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text: metagenome

characteristic: investigation type

text: human metagenome

text: amylase oral stool microbiome

characteristic: project name

text: saliva

characteristic: sample type

text: human metagenome

text: MiSeq

characteristic: sequencing method

characteristic: subjectid

characteristic: timepoint

characteristic: weight


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

characteristic: Submitter Id

characteristic: age

text: high

text: ATACGCATCAAG

characteristic: barcodesequence

characteristic: bmi

characteristic: collection date

text: human metagenome

characteristic: common name

characteristic: description

text: human oral microbiome

text: oral

text: saliva

text: female

text: USA

text: human-oral

text: metagenome

text: human metagenome

characteristic: organism

text: amylase oral stool microbiome

text: saliva

text: human metagenome

text: MiSeq

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: public

text: high

text: GTGTCCGGATTC

text: human metagenome

text: human oral microbiome

characteristic: environment (biome)

text: oral

characteristic: environment (feature)

text: saliva

characteristic: environment (material)

text: male

characteristic: gender

text: USA

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

characteristic: height

text: human-oral

characteristic: human oral environmental package

text: metagenome

characteristic: investigation type

text: human metagenome

text: amylase oral stool microbiome

characteristic: project name

text: saliva

characteristic: sample type

text: human metagenome

text: MiSeq

characteristic: sequencing method

characteristic: subjectid

characteristic: timepoint

characteristic: weight


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

characteristic: Submitter Id

characteristic: age

text: low

text: CATGCGGATCCT

characteristic: barcodesequence

characteristic: bmi

characteristic: collection date

text: human metagenome

characteristic: common name

characteristic: description

text: human oral microbiome

text: oral

text: saliva

text: female

text: USA

text: human-oral

text: metagenome

text: human metagenome

characteristic: organism

text: amylase oral stool microbiome

text: saliva

text: human metagenome

text: MiSeq

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: public

text: high

text: GTTTGCTCGAGA

text: human metagenome

text: human oral microbiome

characteristic: environment (biome)

text: oral

characteristic: environment (feature)

text: saliva

characteristic: environment (material)

text: female

characteristic: gender

text: USA

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

characteristic: height

text: human-oral

characteristic: human oral environmental package

text: metagenome

characteristic: investigation type

text: human metagenome

text: amylase oral stool microbiome

characteristic: project name

text: saliva

characteristic: sample type

text: human metagenome

text: MiSeq

characteristic: sequencing method

characteristic: subjectid

characteristic: timepoint

characteristic: weight


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

characteristic: Submitter Id

characteristic: age

text: high

text: CAGACACTTCCG

characteristic: barcodesequence

characteristic: bmi

characteristic: collection date

text: human metagenome

characteristic: common name

characteristic: description

text: human oral microbiome

text: oral

text: saliva

text: female

text: USA

text: human-oral

text: metagenome

text: human metagenome

characteristic: organism

text: amylase oral stool microbiome

text: saliva

text: human metagenome

text: MiSeq

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: public

text: medium

text: GAACAAAGAGCG

text: human metagenome

text: human oral microbiome

characteristic: environment (biome)

text: oral

characteristic: environment (feature)

text: saliva

characteristic: environment (material)

text: female

characteristic: gender

text: USA

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

characteristic: height

text: human-oral

characteristic: human oral environmental package

text: metagenome

characteristic: investigation type

text: human metagenome

text: amylase oral stool microbiome

characteristic: project name

text: saliva

characteristic: sample type

text: human metagenome

text: MiSeq

characteristic: sequencing method

characteristic: subjectid

characteristic: timepoint

characteristic: weight


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: UNIVERSITY OF BASEL

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

tag: Namespace:UNIVERSITY OF BASEL

characteristic: Submitter Id

text: cattle

characteristic: common name

characteristic: description

text: Bos taurus

characteristic: organism

text: Bos taurus

text: Progressive ataxia case 1

characteristic: title


text: UNIVERSITY OF BASEL

text: public

text: cattle

text: Bos taurus

text: Bos taurus

text: Progressive ataxia case 2


text: NATIONAL VETERINARY INSTITUTE (SVA)

text: public

tag: Namespace:NATIONAL VETERINARY INSTITUTE (SVA)

text: 24 April 2018

characteristic: collection date

text: Atlantic salmon

text: Compare microorganisms' identity in a food matrix tested by shotgun metagenomic sequencing

text: Smoked salmon spiked with mock community containing bacteria, viruses and parasites

characteristic: isolate

characteristic: isolation source

text: Salmo salar

characteristic: receipt date

text: Salmo salar

text: FoodRT-WetLab


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: EMBL

text: public

text: ArrayExpress

characteristic: broker name

characteristic: cell line

text: embryonic stem cell

characteristic: cell type

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). RNAs were extracted from 1 Mio. cells using RNeasy Kit (Qiagen), followed by DNase digestion using TURBO DNase (Thermo Fisher). RNA was quantified using Nanodrop and RIN score quality assessment was determine using Bioanalyzer. PolyA-mRNA was isolated from 1 microg of total RNA using NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB) before sequencing library preparation. mRNAs were isolated from 1 microg of total RNA using a PolyA selection kit (NEB) and sequencing libraries were prepared following instructions from NEBs Ultra Library Preparation Kit for Illumina. All samples were barcoded, amplified in 12x PCR cycles, pooled and sequenced on a HiSeq2500 Sequencer (Illumina) using a 50 bp single-end run.

