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characteristic: host scientific name

characteristic: host subject id

text: begomovirus

characteristic: isolate

text: leaf tissue

characteristic: isolation source host associated

text: Tomato leaf curl Karnataka virus

text: Tomato leaf curl Karnataka virus

text: tomato leaf curl disease complex


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: NIBGE

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: NIBGE

text: Riffat Shahid

text: Pakistan

text: Faisalabad

text: tomato

text: diseased

text: lycopersicon esculentum

text: begomovirus

text: leaf tissue

text: Tomato leaf curl Kerala virus

characteristic: organism

text: Tomato leaf curl Kerala virus

text: tomato leaf curl disease complex

characteristic: title


text: NIBGE

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: NIBGE

characteristic: collecting institution

characteristic: collection date

text: Riffat Shahid

characteristic: collector name

text: Pakistan

characteristic: geographic location (country and/or sea)

text: SWAT

text: tomato

text: diseased

text: lycopersicon esculentum

text: begomovirus

text: leaf tissue

text: Tomato leaf curl Palampur virus

text: Tomato leaf curl Palampur virus

text: tomato leaf curl disease complex


text: NIBGE

text: public

text: NIBGE

text: Riffat Shahid

text: Pakistan

text: SWAT

characteristic: geographic location (region and locality)

text: tomato

characteristic: host common name

text: diseased

characteristic: host health state

text: lycopersicon esculentum

characteristic: host scientific name

characteristic: host subject id

text: begomovirus

characteristic: isolate

text: leaf tissue

characteristic: isolation source host associated

text: Tomato leaf curl New Delhi virus

text: Tomato leaf curl New Delhi virus

text: tomato leaf curl disease complex


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: NIBGE

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: NIBGE

text: Riffat Shahid

text: Pakistan

text: Lahore

text: tomato

text: diseased

text: lycopersicon esculentum

text: begomovirus

text: leaf tissue

text: Tomato leaf curl New Delhi virus

text: Tomato leaf curl New Delhi virus

text: tomato leaf curl disease complex


PST infection Vuka: 0dpi-Rep2

text: The Genome Analysis Centre

text: public

characteristic: INSDC status

characteristic: SRA accession

text: PST infection Vuka: 0dpi-Rep2

tag: Namespace:The Genome Analysis Centre

characteristic: Submitter Id

text: Vuka

characteristic: cultivar

text: wheat

characteristic: host

text: Puccinia striiformis

characteristic: organism

text: Puccinia striiformis

characteristic: strain

text: PST infection Vuka: 0dpi-Rep2

characteristic: title


PST infection Vuka: 0dpi-Rep3

text: The Genome Analysis Centre

text: public

text: PST infection Vuka: 0dpi-Rep3

text: Vuka

text: wheat

text: Puccinia striiformis

text: Puccinia striiformis

text: PST infection Vuka: 0dpi-Rep3


PST infection Vuka: 1dpi-Rep1

text: The Genome Analysis Centre

text: public

text: PST infection Vuka: 1dpi-Rep1

text: Vuka

text: wheat

text: Puccinia striiformis

text: Puccinia striiformis

text: PST infection Vuka: 1dpi-Rep1


PST infection Vuka: 1dpi-Rep2

text: The Genome Analysis Centre

text: public

text: PST infection Vuka: 1dpi-Rep2

text: Vuka

text: wheat

text: Puccinia striiformis

text: Puccinia striiformis

text: PST infection Vuka: 1dpi-Rep2


PST infection Vuka: 1dpi-Rep3

text: The Genome Analysis Centre

text: public

text: PST infection Vuka: 1dpi-Rep3

text: Vuka

text: wheat

text: Puccinia striiformis

text: Puccinia striiformis

text: PST infection Vuka: 1dpi-Rep3


PST infection Vuka: 2dpi-Rep1

text: The Genome Analysis Centre

text: public

text: PST infection Vuka: 2dpi-Rep1

text: Vuka

text: wheat

text: Puccinia striiformis

text: Puccinia striiformis

text: PST infection Vuka: 2dpi-Rep1


PST infection Vuka: 2dpi-Rep2

text: The Genome Analysis Centre

text: public

text: PST infection Vuka: 2dpi-Rep2

text: Vuka

text: wheat

text: Puccinia striiformis

text: Puccinia striiformis

text: PST infection Vuka: 2dpi-Rep2


PST infection Vuka: 2dpi-Rep3

text: The Genome Analysis Centre

text: public

text: PST infection Vuka: 2dpi-Rep3

text: Vuka

text: Wheat

text: Puccinia striiformis

text: Puccinia striiformis

text: PST infection Vuka: 2dpi-Rep3


PST infection Vuka: 3dpi-Rep1

text: The Genome Analysis Centre

text: public

text: PST infection Vuka: 3dpi-Rep1

text: Vuka

text: Wheat

text: Puccinia striiformis

text: Puccinia striiformis

text: PST infection Vuka: 3dpi-Rep1


PST infection Vuka: 3dpi-Rep2

text: The Genome Analysis Centre

text: public

text: PST infection Vuka: 3dpi-Rep2

text: Vuka

text: Wheat

text: Puccinia striiformis

text: Puccinia striiformis

text: PST infection Vuka: 3dpi-Rep2


PST infection Vuka: 3dpi-Rep3

text: The Genome Analysis Centre

text: public

text: PST infection Vuka: 3dpi-Rep3

text: Vuka

text: Wheat

text: Puccinia striiformis

text: Puccinia striiformis

text: PST infection Vuka: 3dpi-Rep3


PST infection Vuka: 5dpi-Rep1

text: The Genome Analysis Centre

text: public

text: PST infection Vuka: 5dpi-Rep1

text: Vuka

text: Wheat

text: Puccinia striiformis

text: Puccinia striiformis

text: PST infection Vuka: 5dpi-Rep1


PST infection Vuka: 5dpi-Rep2

text: The Genome Analysis Centre

text: public

text: PST infection Vuka: 5dpi-Rep2

text: Vuka

text: Wheat

text: Puccinia striiformis

text: Puccinia striiformis

text: PST infection Vuka: 5dpi-Rep2


PST infection Vuka: 5dpi-Rep3

text: The Genome Analysis Centre

text: public

text: PST infection Vuka: 5dpi-Rep3

text: Vuka

text: Wheat

text: Puccinia striiformis

text: Puccinia striiformis

text: PST infection Vuka: 5dpi-Rep3


PST infection Vuka: 7dpi-Rep1

text: The Genome Analysis Centre

text: public

