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text: Homo sapiens

text: Human Postmortem Microbiome

characteristic: project name

text: Cotton Tipped Swab

characteristic: sample collection device or method

characteristic: sample storage temperature

text: Homo sapiens

text: Illumina MiSeq

characteristic: sequencing method

text: 16S rRNA

characteristic: target gene

characteristic: target subfragment

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Michigan State University

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

characteristic: collection date

text: human

characteristic: common name

characteristic: description

text: anthropogenic terrestrial

characteristic: environment (biome)

text: urban

characteristic: environment (feature)

text: Rectum

characteristic: environment (material)

characteristic: estimated postmortem interval

text: USA

text: male

text: human-associated

text: mimarks-survey

text: Homo sapiens

characteristic: organism

text: Human Postmortem Microbiome

text: Cotton Tipped Swab

text: Homo sapiens

text: Illumina MiSeq

text: 16S rRNA


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: Michigan State University

text: public

text: human

text: anthropogenic terrestrial

text: urban

text: Eyes

text: USA

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

characteristic: host body mass index

text: male

characteristic: host sex

characteristic: host subject id

text: human-associated

characteristic: human associated environmental package

text: mimarks-survey

characteristic: investigation type

characteristic: nucleic acid extraction

text: Homo sapiens

text: Human Postmortem Microbiome

characteristic: project name

text: Cotton Tipped Swab

characteristic: sample collection device or method

characteristic: sample storage temperature

text: Homo sapiens

text: Illumina MiSeq

characteristic: sequencing method

text: 16S rRNA

characteristic: target gene

characteristic: target subfragment

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Michigan State University

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

characteristic: collection date

text: human

characteristic: common name

characteristic: description

text: anthropogenic terrestrial

characteristic: environment (biome)

text: urban

characteristic: environment (feature)

text: Nose

characteristic: environment (material)

characteristic: estimated postmortem interval

text: USA

text: male

text: human-associated

text: mimarks-survey

text: Homo sapiens

characteristic: organism

text: Human Postmortem Microbiome

text: Cotton Tipped Swab

text: Homo sapiens

text: Illumina MiSeq

text: 16S rRNA


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: Michigan State University

text: public

text: human

text: anthropogenic terrestrial

text: urban

text: Mouth

text: USA

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

characteristic: host body mass index

text: male

characteristic: host sex

characteristic: host subject id

text: human-associated

characteristic: human associated environmental package

text: mimarks-survey

characteristic: investigation type

characteristic: nucleic acid extraction

text: Homo sapiens

text: Human Postmortem Microbiome

characteristic: project name

text: Cotton Tipped Swab

characteristic: sample collection device or method

characteristic: sample storage temperature

text: Homo sapiens

text: Illumina MiSeq

characteristic: sequencing method

text: 16S rRNA

characteristic: target gene

characteristic: target subfragment

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Michigan State University

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

characteristic: collection date

text: human

characteristic: common name

characteristic: description

text: anthropogenic terrestrial

characteristic: environment (biome)

text: urban

characteristic: environment (feature)

text: Umbilicus

characteristic: environment (material)

characteristic: estimated postmortem interval

text: USA

text: male

text: human-associated

text: mimarks-survey

text: Homo sapiens

characteristic: organism

text: Human Postmortem Microbiome

text: Cotton Tipped Swab

text: Homo sapiens

text: Illumina MiSeq

text: 16S rRNA


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: Michigan State University

text: public

text: human

text: anthropogenic terrestrial

text: urban

text: Rectum

text: USA

characteristic: geographic location (country and/or sea)

text: 42� 6'41.60N

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

characteristic: host body mass index

text: female

characteristic: host sex

characteristic: host subject id

text: human-associated

characteristic: human associated environmental package

text: mimarks-survey

characteristic: investigation type

characteristic: nucleic acid extraction

text: Homo sapiens

text: Human Postmortem Microbiome

characteristic: project name

text: Cotton Tipped Swab

characteristic: sample collection device or method

characteristic: sample storage temperature

text: Homo sapiens

text: Illumina MiSeq

characteristic: sequencing method

text: 16S rRNA

characteristic: target gene

characteristic: target subfragment

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Michigan State University

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

characteristic: collection date

text: human

characteristic: common name

characteristic: description

text: anthropogenic terrestrial

characteristic: environment (biome)

text: urban

characteristic: environment (feature)