text: gene knock out

characteristic: genetic modification

text: H3f3a -/-

characteristic: genotype

text: Mus musculus

text: Mus musculus

text: Mus musculus

unit: day

characteristic: time


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

characteristic: Submitter Id

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

text: public

text: ArrayExpress

text: embryonic stem cell

text: house mouse

characteristic: common name

characteristic: description

text: induced mutation

text: H3f3a -/-; H3f3b K4A

text: Mus musculus

characteristic: organism

text: Mus musculus

text: Mus musculus

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: EMBL

text: public

text: ArrayExpress

characteristic: broker name

characteristic: cell line

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

text: neural precursor

characteristic: cell type

text: house mouse

text: induced mutation

characteristic: genetic modification

text: H3f3a -/-; H3f3b K36A

characteristic: genotype

text: Mus musculus

text: Mus musculus

text: Mus musculus

characteristic: time


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: EMBL

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: ArrayExpress

text: neural precursor

text: house mouse

text: wild type genotype

text: Mus musculus

text: Mus musculus

text: Mus musculus


text: EMBL

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: ArrayExpress

text: neuron

text: house mouse

text: gene knock out

text: H3f3a -/-

text: Mus musculus

text: Mus musculus

text: Mus musculus


text: EMBL

text: public

text: ArrayExpress

text: neuron

text: house mouse

characteristic: common name

characteristic: description

text: induced mutation

text: H3f3a -/-; H3f3b K36A

text: Mus musculus

characteristic: organism

text: Mus musculus

text: Mus musculus

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: EMBL

text: public

text: ArrayExpress

characteristic: broker name

characteristic: cell line

text: neuron

text: house mouse

text: induced mutation

text: H3f3a -/-; H3f3b K4A

text: Mus musculus

text: Mus musculus

text: Mus musculus


text: EMBL

text: public

text: ArrayExpress

text: neuron

characteristic: cell type

text: house mouse

text: wild type genotype

characteristic: genotype

text: Mus musculus

text: Mus musculus

text: Mus musculus

characteristic: time


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: HELMHOLTZ CENTRE FOR INFECTION RESEARCH

characteristic: INSDC center name

text: public

tag: Namespace:HELMHOLTZ CENTRE FOR INFECTION RESEARCH

characteristic: collection date

text: freshwater metagenome

text: Size fractionated (< 1 micron) treatment, sample collected after 0 h of incubation in the dark, replicate A

text: freshwater biome

characteristic: environment (biome)

text: freshwater biome

characteristic: environment (feature)

text: water

characteristic: environment (material)

text: size fractionation < 1 micrometer

characteristic: experimental factor

text: Czech Republic

characteristic: geographic location (country and/or sea)

unit: m

characteristic: geographic location (depth)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: metagenome

characteristic: investigation type

text: freshwater metagenome

text: Rimov Exp

characteristic: project name

text: freshwater metagenome

text: Illumina

characteristic: sequencing method

text: water

characteristic: water environmental package


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: HELMHOLTZ CENTRE FOR INFECTION RESEARCH

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: freshwater metagenome

characteristic: common name

text: Size fractionated (< 1 micron) treatment, sample collected after 0 h of incubation in the dark, replicate B

characteristic: description

text: freshwater biome

text: freshwater biome

text: water

text: size fractionation < 1 micrometer

text: Czech Republic

text: metagenome

text: freshwater metagenome

characteristic: organism

text: Rimov Exp

text: freshwater metagenome

text: Illumina

characteristic: title

text: water


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: HELMHOLTZ CENTRE FOR INFECTION RESEARCH

characteristic: INSDC center name

text: public

characteristic: collection date

text: freshwater metagenome

text: Size fractionated (< 1 micron) treatment, sample collected after 0 h of incubation in the dark, replicate C

text: freshwater biome

characteristic: environment (biome)

text: freshwater biome

characteristic: environment (feature)

text: water

characteristic: environment (material)

text: size fractionation < 1 micrometer

characteristic: experimental factor

text: Czech Republic

characteristic: geographic location (country and/or sea)

characteristic: geographic location (depth)

characteristic: geographic location (latitude)

text: metagenome

text: freshwater metagenome

text: Rimov Exp

text: freshwater metagenome

text: Illumina

text: water


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: HELMHOLTZ CENTRE FOR INFECTION RESEARCH

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: freshwater metagenome

text: Control treatment, sample collected after 0 h of incubation in the dark, replicate A

text: freshwater biome

text: freshwater biome

text: water

text: unfiltered control

text: Czech Republic

characteristic: geographic location (longitude)

text: metagenome

characteristic: investigation type

text: freshwater metagenome

text: Rimov Exp

characteristic: project name

text: freshwater metagenome

text: Illumina

characteristic: sequencing method

text: water

characteristic: water environmental package


NB

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: HELMHOLTZ CENTRE FOR INFECTION RESEARCH

characteristic: INSDC center name

text: public

text: NB

characteristic: Submitter Id

characteristic: collection date

text: freshwater metagenome

characteristic: common name

text: Control treatment, sample collected after 0 h of incubation in the dark, replicate B

characteristic: description

text: freshwater biome

characteristic: environment (biome)

text: freshwater biome

characteristic: environment (feature)

text: water

text: unfiltered control

text: Czech Republic

text: metagenome

text: freshwater metagenome

characteristic: organism

text: Rimov Exp

text: freshwater metagenome

text: Illumina

characteristic: title

text: water


NC

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: HELMHOLTZ CENTRE FOR INFECTION RESEARCH

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: NC

text: freshwater metagenome

text: Control treatment, sample collected after 0 h of incubation in the dark, replicate C

text: freshwater biome

text: freshwater biome

text: water

characteristic: environment (material)

text: unfiltered control

characteristic: experimental factor

text: Czech Republic

characteristic: geographic location (country and/or sea)

characteristic: geographic location (depth)

characteristic: geographic location (latitude)

text: metagenome

text: freshwater metagenome

text: Rimov Exp

text: freshwater metagenome

text: Illumina

text: water


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: HELMHOLTZ CENTRE FOR INFECTION RESEARCH

characteristic: INSDC center name

text: public

characteristic: Submitter Id

characteristic: collection date

text: freshwater metagenome

characteristic: common name

text: Control treatment, sample collected after 45 h of incubation in the dark, replicate B

text: freshwater biome

text: freshwater biome

text: water

text: unfiltered control

text: Czech Republic

characteristic: geographic location (longitude)

text: metagenome

characteristic: investigation type

text: freshwater metagenome

text: Rimov Exp

characteristic: project name

text: freshwater metagenome

text: Illumina

characteristic: sequencing method

text: water

characteristic: water environmental package


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: HELMHOLTZ CENTRE FOR INFECTION RESEARCH

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: freshwater metagenome

text: Control treatment, sample collected after 45 h of incubation in the dark, replicate C

characteristic: description

text: freshwater biome

characteristic: environment (biome)

text: freshwater biome

characteristic: environment (feature)

text: water

text: unfiltered control

text: Czech Republic

text: metagenome

text: freshwater metagenome

characteristic: organism

text: Rimov Exp

text: freshwater metagenome

text: Illumina

characteristic: title

text: water


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: HELMHOLTZ CENTRE FOR INFECTION RESEARCH

characteristic: INSDC center name

text: public

characteristic: Submitter Id

characteristic: collection date

text: freshwater metagenome

characteristic: common name

text: Size fractionated (< 1 micron) treatment, sample collected after 69 h of incubation in the dark, replicate A

text: freshwater biome

text: freshwater biome

text: water

characteristic: environment (material)

text: size fractionation < 1 micrometer

characteristic: experimental factor

text: Czech Republic

characteristic: geographic location (country and/or sea)

characteristic: geographic location (depth)

characteristic: geographic location (latitude)

text: metagenome

text: freshwater metagenome

text: Rimov Exp

text: freshwater metagenome

text: Illumina

text: water


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: HELMHOLTZ CENTRE FOR INFECTION RESEARCH

