was quenched by addition of 10x Quenching buffer (150mM HEPES pH8, 1500mM NaCl, 50 mM EDTA, 30 mM EGTA, 0.2% TritonX-100) and by placing samples on ice. 0.1% sodium deoxycholate, 0.5% sarcosine and 1% Triton-X were added to lysates and samples were sonicated in Bioruptor Pico (Diagenode) to further promote DNA fragmentation. Insoluble material was removed by centrifugation at 20.000rpm for 10 min, 4C and the soluble supernatant was used as ChIP Input. DNA fragment sizes of lysates were checked by agarose gel electrophoresis. Mainly mono-, di-, tri-nucleosomes were obtained. Protein-G Dynabeads were precoated with H3.3 antibody (Millipore) for 4 hours at 4C. Beads were washed, added to lysates and incubated over night at 4C while rotating. On the next day, beads were washed 8x with RIPA buffer (50 mM HEPES pH7.6, 100 mM LiCl, 1 mM EDTA, 1% NP-40, 0.7% Sodium deoxycholate) and gently rinsed once with TE buffer+50 mM NaCl. Elution was carried out using SDS elution buffer (50 mM Tris-HCl ph8.0, 10 mM EDTA, 1% SDS) at 65C for 30 minutes while shaking samples at 1500rpm. Samples were Proteinase K digested (0.2 mg/ml final) for 2 hours at 55C and crosslink was reversed over night at 65C. Samples were purified using Qiagen???s PCR purification kit and used for ChIP-library preparation. Samples were eluted from ProteinG Dynabeads using SDS-elution buffer (50 mM Tris-HCl ph8.0, 10 mM EDTA, 1% SDS) at 65C for 30 minutes, shaking at 1500 rpm. Proteinase K was added (0.2 mg/ml final) to eluted samples and digestion was carried out for 2 hours at 55C followed by PCR purification (Qiagen). For Inputs (MNase-Seq) 300 ng of prepared MNase-digested DNA was used for library preparation. For ChIP, entire IP-eluate was used for library preparation. Sequencing libraries were prepared using DNA Ultra II library preparation kit (NEB) according to the manufacturer???s instructions. Number of Amplification cycles was adjusted depending on ChIP: H3K27ac 10x cycles, H3K4me3 10x cycles, H3K4me1 11x cycles, H3.3 12x cycles, H3K36me3 12x cycles, Inputs 10x cycles. Samples were barcoded, pooled and sequenced on Illumina???s HiSeq2000 Sequencer (50 bp single-end mode) or NextSeq 500 Sequencer (75 bp single-end mode).

characteristic: description

text: gene knock out

text: H3f3a -/-

text: Mus musculus

text: Mus musculus

text: Mus musculus


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: EMBL

characteristic: INSDC center name

text: public

text: ArrayExpress

text: embryonic stem cell

text: house mouse

text: induced mutation

text: H3f3a -/-; H3f3b K36A

text: Mus musculus

text: Mus musculus

text: Mus musculus


text: EMBL

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: ArrayExpress

text: embryonic stem cell

text: house mouse

text: Protocols: mESC growth: Mouse embryonic stem cells (129B-13) were cultured in ESC media containing Knockout-DMEM (Thermo Fisher) with 15% EmbryoMax FBS (Millipore) and 20 ng/ml leukemia inhibitory factor (LIF, produced by Protein Expression Facility at EMBL Heidelberg), 1% non-essential amino acids, 1% Glutamax, 1% Pen/Strep, 1% of 55mM beta-Mercaptoethanol solution. Cells were maintained at 37C with 5% CO2. mESCs were used as neuronal differentiation Day 0 (D0). Neuronal Differentiation: mESCs were differentiated into glutamatergic neurons according to Bibel et al. (Nature Protocols, 2007) with small modifications. mESCs were resuspended in differentiation media without LIF and grown in suspension using non-adherent plates to promote the formation of embryoid bodies. Differentiation media was changed every two days. On day 4 retinoic acid was added to the media. Embryoid bodies were cultured for 4 additional days in the presence of retinoic acid to obtain neural precursor cells on differentiation day 8. For neural monolayer culture, plates were pre-coated with Poly-D-Lysin and Laminin. On day 8, Embryoid bodies were dissociated with trypsin and cells were plated in N2 media (regular DMEM supplemented with 1xN2 and 1xB27-VitaminA (Thermo Fisher)) at a density of 200.000 cells/cm2 on precoated plates. N2 media was changed every two days without exposing neuron culture to oxygen. Four days after plating, neurons were harvested after a total of 12 differentiation days (D12). Lysates were prepared by resuspending crosslinked cells in hypotonic buffer (15 mM HEPES pH8, 5 mM MgCl2, 10 mM KCl, 0.5mM EDTA, 2x Protease Inhibitors) followed by douncing to release intact nuclei. Nuclei were pelleted and resuspended in digestion buffer (15 mM HEPES pH8, 5 mM MgCl2, 30 mM KCl, 3mM CaCl2, 2x Protease Inhibitors) by douncing. In-nuclei MNase digestion was started by addition of 150U MNase (Worthington). Samples were then quickly vortexed and incubated at 37C for 5 min while shaking at 500rpm. Reaction was quenched by addition of 10x Quenching buffer (150mM HEPES pH8, 1500mM NaCl, 50 mM EDTA, 30 mM EGTA, 0.2% TritonX-100) and by placing samples on ice. 0.1% sodium deoxycholate, 0.5% sarcosine and 1% Triton-X were added to lysates and samples were sonicated in Bioruptor Pico (Diagenode) to further promote DNA fragmentation. Insoluble material was removed by centrifugation at 20.000rpm for 10 min, 4C and the soluble supernatant was used as ChIP Input. DNA fragment sizes of lysates were checked by agarose gel electrophoresis. Mainly mono-, di-, tri-nucleosomes were obtained. Protein-G Dynabeads were precoated with H3.3 antibody (Millipore) for 4 hours at 4C. Beads were washed, added to lysates and incubated over night at 4C while rotating. On the next day, beads were washed 8x with RIPA buffer (50 mM HEPES pH7.6, 100 mM LiCl, 1 mM EDTA, 1% NP-40, 0.7% Sodium deoxycholate) and gently rinsed once with TE buffer+50 mM NaCl. Elution was carried out using SDS elution buffer (50 mM Tris-HCl ph8.0, 10 mM EDTA, 1% SDS) at 65C for 30 minutes while shaking samples at 1500rpm. Samples were Proteinase K digested (0.2 mg/ml final) for 2 hours at 55C and crosslink was reversed over night at 65C. Samples were purified using Qiagen???s PCR purification kit and used for ChIP-library preparation. Samples were eluted from ProteinG Dynabeads using SDS-elution buffer (50 mM Tris-HCl ph8.0, 10 mM EDTA, 1% SDS) at 65C for 30 minutes, shaking at 1500 rpm. Proteinase K was added (0.2 mg/ml final) to eluted samples and digestion was carried out for 2 hours at 55C followed by PCR purification (Qiagen). For Inputs (MNase-Seq) 300 ng of prepared MNase-digested DNA was used for library preparation. For ChIP, entire IP-eluate was used for library preparation. Sequencing libraries were prepared using DNA Ultra II library preparation kit (NEB) according to the manufacturer???s instructions. Number of Amplification cycles was adjusted depending on ChIP: H3K27ac 10x cycles, H3K4me3 10x cycles, H3K4me1 11x cycles, H3.3 12x cycles, H3K36me3 12x cycles, Inputs 10x cycles. Samples were barcoded, pooled and sequenced on Illumina???s HiSeq2000 Sequencer (50 bp single-end mode) or NextSeq 500 Sequencer (75 bp single-end mode).