text: Nose

characteristic: environment (material)

characteristic: estimated postmortem interval

text: USA

text: 83� 8'50.99W

text: male

text: human-associated

text: mimarks-survey

text: Homo sapiens

characteristic: organism

text: Human Postmortem Microbiome

text: Cotton Tipped Swab

text: Homo sapiens

text: Illumina MiSeq

text: 16S rRNA


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: Michigan State University

text: public

text: human

text: anthropogenic terrestrial

text: urban

text: Eyes

text: USA

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

text: 83� 3'44.96W

characteristic: geographic location (longitude)

characteristic: host body mass index

text: female

characteristic: host sex

characteristic: host subject id

text: human-associated

characteristic: human associated environmental package

text: mimarks-survey

characteristic: investigation type

characteristic: nucleic acid extraction

text: Homo sapiens

text: Human Postmortem Microbiome

characteristic: project name

text: Cotton Tipped Swab

characteristic: sample collection device or method

characteristic: sample storage temperature

text: Homo sapiens

text: Illumina MiSeq

characteristic: sequencing method

text: 16S rRNA

characteristic: target gene

characteristic: target subfragment

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Michigan State University

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

characteristic: collection date

text: human

characteristic: common name

characteristic: description

text: anthropogenic terrestrial

characteristic: environment (biome)

text: urban

characteristic: environment (feature)

text: Mouth

characteristic: environment (material)

characteristic: estimated postmortem interval

text: USA

text: 83� 6'19.55W

text: male

text: human-associated

text: mimarks-survey

text: Homo sapiens

characteristic: organism

text: Human Postmortem Microbiome

text: Cotton Tipped Swab

text: Homo sapiens

text: Illumina MiSeq

text: 16S rRNA


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: THE ROSLIN INSTITUTE

text: public

tag: Namespace:THE ROSLIN INSTITUTE

text: Environmental E coli

text: Escherichia coli

text: Escherichia coli

text: Environmental E coli

characteristic: title


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: ISTANBUL UNIVERSITY

characteristic: INSDC center name

text: public

tag: Namespace:ISTANBUL UNIVERSITY

text: metagenome

text: metagenome


text: Chinese Academic of Sciences

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

tag: Namespace:Chinese Academic of Sciences

text: 16S rRNA pyrosequencing

text: microorganisms

text: dark brown forest soil

text: soil

text: China

characteristic: geographic location (country and/or sea)

unit: m

characteristic: geographic location (depth)

characteristic: geographic location (elevation)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: metagenome

characteristic: investigation type

text: soil metagenome

text: Investigating microbial control on soil organic matter dynamics during forest succession

characteristic: project name

text: soil metagenome

text: Mesiq

characteristic: sequencing method

text: soil

characteristic: soil environmental package

text: Soil microbes


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: RU

text: public

characteristic: SRA accession

characteristic: Submitter Id

characteristic: collection date

text: Planktonic Kuenenia cells sustained in a anoxic membrane bioreactor. The culture was obtained by Strous et. al (2006) by inoculating a gas lift bioreactor with nitrifying activated sludge in 2002. This resulted in a enrichment of Kuenenia cells occurring as flocs. The culture was transferred into a sequencing batch reactor in 2004. The current culturing setup, in operation since 2009, utilizes a membrane bioreactor. This change in cultivation enabled obtaining planktonic cells instead of flocs which resulted in an enrichment of up to 95%.

characteristic: description

text: anaerobic bioreactor

characteristic: environment (biome)

text: anaerobic bioreactor

characteristic: environment (feature)

text: anaerobic bioreactor

characteristic: environment (material)

text: Netherlands

text: metagenome

text: miscellaneous natural or artificial environment

characteristic: miscellaneous environmental package

text: Candidatus Kuenenia stuttgartiensis

characteristic: organism

text: Resolving the complete genome of Kuenenia stuttgartiensis from a membrane bioreactor enrichment using Single Molecule Real-Time sequencing

text: Candidatus Kuenenia stuttgartiensis

text: Single Molecule Real-Time sequencing - PacBio RS II

text: Kuenenia stuttgartiensis anoxic membrane bioreactor enrichment culture

type: has member


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Chinese Academic of Sciences