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: freshwater metagenome

text: Size fractionated (< 1 micron) treatment, sample collected after 69 h of incubation in the dark, replicate B

text: freshwater biome

text: freshwater biome

text: water

text: size fractionation < 1 micrometer

text: Czech Republic

characteristic: geographic location (longitude)

text: metagenome

characteristic: investigation type

text: freshwater metagenome

text: Rimov Exp

characteristic: project name

text: freshwater metagenome

text: Illumina

characteristic: sequencing method

text: water

characteristic: water environmental package


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: HELMHOLTZ CENTRE FOR INFECTION RESEARCH

characteristic: INSDC center name

text: public

characteristic: Submitter Id

characteristic: collection date

text: freshwater metagenome

characteristic: common name

text: Size fractionated (< 1 micron) treatment, sample collected after 69 h of incubation in the dark, replicate C

characteristic: description

text: freshwater biome

characteristic: environment (biome)

text: freshwater biome

characteristic: environment (feature)

text: water

text: size fractionation < 1 micrometer

text: Czech Republic

text: metagenome

text: freshwater metagenome

characteristic: organism

text: Rimov Exp

text: freshwater metagenome

text: Illumina

characteristic: title

text: water


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: HELMHOLTZ CENTRE FOR INFECTION RESEARCH

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: freshwater metagenome

text: Control treatment, sample collected after 69 h of incubation in the dark, replicate A

text: freshwater biome

text: freshwater biome

text: water

characteristic: environment (material)

text: unfiltered control

characteristic: experimental factor

text: Czech Republic

characteristic: geographic location (country and/or sea)

characteristic: geographic location (depth)

characteristic: geographic location (latitude)

text: metagenome

text: freshwater metagenome

text: Rimov Exp

text: freshwater metagenome

text: Illumina

text: water


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: HELMHOLTZ CENTRE FOR INFECTION RESEARCH

characteristic: INSDC center name

text: public

characteristic: Submitter Id

characteristic: collection date

text: freshwater metagenome

characteristic: common name

text: Control treatment, sample collected after 69 h of incubation in the dark, replicate B

text: freshwater biome

text: freshwater biome

text: water

text: unfiltered control

text: Czech Republic

characteristic: geographic location (longitude)

text: metagenome

characteristic: investigation type

text: freshwater metagenome

text: Rimov Exp

characteristic: project name

text: freshwater metagenome

text: Illumina

characteristic: sequencing method

text: water

characteristic: water environmental package


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: HELMHOLTZ CENTRE FOR INFECTION RESEARCH

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: freshwater metagenome

text: Control treatment, sample collected after 69 h of incubation in the dark, replicate C

characteristic: description

text: freshwater biome

characteristic: environment (biome)

text: freshwater biome

characteristic: environment (feature)

text: water

text: unfiltered control

text: Czech Republic

text: metagenome

text: freshwater metagenome

characteristic: organism

text: Rimov Exp

text: freshwater metagenome

text: Illumina

characteristic: title

text: water


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: HELMHOLTZ CENTRE FOR INFECTION RESEARCH

characteristic: INSDC center name

text: public

characteristic: Submitter Id

characteristic: collection date

text: freshwater metagenome

characteristic: common name

text: Size fractionated (< 1 micron) treatment, sample collected after 12 h of incubation in the dark, replicate A

text: freshwater biome

text: freshwater biome

text: water

characteristic: environment (material)

text: size fractionation < 1 micrometer

characteristic: experimental factor

text: Czech Republic

characteristic: geographic location (country and/or sea)

characteristic: geographic location (depth)

characteristic: geographic location (latitude)

text: metagenome

text: freshwater metagenome

text: Rimov Exp

text: freshwater metagenome

text: Illumina

text: water


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: HELMHOLTZ CENTRE FOR INFECTION RESEARCH

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: freshwater metagenome

text: Size fractionated (< 1 micron) treatment, sample collected after 12 h of incubation in the dark, replicate B

text: freshwater biome

text: freshwater biome

text: water

text: size fractionation < 1 micrometer

text: Czech Republic

characteristic: geographic location (longitude)

text: metagenome

characteristic: investigation type

text: freshwater metagenome

text: Rimov Exp

characteristic: project name

text: freshwater metagenome

text: Illumina

characteristic: sequencing method

text: water

characteristic: water environmental package


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: HELMHOLTZ CENTRE FOR INFECTION RESEARCH

characteristic: INSDC center name

text: public

characteristic: Submitter Id

characteristic: collection date

text: freshwater metagenome

characteristic: common name

text: Size fractionated (< 1 micron) treatment, sample collected after 12 h of incubation in the dark, replicate C

characteristic: description

text: freshwater biome

characteristic: environment (biome)

text: freshwater biome

characteristic: environment (feature)

text: water

text: size fractionation < 1 micrometer

text: Czech Republic

text: metagenome

text: freshwater metagenome

characteristic: organism

text: Rimov Exp

text: freshwater metagenome

text: Illumina

characteristic: title

text: water


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: HELMHOLTZ CENTRE FOR INFECTION RESEARCH

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: freshwater metagenome

text: Control treatment, sample collected after 12 h of incubation in the dark, replicate A

text: freshwater biome

text: freshwater biome

text: water

characteristic: environment (material)

text: unfiltered control

characteristic: experimental factor

text: Czech Republic

characteristic: geographic location (country and/or sea)

characteristic: geographic location (depth)

characteristic: geographic location (latitude)

text: metagenome

text: freshwater metagenome

text: Rimov Exp

text: freshwater metagenome

text: Illumina

text: water


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: HELMHOLTZ CENTRE FOR INFECTION RESEARCH

characteristic: INSDC center name

text: public

characteristic: Submitter Id

characteristic: collection date

text: freshwater metagenome

characteristic: common name

text: Control treatment, sample collected after 12 h of incubation in the dark, replicate B

text: freshwater biome

text: freshwater biome

text: water

text: unfiltered control

text: Czech Republic

characteristic: geographic location (longitude)

text: metagenome

characteristic: investigation type

text: freshwater metagenome

text: Rimov Exp

characteristic: project name

text: freshwater metagenome

text: Illumina

characteristic: sequencing method

text: water

characteristic: water environmental package


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: HELMHOLTZ CENTRE FOR INFECTION RESEARCH