text: induced mutation

text: H3f3a -/-; H3f3b K36A

text: Mus musculus

text: Mus musculus

text: Mus musculus


text: EMBL

text: public

text: ArrayExpress

characteristic: broker name

characteristic: cell line

text: neural precursor

characteristic: cell type

text: house mouse

text: induced mutation

characteristic: genetic modification

text: H3f3a -/-; H3f3b K36A

text: Mus musculus

text: Mus musculus

text: Mus musculus


text: EMBL

text: public

text: E-MTAB-6822:ChIP_H3K36me3_H3.3K36A-1_D12

text: ArrayExpress

text: neuron

text: house mouse

text: induced mutation

text: H3f3a -/-; H3f3b K36A

characteristic: genotype

text: Mus musculus

characteristic: organism

text: Mus musculus

text: Mus musculus

characteristic: time

characteristic: title


characteristic: ENA-CHECKLIST

text: EMBL

text: public

characteristic: Submitter Id

text: ArrayExpress

text: embryonic stem cell

text: house mouse

characteristic: common name

characteristic: description

text: induced mutation

text: H3f3a -/-; H3f3b K4A

text: Mus musculus

text: Mus musculus

text: Mus musculus


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: EMBL

characteristic: INSDC center name

text: public

text: ArrayExpress

text: embryonic stem cell

text: house mouse

text: induced mutation

text: H3f3a -/-; H3f3b K4A

text: Mus musculus

text: Mus musculus

text: Mus musculus


text: EMBL

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: ArrayExpress

text: embryonic stem cell

text: house mouse

text: wild type genotype

text: Mus musculus

text: Mus musculus

text: Mus musculus


text: EMBL

text: public

text: ArrayExpress

characteristic: broker name

characteristic: cell line

text: neural precursor

characteristic: cell type

text: house mouse

text: wild type genotype

text: Mus musculus

text: Mus musculus

text: Mus musculus


text: EMBL

text: public

text: ArrayExpress

text: neuron

text: house mouse

text: wild type genotype

characteristic: genotype

text: Mus musculus

characteristic: organism

text: Mus musculus

text: Mus musculus

characteristic: time


characteristic: ENA-CHECKLIST

text: MPI-MM

text: public

characteristic: Submitter Id

characteristic: collection date

text: water

characteristic: environment (biome)

text: chemocline

characteristic: environment (feature)

text: water

characteristic: environment (material)

text: Switzerland

characteristic: geographic location (country and/or sea)

characteristic: geographic location (depth)

text: 8°42'24.59 E

characteristic: geographic location (latitude)

text: 46°32'35.39 N

characteristic: geographic location (longitude)

text: metagenome

characteristic: investigation type

text: metagenome

text: Cadagno chemocline

characteristic: project name

text: metagenome

text: Illumina HiSeq

characteristic: sequencing method

text: Cadagno chemocline sequencing

characteristic: title

text: water

characteristic: water environmental package


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: SIB

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: not collected

text: not collected

characteristic: host health state

text: Capra aegagrus

characteristic: host scientific name

text: synthetic

characteristic: isolate

text: not collected

characteristic: isolation source

text: not collected

characteristic: lat lon

text: Mycoplasma mycoides subsp. capri

characteristic: organism

text: Mycoplasma mycoides subsp. capri

text: not collected

characteristic: serovar

characteristic: strain

text: Construction of deletion clone MMC68


text: Tumour

characteristic: ArrayExpress-Phenotype

text: Homo Sapien

characteristic: ArrayExpress-Species

characteristic: ENA-CHECKLIST

text: SC

text: public

characteristic: Submitter Id

text: human

characteristic: common name

text: Homo sapiens

characteristic: sample description

text: Homo sapiens

characteristic: title


RMR-D

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: MPI-MM

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: RMR-D

characteristic: collection date

text: hydrothermal vent

characteristic: environment (biome)

text: hydrothermal chimney

characteristic: environment (feature)

text: rock

characteristic: environment (material)

text: Pacific Ocean

characteristic: geographic location (country and/or sea)

text: -3° 43'

characteristic: geographic location (latitude)

text: 151° 42'

characteristic: geographic location (longitude)

text: metagenome

characteristic: investigation type

text: miscellaneous natural or artificial environment

characteristic: miscellaneous environmental package

text: metagenome

text: Active hydrothermal chimney metagenomics

characteristic: project name

text: metagenome

text: Illumina HiSeq

characteristic: sequencing method


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: MPI-MM

text: public

characteristic: SRA accession

characteristic: Submitter Id

text: hydrothermal vent

text: hydrothermal chimney

text: rock

text: Pacific Ocean

text: -3° 43'

text: 151° 42'

text: metagenome

text: metagenome

characteristic: organism

text: metagenome

text: Illumina HiSeq

characteristic: title


characteristic: External Id

text: LMU

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: Dr Jaume Forcada

characteristic: collected by

text: antarctic fur seal

characteristic: common name

text: Adult

characteristic: dev stage

text: Bird Island, South Georgia

characteristic: geographic location (region and locality)