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: soil

text: forest

text: soil

text: soil

text: China

characteristic: geographic location (country and/or sea)

characteristic: geographic location (depth)

characteristic: geographic location (elevation)

characteristic: geographic location (latitude)

text: metagenome

text: soil metagenome

text: soil

text: soil metagenome

text: Mesiq

text: soil

text: soil

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: Chinese Academic of Sciences

text: public

characteristic: SRA accession

characteristic: Submitter Id

characteristic: collection date

text: microbe

text: Alfisols

text: soil

text: China

characteristic: geographic location (longitude)

text: metagenome

characteristic: investigation type

text: soil metagenome

text: 16S rRNA pyrosequencing

characteristic: project name

text: soil metagenome

text: Mesiq

characteristic: sequencing method

text: soil

characteristic: soil environmental package

text: 16S rRNA pyrosequencing


LM_JF5203 complete genome

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: UNIVERSITY OF BERN

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: LM_JF5203 complete genome

tag: Namespace:UNIVERSITY OF BERN

text: Listeria monocytogenes

characteristic: organism

text: Listeria monocytogenes

text: LM_JF5203 complete genome


JF4839 complete genome

text: UNIVERSITY OF BERN

text: public

characteristic: INSDC status

text: JF4839 complete genome

text: JF4839 complete genome

characteristic: description

text: Listeria monocytogenes

text: Listeria monocytogenes

text: JF4839 complete genome

characteristic: title


JF5203 complete chromosome

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: UNIVERSITY OF BERN

text: public

characteristic: SRA accession

text: JF5203 complete chromosome

text: JF5203 complete chromosome

text: Listeria monocytogenes

text: Listeria monocytogenes

text: JF5203 complete chromosome


JF5861 complete genome

text: UNIVERSITY OF BERN

text: public

text: JF5861 complete genome

characteristic: Submitter Id

text: JF5861 complete genome

text: Listeria monocytogenes

text: Listeria monocytogenes

text: JF5861 complete genome


LMNC088 complete genome

text: UNIVERSITY OF BERN

text: public

text: LMNC088 complete genome

text: LMNC088 complete genome

text: Listeria monocytogenes

text: Listeria monocytogenes

text: LMNC088 complete genome


102.100.100/14730 220bp

text: public

text: 102.100.100/14730 220bp

text: Acropora hyacinthus

text: Acropora hyacinthus

text: Acropora hyacinthus

text: REFUGE2020, Acropora hyacinthus genome from sperm DNA


102.100.100/14730 450bp

text: public

text: 102.100.100/14730 450bp

text: Acropora hyacinthus

text: Acropora hyacinthus

text: Acropora hyacinthus

text: REFUGE2020, Acopora hyacinthus genome from sperm DNA


text: UNIVERSITY OF BERN

text: public

text: Listeria monocytogenes

characteristic: common name

text: Food

text: Listeria monocytogenes

text: Listeria monocytogenes


text: UNIVERSITY OF BERN

text: public

text: Listeria monocytogenes

text: Cattle brain

text: Listeria monocytogenes

text: Listeria monocytogenes


text: UNIVERSITY OF BERN

text: public

text: Listeria monocytogenes

text: Goat brain

text: Listeria monocytogenes

text: Listeria monocytogenes


text: UNIVERSITY OF BERN

text: public

text: Listeria monocytogenes

text: Sheep brain

text: Listeria monocytogenes

text: Listeria monocytogenes


text: UNIVERSITY OF BERN

text: public

text: Listeria monocytogenes

text: Cattle abortion

text: Listeria monocytogenes

text: Listeria monocytogenes


text: UNIVERSITY OF BERN

text: public

text: Listeria monocytogenes

text: Sheep enteritis

text: Listeria monocytogenes

text: Listeria monocytogenes


text: UNIVERSITY OF BERN

text: public

text: Listeria monocytogenes

text: Sheep abortion

text: Listeria monocytogenes

text: Listeria monocytogenes


text: UNIVERSITY OF BERN

text: public

text: Listeria monocytogenes

text: Cattle mastitis

text: Listeria monocytogenes

text: Listeria monocytogenes


text: UNIVERSITY OF BERN

text: public

text: Listeria monocytogenes

text: Environment

text: Listeria monocytogenes

text: Listeria monocytogenes


text: UNIVERSITY OF BERN

text: public

text: Listeria monocytogenes

text: Goat abortion

text: Listeria monocytogenes

text: Listeria monocytogenes


text: UNIVERSITY OF BERN

text: public

text: Listeria monocytogenes

text: Human brain

text: Listeria monocytogenes

text: Listeria monocytogenes


text: UNIVERSITY OF BERN

text: public

text: Listeria monocytogenes

text: Sheep septicemia

text: Listeria monocytogenes

text: Listeria monocytogenes


text: Chinese Academic of Sciences

text: public

characteristic: collection date

text: microbe

characteristic: environment (biome)