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: freshwater metagenome

text: Control treatment, sample collected after 12 h of incubation in the dark, replicate C

characteristic: description

text: freshwater biome

characteristic: environment (biome)

text: freshwater biome

characteristic: environment (feature)

text: water

text: unfiltered control

text: Czech Republic

text: metagenome

text: freshwater metagenome

characteristic: organism

text: Rimov Exp

text: freshwater metagenome

text: Illumina

characteristic: title

text: water


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: HELMHOLTZ CENTRE FOR INFECTION RESEARCH

characteristic: INSDC center name

text: public

characteristic: Submitter Id

characteristic: collection date

text: freshwater metagenome

characteristic: common name

text: Size fractionated (< 1 micron) treatment, sample collected after 21 h of incubation in the dark, replicate A

text: freshwater biome

text: freshwater biome

text: water

characteristic: environment (material)

text: size fractionation < 1 micrometer

characteristic: experimental factor

text: Czech Republic

characteristic: geographic location (country and/or sea)

characteristic: geographic location (depth)

characteristic: geographic location (latitude)

text: metagenome

text: freshwater metagenome

text: Rimov Exp

text: freshwater metagenome

text: Illumina

text: water


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: HELMHOLTZ CENTRE FOR INFECTION RESEARCH

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: freshwater metagenome

text: Size fractionated (< 1 micron) treatment, sample collected after 21 h of incubation in the dark, replicate B

text: freshwater biome

text: freshwater biome

text: water

text: size fractionation < 1 micrometer

text: Czech Republic

characteristic: geographic location (longitude)

text: metagenome

characteristic: investigation type

text: freshwater metagenome

text: Rimov Exp

characteristic: project name

text: freshwater metagenome

text: Illumina

characteristic: sequencing method

text: water

characteristic: water environmental package


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: HELMHOLTZ CENTRE FOR INFECTION RESEARCH

characteristic: INSDC center name

text: public

characteristic: Submitter Id

characteristic: collection date

text: freshwater metagenome

characteristic: common name

text: Size fractionated (< 1 micron) treatment, sample collected after 21 h of incubation in the dark, replicate C

characteristic: description

text: freshwater biome

characteristic: environment (biome)

text: freshwater biome

characteristic: environment (feature)

text: water

text: size fractionation < 1 micrometer

text: Czech Republic

text: metagenome

text: freshwater metagenome

characteristic: organism

text: Rimov Exp

text: freshwater metagenome

text: Illumina

characteristic: title

text: water


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: HELMHOLTZ CENTRE FOR INFECTION RESEARCH

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: freshwater metagenome

text: Control treatment, sample collected after 21 h of incubation in the dark, replicate A

text: freshwater biome

text: freshwater biome

text: water

characteristic: environment (material)

text: unfiltered control

characteristic: experimental factor

text: Czech Republic

characteristic: geographic location (country and/or sea)

characteristic: geographic location (depth)

characteristic: geographic location (latitude)

text: metagenome

text: freshwater metagenome

text: Rimov Exp

text: freshwater metagenome

text: Illumina

text: water


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: HELMHOLTZ CENTRE FOR INFECTION RESEARCH

characteristic: INSDC center name

text: public

characteristic: Submitter Id

characteristic: collection date

text: freshwater metagenome

characteristic: common name

text: Control treatment, sample collected after 21 h of incubation in the dark, replicate B

text: freshwater biome

text: freshwater biome

text: water

text: unfiltered control

text: Czech Republic

characteristic: geographic location (longitude)

text: metagenome

characteristic: investigation type

text: freshwater metagenome

text: Rimov Exp

characteristic: project name

text: freshwater metagenome

text: Illumina

characteristic: sequencing method

text: water

characteristic: water environmental package


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: HELMHOLTZ CENTRE FOR INFECTION RESEARCH

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: freshwater metagenome

text: Control treatment, sample collected after 21 h of incubation in the dark, replicate C

characteristic: description

text: freshwater biome

characteristic: environment (biome)

text: freshwater biome

characteristic: environment (feature)

text: water

text: unfiltered control

text: Czech Republic

text: metagenome

text: freshwater metagenome

characteristic: organism

text: Rimov Exp

text: freshwater metagenome

text: Illumina

characteristic: title

text: water


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: HELMHOLTZ CENTRE FOR INFECTION RESEARCH

characteristic: INSDC center name

text: public

characteristic: Submitter Id

characteristic: collection date

text: freshwater metagenome

characteristic: common name

text: Size fractionated (< 1 micron) treatment, sample collected after 45 h of incubation in the dark, replicate A

text: freshwater biome

text: freshwater biome

text: water

characteristic: environment (material)

text: size fractionation < 1 micrometer

characteristic: experimental factor

text: Czech Republic

characteristic: geographic location (country and/or sea)

characteristic: geographic location (depth)

characteristic: geographic location (latitude)

text: metagenome

text: freshwater metagenome

text: Rimov Exp

text: freshwater metagenome

text: Illumina

text: water


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: HELMHOLTZ CENTRE FOR INFECTION RESEARCH

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: freshwater metagenome

text: Size fractionated (< 1 micron) treatment, sample collected after 45 h of incubation in the dark, replicate B

text: freshwater biome

text: freshwater biome

text: water

text: size fractionation < 1 micrometer

text: Czech Republic

characteristic: geographic location (longitude)

text: metagenome

characteristic: investigation type

text: freshwater metagenome

text: Rimov Exp

characteristic: project name

text: freshwater metagenome

text: Illumina

characteristic: sequencing method

text: water

characteristic: water environmental package


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: DTU-GE

characteristic: INSDC center name

text: public

text: DTU2018-1342-PRJCompare-1A-microbiome-salmon-mock-QIAFast_S16

characteristic: Submitter Id

text: DTU-GE

characteristic: broker name

text: Yes

characteristic: environmental sample

text: Salmo salar

characteristic: host scientific name

text: Yes

characteristic: is the sequenced pathogen host associated?