text: Arctocephalus gazella

text: Arctocephalus gazella

text: Female

characteristic: sex

text: liver and skin

characteristic: tissue type

text: Sample from Arctocephalus gazella for genome assembly


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: CIGENE

text: public

text: Atlantic cod

text: Gadus morhua

text: Gadus morhua

text: mRNA miseq 12 days post hatching


characteristic: ENA-LAST-UPDATE

text: CIGENE

text: public

characteristic: SRA accession

text: Atlantic cod

text: Gadus morhua

text: Gadus morhua

text: mRNA miseq 35 days post hatching


text: MEDICAL UNIVERSITY GRAZ

text: public

tag: Namespace:MEDICAL UNIVERSITY GRAZ

characteristic: Submitter Id

text: human

text: blank extraction made from the kit used for DNA isolation

characteristic: description

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: blank extraction


characteristic: External Id

text: MEDICAL UNIVERSITY GRAZ

characteristic: INSDC center name

text: public

text: human

text: extraction made from the adjacent paraffin of the paraffin blocks

text: Homo sapiens

text: Homo sapiens

text: paraffin extraction

characteristic: title


text: MEDICAL UNIVERSITY GRAZ

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: human

text: no template for the 16S qPCR used for sequencing

text: Homo sapiens

text: Homo sapiens

text: negative control


RG-chemicline

text: MPI-MM

text: public

text: RG-chemicline

characteristic: collection date

text: chemocline and hypolimnion metagenomes

text: stratified lake

characteristic: environment (biome)

text: anoxic water column

characteristic: environment (feature)

text: water

characteristic: environment (material)

text: Croatia

characteristic: geographic location (country and/or sea)

characteristic: geographic location (depth)

text: 43° 31'

characteristic: geographic location (latitude)

text: 15° 578

characteristic: geographic location (longitude)

text: metagenome

characteristic: investigation type

text: metagenome

text: Lake Rogoznica

characteristic: project name

text: metagenome

text: Illumina HiSeq

characteristic: sequencing method

text: Lake Rogoznica

text: water

characteristic: water environmental package


RG-hypolimnion

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: MPI-MM

characteristic: INSDC center name

text: public

characteristic: SRA accession

text: RG-hypolimnion

characteristic: Submitter Id

text: chemocline and hypolimnion metagenomes

characteristic: description

text: stratified lake

text: anoxic water column

text: water

text: Croatia

text: 43° 31'