text: Alfisols

characteristic: environment (feature)

text: forest soil

characteristic: environment (material)

text: China

characteristic: geographic location (country and/or sea)

characteristic: geographic location (depth)

characteristic: geographic location (elevation)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: metagenome

characteristic: investigation type

text: soil metagenome

text: 16S rRNA pyrosequencing

characteristic: project name

text: soil metagenome

text: Mesiq

text: soil

text: 16S rRNA pyrosequencing


characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

tag: Namespace:University of Chinese Academy of Sciences

text: wheat

text: agriculture

text: soil

text: China

text: metagenome

text: soil metagenome

characteristic: organism

text: soil

text: soil metagenome

text: Illumina

characteristic: sequencing method

text: soil

characteristic: soil environmental package

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: University of Chinese Academy of Sciences

text: public

characteristic: SRA accession

characteristic: Submitter Id

characteristic: collection date

text: wheat

characteristic: environment (biome)

text: agriculture

characteristic: environment (feature)

text: soil

characteristic: environment (material)

text: China

characteristic: geographic location (country and/or sea)

text: metagenome

text: soil metagenome

text: soil

text: soil metagenome

text: soil


characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC center name

text: public

text: wheat

text: agriculture

text: soil

text: China

characteristic: geographic location (depth)

characteristic: geographic location (elevation)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: metagenome

characteristic: investigation type

text: soil metagenome

text: soil

characteristic: project name

text: soil metagenome

text: Illumina

text: soil


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: UWS

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: arid steppe

text: common field soil after 1 year in pots without plants

text: soil

text: Spain

text: mimarks-survey

text: soil metagenome

characteristic: organism

text: Maytenus-Lycium

text: soil metagenome

text: pyrosequencing

characteristic: sequencing method

text: soil

characteristic: soil environmental package

text: soil from control pots

characteristic: title


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: UWS

text: public

characteristic: SRA accession

characteristic: Submitter Id

characteristic: collection date

text: arid steppe

characteristic: environment (biome)

text: common field soil after 1 year in pots with 2 Lycium plants

characteristic: environment (feature)

text: soil

characteristic: environment (material)

text: Spain

characteristic: geographic location (country and/or sea)

text: mimarks-survey

text: soil metagenome

text: Maytenus-Lycium

text: soil metagenome

text: pyrosequencing

text: soil

text: soil from pots with Lycium plants


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: UWS

characteristic: INSDC center name

text: public

text: arid steppe

text: common field soil after 1 year in pots with 2 Maytenus plants

text: soil

text: Spain

characteristic: geographic location (depth)

characteristic: geographic location (elevation)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: mimarks-survey

characteristic: investigation type

text: soil metagenome

text: Maytenus-Lycium

characteristic: project name

text: soil metagenome

text: pyrosequencing

text: soil

text: soil from pots with Maytenus plants


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: UWS

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: arid steppe

text: common field soil after 1 year in pots with 1 Lycium and 1 Maytenus plants

text: soil

text: Spain

text: mimarks-survey

text: soil metagenome

characteristic: organism

text: Maytenus-Lycium

text: soil metagenome

text: pyrosequencing

characteristic: sequencing method

text: soil

characteristic: soil environmental package

text: soil from pots with Lycium and Maytenus

characteristic: title


E-MTAB-6067:ew 1

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: public

characteristic: SRA accession

text: E-MTAB-6067:ew 1

tag: Namespace:University of Muenster, Medical Faculty, Institute of Bioinformatics