text: PST infection Vuka: 7dpi-Rep1

text: Vuka

text: Wheat

text: Puccinia striiformis

text: Puccinia striiformis

text: PST infection Vuka: 7dpi-Rep1


PST infection Vuka: 7dpi-Rep2

text: The Genome Analysis Centre

text: public

text: PST infection Vuka: 7dpi-Rep2

text: Vuka

text: Wheat

text: Puccinia striiformis

text: Puccinia striiformis

text: PST infection Vuka: 7dpi-Rep2


PST infection Vuka: 7dpi-Rep3

text: The Genome Analysis Centre

text: public

text: PST infection Vuka: 7dpi-Rep3

text: Vuka

text: Wheat

text: Puccinia striiformis

text: Puccinia striiformis

text: PST infection Vuka: 7dpi-Rep3


PST infection Vuka: 9dpi-Rep1

text: The Genome Analysis Centre

text: public

text: PST infection Vuka: 9dpi-Rep1

text: Vuka

text: Wheat

text: Puccinia striiformis

text: Puccinia striiformis

text: PST infection Vuka: 9dpi-Rep1


PST infection Vuka: 9dpi-Rep2

text: The Genome Analysis Centre

text: public

text: PST infection Vuka: 9dpi-Rep2

text: Vuka

text: Wheat

text: Puccinia striiformis

text: Puccinia striiformis

text: PST infection Vuka: 9dpi-Rep2


PST infection Vuka: 9dpi-Rep3

text: The Genome Analysis Centre

text: public

text: PST infection Vuka: 9dpi-Rep3

text: Vuka

text: Wheat

text: Puccinia striiformis

text: Puccinia striiformis

text: PST infection Vuka: 9dpi-Rep3


PST infection Vuka: 11dpi-Rep1

text: The Genome Analysis Centre

text: public

text: PST infection Vuka: 11dpi-Rep1

text: Vuka

text: Wheat

text: Puccinia striiformis

text: Puccinia striiformis

text: PST infection Vuka: 11dpi-Rep1


PST infection Vuka: 11dpi-Rep2

text: The Genome Analysis Centre

text: public

text: PST infection Vuka: 11dpi-Rep2

text: Vuka

text: Wheat

text: Puccinia striiformis

text: Puccinia striiformis

text: PST infection Vuka: 11dpi-Rep2


PST infection Vuka: 11dpi-Rep3

text: The Genome Analysis Centre

text: public

text: PST infection Vuka: 11dpi-Rep3

text: Vuka

text: Wheat

text: Puccinia striiformis

text: Puccinia striiformis

text: PST infection Vuka: 11dpi-Rep3


name: PST infection Vuka: PST - germinating spores Rep1

text: The Genome Analysis Centre

text: public

text: Puccinia striiformis

text: Puccinia striiformis


name: PST infection Vuka: PST - germinating spores Rep2

text: The Genome Analysis Centre

text: public

text: Puccinia striiformis

text: Puccinia striiformis


name: PST infection Vuka: PST - germinating spores Rep3

text: The Genome Analysis Centre

text: public

text: Puccinia striiformis

text: Puccinia striiformis


PST infection Yr5 wheat:  0dpi-Rep1

text: The Genome Analysis Centre

text: public

text: PST infection Yr5 wheat: 0dpi-Rep1

text: Avocet Yr5

text: Wheat

text: Puccinia striiformis

text: Puccinia striiformis

text: PST infection Yr5 wheat: 0dpi-Rep1


PST infection Yr5 wheat:  0dpi-Rep2

text: The Genome Analysis Centre

text: public

text: PST infection Yr5 wheat: 0dpi-Rep2

text: Avocet Yr5

text: Wheat

text: Puccinia striiformis

text: Puccinia striiformis

text: PST infection Yr5 wheat: 0dpi-Rep2


PST infection Yr5 wheat:  0dpi-Rep3

text: The Genome Analysis Centre

text: public

text: PST infection Yr5 wheat: 0dpi-Rep3

text: Avocet Yr5

text: Wheat

text: Puccinia striiformis

text: Puccinia striiformis

text: PST infection Yr5 wheat: 0dpi-Rep3


PST infection Yr5 wheat:  1dpi-Rep1

text: The Genome Analysis Centre

text: public

text: PST infection Yr5 wheat: 1dpi-Rep1

text: Avocet Yr5

text: Wheat

text: Puccinia striiformis

text: Puccinia striiformis

text: PST infection Yr5 wheat: 1dpi-Rep1


PST infection Yr5 wheat:  1dpi-Rep2

text: The Genome Analysis Centre

text: public

text: PST infection Yr5 wheat: 1dpi-Rep2

text: Avocet Yr5

text: Wheat

text: Puccinia striiformis

text: Puccinia striiformis

text: PST infection Yr5 wheat: 1dpi-Rep2


PST infection Yr5 wheat:  1dpi-Rep3

text: The Genome Analysis Centre

text: public

text: PST infection Yr5 wheat: 1dpi-Rep3

text: Avocet Yr5

text: Wheat

text: Puccinia striiformis

text: Puccinia striiformis

text: PST infection Yr5 wheat: 1dpi-Rep3


PST infection Yr5 wheat:  2dpi-Rep1

text: The Genome Analysis Centre

text: public

text: PST infection Yr5 wheat: 2dpi-Rep1

text: Avocet Yr5

text: Wheat

text: Puccinia striiformis

text: Puccinia striiformis

text: PST infection Yr5 wheat: 2dpi-Rep1


PST infection Yr5 wheat:  2dpi-Rep2

text: The Genome Analysis Centre

text: public

text: PST infection Yr5 wheat: 2dpi-Rep2

text: Avocet Yr5

text: Wheat

text: Puccinia striiformis

text: Puccinia striiformis

text: PST infection Yr5 wheat: 2dpi-Rep2


PST infection Yr5 wheat:  2dpi-Rep3

text: The Genome Analysis Centre

text: public

text: PST infection Yr5 wheat: 2dpi-Rep3

text: Avocet Yr5

text: Wheat

text: Puccinia striiformis

text: Puccinia striiformis

text: PST infection Yr5 wheat: 2dpi-Rep3


PST infection Yr5 wheat:  3dpi-Rep1

text: The Genome Analysis Centre

text: public

text: PST infection Yr5 wheat: 3dpi-Rep1

text: Avocet Yr5

text: Wheat

text: Puccinia striiformis

text: Puccinia striiformis

text: PST infection Yr5 wheat: 3dpi-Rep1


PST infection Yr5 wheat:  3dpi-Rep2

text: The Genome Analysis Centre

text: public

text: PST infection Yr5 wheat: 3dpi-Rep2

text: Avocet Yr5

text: Wheat

text: Puccinia striiformis

text: Puccinia striiformis

text: PST infection Yr5 wheat: 3dpi-Rep2


PST infection Yr5 wheat:  3dpi-Rep3

text: The Genome Analysis Centre

text: public

text: PST infection Yr5 wheat: 3dpi-Rep3

text: Avocet Yr5

text: Wheat

text: Puccinia striiformis

text: Puccinia striiformis

text: PST infection Yr5 wheat: 3dpi-Rep3


PST infection Yr5 wheat:  5dpi-Rep1

text: The Genome Analysis Centre

text: public

text: PST infection Yr5 wheat: 5dpi-Rep1

text: Avocet Yr5

text: Wheat

text: Puccinia striiformis

text: Puccinia striiformis

text: PST infection Yr5 wheat: 5dpi-Rep1


PST infection Yr5 wheat:  5dpi-Rep2