text: 15° 578

text: metagenome

text: metagenome

characteristic: organism

text: Lake Rogoznica

text: metagenome

text: Illumina HiSeq

text: Lake Rogoznica

text: water


characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: human

characteristic: common name

text: Homo sapiens

text: Homo sapiens

text: mitochondrial genome sequence for Th703

characteristic: title


text: public

text: human

text: Homo sapiens

text: Homo sapiens

text: mitochondrial genome sequence for In661


text: public

text: human

text: Homo sapiens

text: Homo sapiens

text: mitochondrial genome sequence for In662


text: public

text: human

text: Homo sapiens

text: Homo sapiens

text: mitochondrial genome sequence for La727


text: public

text: human

text: Homo sapiens

text: Homo sapiens

text: mitochondrial genome sequence for Vt833


text: public

text: human

text: Homo sapiens

text: Homo sapiens

text: mitochondrial genome sequence for Th519


text: public

text: human

text: Homo sapiens

text: Homo sapiens

text: mitochondrial genome sequence for Th521


text: public

text: human

text: Homo sapiens

text: Homo sapiens

text: mitochondrial genome sequence for Th522


text: public

text: human

text: Homo sapiens

text: Homo sapiens

text: mitochondrial genome sequence for Th523


text: public

text: human

text: Homo sapiens

text: Homo sapiens

text: mitochondrial genome sequence for Th530


text: public

text: human

text: Homo sapiens

text: Homo sapiens

text: mitochondrial genome sequence for Th531


text: public

text: human

text: Homo sapiens

text: Homo sapiens

text: mitochondrial genome sequence for Ma525


text: public

text: human

text: Homo sapiens

text: Homo sapiens

text: mitochondrial genome sequence for Phl533


text: public

text: human

text: Homo sapiens

text: Homo sapiens

text: mitochondrial genome sequence for Phl534


text: public

text: human

text: Homo sapiens

text: Homo sapiens

text: mitochondrial genome sequence for Ma548


text: public

text: human

text: Homo sapiens

text: Homo sapiens

text: mitochondrial genome sequence for Ma554


text: public

text: human

text: Homo sapiens

text: Homo sapiens

text: mitochondrial genome sequence for Ma555


text: public

text: human

text: Homo sapiens

text: Homo sapiens

text: mitochondrial genome sequence for Vt719


text: public

text: human

text: Homo sapiens

text: Homo sapiens

text: mitochondrial genome sequence for Vt739


text: public

text: human

text: Homo sapiens

text: Homo sapiens

text: mitochondrial genome sequence for Vt743


text: public

text: human

text: Homo sapiens

text: Homo sapiens

text: mitochondrial genome sequence for Vt744


text: public

text: human

text: Homo sapiens

text: Homo sapiens

text: mitochondrial genome sequence for Vt880


text: public

text: human

text: Homo sapiens

text: Homo sapiens

text: mitochondrial genome sequence for La898


text: public

text: human

text: Homo sapiens

text: Homo sapiens

text: mitochondrial genome sequence for Ma911


text: public

text: human

text: Homo sapiens

text: Homo sapiens

text: mitochondrial genome sequence for Ma912


text: public

text: human

text: Homo sapiens

text: Homo sapiens

text: mitochondrial genome sequence for La364


text: public

text: human

text: Homo sapiens

text: Homo sapiens

text: mitochondrial genome sequence for La368


text: public

text: human

text: Homo sapiens

text: Homo sapiens

text: mitochondrial genome sequence for Vt777


text: public

text: human

text: Homo sapiens

text: Homo sapiens

text: mitochondrial genome sequence for Vt778


text: public

text: human

text: Homo sapiens

text: Homo sapiens

text: mitochondrial genome sequence for Vt779


text: public

text: human

text: Homo sapiens

text: Homo sapiens

text: mitochondrial genome sequence for Vt781


text: public

text: human

text: Homo sapiens

text: Homo sapiens

text: mitochondrial genome sequence for Vt796


text: public

text: human

text: Homo sapiens

text: Homo sapiens

text: mitochondrial genome sequence for Vt808


text: public

text: human

text: Homo sapiens

text: Homo sapiens

text: mitochondrial genome sequence for Th387


text: public

text: human

text: Homo sapiens

text: Homo sapiens

text: mitochondrial genome sequence for Th391


text: public

text: human

text: Homo sapiens

text: Homo sapiens

text: mitochondrial genome sequence for Th392


text: public

text: human

text: Homo sapiens

text: Homo sapiens

text: mitochondrial genome sequence for Th389


text: public

text: human

text: Homo sapiens

text: Homo sapiens

text: mitochondrial genome sequence for Th126


text: public

text: human

text: Homo sapiens

text: Homo sapiens

text: mitochondrial genome sequence for Th127


text: public

text: human

text: Homo sapiens

text: Homo sapiens

text: mitochondrial genome sequence for Th238


text: public

text: human

text: Homo sapiens

text: Homo sapiens

text: mitochondrial genome sequence for Th248


text: Human

characteristic: ArrayExpress-SPECIES

text: SC

text: public

text: human

text: Homo sapiens

text: Homo sapiens

characteristic: subject id

text: Homo Sapien


text: HUMAN

text: SC

text: public

text: human

text: Homo sapiens

text: Homo sapiens

text: HOMO SAPIENS


text: Leishmania infected iPSC-derived macrophages

characteristic: ArrayExpress-PHENOTYPE

text: Homo sapiens

text: SC

text: public

text: human

text: Homo sapiens

characteristic: phenotype

text: Homo sapiens


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: INSTITUT PASTEUR

text: public

tag: Namespace:INSTITUT PASTEUR

characteristic: isolate

text: Escherichia coli

characteristic: receipt date

text: Escherichia coli


E-MTAB-6713:Sample 1

characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC center name

text: public

characteristic: SRA accession

text: E-MTAB-6713:Sample 1

tag: Namespace:Center for Medical Genetics Ghent (CMGG) Cancer Research Institute Ghent (CRIG)

text: ArrayExpress

characteristic: broker name

characteristic: cell line

text: human

text: Protocols: The cells were grown in RPMI 1640 (Invitrogen) supplemented with 10% FCS, 100 IU/ml penicillin/streptomycin, 2 mM L-glutamin and 25 mM HEPES (Life Technologies). ETV5 mission shRNAs were obtained from the TRC1 library (Sigma-Aldrich, TRCN0000013938-42). The ETV5 mission lentiviral shRNA TRCN0000013938 (referred to as shETV5) was used throughout this manuscript as optimal shRNA (target sequence: CCGGCCGTGACACTTAGTACATTAACTCGAGTTAATGTACTAAGTGTCACGGTTTTT). Lentiviral particle production was done by seeding 3x106 HEK-293TN cells in a 10-cm dish 24h prior to transfection. The transfection of the HEK-293TN was subsequently done with trans-lentiviral packaging mix and lentiviral transfection vector DNA according to the Thermo Scientific Trans-Lentiviral Packaging Kit (TLP5913). 16h after transfection cells were refreshed with reduced serum medium and lentivirus-containing medium was harvested 48h later. Virus was concentrated by adding 2.5 ml ice-cold PEG-IT (LV810A-1, System Biosciences) to 10 ml of the harvested viral supernatants. This mixture was then incubated overnight at 4°C and FCS and antibiotic-containing medium was added to the remaining pellet upon centrifugation. NB cells CLB-GA, SH-SY5Y, IMR-32, SK-N-SH and SK-N-AS and PDX-derived Lu-NB-2 cells were transduced with concentrated virus and refreshed 24h post-transduction with normal cell culture medium. 48h post-transduction, cells were selected using 0.5-1 µg/ml puromycin (P8833, Sigma-Aldrich). The transduction efficiency was determined by qPCR. Subsequently, cells were used for functional assay profiling. pLKO.1-puro Non-Mammalian shRNA control plasmid (SHC002, Sigma-Aldrich) was used as a negative control. Cell line samples were washed with PBS, whereafter they were scraped on ice in PBS. The samples were then centrifuged at 200g for 5 min and supernatans discarted. The remaining cell pellet was dissolved in 700 µl of Trizol and snap frozen in liquid nitrogen. The samples were stored at -80°C.Tumor samples were dissociated in the Tissuelyser with 700 µl of Trizol was added and samples were snap frozen in liquid nitrogen. The samples were stored at -80°C. Total RNA was isolated using the miRNeasy kit (217004, Qiagen) according to manufacturer’s instructions, including on-column DNase treatment. RNA concentration was determined with Nanodrop (Thermo Scientific). Libraries for mRNA sequencing were prepared using the TruSeq stranded mRNA sample prep kit (Illumina), involving polyA-selection, fragmentation, adapter ligation, reverse transcription and PCR amplification. Libraries were quantified using the Qubit 2.0 Fluorometer.

text: neuroblastoma

characteristic: disease

text: wild type genotype

characteristic: genotype

text: in vitro

characteristic: growth condition

text: Homo sapiens

text: Homo sapiens

text: bone marrow

characteristic: organism part

text: Homo sapiens

text: Sample 1


E-MTAB-6713:Sample 13

text: Center for Medical Genetics Ghent (CMGG) Cancer Research Institute Ghent (CRIG)