characteristic: Submitter Id

unit: year

characteristic: age

text: ArrayExpress

characteristic: broker name

text: Ewings sarcoma

characteristic: cell type

text: human

characteristic: common name

text: Protocols: Ewing Sarcoma cell lines CADO-ES1, was purchased form DSMZ. All other Ewing sarccoma cell lines were kindly supplied by Franz von Valen. Ewing sarcoma cell lines were cultivated in RPMI1640 medium, supplemented with 10% (v/v) FCS, 1% Glutamin and 1% of an antibiotic cocktail containing penicillin and streptomycin. All Ewing sarcoma cell lines were maintained on cell culture plastic coated with collagen (0,5mg/ml). Mesenchymal stem cells (MSC) were isolated from BM biopsies. Human skin fibroblast (hfib) were obtained from genital skin biopsies. MSCs and hFBs were cultivated on untreated cell culture plastic in DMEM, 10% (v/v) FCS, 1% Glutamin and 1% of an antibiotic cocktail containing penicillin and streptomycin. All cell lines were incubated at 37°C and 5%CO2 in a humidified atmosphere. Routine microbiological analysis was done using a PCR Mycoplasma Detection Kit according to suggested protocols (Applied Biosystems, Darmstadt, Germany). The extraction of nucleic acids from cell cultures was performed by the use of the RNAeasy Kit (Qiagen) according to the supplier's recommendations. For RNA library preparation 500 - 5000ng RNA were used. ERCCs as an additional internal quality control were added to the libraries. We followed exactly the Thermo-Fischer/Life-Technology(ABI) protocols for the SOLID-5500XL Technology for RNAseq. Most of the procedures were run in a core lab facility of Life-Technology as a commercial service.

characteristic: description

text: Ewing sarcoma

characteristic: disease

text: EWS-ERG

characteristic: genotype

text: Homo sapiens

text: Homo sapiens

text: bone

characteristic: organism part

text: Homo sapiens

text: male

characteristic: sex

text: ew 1


E-MTAB-6067:ew 2

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: University of Muenster, Medical Faculty, Institute of Bioinformatics