characteristic: isolate

text: proficiency test

characteristic: isolation source host associated

text: fish metagenome

characteristic: organism

text: fish metagenome

characteristic: strain


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: DTU-GE

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: DTU2018-1343-PRJCompare-1B-microbiome-salmon-mock-supernatant-QIAFast_S11

text: DTU-GE

text: Yes

text: Salmo salar

text: Yes

text: proficiency test

text: fish metagenome

text: fish metagenome


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: DTU-GE

text: public

text: DTU2018-1344-PRJCompare-1C-microbiome-salmon-QIAFast_S14

text: DTU-GE

text: Yes

text: Salmo salar

text: Yes

text: proficiency test

text: fish metagenome

text: fish metagenome


text: DTU-GE

characteristic: INSDC center name

text: public

text: DTU2018-1345-PRJCompare-1D-microbiome-EC-QIAFast_S13

characteristic: Submitter Id

text: DTU-GE

text: Yes

text: Salmo salar

text: Yes

text: proficiency test

text: fish metagenome

text: fish metagenome


text: DTU-GE

text: public

text: DTU2018-1346-PRJCompare-2A-microbiome-salmon-mock-QIAUCP_S10

text: DTU-GE

characteristic: broker name

text: Yes

characteristic: environmental sample

text: Salmo salar

text: Yes

text: proficiency test

text: fish metagenome

text: fish metagenome


text: DTU-GE

text: public

text: DTU2018-1347-PRJCompare-2B-microbiome-salmon-mock-supernatant-QIAUCP_S7

text: DTU-GE

text: Yes

text: Salmo salar

characteristic: host scientific name

text: Yes

characteristic: is the sequenced pathogen host associated?

text: proficiency test

text: fish metagenome

text: fish metagenome


text: DTU-GE

text: public

text: DTU2018-1348-PRJCompare-2C-microbiome-salmon-QIAUCP_S4

text: DTU-GE

text: Yes

text: Salmo salar

text: Yes

characteristic: isolate

text: proficiency test

characteristic: isolation source host associated

text: fish metagenome

text: fish metagenome


text: DTU-GE

text: public

text: DTU2018-1349-PRJCompare-2D-microbiome-EC-QIAUCP_S3

text: DTU-GE

text: Yes

text: Salmo salar

text: Yes

text: proficiency test

text: fish metagenome

characteristic: organism

text: fish metagenome

characteristic: strain


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: DTU-GE

text: public

text: DTU2018-1350-PRJCompare-3A-microbiome-salmon-mock-MoBioFood_S6

text: DTU-GE

text: Yes

text: Salmo salar

text: Yes

text: proficiency test

text: fish metagenome

text: fish metagenome


text: DTU-GE

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: DTU2018-1351-PRJCompare-3B-microbiome-salmon-mock-supernatant-MoBioFood_S12

text: DTU-GE

text: Yes

text: Salmo salar

text: Yes

text: proficiency test

text: fish metagenome

text: fish metagenome


text: DTU-GE

text: public

characteristic: INSDC status

characteristic: SRA accession

text: DTU2018-1352-PRJCompare-3C-microbiome-salmon-MoBioFood_S9

text: DTU-GE

text: Yes

text: Salmo salar

text: Yes

text: proficiency test

text: fish metagenome

text: fish metagenome


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: DTU-GE

text: public

text: DTU2018-1353-PRJCompare-3D-microbiome-EC-MoBioFood_S8

text: DTU-GE

text: Yes

text: Salmo salar

text: Yes

text: proficiency test

text: fish metagenome

text: fish metagenome


text: DTU-GE

characteristic: INSDC center name

text: public

text: DTU2018-1354-PRJCompare-4A-microbiome-salmon-mock-Rneasy_S2

characteristic: Submitter Id

text: DTU-GE

text: Yes

text: Salmo salar

text: Yes

text: proficiency test

text: fish metagenome

text: fish metagenome


text: DTU-GE

text: public

text: DTU2018-1355-PRJCompare-4B-microbiome-salmon-mock-supernatant-Rneasy_S5

text: DTU-GE

characteristic: broker name

text: Yes

characteristic: environmental sample

text: Salmo salar

text: Yes

text: proficiency test

text: fish metagenome

text: fish metagenome


text: DTU-GE

text: public

text: DTU2018-1356-PRJCompare-4C-microbiome-salmon-Rneasy_S1

text: DTU-GE

text: Yes

text: Salmo salar

characteristic: host scientific name

text: Yes

characteristic: is the sequenced pathogen host associated?

text: proficiency test

text: fish metagenome

text: fish metagenome


text: DTU-GE

text: public

text: DTU2018-1357-PRJCompare-4D-microbiome-EC-Rneasy_S15

text: DTU-GE

text: Yes

text: Salmo salar

text: Yes

characteristic: isolate

text: proficiency test

characteristic: isolation source host associated

text: fish metagenome

text: fish metagenome


text: EMBL

text: public

text: E-MTAB-68221529059880:Input_H3.3ctrl-1_D0

text: ArrayExpress

characteristic: cell line

text: embryonic stem cell

characteristic: cell type

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. 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 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

characteristic: genetic modification

text: H3f3a -/-

characteristic: genotype

text: Mus musculus

characteristic: organism

text: Mus musculus

text: Mus musculus

characteristic: time

characteristic: title


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: E-MTAB-68221529059880:Input_H3.3K36A-1_D0

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

text: public

text: E-MTAB-68221529059880:Input_H3.3K4A-1_D0

characteristic: Submitter Id

text: ArrayExpress

characteristic: broker name

characteristic: cell line

text: embryonic stem cell

characteristic: cell type

text: house mouse

text: induced mutation

text: H3f3a -/-; H3f3b K4A

text: Mus musculus

text: Mus musculus

text: Mus musculus


text: Mycobacterium avium

characteristic: ArrayExpress-SPECIES

text: SC

text: public

text: Mycobacterium avium

characteristic: common name

text: Mycobacterium avium 05-4293

text: Mycobacterium avium 05-4293

characteristic: subject id


text: Salmonella enterica subsp. enterica serovar Typhimurium

text: SC

text: public

characteristic: organism

characteristic: title


characteristic: ENA checklist

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: University Hospital Galway

text: public

text: sam_adb27551-3cab-45c5-aafd-87b47b435c68

tag: Namespace:University Hospital Galway

text: University Hospital Galway

characteristic: collected by

characteristic: collection date

text: Ireland

characteristic: geographic location (country and/or sea)

text: Homo sapien

characteristic: host scientific name

characteristic: isolate

text: Salmonella enterica subsp. enterica serovar Coeln


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: University Hospital Galway