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: E-MTAB-6713:Sample 13

characteristic: Submitter Id

text: ArrayExpress

text: human

characteristic: common name

characteristic: description

text: neuroblastoma

text: wild type genotype

text: in vitro

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: bone marrow

text: Homo sapiens

text: Sample 13

characteristic: title


E-MTAB-6713:Sample 15

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: public

text: E-MTAB-6713:Sample 15

text: ArrayExpress

text: human

text: neuroblastoma

text: ETV5 knockdown by shRNA

text: in vitro

text: Homo sapiens

text: Homo sapiens

text: bone marrow

text: Homo sapiens

text: Sample 15


E-MTAB-6713:Sample 2

characteristic: INSDC center name

text: public

characteristic: SRA accession

text: E-MTAB-6713:Sample 2

text: ArrayExpress

characteristic: broker name

characteristic: cell line

text: human

text: neuroblastoma

text: ETV5 knockdown by shRNA

text: in vitro

text: Homo sapiens

text: Homo sapiens

text: bone marrow

text: Homo sapiens

text: Sample 2


E-MTAB-6713:Sample 3

text: public

text: E-MTAB-6713:Sample 3

text: ArrayExpress

text: human

text: neuroblastoma

characteristic: disease

text: ETV5 knockdown by shRNA

characteristic: genotype

text: in vitro

characteristic: growth condition

text: Homo sapiens

text: Homo sapiens

text: bone marrow

characteristic: organism part

text: Homo sapiens

text: Sample 3


E-MTAB-6713:Sample 6

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: E-MTAB-6713:Sample 6

characteristic: Submitter Id

text: ArrayExpress

text: human

text: neuroblastoma

text: wild type genotype

text: in vitro

text: Homo sapiens

text: Homo sapiens

text: bone marrow

text: Homo sapiens

text: Sample 6


E-MTAB-6713:Sample 10

text: public

text: E-MTAB-6713:Sample 10

text: ArrayExpress

text: human

characteristic: common name

text: Protocols: The cells were grown in RPMI 1640 (Invitrogen) supplemented with 10% FCS, 100 IU/ml penicillin/streptomycin, 2 mM L-glutamin and 25 mM HEPES (Life Technologies). All animal experiments were performed according to the Guide for the Care and Use of Laboratory Animals (Eight Edition) following approval of the Committee on the Ethics of Animal Experiments of Ghent University (Permit number: ECD 12/22) 22. Persons who carried out the described experiment received appropriate training in animal care and handling. The mice were allowed to acclimatize for 1 week before experimental procedure started and were randomly assigned into two groups. Stable ETV5 knockdown SH-SY5Y were used to investigate the role of ETV5 in vivo. SH-SY5Y parental or SH-SY5Y shETV5 cells were cultured as described above. Next, 6x10^6 cells were mixed with Matrigel® (354230, Corning) and subsequently injected subcutaneously in the left flank of female Crl:NU-Foxn1nu nude mice. Tumour growth was followed for 33 days and tumour volume was assessed by Caliper measurements and calculated according to the spheroid formula: V=0.5*a²*b with a the smallest superficial diameter and b the largest superficial diameter. Body weight and physical status of the animals were recorded daily until they were judged to be in discomfort by animal caretakers or maximum tumour volume was reached (2000 mm³) upon which the animal was euthanized by cervical dislocation. ETV5 mission shRNAs were obtained from the TRC1 library (Sigma-Aldrich, TRCN0000013938-42). The ETV5 mission lentiviral shRNA TRCN0000013938 (referred to as shETV5) was used throughout this manuscript as optimal shRNA (target sequence: CCGGCCGTGACACTTAGTACATTAACTCGAGTTAATGTACTAAGTGTCACGGTTTTT). Lentiviral particle production was done by seeding 3x106 HEK-293TN cells in a 10-cm dish 24h prior to transfection. The transfection of the HEK-293TN was subsequently done with trans-lentiviral packaging mix and lentiviral transfection vector DNA according to the Thermo Scientific Trans-Lentiviral Packaging Kit (TLP5913). 16h after transfection cells were refreshed with reduced serum medium and lentivirus-containing medium was harvested 48h later. Virus was concentrated by adding 2.5 ml ice-cold PEG-IT (LV810A-1, System Biosciences) to 10 ml of the harvested viral supernatants. This mixture was then incubated overnight at 4°C and FCS and antibiotic-containing medium was added to the remaining pellet upon centrifugation. NB cells CLB-GA, SH-SY5Y, IMR-32, SK-N-SH and SK-N-AS and PDX-derived Lu-NB-2 cells were transduced with concentrated virus and refreshed 24h post-transduction with normal cell culture medium. 48h post-transduction, cells were selected using 0.5-1 µg/ml puromycin (P8833, Sigma-Aldrich). The transduction efficiency was determined by qPCR. Subsequently, cells were used for functional assay profiling. pLKO.1-puro Non-Mammalian shRNA control plasmid (SHC002, Sigma-Aldrich) was used as a negative control. Cell line samples were washed with PBS, whereafter they were scraped on ice in PBS. The samples were then centrifuged at 200g for 5 min and supernatans discarted. The remaining cell pellet was dissolved in 700 µl of Trizol and snap frozen in liquid nitrogen. The samples were stored at -80°C.Tumor samples were dissociated in the Tissuelyser with 700 µl of Trizol was added and samples were snap frozen in liquid nitrogen. The samples were stored at -80°C. Total RNA was isolated using the miRNeasy kit (217004, Qiagen) according to manufacturer’s instructions, including on-column DNase treatment. RNA concentration was determined with Nanodrop (Thermo Scientific). Libraries for mRNA sequencing were prepared using the TruSeq stranded mRNA sample prep kit (Illumina), involving polyA-selection, fragmentation, adapter ligation, reverse transcription and PCR amplification. Libraries were quantified using the Qubit 2.0 Fluorometer.