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: E-MTAB-6067:ew 2

text: ArrayExpress

text: Ewings sarcoma

text: human

text: Ewing sarcoma

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: bone

text: Homo sapiens

text: male

text: ew 2


E-MTAB-6067:hfib 1

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: public

characteristic: SRA accession

text: E-MTAB-6067:hfib 1

characteristic: Submitter Id

text: less than 2

text: ArrayExpress

text: fibroblast of dermis

text: human

text: normal

text: wild type genotype

text: Homo sapiens

text: Homo sapiens

text: foreskin

text: Homo sapiens

text: male

text: hfib 1

characteristic: title


E-MTAB-6067:hfib 2

text: public

text: E-MTAB-6067:hfib 2

text: less than 2

characteristic: age

text: ArrayExpress

characteristic: broker name

text: fibroblast of dermis

characteristic: cell type

text: human

characteristic: common name

characteristic: description

text: normal

text: wild type genotype

text: Homo sapiens

text: Homo sapiens

text: foreskin

text: Homo sapiens

text: male

text: hfib 2


E-MTAB-6067:hfib 3

characteristic: ENA-LAST-UPDATE

text: public

text: E-MTAB-6067:hfib 3

text: less than 2

text: ArrayExpress

text: fibroblast of dermis

text: human

text: normal

characteristic: disease

text: wild type genotype

characteristic: genotype

text: Homo sapiens

text: Homo sapiens

text: foreskin

characteristic: organism part

text: Homo sapiens

text: male

characteristic: sex

text: hfib 3


E-MTAB-6067:hfib 4

characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: E-MTAB-6067:hfib 4

text: less than 2

text: ArrayExpress

text: fibroblast of dermis

text: human

text: normal

text: wild type genotype

text: Homo sapiens

text: Homo sapiens

text: foreskin

text: Homo sapiens

text: male

text: hfib 4


E-MTAB-6067:msc 1

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: public

characteristic: SRA accession

text: E-MTAB-6067:msc 1

characteristic: Submitter Id

text: ArrayExpress

text: mesenchymal stem cell

text: human

text: normal

text: wild type genotype

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: bone marrow

text: Homo sapiens

text: female

text: msc 1


E-MTAB-6067:msc 2

text: public

text: E-MTAB-6067:msc 2

characteristic: age

text: ArrayExpress

characteristic: broker name

text: mesenchymal stem cell

characteristic: cell type

text: human

characteristic: common name

text: normal

text: wild type genotype

text: Homo sapiens

text: Homo sapiens

text: bone marrow

text: Homo sapiens

text: male

text: msc 2

characteristic: title


E-MTAB-6067:msc 3

characteristic: ENA-LAST-UPDATE

text: public

text: E-MTAB-6067:msc 3

text: ArrayExpress

text: mesenchymal stem cell

text: human

characteristic: description

text: normal

characteristic: disease

text: wild type genotype

characteristic: genotype

text: Homo sapiens

text: Homo sapiens

text: bone marrow

characteristic: organism part

text: Homo sapiens

text: male

text: msc 3


E-MTAB-6067:msc 4

characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: E-MTAB-6067:msc 4

text: ArrayExpress

text: mesenchymal stem cell

text: human

text: normal

text: wild type genotype

text: Homo sapiens

text: Homo sapiens

text: bone marrow

text: Homo sapiens

text: female

characteristic: sex

text: msc 4


E-MTAB-6067:nso 1

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-6067:nso 1

characteristic: Submitter Id

text: ArrayExpress

text: CADO ES1

characteristic: cell line

text: Ewings sarcoma

text: human

text: Ewing sarcoma

text: EWS-ERG

text: pleural fluid

characteristic: metastatic site

text: Homo sapiens

text: Homo sapiens

text: bone

text: Homo sapiens

text: female

text: nso 1


E-MTAB-6067:nso 2

characteristic: ENA-LAST-UPDATE

text: public

text: E-MTAB-6067:nso 2

characteristic: age

text: ArrayExpress

characteristic: broker name

text: CADO ES1

text: Ewings sarcoma

characteristic: cell type

text: human

characteristic: common name

text: Ewing sarcoma

text: EWS-ERG

text: pleural fluid

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: bone

text: Homo sapiens

text: female

text: nso 2

characteristic: title


E-MTAB-6067:nso 3

characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: E-MTAB-6067:nso 3