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: sam_f9e39395-c0eb-484c-8395-e668deecbaab

characteristic: Submitter Id

text: University Hospital Galway

text: Ireland

text: Homo sapien

text: Salmonella enterica subsp. enterica serovar Brandenburg


text: University Hospital Galway

text: public

text: sam_9fe68893-45ee-47e4-9473-59f595c8b8a7

text: University Hospital Galway

text: Ireland

text: Homo sapien

characteristic: organism

characteristic: title


characteristic: ENA checklist

characteristic: ENA-CHECKLIST

text: University Hospital Galway

text: public

text: sam_4e007ad0-4d06-4616-91f4-054f3fb27dd4

text: University Hospital Galway

text: Ireland

text: Homo sapien

text: Salmonella enterica subsp. enterica serovar Litchfield


characteristic: ENA-FIRST-PUBLIC

text: University Hospital Galway

text: public

text: sam_138d57b9-c43a-44a0-af4a-27de9985fa66

text: University Hospital Galway

characteristic: collected by

text: Ireland

text: Homo sapien

text: Salmonella enterica subsp. enterica serovar Kentucky


text: University Hospital Galway

text: public

text: sam_04b62a33-0674-4cee-8175-a05a0033839d

text: University Hospital Galway

characteristic: collection date

text: Ireland

characteristic: geographic location (country and/or sea)

text: Homo sapien

text: Salmonella enterica subsp. enterica serovar Give


text: Plasmodium falciparum

characteristic: ArrayExpress-SPECIES

text: SC

text: public

text: malaria parasite P. falciparum

characteristic: common name

text: Plasmodium falciparum

text: Plasmodium falciparum

characteristic: subject id


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: UTRECHT UNIVERSITY

characteristic: INSDC center name

text: public

tag: Namespace:UTRECHT UNIVERSITY

text: Streptococcus equi subsp. zooepidemicus

text: Streptococcus equi subsp. zooepidemicus

text: Streptococcus equi subsp. zooepidemicus WGS reads human sample


text: UTRECHT UNIVERSITY

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: Streptococcus equi subsp. zooepidemicus

text: Streptococcus equi subsp. zooepidemicus

text: Streptococcus equi subsp. zooepidemicus WGS reads horse D


text: UTRECHT UNIVERSITY

text: public

characteristic: SRA accession

characteristic: Submitter Id

text: Streptococcus equi subsp. zooepidemicus

characteristic: organism

text: Streptococcus equi subsp. zooepidemicus

text: Streptococcus equi subsp. zooepidemicus WGS reads horse A


characteristic: ENA-CHECKLIST

text: UTRECHT UNIVERSITY

text: public

text: Streptococcus equi subsp. zooepidemicus

text: Streptococcus equi subsp. zooepidemicus

text: Streptococcus equi subsp. zooepidemicus WGS reads horse A sample 2

characteristic: title


characteristic: ENA-FIRST-PUBLIC

text: UTRECHT UNIVERSITY

text: public

text: Streptococcus equi subsp. zooepidemicus

text: Streptococcus equi subsp. zooepidemicus

text: Streptococcus equi subsp. zooepidemicus WGS reads horse B


text: UTRECHT UNIVERSITY

text: public

text: Streptococcus equi subsp. zooepidemicus

text: Streptococcus equi subsp. zooepidemicus

text: Streptococcus equi subsp. zooepidemicus WGS reads horse B sample 2


text: UTRECHT UNIVERSITY

text: public

text: Streptococcus equi subsp. zooepidemicus

text: Streptococcus equi subsp. zooepidemicus

text: Streptococcus equi subsp. zooepidemicus WGS reads horse B sample 3


text: UTRECHT UNIVERSITY

text: public

text: Streptococcus equi subsp. zooepidemicus

text: Streptococcus equi subsp. zooepidemicus

text: Streptococcus equi subsp. zooepidemicus WGS reads horse B sample 4


text: UTRECHT UNIVERSITY

text: public

text: Streptococcus equi subsp. zooepidemicus

text: Streptococcus equi subsp. zooepidemicus

text: Streptococcus equi subsp. zooepidemicus WGS reads horse C


text: UTRECHT UNIVERSITY

text: public

text: Streptococcus equi subsp. zooepidemicus

text: Streptococcus equi subsp. zooepidemicus

text: Streptococcus equi subsp. zooepidemicus WGS reads horse C sample 2


characteristic: ENA checklist

text: University Hospital Galway

text: public

text: sam_e34fe34a-ee9c-4d9a-8da5-73131884aece

text: University Hospital Galway

characteristic: collected by

characteristic: collection date

text: Ireland

text: Homo sapien

characteristic: host scientific name

characteristic: isolate

text: Salmonella enterica subsp. enterica serovar Enteritidis


characteristic: ENA-LAST-UPDATE

text: University Hospital Galway

text: public

text: sam_2c245506-e6a1-4a6d-a922-630da47117cd

text: University Hospital Galway

text: Ireland

characteristic: geographic location (country and/or sea)

text: Homo sapien

text: Salmonella enterica subsp. enterica serovar Rissen


characteristic: External Id

characteristic: INSDC center name

text: public

text: E-MTAB-6927:iCLIP_IgG_HEK293_NoAb_rep1_Hs_NNNCAATNN

tag: Namespace:European Molecular Biology Laboratory (EMBL)