characteristic: description

text: neuroblastoma

text: wild type genotype

text: tumour growth in mouse xenograft

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: bone marrow

text: Homo sapiens

text: Sample 10

characteristic: title


E-MTAB-6713:Sample 11

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: public

text: E-MTAB-6713:Sample 11

text: ArrayExpress

text: human

text: neuroblastoma

text: ETV5 knockdown by shRNA

text: tumour growth in mouse xenograft

text: Homo sapiens

text: Homo sapiens

text: bone marrow

text: Homo sapiens

text: Sample 11


E-MTAB-6713:Sample 12

characteristic: INSDC center name

text: public

characteristic: SRA accession

text: E-MTAB-6713:Sample 12

text: ArrayExpress

characteristic: broker name

characteristic: cell line

text: human

text: neuroblastoma

text: wild type genotype

text: tumour growth in mouse xenograft

text: Homo sapiens

text: Homo sapiens

text: bone marrow

text: Homo sapiens

text: Sample 12


E-MTAB-6713:Sample 14

text: public

text: E-MTAB-6713:Sample 14

text: ArrayExpress

text: human

text: neuroblastoma

characteristic: disease

text: wild type genotype

characteristic: genotype

text: tumour growth in mouse xenograft

characteristic: growth condition

text: Homo sapiens

text: Homo sapiens

text: bone marrow

characteristic: organism part

text: Homo sapiens

text: Sample 14


E-MTAB-6713:Sample 4

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: E-MTAB-6713:Sample 4

characteristic: Submitter Id

text: ArrayExpress

text: human

text: neuroblastoma

text: ETV5 knockdown by shRNA

text: tumour growth in mouse xenograft

text: Homo sapiens

text: Homo sapiens

text: bone marrow

text: Homo sapiens

text: Sample 4


E-MTAB-6713:Sample 5

text: public

text: E-MTAB-6713:Sample 5

text: ArrayExpress

text: human

characteristic: common name

characteristic: description

text: neuroblastoma

text: ETV5 knockdown by shRNA

text: tumour growth in mouse xenograft

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: bone marrow

text: Homo sapiens

text: Sample 5

characteristic: title


E-MTAB-6713:Sample 7

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: public

text: E-MTAB-6713:Sample 7

text: ArrayExpress

text: human

text: neuroblastoma

text: wild type genotype

text: tumour growth in mouse xenograft

text: Homo sapiens

text: Homo sapiens

text: bone marrow

text: Homo sapiens

text: Sample 7


E-MTAB-6713:Sample 8

characteristic: INSDC center name

text: public

characteristic: SRA accession

text: E-MTAB-6713:Sample 8

text: ArrayExpress

characteristic: broker name

characteristic: cell line

text: human

text: neuroblastoma

text: ETV5 knockdown by shRNA

text: tumour growth in mouse xenograft

text: Homo sapiens

text: Homo sapiens

text: bone marrow

text: Homo sapiens

text: Sample 8


E-MTAB-6713:Sample 9

text: public

text: E-MTAB-6713:Sample 9

text: ArrayExpress

text: human

text: neuroblastoma

characteristic: disease

text: ETV5 knockdown by shRNA

characteristic: genotype

text: tumour growth in mouse xenograft

characteristic: growth condition

text: Homo sapiens

text: Homo sapiens

text: bone marrow

characteristic: organism part

text: Homo sapiens

text: Sample 9


text: Homo sapiens

characteristic: ArrayExpress-SPECIES

text: SC

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: Submitter Id

text: human

text: Homo sapiens

text: Homo sapiens

characteristic: subject id


E-MTAB-6789:Sample 1

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: public

text: E-MTAB-6789:Sample 1

tag: Namespace:East China University of Science and Technology

text: ArrayExpress

text: Protocols: All mycobacteria strains were aerobically cultured in MYC/01 medium at 30 degrees celsius with a shaking speed of 200 rpm in the work. For sterol biotransformation, strains Mn-CC, Mn-9OHAD, Mn-ADD, and Mn-HBC were fermented in MYC/02 medium by adding 10.0 g/l glucose and 0.5 g/l phytosterols to replace glycerol in MYC/01 medium. As a control, strain Mn-C was fermented in MYC/02 medium by adding 10.0 g/l glucose to replace glycerol (without sterol addition) in MYC/01. The samples for strains Mn-C, Mn-CC, Mn-9OHAD, Mn-ADD, and Mn-HBC were taken at 48 h after fermentation. For RNA isolation, strains Mn-C, Mn-CC, Mn-9OHAD, Mn-ADD, and Mn-BNA were cultured in MYC/02 medium. After 48 h fermentation in MYC/02 medium, total RNA of strains Mn-C, Mn-CC, Mn-9OHAD, Mn-ADD, and Mn-BNA were isolated using the FastRNA™ Pro Blue Kit and the Fast Prep-24™ Instrument (MP Biomedicals, SantaAna, CA). RNA of each sample was dissolved in RNase-free water to verify the concentration and quality using NanoDrop (NanoDrop Technologies,Wilmington, DE) and 2% (w/v) agarose gel electrophoresis. For the removal of DNA, total RNA was incubated with Rnase-free DNase Set (Qiagen) according to the manufacturer’s instructions. Messenger RNA (mRNA) was further purified by depleting ribosomal RNA (rRNA) and tRNA with TerminatorTM 5’-phosphate dependent exonuclease (Epicenter, Madison, WI) digestion. The cDNA was synthesized using a kit obtained from Beijing Dingguo Changsheng Biotechnology Co., Ltd., (Beijing, China).

characteristic: description

text: wild type genotype

text: MYC/01 medium

text: Mycobacterium neoaurum

characteristic: organism

text: Mycobacterium neoaurum

text: Mycobacterium neoaurum

text: ATCC 25795

characteristic: strain

text: Sample 1

characteristic: title


E-MTAB-6789:Sample 2

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: East China University of Science and Technology

characteristic: INSDC center name

text: public

characteristic: SRA accession

text: E-MTAB-6789:Sample 2

text: ArrayExpress

characteristic: broker name

text: wild type genotype

text: MYC/02 medium

text: Mycobacterium neoaurum

text: Mycobacterium neoaurum

text: Mycobacterium neoaurum

text: ATCC 25795

text: Sample 2


E-MTAB-6789:Sample 3

text: public

text: E-MTAB-6789:Sample 3

text: ArrayExpress

text: kstd1 knockout

characteristic: genotype

text: MYC/02 medium

characteristic: growth condition

text: Mycobacterium neoaurum

text: Mycobacterium neoaurum

text: Mycobacterium neoaurum

text: ATCC 25795

text: Sample 3


E-MTAB-6789:Sample 4

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: E-MTAB-6789:Sample 4

text: ArrayExpress

text: kshA1 knockout

text: MYC/02 medium

text: Mycobacterium neoaurum

text: Mycobacterium neoaurum

text: Mycobacterium neoaurum

text: ATCC 25795

text: Sample 4


E-MTAB-6789:Sample 5

text: public

characteristic: INSDC status

text: E-MTAB-6789:Sample 5

characteristic: Submitter Id

text: ArrayExpress

text: kshA1 and hsd4A double knockout

text: MYC/02 medium

text: Mycobacterium neoaurum

text: Mycobacterium neoaurum

text: Mycobacterium neoaurum

text: ATCC 25795

text: Sample 5


text: mouse

characteristic: ArrayExpress-SPECIES

characteristic: ENA-CHECKLIST

text: SC

text: public

text: house mouse

characteristic: common name

text: Mus musculus

text: Mus musculus

characteristic: subject id

text: Mus musculus


characteristic: ENA-FIRST-PUBLIC

text: public

tag: Namespace:Alfred-Wegener-Institut Helmholtz-Zentrum fuer Polar- und Meeresforschung