text: ArrayExpress

text: CADO ES1

text: Ewings sarcoma

text: human

characteristic: description

text: Ewing sarcoma

characteristic: disease

text: EWS-ERG

characteristic: genotype

text: pleural fluid

text: Homo sapiens

text: Homo sapiens

text: bone

characteristic: organism part

text: Homo sapiens

text: female

text: nso 3


E-MTAB-6067:nsp 1

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-6067:nsp 1

characteristic: Submitter Id

text: ArrayExpress

text: CADO ES1

text: Ewings sarcoma

text: human

text: Ewing sarcoma

text: EWS-ERG

text: pleural fluid

text: Homo sapiens

text: Homo sapiens

text: bone

text: Homo sapiens

text: female

characteristic: sex

text: nsp 1


E-MTAB-6067:nsp 2

characteristic: ENA-LAST-UPDATE

text: public

text: E-MTAB-6067:nsp 2

characteristic: age

text: ArrayExpress

characteristic: broker name

text: CADO ES1

characteristic: cell line

text: Ewings sarcoma

characteristic: cell type

text: human

characteristic: common name

text: Ewing sarcoma

text: EWS-ERG

text: pleural fluid

characteristic: metastatic site

text: Homo sapiens

text: Homo sapiens

text: bone

text: Homo sapiens

text: female

text: nsp 2


E-MTAB-6067:nsp 3

characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: E-MTAB-6067:nsp 3

text: ArrayExpress

text: CADO ES1

text: Ewings sarcoma

text: human

characteristic: description

text: Ewing sarcoma

characteristic: disease

text: EWS-ERG

text: pleural fluid

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: bone

text: Homo sapiens

text: female

text: nsp 3

characteristic: title


E-MTAB-6067:nst 1

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-6067:nst 1

text: ArrayExpress

text: CADO ES1

text: Ewings sarcoma

text: human

text: Ewing sarcoma

text: EWS-ERG

characteristic: genotype

text: pleural fluid

text: Homo sapiens

text: Homo sapiens

text: bone

characteristic: organism part

text: Homo sapiens

text: female

text: nst 1


E-MTAB-6067:nst 2

characteristic: ENA-LAST-UPDATE

text: public

text: E-MTAB-6067:nst 2

characteristic: Submitter Id

characteristic: age

text: ArrayExpress

characteristic: broker name

text: CADO ES1

characteristic: cell line

text: Ewings sarcoma

characteristic: cell type

text: human

text: Ewing sarcoma

text: EWS-ERG

text: pleural fluid

text: Homo sapiens

text: Homo sapiens

text: bone

text: Homo sapiens

text: female

characteristic: sex

text: nst 2


E-MTAB-6067:nst 3

characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: E-MTAB-6067:nst 3

text: ArrayExpress

text: CADO ES1

text: Ewings sarcoma

text: human

characteristic: common name

characteristic: description

text: Ewing sarcoma

characteristic: disease

text: EWS-ERG

text: pleural fluid

characteristic: metastatic site

text: Homo sapiens

text: Homo sapiens

text: bone

text: Homo sapiens

text: female

text: nst 3


E-MTAB-6067:sp 1

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-6067:sp 1

text: ArrayExpress

text: CADO ES1

text: Ewings sarcoma

text: human

text: Ewing sarcoma

text: EWS-ERG

text: pleural fluid

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: bone

text: Homo sapiens

text: female

text: sp 1

characteristic: title


E-MTAB-6067:sp 2

characteristic: ENA-LAST-UPDATE

text: public

text: E-MTAB-6067:sp 2

characteristic: Submitter Id

characteristic: age

text: ArrayExpress

characteristic: broker name

text: CADO ES1

characteristic: cell line

text: Ewings sarcoma

text: human

text: Ewing sarcoma

text: EWS-ERG

characteristic: genotype

text: pleural fluid

text: Homo sapiens

text: Homo sapiens

text: bone

characteristic: organism part

text: Homo sapiens

text: female

text: sp 2


E-MTAB-6067:sp 3

characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: E-MTAB-6067:sp 3

text: ArrayExpress

text: CADO ES1

text: Ewings sarcoma

characteristic: cell type

text: human

characteristic: common name

characteristic: description

text: Ewing sarcoma

text: EWS-ERG

text: pleural fluid

text: Homo sapiens

text: Homo sapiens

text: bone

text: Homo sapiens

text: female

characteristic: sex

text: sp 3


Caenorhabditis sp. 1 JU166711

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: BANG

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: Caenorhabditis sp. 1 JU166711