text: The Genome Analysis Centre

text: public

text: PST infection Yr5 wheat: 5dpi-Rep2

text: Avocet Yr5

text: Wheat

text: Puccinia striiformis

text: Puccinia striiformis

text: PST infection Yr5 wheat: 5dpi-Rep2


PST infection Yr5 wheat:  5dpi-Rep3

text: The Genome Analysis Centre

text: public

text: PST infection Yr5 wheat: 5dpi-Rep3

text: Avocet Yr5

text: Wheat

text: Puccinia striiformis

text: Puccinia striiformis

text: PST infection Yr5 wheat: 5dpi-Rep3


text: NYU LANGONE MEDICAL CENTER

text: public

tag: Namespace:NYU LANGONE MEDICAL CENTER

characteristic: body site

text: F

characteristic: gender

text: Y

characteristic: lens wearer

text: metagenome

text: proparacaine anesthetic

characteristic: pre-sampling step

characteristic: sampling point

text: metagenome

characteristic: subject no

text: Altered eye microbiota by wearing contact lenses


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: NYU LANGONE MEDICAL CENTER

characteristic: INSDC center name

text: public

text: M

text: Y

text: metagenome

text: proparacaine anesthetic

text: metagenome


text: NYU LANGONE MEDICAL CENTER

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: F

text: N

text: metagenome

text: proparacaine anesthetic

text: metagenome


text: NYU LANGONE MEDICAL CENTER

text: public

text: M

text: N

text: metagenome

characteristic: organism

text: proparacaine anesthetic

text: metagenome

characteristic: title


text: NYU LANGONE MEDICAL CENTER

text: public

characteristic: body site

text: F

characteristic: gender

text: Y

text: metagenome

text: metagenome


text: NYU LANGONE MEDICAL CENTER

text: public

text: M

text: Y

characteristic: lens wearer

text: metagenome

text: metagenome


text: NYU LANGONE MEDICAL CENTER

text: public

text: Contact Lens_L

text: F

text: Y

text: metagenome

characteristic: sampling point

text: metagenome


text: NYU LANGONE MEDICAL CENTER

text: public

text: Contact Lens_R

text: F

text: Y

text: metagenome

text: metagenome

characteristic: subject no


characteristic: ENA-CHECKLIST

text: NYU LANGONE MEDICAL CENTER

text: public

text: Contact Lens_R

text: M

text: Y

text: metagenome

text: metagenome


characteristic: ENA-FIRST-PUBLIC

text: NYU LANGONE MEDICAL CENTER

text: public

text: Contact Lens_L

text: M

text: Y

text: metagenome

text: metagenome


characteristic: ENA-LAST-UPDATE

text: NYU LANGONE MEDICAL CENTER

text: public

text: Skin under Eye_L

text: F

text: Y

text: metagenome

text: metagenome


characteristic: External Id

text: NYU LANGONE MEDICAL CENTER

text: public

text: Skin under Eye_R

text: F

text: Y

text: metagenome

text: metagenome


text: NYU LANGONE MEDICAL CENTER

characteristic: INSDC center name

text: public

text: Skin under Eye_R

text: M

text: Y

text: metagenome

text: metagenome


text: NYU LANGONE MEDICAL CENTER

characteristic: INSDC first public

text: public

text: Skin under Eye_L

text: M

text: Y

text: metagenome

text: metagenome


text: NYU LANGONE MEDICAL CENTER

characteristic: INSDC last update

text: public

text: F

text: N

text: metagenome

text: metagenome


text: NYU LANGONE MEDICAL CENTER

text: public

characteristic: INSDC status

text: M

text: N

text: metagenome

text: metagenome


text: NYU LANGONE MEDICAL CENTER

text: public

characteristic: SRA accession

text: Skin under Eye_R

text: M

text: N

text: metagenome

text: metagenome


text: NYU LANGONE MEDICAL CENTER

text: public

characteristic: Submitter Id

text: Skin under Eye_L

text: M

text: N

text: metagenome

text: metagenome


text: NYU LANGONE MEDICAL CENTER

text: public

text: Skin under Eye_R

text: F

text: N

text: metagenome

characteristic: organism

text: metagenome


text: NYU LANGONE MEDICAL CENTER

text: public

text: Skin under Eye_L

text: F

text: N

text: metagenome

text: metagenome

characteristic: title


text: UNIVERSITY OF MELBOURNE

text: public

tag: Namespace:UNIVERSITY OF MELBOURNE

characteristic: collection date

text: New Zealand

characteristic: geographic location (country and/or sea)

text: Human

characteristic: host

text: Diseased

characteristic: host health state

text: Skin

characteristic: isolation source

text: Staphylococcus aureus

text: Staphylococcus aureus

characteristic: strain


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: ESTONIAN BIOCENTRE, ESTONIA

text: public

tag: Namespace:ESTONIAN BIOCENTRE, ESTONIA

text: human

characteristic: common name

text: Homo sapiens

text: Homo sapiens

text: human complete genome


text: Group B Streptococcus

characteristic: ArrayExpress-Species

characteristic: ArrayExpress-StrainOrLine

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: SC

characteristic: INSDC center name

text: public

text: Group B Streptococcus

text: Streptococcus sp. 'group B'

text: Streptococcus sp. 'group B'


text: Yeast

characteristic: ArrayExpress-Phenotype

text: Saccharomyces cerevisiae

text: SC

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: baker's yeast

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae


text: UNIVERSITY OF ZUERICH

text: public

tag: Namespace:UNIVERSITY OF ZUERICH

text: Monocyte derived dendritic cell

characteristic: cell type

text: house mouse

text: WT CD45.1 MoDCs isolated from the inflamed CNS at EAE peak disease, Experiment 1

characteristic: description

text: Mus musculus

characteristic: organism

text: Mus musculus

text: Inflamed CNS (EAE)

characteristic: tissue type

text: Monocyte derived DCs derived from inflamed CNS

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: UNIVERSITY OF ZUERICH

text: public

text: Monocyte derived dendritic cell

text: house mouse

characteristic: common name

text: WT CD45.1 MoDCs isolated from the inflamed CNS at EAE peak disease, Experiment 2

text: Mus musculus

text: Mus musculus

characteristic: strain

text: Inflamed CNS (EAE)