text: ArrayExpress

characteristic: broker name

characteristic: cell line

text: epithelial cell

characteristic: cell type

text: human

characteristic: common name

text: Protocols: The modified iCLIP protocol is based on the previously described protocol with modifications that enable the definition of read-through cDNAs (Huppertz el al., 2014). HEK293 cells were crosslinked with 0.15 mJ/cm2 254 nm UV light. To prepare the cell lysate, the cells were lysed with 1 ml iCLIP lysis buffer (50 mM Tris-HCl pH 7.4, 100 mM NaCl, 1% NP-40, 0.1% SDS, 0.5% sodium deoxycholate, final concentration 2mg/ml) and sonicated (Bioruptor, 5x5 sec on/off). For the iCLIP library preparation of PTBP1, the sonicated lysates were initially centrifuged and the supernatant was kept as the first lysate. The remaining cell pellet was dissolved in 50 µL MSB lysis buffer (50 mM Tris-HCl, pH 7.4, 100 mM NaH2PO4, 7 M urea, 1 mM DTT). After the pellet had dissolved, the mixture was diluted with H2O to 1000 μL and an additional centrifugation was performed (second lysate). The two lysates were combined and incubated with RNase I (AM2295, Thermo Scientific) at 37°C for 3 min at 4 U/ml. Protein A Dynabeads were used for the IP of PTBP1. For each IP, 100 µl of beads were washed in iCLIP lysis buffer and incubated with the mouse monoclonal BB7 serum anti-PTBP1 (a gift from C. Smith, available from ATCC CRL-2501). The samples were then rotated at 4°C for 2 h (final urea concentration 175 mM). The beads were washed with high-salt washing buffer (50 mM Tris-HCl pH 7.4, 1 M NaCl, 1% NP-40, 0.1% SDS, 0.5% sodium deoxycholate). After the first round of washes, the samples proceed through 3´ adapter addition, an additional phosphorylation (0.2 µl PNK, 0.4 µl cold ATP (1 mM), 0.4 µl 10x PNK buffer, 3 µl water) and a 5´marker ligation (6 µl water, 5 µl 4X ligation buffer, 2 µl RNA ligase, 1 µl RNasin, 2 µl 5´ marker (100 µM), 4 µl PEG400). The sequence of the 5´ marker is CAGUCCGACGAUC, which corresponds to the Illumina short RNA 5´ Adapter (RA5), part #15013205; this sequence is not complementary to the primers used for amplification of iCLIP cDNA libraries (Huppertz el al., 2014). We followed the protocol as described in Huppertz et al., 2014

characteristic: description

text: embryo

characteristic: developmental stage

text: normal

characteristic: disease

text: Homo sapiens

text: Homo sapiens

text: kidney

characteristic: organism part

text: Homo sapiens


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: European Molecular Biology Laboratory (EMBL)

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-6927:iCLIP_IgG_HEK293_NoAb_rep2_Hs_NNNTTGTNN

characteristic: Submitter Id

text: ArrayExpress

text: epithelial cell

text: human

text: embryo

text: normal

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: kidney

text: Homo sapiens

characteristic: title


characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC center name

text: public

text: E-MTAB-6927:iCLIP_PTBP1_HEK293_rep1.1_Hs_NNNCCACNN

text: ArrayExpress

characteristic: broker name

text: epithelial cell

text: human

text: embryo

text: normal

text: Homo sapiens

text: Homo sapiens

text: kidney

text: Homo sapiens


text: public

text: E-MTAB-6927:iCLIP_PTBP1_HEK293_rep1.2_Hs_NNNAATANN

text: ArrayExpress

characteristic: cell line

text: epithelial cell

characteristic: cell type

text: human

characteristic: common name

characteristic: description

text: embryo

text: normal

text: Homo sapiens

text: Homo sapiens

text: kidney

text: Homo sapiens


characteristic: ENA-CHECKLIST

text: public

text: E-MTAB-6927:iCLIP_PTBP1_HEK293_rep2.1_Hs_NNNTTAANN

text: ArrayExpress

text: epithelial cell

text: human

text: embryo

characteristic: developmental stage

text: normal

characteristic: disease

text: Homo sapiens

text: Homo sapiens

text: kidney

characteristic: organism part

text: Homo sapiens


characteristic: ENA-FIRST-PUBLIC

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: E-MTAB-6927:iCLIP_PTBP1_HEK293_rep2.2_Hs_NNNTGGCNN

text: ArrayExpress

text: epithelial cell

text: human

text: embryo

text: normal

text: Homo sapiens

text: Homo sapiens

text: kidney

text: Homo sapiens


text: Homo sapiens

characteristic: ArrayExpress-SPECIES

text: SC

text: public

characteristic: SRA accession

characteristic: Submitter Id

text: human

text: Homo sapiens

characteristic: organism

text: Homo sapiens

characteristic: subject id

characteristic: title


characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC center name

text: public

tag: Namespace:SCIENCE FOR LIFE LABORATORY, KTH ROYAL INSTITUTE OF TECHNOLOGY

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text: We applied nanopore sequencing to trace the fecal contamination from the stormwater system in Stockholm County

text: urban biome

characteristic: environment (biome)

text: urban stormwater

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characteristic: geographic location (country and/or sea)

characteristic: geographic location (depth)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

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text: Stationary and portable sequencing approaches for tracking fecal contamination in an urban stormwater system

characteristic: project name

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characteristic: sequencing method

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characteristic: water environmental package


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: SCIENCE FOR LIFE LABORATORY, KTH ROYAL INSTITUTE OF TECHNOLOGY

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

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text: metagenome

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characteristic: organism

text: metagenome

text: Oxford Nanopore

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characteristic: ENA-LAST-UPDATE

characteristic: External Id

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characteristic: INSDC center name

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text: barber pole worm

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characteristic: subject id

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text: UANTW

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characteristic: collection date

text: human skin metagenome

text: Human skin microbiome sample using the V4 region of the 16S rRNA gene from the CON group. The sample belongs to participant 01 who affiliates with the gender F. The structure of the samplenames shows this metadata as follows: region - group - participant - gender - visit - techrep - biolrep

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characteristic: geographic location (country and/or sea)

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characteristic: geographic location (latitude)

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characteristic: ENA-FIRST-PUBLIC

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characteristic: INSDC first public

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characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: human skin metagenome

text: Human skin microbiome sample using the V4 region of the 16S rRNA gene from the CON group. The sample belongs to participant 02 who affiliates with the gender F. The structure of the samplenames shows this metadata as follows: region - group - participant - gender - visit - techrep - biolrep

characteristic: description

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text: skin environment

text: swab

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text: 4.416253 DD

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text: metagenome

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characteristic: organism

text: Acne microbiome modulation

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text: Illumina MiSeq


characteristic: External Id

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characteristic: INSDC center name

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characteristic: collection date

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characteristic: common name

text: Human skin microbiome sample using the V4 region of the 16S rRNA gene from the CON group. The sample belongs to participant 03 who affiliates with the gender F. The structure of the samplenames shows this metadata as follows: region - group - participant - gender - visit - techrep - biolrep

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characteristic: environment (biome)

text: skin environment

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characteristic: geographic location (country and/or sea)

text: 51.179043 DD

text: 4.416253 DD

text: human-skin

text: metagenome

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text: Illumina MiSeq

characteristic: title


characteristic: ENA-CHECKLIST

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characteristic: ENA-LAST-UPDATE

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text: human skin metagenome

text: Human skin microbiome sample using the V4 region of the 16S rRNA gene from the CON group. The sample belongs to participant 04 who affiliates with the gender F. The structure of the samplenames shows this metadata as follows: region - group - participant - gender - visit - techrep - biolrep

text: Homo Sapiens

text: skin environment

text: swab

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text: 51.179043 DD

characteristic: geographic location (latitude)