text: Caenorhabditis sp. 1 KK-2011

text: Caenorhabditis sp. 1 KK-2011

characteristic: strain

text: whole organism

characteristic: tissue type

text: Caenorhabditis sp. 1 JU16671


characteristic: ENA-LAST-UPDATE

text: GSC

text: public

characteristic: Submitter Id

text: Xiphinema index

characteristic: organism

text: Xiphinema index


E-MTAB-6057:19pcw total retina

characteristic: External Id

text: UCL GOS Institute of Child Health

text: public

text: E-MTAB-6057:19pcw total retina

tag: Namespace:UCL GOS Institute of Child Health

unit: week

characteristic: age

text: ArrayExpress

characteristic: broker name

text: human

text: Protocols: Human foetal eyes were obtained from the Joint Medical Research Council UK (grant # G0700089)/Wellcome Trust (grant # GR082557) Human Developmental Biology Resource (http://www.hdbr.org/. Human foetal retinae were dissected under sterile conditions to remove all surrounding ocular tissue using stainless steel 8mm blade curved micro scissors and 0.1mm straight forceps (World Precision Instruments). Human foetal retinal explants and iPSC-derived retinal differentiation cultures were dissociated enzymatically into a single cell suspension using the papain dissociation system (Worthington Biochemical, Lorne Laboratories) following manufacturer’s protocol. For large foetal retinae (16-22pcw), samples were cut into smaller pieces (5mm x 5mm) before the addition of papain (approx. 100µl per piece). For retinal differentiation cultures, tissue was cut into smaller pieces using micro dissection scissors before adding 1ml of papain per well of 6 well culture plate. 70µm cell strainers were used to ensure cell single density of cell suspension. For GFP cell isolation, cells were resuspended in a final volume of 500µl blocking solution (1% (w/v) BSA in PBS), whereas cells for immunocytochemistry were resuspended in 1ml of blocking solution and counted using a haemocytometer before being diluted to 1x10⁶ cells per 100µl. A human induced pluripotent stem cell line (NCUS:7) was generated by Cambridge BRC hiPSC Core Facility from skin fibroblasts from an individual with normal ophthalmological examination. iPSCs were cultured on irradiated mouse embryonic fibroblast layer (GlobalStem) in knockout serum replacement medium (KSR; DMEM/F12 1:1, Knockout Serum Replacement (KOSR), MEM non-essential amino acids, glutamax, β-mercaptoethanol) with 4ng/ml fibroblastic growth factor (FGF; Peprotech). The retinal differentiation protocol for transcriptome profiling stem cell-derived cones was based on Meyer et al., 2009 (Protocol 1). iPSC colonies were enzymatically lifted using dispase (Life Technologies) on Day 0 and transfer into T25 flasks containing KSR medium without FGF to induce the formation of embryoid bodies (EBs). Medium was changed daily before substituting into neural induction medium (NIM) containing DMEM/F12 1:1 (Gibco), MEM non-essential amino acids (Gibo), N2 supplement (Gibo), heparin (Sigma) on Day 4. To promote neural rosette formation, EBs were transferred onto 30% laminin (Sigma) coated plates in NIM on Day 6, which appeared by differentiation day 8/9. Cultures were then fed every 2 days with NIM until Day 16, where the media was substituted for retinal differentiation media (RDM; DMEM (Gibo), F12 (Gibo) and B27 supplement (Gibo). Optic vesicle structures were visible from Day 18-20 onwards and media was changed every 2-3 days. 10% FBS (Gibo) was added to cultures at week 14 for late stage cultures. Intact human foetal retina were cultured free floating in 12 well plates with retinal differentiation media (RDM) containing DMEM-F12 (Gibo), Glutamax (Gibo), 1x N2 and 1x B27 neural supplements (Invitrogen), 10% FBS (Invitrogen) and 1.5x penicillin/streptomycin (Invitrogen). Cell culture media was changed every 2 days. AAV2/9.pR2.1:GFP production and application: 293T cells were cultured in D10 medium containing DMEM+Glutamax, 10% (v/w) FBS and 1x pencillin/streptomycin in 150cm plates and grown to 80% confluency. pd10/pR2.1.L/Mopsin-eGFP construct, pHGT1 helper vector, AAV2/9 caspid were transfected into 293T cells using polyethylenimine (PEI), before harvesting cells after 72 hours and performing four thaw-vortex-freeze cycles for viral release. pR2.1.L/M-opsin promoter was originally generated by the Jeremy Nathans group (Wang et al., 1992). Virus lysate underwent benzonase treatment and was prepared for purification through multiple centrifugation steps and sequential filtering with 5µm, 0.45µm and 0.22µm PES membranes. Virus was purified via ion exchange chromatography using AKTA Prime (GE Life Sciences) and concentrated using a Vivaspin 4 concentrator (Vivaproducts). Viral genomic titer was determined through qRT PCR and the virus titer used in this study ranged from 1.48x1013-1.01x1014. Virus was added to human foetal retinal explant and iPSC-derived retinal differentiation cultures at a MOI of 40,000-45,000 through addition to culture media. Human foetal and iPSC-derived retinal explants were cultured for 7 days to allow for pR2.1:GFP expression to be visualised. On day 7, human foetal retinal explants and iPSC-derived retinal differentiation cultures were dissociated enzymatically into a single cell suspension using the papain dissociation system (Worthington Biochemical, Lorne Laboratories) following manufacturer’s protocol. Total retina without pR2.1:GFP transfection were dissected and dissociated into single cell suspension using the same method. For large foetal retinae (16-22pcw), samples were cut into smaller pieces (5mm x 5mm) before the addition of papain (approx. 100µl per piece). For retinal differentiation cultures, tissue was cut into smaller pieces using micro dissection scissors before adding 1ml of papain per well of 6 well culture plate. 70µm cell strainers were used to ensure cell single density of cell suspension. For GFP cell isolation, cells were resuspended in a final volume of 500µl blocking solution (1% (w/v) BSA in PBS). Cell populations (GFP+ and GFP-) were collected into eppendorf tubes containing 500µl of 50% v/v FBS (DMEM). After sorting, cell populations were collected via centrifugation for 20 minutes at 200 x g; the supernatant was subsequently removed and RNA extraction was performed on cell pellets. mirVana miRNA Isolation Kit used for all extractions. Uses organic extraction followed by purification on a glass fiber filter under specialised binding and wash conditions collect all RNAs. RNA-seq samples were amplified using the SMART-Seq v4 Ultra Low Input RNA kit (Clontech Laboratories) and cDNA libraries were prepared using the Nextera XT DNA Library Preparation Kit (Illumina).

text: late embryo

characteristic: developmental stage

text: wild type genotype

characteristic: genotype

text: Homo sapiens

text: Homo sapiens

text: retina

characteristic: organism part

text: Homo sapiens

text: 19pcw total retina

characteristic: title