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: UNIVERSITY OF ZUERICH

text: public

text: Monocyte derived dendritic cell

text: house mouse

text: WT CD45.1 MoDCs isolated from the inflamed CNS at EAE peak disease, Experiment 3

text: Mus musculus

text: Mus musculus

text: Inflamed CNS (EAE)


text: UNIVERSITY OF ZUERICH

characteristic: INSDC center name

text: public

text: Monocyte derived dendritic cell

text: house mouse

text: WT CD45.1 MoDCs isolated from the inflamed CNS at EAE peak disease, Experiment 4

text: Mus musculus

text: Mus musculus

text: Inflamed CNS (EAE)


text: UNIVERSITY OF ZUERICH

characteristic: INSDC first public

text: public

text: Monocyte derived dendritic cell

text: house mouse

text: GMRKO CD45.2 MoDCs isolated from the inflamed CNS at EAE peak disease, Experiment 1

text: Mus musculus

text: Mus musculus

text: Inflamed CNS (EAE)


text: UNIVERSITY OF ZUERICH

characteristic: INSDC last update

text: public

text: Monocyte derived dendritic cell

text: house mouse

text: GMRKO CD45.2 MoDCs isolated from the inflamed CNS at EAE peak disease, Experiment 2

text: Mus musculus

text: Mus musculus

text: Inflamed CNS (EAE)


text: UNIVERSITY OF ZUERICH

text: public

characteristic: INSDC status

text: Monocyte derived dendritic cell

text: house mouse

text: GMRKO CD45.2 MoDCs isolated from the inflamed CNS at EAE peak disease, Experiment 3

text: Mus musculus

text: Mus musculus

text: Inflamed CNS (EAE)


text: UNIVERSITY OF ZUERICH

text: public

characteristic: SRA accession

text: Monocyte derived dendritic cell

text: house mouse

text: GMRKO CD45.2 MoDCs isolated from the inflamed CNS at EAE peak disease, Experiment 4

text: Mus musculus

text: Mus musculus

text: Inflamed CNS (EAE)


text: WEIZMANN INSTITUE OF SCIENCE

text: public

tag: Namespace:WEIZMANN INSTITUE OF SCIENCE

characteristic: Submitter Id

text: Citrobacter rodentium

text: Citrobacter rodentium


text: DUKE-NUS

text: public

characteristic: anonymized name

text: human

text: Patient's whole blood

text: Homo sapiens

text: Homo sapiens


text: DUKE-NUS

text: public

text: human

text: Type II enteropathy associated T-cell lymphoma tumor

characteristic: description

text: Homo sapiens

text: Homo sapiens


text: NEW ENGLAND BIOLABS

text: public

tag: Namespace:NEW ENGLAND BIOLABS

text: E.coli total RNA subject to the cappable-seq protocol as describe in the publication

text: Escherichia coli K-12

characteristic: organism

text: Escherichia coli K-12

text: Cappable-seq treated RNA


text: NEW ENGLAND BIOLABS

text: public

text: E.coli total RNA subject to the cappable-seq protocol (control) as describe in the publication

text: Escherichia coli K-12

text: Escherichia coli K-12

text: Cappable-seq treated RNA without selection on Streptavidin beads


Mimivirus amazonia

text: URMITE

text: public

text: Mimivirus amazonia

text: Mimivirus amazonia

text: Mimivirus amazonia

text: PUMIVIRE


Afrovirus Urmite69

text: URMITE

text: public

text: Afrovirus Urmite69

text: Afrovirus Urmite69

text: Afrovirus Urmite69

text: PUMIVIRE


Megavirus avenue9

text: URMITE

text: public

text: Megavirus avenue9

text: Megavirus avenue9

text: Megavirus avenue9

text: PUMIVIRE


text: STATENS SERUM INSTITUT

text: public

tag: Namespace:STATENS SERUM INSTITUT

text: blood

characteristic: bio material

text: Denmark

characteristic: geographic location (country and/or sea)

text: homo sapiens

characteristic: host

text: Human immunodeficiency virus 1

text: Human immunodeficiency virus 1

text: HIV-1 integrase


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: CAM

text: public

text: metagenome

text: metagenome

text: SEAR-WWTP

characteristic: title


characteristic: ENA-LAST-UPDATE

text: public

tag: Namespace:Department of Biomedical Sciences, Seoul National University Graduate School

text: human

characteristic: common name

text: Homo sapiens

text: Homo sapiens

text: Gastric tumor and paired normal tissue


characteristic: External Id

text: Department of Biomedical Sciences, Seoul National University Graduate School