text: marine plankton metagenome

characteristic: organism

text: marine plankton metagenome

text: Mixed Plankton Brudenell River (Canada)


text: Teladorsagia circumcincta

text: field

characteristic: ENA-LAST-UPDATE

text: SC

text: public

text: Teladorsagia circumcincta

text: Teladorsagia circumcincta

text: Teladorsagia circumcincta

text: Teladorsagia circumcincta

characteristic: title


characteristic: External Id

characteristic: INSDC center name

text: public

tag: Namespace:MRC Centre for Regenerative Medicine, University of Edinburgh, Edinburgh, UK

text: ArrayExpress

text: c-Kit+ cell

characteristic: cell type

text: house mouse

text: Protocols: Meis1/Hoxa9-transduced foetal liver c-Kit+ cells were collected after three rounds of serial re-plating in methylcellulose. Total RNA was extracted using TRIzol (Thermo Fisher Scientific). mRNA was purified from total RNA using PolyATtract mRNA Isolation Systems (Promega). The library was constructed using TruSeq Stranded mRNA Sample Prep Kits (Illumina RS-122-2101).

characteristic: description

text: embryonic day 14.5

characteristic: developmental stage

text: Ythdf2 fl/fl; Meis1/Hoxa9 overexpression

text: Mus musculus

text: Mus musculus

text: liver

characteristic: organism part

text: Mus musculus


text: MRC Centre for Regenerative Medicine, University of Edinburgh, Edinburgh, UK

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: SRA accession

text: ArrayExpress

characteristic: broker name

text: c-Kit+ cell

text: house mouse

text: embryonic day 14.5

characteristic: genotype

text: Mus musculus

text: Mus musculus

text: liver

text: Mus musculus


characteristic: ENA-CHECKLIST

text: public

characteristic: INSDC status

characteristic: Submitter Id

text: ArrayExpress

text: c-Kit+ cell

text: house mouse

characteristic: common name

text: Protocols: Meis1/Hoxa9-transduced foetal liver c-Kit+ cells were collected after three rounds of serial re-plating in methylcellulose. Total RNA was extracted using TRIzol (Thermo Fisher Scientific). mRNA was purified from total RNA using PolyATtract mRNA Isolation Systems (Promega), fragmented and immunoprecipitated with anti-m6A antibody (Synaptic Systems, 202003). The library was constructed using TruSeq Stranded mRNA Sample Prep Kits (Illumina RS-122-2101)

text: embryonic day 14.5

text: Mus musculus

text: Mus musculus

text: liver

text: Mus musculus


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: DKFZ-IBIOS

text: public

text: human

text: scRNA-seq of breast cancer cell line MCF10CA cultured in 3D

text: Homo sapiens

characteristic: organism

text: Homo sapiens


characteristic: External Id

text: DKFZ-IBIOS

characteristic: INSDC center name

text: public

text: human

text: manual pheno-seq of aberrant MCF10CA spheroids

text: Homo sapiens

text: Homo sapiens

characteristic: title


text: DKFZ-IBIOS

text: public

text: human

text: manual pheno-seq of round MCF10CA spheroids

characteristic: description

text: Homo sapiens

text: Homo sapiens


text: DKFZ-IBIOS

text: public

text: human

text: high thoughput pheno-seq of MCF10CA spheroids

text: Homo sapiens

text: Homo sapiens


text: Universidad San Francisco de Quito

text: public

tag: Namespace:Universidad San Francisco de Quito

characteristic: collection date

text: Controls

text: oropharynx

characteristic: environment (biome)

characteristic: environment (feature)

characteristic: environment (material)

text: Ecuador

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

unit: centuries

characteristic: host age

text: oropharynx

characteristic: host body site

characteristic: host subject id

text: human-oral

characteristic: human oral environmental package

text: metagenome

characteristic: investigation type

text: Controls

characteristic: miscellaneous parameter

text: CTGTTCGTAGAG

characteristic: multiplex identifiers

text: bacterium

text: CCGTCAATTCMTTTRAGT

characteristic: pcr primers

characteristic: project name

text: swab

characteristic: sample collection device or method

text: bacterium

text: pyrosequencing

characteristic: sequencing method


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Universidad San Francisco de Quito

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

characteristic: description

text: oropharynx

characteristic: environment (biome)

text: Ecuador

text: oropharynx

text: human-oral

text: metagenome

text: Controls

text: GATCAGAAGATG

text: bacterium

characteristic: organism

text: CCGTCAATTCMTTTRAGT

text: swab

text: bacterium

text: pyrosequencing

characteristic: title


text: Universidad San Francisco de Quito

text: public

text: oropharynx

characteristic: environment (feature)

characteristic: environment (material)

text: Ecuador

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

characteristic: host age

text: oropharynx

characteristic: host body site

characteristic: host subject id

text: human-oral

characteristic: human oral environmental package

text: metagenome

characteristic: investigation type

text: Cases

characteristic: miscellaneous parameter

text: TAGTTGCGAGTC

characteristic: multiplex identifiers

text: bacterium

text: CCGTCAATTCMTTTRAGT

characteristic: pcr primers

characteristic: project name

text: swab

characteristic: sample collection device or method

text: bacterium

text: pyrosequencing


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Universidad San Francisco de Quito

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

characteristic: description

text: oropharynx

characteristic: environment (biome)

text: Ecuador

text: oropharynx

text: human-oral

text: metagenome

text: Controls

text: TCGTTCACATGA

text: bacterium

characteristic: organism

text: CCGTCAATTCMTTTRAGT

text: swab

text: bacterium

text: pyrosequencing

characteristic: sequencing method


text: Universidad San Francisco de Quito

text: public

text: oropharynx

characteristic: environment (feature)

characteristic: environment (material)

text: Ecuador

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

characteristic: host age

text: oropharynx

characteristic: host body site

characteristic: host subject id

text: human-oral

characteristic: human oral environmental package

text: metagenome

characteristic: investigation type

text: Cases

characteristic: miscellaneous parameter

text: AGTGAGAGAAGC

characteristic: multiplex identifiers

text: bacterium

text: CCGTCAATTCMTTTRAGT

characteristic: pcr primers

characteristic: project name

text: swab

text: bacterium

text: pyrosequencing

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Universidad San Francisco de Quito