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characteristic: geographic location (longitude)

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characteristic: project name

text: human skin metagenome

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characteristic: External Id

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characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

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characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: human skin metagenome

text: Human skin microbiome sample using the V4 region of the 16S rRNA gene from the CON group. The sample belongs to participant 05 who affiliates with the gender F. The structure of the samplenames shows this metadata as follows: region - group - participant - gender - visit - techrep - biolrep

characteristic: description

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text: skin environment

text: swab

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text: 4.416253 DD

text: human-skin

text: metagenome

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characteristic: organism

text: Acne microbiome modulation

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text: Illumina MiSeq


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: UANTW

text: public

characteristic: collection date

text: human skin metagenome

characteristic: common name

text: Human skin microbiome sample using the V4 region of the 16S rRNA gene from the CON group. The sample belongs to participant 06 who affiliates with the gender F. The structure of the samplenames shows this metadata as follows: region - group - participant - gender - visit - techrep - biolrep

text: Homo Sapiens

characteristic: environment (biome)

text: skin environment

characteristic: environment (feature)

text: swab

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characteristic: geographic location (country and/or sea)

text: 51.179043 DD

text: 4.416253 DD

text: human-skin

text: metagenome

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text: Acne microbiome modulation

text: human skin metagenome

text: Illumina MiSeq

characteristic: title


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: UANTW

characteristic: INSDC center name

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text: human skin metagenome

text: Human skin microbiome sample using the V4 region of the 16S rRNA gene from the CON group. The sample belongs to participant 07 who affiliates with the gender F. The structure of the samplenames shows this metadata as follows: region - group - participant - gender - visit - techrep - biolrep

text: Homo Sapiens

text: skin environment

text: swab

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characteristic: geographic location (latitude)

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characteristic: geographic location (longitude)

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characteristic: human skin environmental package

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characteristic: project name

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characteristic: sequencing method


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text: UANTW

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: human skin metagenome

text: Human skin microbiome sample using the V4 region of the 16S rRNA gene from the CON group. The sample belongs to participant 08 who affiliates with the gender F. The structure of the samplenames shows this metadata as follows: region - group - participant - gender - visit - techrep - biolrep

characteristic: description

text: Homo Sapiens

text: skin environment

text: swab

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text: 4.416253 DD

text: human-skin

text: metagenome

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characteristic: organism

text: Acne microbiome modulation

text: human skin metagenome

text: Illumina MiSeq


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: UANTW

text: public

characteristic: collection date

text: human skin metagenome

characteristic: common name

text: Human skin microbiome sample using the V4 region of the 16S rRNA gene from the CON group. The sample belongs to participant 09 who affiliates with the gender F. The structure of the samplenames shows this metadata as follows: region - group - participant - gender - visit - techrep - biolrep

text: Homo Sapiens

characteristic: environment (biome)

text: skin environment

characteristic: environment (feature)

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characteristic: geographic location (country and/or sea)

text: 51.179043 DD

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text: human-skin

text: metagenome

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text: Illumina MiSeq

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

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characteristic: INSDC center name

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text: Human skin microbiome sample using the V4 region of the 16S rRNA gene from the CON group. The sample belongs to participant 10 who affiliates with the gender F. The structure of the samplenames shows this metadata as follows: region - group - participant - gender - visit - techrep - biolrep

text: Homo Sapiens

text: skin environment

text: swab

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characteristic: geographic location (latitude)

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characteristic: geographic location (longitude)

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characteristic: project name

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characteristic: sequencing method


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text: UANTW

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: human skin metagenome

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characteristic: description

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text: skin environment

text: swab

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text: human-skin

text: metagenome

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characteristic: organism

text: Acne microbiome modulation

text: human skin metagenome

text: Illumina MiSeq


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: UANTW

text: public

characteristic: collection date

text: human skin metagenome

characteristic: common name

text: Human skin microbiome sample using the V4 region of the 16S rRNA gene from the CON group. The sample belongs to participant 12 who affiliates with the gender F. The structure of the samplenames shows this metadata as follows: region - group - participant - gender - visit - techrep - biolrep

text: Homo Sapiens

characteristic: environment (biome)

text: skin environment

characteristic: environment (feature)

text: swab

characteristic: environment (material)

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characteristic: geographic location (country and/or sea)

text: 51.179043 DD

text: 4.416253 DD

text: human-skin

text: metagenome

text: human skin metagenome

text: Acne microbiome modulation

text: human skin metagenome

text: Illumina MiSeq

characteristic: title


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: UANTW

characteristic: INSDC center name

text: public

text: human skin metagenome

text: Human skin microbiome sample using the V4 region of the 16S rRNA gene from the CON group. The sample belongs to participant 13 who affiliates with the gender F. The structure of the samplenames shows this metadata as follows: region - group - participant - gender - visit - techrep - biolrep

text: Homo Sapiens

text: skin environment

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text: 51.179043 DD

characteristic: geographic location (latitude)

text: 4.416253 DD

characteristic: geographic location (longitude)

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text: metagenome

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characteristic: project name

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characteristic: sequencing method


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characteristic: INSDC first public

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characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: human skin metagenome

text: Human skin microbiome sample using the V4 region of the 16S rRNA gene from the CON group. The sample belongs to participant 14 who affiliates with the gender F. The structure of the samplenames shows this metadata as follows: region - group - participant - gender - visit - techrep - biolrep

characteristic: description

text: Homo Sapiens

text: skin environment

text: swab

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text: 4.416253 DD

text: human-skin

text: metagenome

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characteristic: organism

text: Acne microbiome modulation

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text: Illumina MiSeq


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: UANTW

text: public

characteristic: collection date

text: human skin metagenome

characteristic: common name

text: Human skin microbiome sample using the V4 region of the 16S rRNA gene from the CON group. The sample belongs to participant 15 who affiliates with the gender F. The structure of the samplenames shows this metadata as follows: region - group - participant - gender - visit - techrep - biolrep

text: Homo Sapiens

characteristic: environment (biome)

text: skin environment

characteristic: environment (feature)

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characteristic: geographic location (country and/or sea)

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text: 4.416253 DD

text: human-skin

text: metagenome

text: human skin metagenome

text: Acne microbiome modulation

text: human skin metagenome

text: Illumina MiSeq

characteristic: title