characteristic: INSDC center name

text: public

text: human

text: Homo sapiens

text: Homo sapiens

text: Gastric tumor and paired normal tissue


Sloth bear

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: Sloth bear

tag: Namespace:BIODIVERSITY AND CLIMATE RESEARCH CENTER, FRANKFUR

text: sloth bear

text: Melursus ursinus

text: Melursus ursinus

text: Sloth bear


Asiatic black bear

text: BIODIVERSITY AND CLIMATE RESEARCH CENTER, FRANKFUR

text: public

characteristic: INSDC status

characteristic: SRA accession

text: Asiatic black bear

text: Asiatic black bear

text: Ursus thibetanus

text: Ursus thibetanus

text: Asiatic black bear


Spectacled bear - Nobody

text: public

text: Spectacled bear - Nobody

characteristic: Submitter Id

text: spectacled bear

text: Tremarctos ornatus

text: Tremarctos ornatus

text: Spectacled bear - Nobody


E-MTAB-3699:pBAD24 Rep1

text: public

text: E-MTAB-3699:pBAD24 Rep1

tag: Namespace:Wadsworth Center, NY Department of Health

text: ArrayExpress

characteristic: broker name

text: Protocols: Overnight cultures were started from single colonies in 2 mL M9+0.4% glycerol at 30 degrees Celsius shaking at 225 rpm and grown for ~36 hours. 40 ml subcultures were grown in M9+0.4% glycerol at 30 degrees Celsius to an OD600 of approximately 0.5. Arabinose was added to the culture at a final concentration of 0.2% and incubated for 10 minutes at 30 degrees Celsius and shaking at 225 rpm. Hot phenol RNA prep: transfer 1mL of subculture to two microcentrifuge tubes. Spin each 1mL at max speed for 1 min and remove supernatant. Resuspend each in 0.4mL ethanol+5% acid phenol/chloroform, spin 1 min at max speed and remove supernatant. Resuspend each in 1mL 1x TBS, spin 1 min at max speed and remove supernatant. Resuspend each in 0.25mL RNA Lysis Buffer (2% SDS, 4mM EDTA), combine and boil samples for 3 min. Add 0.5mL acid phenol/chloroform to each tube and incubate for 6 min at 65 °C. Incubate 5 min on ice then spin tubes at max speed for 6 min. Transfer upper phase to phase lock tube, add equal volume (0.4mL) chloroform:isoamyl alcohol 24:1 and spin 6 min at max speed. Transfer upper phase to new phase lock tube, add equal volume (0.4mL) chloroform:isoamyl alcohol 24:1 and spin 6 min at max speed. Transfer upper phase to new tube containing 40uL 3M Na Acetate+2uL glycogen (20mg/mL stock). Add 1mL ice cold EtOH and precipitate at -20 °C overnight. Spin samples for 30 min at 4 °C at max speed. Pipet off supernatant. Wash with 0.7mL of 70% EtOH (in DEPC H2O), spin 5 min at max speed at 4 °C and remove supernatant. Wash again with 0.7mL of 70% EtOH (in DEPC H2O), spin for 5 min at max speed at 4 °C and pipet off supernatant. Dry pellet at room temperature and resuspend in 15uL nuclease free water. DNase treat RNA - set up 50uL reaction including 8-10ug RNA, 5uL of 10X buffer and 1uL DNase enzyme (Ambion). Incubate 30 min at 37 °C. Stop reaction by adding 352uL DEPC H2O + 134uL acid phenol:chloroform + 268uL chloroform:isoamyl alcohol 24:1. Transfer all to phase lock tube and spin at max speed for 6 min. Transfer upper phase to new microcentrifuge tube containing 40uL 3M Na Acetate + 2uL glycogen (20mg/mL stock). Add 1mL ice cold EtOH and precipitate at -20 °C overnight. Spin samples for 30 min at 4 °C at max speed. Pipet off supernatant. Wash with 0.7mL of 70% EtOH (in DEPC H2O), spin 5 min at max speed at 4 °C and remove supernatant. Wash again with 0.7mL of 70% EtOH (in DEPC H2O), spin for 5 min at max speed at 4 °C and pipet off supernatant. Dry pellet at room temperature and resuspend in 15uL nuclease free water. Remove ribosomal RNA using the RiboZero kit from EpiCentre - wash magnetic beads 2x in RNase free water, then resuspend in Resuspension Solution. Add 32.5uL beads to each tube then add 0.5uL RNase inhibitor. Mix together in final volume of 20uL: 2.5ug DNase treated RNA + 2uL Ribozero reaction buffer + 4uL Ribozero rRNA removal solution. Incubate at 68 °C for 10 min followed by RT for 5 min. Add RNA to beads, mix by pipetting and vortexing for 10 s. Incubate at RT for 5 min. Vortex for 5 s then incubate at 50 °C for 5 min. Place tubes on magnetic stand for 1 min and transfer RNA to new tube. Bring volume to 180uL with DEPC H2O, then add 18uL 3M Na Acetate + 2uL glycogen (20mg/mL stock). Add 0.6mL ice cold EtOH and precipitate at -20 °C overnight. Spin samples for 30 min at 4 °C at max speed. Pipet off supernatant. Wash with 0.7mL of 70% EtOH (in DEPC H2O), spin 5 min at max speed at 4 °C and remove supernatant. Wash again with 0.7mL of 70% EtOH (in DEPC H2O), spin for 5 min at max speed at 4 °C and pipet off supernatant. Dry pellet at room temperature and resuspend in 8uL nuclease free water. Prepare libraries using EpiCentre ScriptSeq v2 kit following kit protocol. Fragment RNA and anneal cDNA synthesis primer in 12uL reaction containing nuclease free water + 40ng rRNA depleted RNA + 1uL RNA Fragmentation solution + 2uL cDNA Synthesis primer. Incubate at 85 °C for 5 min then place tubes on ice. Synthesize DNA by adding 3uL cDNA Synthesis Premix + 0.5uL 100mM DTT + 0.5uL StarScript Reverse Transcriptase. Incubate at 25 °C for 5 min then 42 °C for 20 min. Cool tubes to 37 °C. Add 1uL Finishing solution and incubate at 37 °C for 10 min then 95 °C for 3 min. Cool tubes to 25 °C then add 7.5uL Terminal Tagging Premix + 0.5uL DNA Polymerase to terminally tag the cDNA. Incubate at 25 °C for 15 min, 95 °C for 3 min, then cool to 4 °C. Purify the cDNA using the Qiagen MinElute PCR Purification Kit - Add 5V Buffer PB to sample and transfer all to MinElute column. Spin 1 min at max speed. Discard flow through. Add 0.75mL Buffer PE to column and spin 1 min at max speed. Discard flow through. Spin column for 1 min at max speed then transfer column to new tube. Add 23.4uL Buffer EB to column, incubate 1 min at room temp, then spin 1 min at max speed. Amplify library by setting up 50uL PCR using 22.5uL purified DNA. Add 25uL FailSafe PCR Premix E + 1uL Forward PCR primer + 1uL ScriptSeq Index PCR Primer + 0.5uL FailSafe PCR Enzyme (1.25U). Heat at 95 °C for 1 min, then 12 cycles of 95 °C for 30 sec, 55 °C for 30 sec and 68 °C for 3 min. Incubate at 68 °C for 7 minutes. Purify sample using AMPure XP Purification protocol. Add 50uL beads to each PCR sample. Mix by pipetting 10x. Transfer beads+sample to new tube and incubate at room temp for 15 min. Put tubes on magnetic stand for 5 min then remove supernatant. Wash beads 2x, each time with 0.2mL of 80% EtOH, let stand 1 min then remove supernatant. Air dry beads at room temp for 15 min. Add 12uL nuclease free water, remove tubes from magnetic stand and resuspend beads in water. Incubate at room temp for 2 min. Place tubes on magnetic stand for 5 min. Library is in supernatant. Transfer to new tube. Quantify using Qubit.