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

characteristic: description

text: oropharynx

characteristic: environment (biome)

text: Ecuador

text: oropharynx

text: human-oral

text: metagenome

text: Cases

text: ATTATCGTGCAC

text: bacterium

characteristic: organism

text: CCGTCAATTCMTTTRAGT

text: swab

characteristic: sample collection device or method

text: bacterium

text: pyrosequencing


text: SLU

text: public

text: Plasmodiophora brassicae

text: Plasmodiophora brassicae

text: Plasmodiophora brassicacae e3


text: J CRAIG VENTER INSTITUTE

text: public

tag: Namespace:J CRAIG VENTER INSTITUTE

text: Assembly of marine microbial communities from oxygen minimum zone in mesopelagic equatorial Pacific

text: Yes

characteristic: environmental sample

text: Pacific Ocean

characteristic: geographic location (country and/or sea)

text: Pacific Ocean

characteristic: isolation source

text: 0 N 158 W

characteristic: lat lon

text: marine metagenome

text: marine metagenome

text: Metzyme Assembly


AMf1/12 run1 r3

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: CNRS and university of Rennes 1

text: public

text: AMf1/12 run1 r3

tag: Namespace:CNRS and university of Rennes 1

text: Glomeromycotina sp. S46

text: Glomeromycotina sp. S46

text: AMF rules of community assembly

characteristic: title


AMf2/12 run1 r4

characteristic: External Id

text: CNRS and university of Rennes 1

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: AMf2/12 run1 r4

text: Glomeromycotina sp. S46

text: Glomeromycotina sp. S46

text: AMF rules of community assembly


AMf3/12 run2 r2

text: CNRS and university of Rennes 1

text: public

characteristic: INSDC status

characteristic: SRA accession

text: AMf3/12 run2 r2

characteristic: Submitter Id

text: Glomeromycotina sp. S46

text: Glomeromycotina sp. S46

text: AMF rules of community assembly


AMf4/12 run2 r4

text: CNRS and university of Rennes 1

text: public

text: AMf4/12 run2 r4

text: Glomeromycotina sp. S46

characteristic: organism

text: Glomeromycotina sp. S46

text: AMF rules of community assembly


AMf5/12 run3 r1

text: CNRS and university of Rennes 1

text: public

text: AMf5/12 run3 r1

text: Glomeromycotina sp. S46

text: Glomeromycotina sp. S46

text: AMF rules of community assembly


AMf6/12 run3 r2

text: CNRS and university of Rennes 1

text: public

text: AMf6/12 run3 r2

text: Glomeromycotina sp. S46

text: Glomeromycotina sp. S46

text: AMF rules of community assembly


AMf7/12 run3 r3

text: CNRS and university of Rennes 1

text: public

text: AMf7/12 run3 r3

text: Glomeromycotina sp. S46

text: Glomeromycotina sp. S46

text: AMF rules of community assembly


AMf8/12 run3 r4

text: CNRS and university of Rennes 1

text: public

text: AMf8/12 run3 r4

text: Glomeromycotina sp. S46

text: Glomeromycotina sp. S46

text: AMF rules of community assembly


AMf9/12 run4 r1

text: CNRS and university of Rennes 1

text: public

text: AMf9/12 run4 r1

text: Glomeromycotina sp. S46

text: Glomeromycotina sp. S46

text: AMF rules of community assembly


AMf10/12 run4 r2

text: CNRS and university of Rennes 1

text: public

text: AMf10/12 run4 r2

text: Glomeromycotina sp. S46

text: Glomeromycotina sp. S46

text: AMF rules of community assembly


AMf11/12 run4 r3

text: CNRS and university of Rennes 1

text: public

text: AMf11/12 run4 r3

text: Glomeromycotina sp. S46

text: Glomeromycotina sp. S46

text: AMF rules of community assembly


AMf12/12 run4 r4

text: CNRS and university of Rennes 1

text: public

text: AMf12/12 run4 r4

text: Glomeromycotina sp. S46

text: Glomeromycotina sp. S46

text: AMF rules of community assembly


text: public

text: metagenome

text: metagenome


text: UNIVERSITY OF KAISERSLAUTERN

text: public

tag: Namespace:UNIVERSITY OF KAISERSLAUTERN

unit: L

characteristic: amount or size of sample collected

characteristic: collection date

text: freshwater river

characteristic: environment (biome)

text: flood plain

characteristic: environment (feature)

text: water

characteristic: environment (material)

text: Brazil

characteristic: geographic location (depth)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: mimarks-survey

characteristic: investigation type

text: uncultured eukaryote

text: ATTAGGGTTCGATTCCGGAGAGG, CTGGAATTACCGCGGSTGCTG

characteristic: pcr primers

text: Protists of Brazilian Várzea Floodplains

characteristic: project name

unit: °C

characteristic: sample storage temperature

unit: g

characteristic: sample volume or weight for DNA extraction

text: uncultured eukaryote

text: Illumina MiSeq

characteristic: sequencing method

text: 18S rRNA

characteristic: target gene

characteristic: target subfragment

text: Amazonia Monte Cristo

text: water

characteristic: water environmental package


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: UNIVERSITY OF KAISERSLAUTERN

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

characteristic: amount or size of sample collected

text: freshwater river

text: flood plain

text: water

text: Brazil

characteristic: geographic location (country and/or sea)

text: mimarks-survey

text: uncultured eukaryote

characteristic: organism

text: uncultured eukaryote

text: Illumina MiSeq

text: 18S rRNA

text: Amazonia Calado

characteristic: title

text: water


text: UNIVERSITY OF KAISERSLAUTERN

text: public

characteristic: collection date

text: freshwater river

characteristic: environment (biome)

text: flood plain

characteristic: environment (feature)

text: water

characteristic: environment (material)

text: Brazil

characteristic: geographic location (depth)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: mimarks-survey

characteristic: investigation type

text: uncultured eukaryote

characteristic: pcr primers

characteristic: project name

characteristic: sample storage temperature

characteristic: sample volume or weight for DNA extraction

text: uncultured eukaryote

text: Illumina MiSeq

characteristic: sequencing method

text: 18S rRNA

characteristic: target gene

text: Amazonia Castanho

text: water