characteristic: description

text: deletion

characteristic: genetic modification

characteristic: genotype

text: Escherichia coli

text: Escherichia coli

text: Escherichia coli

text: K-12 substr. MG1655 delta rpoN

characteristic: strain

text: pBAD24 Rep1


E-MTAB-3699:pBAD24 Rep2

characteristic: ENA-CHECKLIST

text: Wadsworth Center, NY Department of Health

text: public

text: E-MTAB-3699:pBAD24 Rep2

text: ArrayExpress

text: deletion

text: Escherichia coli

characteristic: organism

text: Escherichia coli

text: Escherichia coli

text: K-12 substr. MG1655 delta rpoN

text: pBAD24 Rep2


E-MTAB-3699:pRpoN Rep1

characteristic: ENA-FIRST-PUBLIC

text: public

text: E-MTAB-3699:pRpoN Rep1

text: ArrayExpress

text: deletion

text: pRpoN

text: Escherichia coli

text: Escherichia coli

text: Escherichia coli

text: K-12 substr. MG1655 delta rpoN

text: pRpoN Rep1

characteristic: title


E-MTAB-3699:pRpoN Rep2

characteristic: ENA-LAST-UPDATE

text: public

text: E-MTAB-3699:pRpoN Rep2

text: ArrayExpress

text: deletion

text: pRpoN

text: Escherichia coli

text: Escherichia coli

text: Escherichia coli

text: K-12 substr. MG1655 delta rpoN

text: pRpoN Rep2


E-MTAB-3697:MG1655 Beta ChIP-seq Rep2

characteristic: External Id

text: public

text: E-MTAB-3697:MG1655 Beta ChIP-seq Rep2

text: ArrayExpress

text: Protocols: Overnight cultures were started from single colonies in 2 mL M9+0.4% glycerol at 30 degrees Celsius shaking at 225 rpm and grown for ~36 hours. 40 ml subcultures were grown in M9+0.4% glycerol at 30 degrees Celsius to an OD600 of approximately 0.5 Cells were crosslinked for 20 minutes with formaldehyde (1% final concentration), pelleted by centrifugation and washed once with Tris-buffered saline (TBS). Cell pellets were resuspended in 1 ml FA lysis buffer (50 mM Hepes-KOH, pH 7, 150 mM NaCl, 1 mM EDTA, 1% Triton X-100, 0.1% sodium deoxycholate, 0.1% SDS) with 4 mg/ml lysozyme and incubated at 37 degrees Celsius for 30 minutes. Samples were then chilled and sonicated for 30 minutes in a Bioruptor sonicator (Diagenode) with 30 s on/30 s off pulsing at maximum amplitude. Samples were pelleted in a microcentrifuge to remove debris and supernatants (chromatin) were saved, 2.5 ml FA lysis buffer was added, and samples were stored indefinitely at -20 degrees Celsius. For the immunoprecipitation (IP), 800 ul chromatin was incubated with 25 ul Protein A Sepharose slurry (50%) in TBS and 1 ul anti-RNA polymerase beta subunit antibody (BioLegend) for 90 minutes at room temperature with gentle mixing on a rotisserie rotator. Following the 90 min incubation, beads were washed twice with FA lysis buffer and twice with 10 mM Tris-HCl, pH 7.5 (please note: all wash steps involved incubation of samples with the wash solution for 3 min with gentle mixing on a rotisserie rotator before pelleting beads at 1,500 x g in a microcentrifuge for 1 min). Beads were resuspended in 100 uL 1X Quick Blunting Buffer (NEB) containing dNTPs (concentration specified by NEB Quick Blunting kit) and 1 uL Quick Blunting enzyme mix (NEB), and incubated at room temperature for 30 min with gentle mixing. Beads were washed twice with FA lysis buffer and twice with 10 mM Tris-HCl, pH 8.0. Beads were resuspended in 100 uL Buffer 2 (NEB) containing 2 mM dATP and 2 uL Klenow DNA polymerase (NEB), and incubated for 30 min at 37 degrees Celsius with gentle mixing. Beads were washed twice with FA lysis buffer and twice with 10 mM Tris-HCl, pH 7.5. Beads were resuspended in 1X DNA Quick Ligase buffer (NEB), 1 uL NEXTflex ChIP-seq Barcoded adapter (BioO) and 2 uL Quick DNA Ligase (NEB), and incubated at room temperature for 15 min with gentle mixing. Beads were washed twice with FA lysis buffer, and once each with high salt FA lysis buffer (50 mM Hepes-KOH, pH 7, 500 mM NaCl, 1 mM EDTA, 1% Triton X-100, 0.1% sodium deoxycholate, 0.1% SDS), ChIP wash buffer (10 mM Tris-HCl, pH 8.0, 250 mM LiCl, 1 mM EDTA, 0.5% Nonidet-P40, 0.5% sodium deoxycholate) and TE (10 mM Tris-HCl, pH 7.5, 1 mM EDTA). After the TE wash, beads were transferred to a fresh Spin-X column and eluted with 100 ul ChIP elution buffer (50 mM Tris-HCl, pH 7.5, 10 mM EDTA, 1% SDS) for 10 minutes at 65 degrees Celsius with occasional agitation. Samples were decrosslinked by boiling for 10 minutes. DNA was extracted with phenol/chlorofom/isoamyl alcohol, ethanol precipitated, and resuspended in 11 uL H2O. 1 uL DNA was diluted 1:8 and 2 ul were used for real time PCR amplification (three technical replicates)with NEXTflex ChIP-seq Primer Mix (JW3764-AATGATACGGCGACCACCGAGATCTACAC and JW3765-CAAGCAGAAGACGGCATACGAGAT) using an ABI 7500 Fast real time PCR machine. The number of cycles required to reach a Delta Rn score of 0.1 was recorded (OXO). 8 uL of the remaining DNA was amplified using conventional PCR with oligonucleotides JW3764 and JW3765 ( 100 uM) for X+3 cycles with an annealing temperature of 60 degrees Celsius. PCR products were purified using Ampure XP magnetic beads (Ampure) and resuspended in 20 uL H2O. Purified PCR products between 200 bp and 600 bp were gel purified from an 8% non-denaturing polyacrylamide gel, eluted overnight in DNA extraction buffer (0.3 M NaCl, 10 mM Tris-HCl pH 8.0, 1 mM EDTA) and ethanol precipitated to generate the final ChIP-seq library. The library was resuspended in 11 uL H2O and quantified using a Qubit fluorimeter (Invitrogen). The library was sequenced using a HiSeq 2000 sequencer (Illumina; University at Buffalo Next Generation Sequencing Core Facility).

text: Escherichia coli

text: Escherichia coli

text: Escherichia coli

text: K-12 substr. MG1655

text: MG1655 Beta ChIP-seq Rep2


E-MTAB-3697:MG1655 Beta ChIP-seq Rep1

characteristic: INSDC center name

text: public

text: E-MTAB-3697:MG1655 Beta ChIP-seq Rep1

text: ArrayExpress

text: Escherichia coli

text: Escherichia coli

text: Escherichia coli

text: K-12 substr. MG1655

text: MG1655 Beta ChIP-seq Rep1


name: E-MTAB-3697:MG1655 Sigma54 ChIP-seq Rep1

characteristic: INSDC first public

text: public

text: ArrayExpress

text: Protocols: Overnight cultures were started from single colonies in 2 mL M9+0.4% glycerol at 30 degrees Celsius shaking at 225 rpm and grown for ~36 hours. 40 ml subcultures were grown in M9+0.4% glycerol at 30 degrees Celsius to an OD600 of approximately 0.5 Cells were crosslinked for 20 minutes with formaldehyde (1% final concentration), pelleted by centrifugation and washed once with Tris-buffered saline (TBS). Cell pellets were resuspended in 1 ml FA lysis buffer (50 mM Hepes-KOH, pH 7, 150 mM NaCl, 1 mM EDTA, 1% Triton X-100, 0.1% sodium deoxycholate, 0.1% SDS) with 4 mg/ml lysozyme and incubated at 37 degrees Celsius for 30 minutes. Samples were then chilled and sonicated for 30 minutes in a Bioruptor sonicator (Diagenode) with 30 s on/30 s off pulsing at maximum amplitude. Samples were pelleted in a microcentrifuge to remove debris and supernatants (chromatin) were saved, 2.5 ml FA lysis buffer was added, and samples were stored indefinitely at -20 degrees Celsius. For the immunoprecipitation (IP), 800 ul chromatin was incubated with 25 ul Protein A Sepharose slurry (50%) in TBS and 5 ul anti-sigma 54 antibody (BioLegend) for 90 minutes at room temperature with gentle mixing on a rotisserie rotator. Following the 90 min incubation, beads were washed twice with FA lysis buffer and twice with 10 mM Tris-HCl, pH 7.5 (please note: all wash steps involved incubation of samples with the wash solution for 3 min with gentle mixing on a rotisserie rotator before pelleting beads at 1,500 x g in a microcentrifuge for 1 min). Beads were resuspended in 100 uL 1X Quick Blunting Buffer (NEB) containing dNTPs (concentration specified by NEB Quick Blunting kit) and 1 uL Quick Blunting enzyme mix (NEB), and incubated at room temperature for 30 min with gentle mixing. Beads were washed twice with FA lysis buffer and twice with 10 mM Tris-HCl, pH 8.0. Beads were resuspended in 100 uL Buffer 2 (NEB) containing 2 mM dATP and 2 uL Klenow DNA polymerase (NEB), and incubated for 30 min at 37 degrees Celsius with gentle mixing. Beads were washed twice with FA lysis buffer and twice with 10 mM Tris-HCl, pH 7.5. Beads were resuspended in 1X DNA Quick Ligase buffer (NEB), 1 uL NEXTflex ChIP-seq Barcoded adapter (BioO) and 2 uL Quick DNA Ligase (NEB), and incubated at room temperature for 15 min with gentle mixing. Beads were washed twice with FA lysis buffer, and once each with high salt FA lysis buffer (50 mM Hepes-KOH, pH 7, 500 mM NaCl, 1 mM EDTA, 1% Triton X-100, 0.1% sodium deoxycholate, 0.1% SDS), ChIP wash buffer (10 mM Tris-HCl, pH 8.0, 250 mM LiCl, 1 mM EDTA, 0.5% Nonidet-P40, 0.5% sodium deoxycholate) and TE (10 mM Tris-HCl, pH 7.5, 1 mM EDTA). After the TE wash, beads were transferred to a fresh Spin-X column and eluted with 100 ul ChIP elution buffer (50 mM Tris-HCl, pH 7.5, 10 mM EDTA, 1% SDS) for 10 minutes at 65 degrees Celsius with occasional agitation. Samples were decrosslinked by boiling for 10 minutes. DNA was extracted with phenol/chlorofom/isoamyl alcohol, ethanol precipitated, and resuspended in 11 uL H2O. 1 uL DNA was diluted 1:8 and 2 ul were used for real time PCR amplification (three technical replicates)with NEXTflex ChIP-seq Primer Mix (JW3764-AATGATACGGCGACCACCGAGATCTACAC and JW3765-CAAGCAGAAGACGGCATACGAGAT) using an ABI 7500 Fast real time PCR machine. The number of cycles required to reach a Delta Rn score of 0.1 was recorded (OXO). 8 uL of the remaining DNA was amplified using conventional PCR with oligonucleotides JW3764 and JW3765 ( 100 uM) for X+3 cycles with an annealing temperature of 60 degrees Celsius. PCR products were purified using Ampure XP magnetic beads (Ampure) and resuspended in 20 uL H2O. Purified PCR products between 200 bp and 600 bp were gel purified from an 8% non-denaturing polyacrylamide gel, eluted overnight in DNA extraction buffer (0.3 M NaCl, 10 mM Tris-HCl pH 8.0, 1 mM EDTA) and ethanol precipitated to generate the final ChIP-seq library. The library was resuspended in 11 uL H2O and quantified using a Qubit fluorimeter (Invitrogen). The library was sequenced using a HiSeq 2000 sequencer (Illumina; University at Buffalo Next Generation Sequencing Core Facility).

text: Escherichia coli

text: Escherichia coli

text: Escherichia coli

text: K-12 substr. MG1655

text: MG1655 Sigma54 ChIP-seq Rep1


name: E-MTAB-3697:MG1655 Sigma54 ChIP-seq Rep2

characteristic: INSDC last update

text: public

text: ArrayExpress

text: Escherichia coli

text: Escherichia coli

text: Escherichia coli

text: K-12 substr. MG1655

text: MG1655 Sigma54 ChIP-seq Rep2


Anaeromassilibacillus senegalense

text: URMITE

text: public

characteristic: INSDC status

text: Anaeromassilibacillus senegalense

text: Ruminococcaceae bacterium mt9

text: Ruminococcaceae bacterium mt9

text: Anaeromassilibacillus senegalense genome


text: KAUST

text: public

characteristic: SRA accession

text: Mecca

characteristic: isolate

text: Stenotrophomonas maltophilia

text: Stenotrophomonas maltophilia

text: Stenotrophomonas maltophilia mecca isolate


text: STATENS SERUM INSTITUT

text: public

characteristic: Submitter Id

text: blood

characteristic: bio material

text: Denmark

characteristic: geographic location (country and/or sea)

text: homo sapiens

characteristic: host

text: Human immunodeficiency virus 1

text: Human immunodeficiency virus 1

text: HIV-1 integrase


text: WEHI

text: public

text: house mouse

characteristic: common name

text: Whole genome sequencing of a Her-2 transgenic mouse

characteristic: description

text: Mus musculus

text: Mus musculus

text: Her-2 transgene


Fructose Rep.1

characteristic: ENA-CHECKLIST

text: UMASS

text: public

text: Fructose Rep.1

text: Clostridium ljungdahlii DSM 13528

characteristic: organism

text: Clostridium ljungdahlii DSM 13528

text: Fructose Rep.1


Fructose Rep.2

characteristic: ENA-FIRST-PUBLIC

text: UMASS

text: public

text: Fructose Rep.2

text: Clostridium ljungdahlii DSM 13528

text: Clostridium ljungdahlii DSM 13528

text: Fructose Rep.2

characteristic: title


Fructose Rep.3

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: UMASS

text: public

text: Fructose Rep.3

text: Clostridium ljungdahlii DSM 13528

text: Clostridium ljungdahlii DSM 13528

text: Fructose Rep. 3


H2/CO2 Rep. 1

text: UMASS

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: H2/CO2 Rep. 1

text: Clostridium ljungdahlii DSM 13528

text: Clostridium ljungdahlii DSM 13528

text: H2/CO2 Rep. 1


H2/CO2 Rep. 2

text: UMASS

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: H2/CO2 Rep. 2

text: Clostridium ljungdahlii DSM 13528

text: Clostridium ljungdahlii DSM 13528

text: Fructose Rep.2


H2/CO2 Rep. 3

text: UMASS

text: public

characteristic: SRA accession

text: H2/CO2 Rep. 3

text: Clostridium ljungdahlii DSM 13528

text: Clostridium ljungdahlii DSM 13528

text: H2/CO2 Rep. 3


text: MPI-TUEBINGEN

text: public

characteristic: Submitter Id

characteristic: collection date

text: Potato sample from Kew Royal Botanical Gardens

text: England

text: Solanaceae

text: Solanaceae


text: public

text: human

text: Homo sapiens

text: Homo sapiens

text: Gastric tumor and paired normal tissue


Control I

text: SRA-Webin

characteristic: ENA-SUBMISSION-TOOL

text: FIMM

text: public

text: Control I

text: human

text: Homo sapiens

text: Homo sapiens

text: Healthy control sample, female


Escherichia coli DH10B

text: ION

text: public

text: Escherichia coli DH10B

text: Escherichia coli DH10B

text: Escherichia coli

text: Escherichia coli


text: UU

text: public

text: chimpanzee

text: cDNA from liver, tissue derived from female chimpanzee that died at the age of three days

text: Pan troglodytes

text: Pan troglodytes


text: UU

text: public

text: chimpanzee

text: cDNA from liver, tissue derived from stillborn male chimpanzee

text: Pan troglodytes

text: Pan troglodytes


text: UU

text: public

text: chimpanzee

text: cDNA from frontal cortex, tissue derived from female chimpanzee that died at the age of three days

text: Pan troglodytes

text: Pan troglodytes


text: UU

text: public

text: chimpanzee

text: cDNA from frontal cortex, tissue derived from stillborn male chimpanzee

text: Pan troglodytes

text: Pan troglodytes


text: L2 and L4 stage

characteristic: Age

text: Guilin Wand/Valerie Reinke (Yale, USA)

characteristic: BioSourceProvider

text: LGTF

text: public

text: Caenorhabditis elegans

characteristic: Organism

text: hemaphrodite

characteristic: Sex

text: ArrayExpress

characteristic: broker name

text: Protocols: Total RNA from N2 worms was isolated using Trizol. Selected targets were then amplified by RT-PCR.

text: Caenorhabditis elegans

text: Caenorhabditis elegans


text: UNIVIE-CSB

text: public

characteristic: common name

text: Shotgun sequencing of Yersinia enterocolitica strain W22703

characteristic: description

text: Yersinia enterocolitica W22703

characteristic: organism

text: Yersinia enterocolitica W22703


name: Schizosaccharomyces japonicus genome sample

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: ED

text: public

text: DNA from Schizosaccharomyces japonicus

characteristic: Source

text: Schizosaccharomyces japonicus genome

text: Schizosaccharomyces japonicus

text: Schizosaccharomyces japonicus


text: UU

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: Number of individuals in pool

text: human

text: Pooled DNA samples of individuals from the 'Microisolates in South Tyrol Study'. Four chromosomal regions surrounding the genes LASS4, LIPC, ATP10D and SLC2A9 were selected by long-range PCR.

text: Homo sapiens

text: Homo sapiens


text: UU

text: public

characteristic: SRA accession

characteristic: Submitter Id

text: human

text: Pooled DNA samples of individuals from a study on the Dalmatian island of Vis, Croatia. Four chromosomal regions surrounding the genes LASS4, LIPC, ATP10D and SLC2A9 were selected by long-range PCR.

text: Homo sapiens

text: Homo sapiens


text: UU

text: public

text: human

text: Pooled DNA samples of individuals from the 'Erasmus Rucphen Family Study'. Four chromosomal regions surrounding the genes LASS4, LIPC, ATP10D and SLC2A9 were selected by long-range PCR.

text: Homo sapiens

text: Homo sapiens


text: UU

text: public

text: human

text: Pooled DNA samples of individuals from the 'Northern Swedish Population Health Study'. Four chromosomal regions surrounding the genes LASS4, LIPC, ATP10D and SLC2A9 were selected by long-range PCR.

text: Homo sapiens

text: Homo sapiens


text: UU

text: public

text: human

text: Pooled DNA samples of individuals from the 'Orkney Complex Disease Study'. Four chromosomal regions surrounding the genes LASS4, LIPC, ATP10D and SLC2A9 were selected by long-range PCR.

text: Homo sapiens

text: Homo sapiens


text: INRA

text: public

text: bread wheat

text: 3B chromosomes sorted by flow cytometry and amplified

text: Triticum aestivum

text: Triticum aestivum


text: 1 month

characteristic: Age

text: mature

characteristic: DevelopmentalStage

text: CRI

text: public

text: Cleome gynandra

characteristic: Organism

text: leaf

characteristic: OrganismPart

text: ArrayExpress

text: Protocols: standard growth condition in LD Qiagen plant RNAeasy kit. Illumina RNA-seq protocol

text: Cleome gynandra

text: Cleome gynandra

characteristic: title


text: 1 month

text: young

text: CRI

text: public

text: Cleome gynandra

text: leaf

text: ArrayExpress

characteristic: broker name

characteristic: description

text: Cleome gynandra

characteristic: organism

text: Cleome gynandra


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: Genome-MPET Library. 5000ng starting material, 15 PCR cycles

characteristic: Experimental factor

characteristic: External Id

text: SHR/Olalpcv

characteristic: Host

text: BCCAGSC

text: public

text: Female

characteristic: Sex

text: Liver

characteristic: Tissue

text: Norway rat

characteristic: common name

text: Spontaneously Hypertensive Rat

text: Rattus norvegicus

text: Rattus norvegicus


text: Genome-MPET Library. 10000ng starting material, 15 PCR cycles

text: SHR/Olalpcv

text: BCCAGSC

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: Female

characteristic: Submitter Id

text: Liver

text: Norway rat

text: Spontaneously Hypertensive Rat

text: Rattus norvegicus

text: Rattus norvegicus


text: Genome-PET Library. Genomic DNA was prepared by collaborator. with post PCR purification

text: SHR/Olalpcv

text: BCCAGSC

text: public

text: Female

text: Liver

text: Norway rat

text: Spontaneously Hypertensive Rat

text: Rattus norvegicus

text: Rattus norvegicus


text: Genome-PET Library. Genomic DNA was prepared by collaborator

text: SHR/Olalpcv

text: BCCAGSC

text: public

text: Female

text: Liver

text: Norway rat

text: Spontaneously Hypertensive Rat

text: Rattus norvegicus

text: Rattus norvegicus


text: Genome-MPET Library. 5000ng starting material, 13 PCR cycles

text: SHR/Olalpcv

text: BCCAGSC

text: public

text: Female

text: Liver

text: Norway rat

text: Spontaneously Hypertensive Rat

text: Rattus norvegicus

text: Rattus norvegicus


text: Genome-PET Library. Genomic DNA extraction was done at GSC

text: SHR/Olalpcv

text: BCCAGSC

text: public

text: Female

text: Liver

text: Norway rat

text: Spontaneously Hypertensive Rat

text: Rattus norvegicus

text: Rattus norvegicus


plate1_index_lib/mix 2

text: SC

text: public

text: plate1_index_lib/mix 2

text: human

text: Homo sapiens

text: Homo sapiens


plate1_index_lib/mix 1

text: SC

text: public

text: plate1_index_lib/mix 1

text: human

text: Homo sapiens

text: Homo sapiens


text: MT

characteristic: Genotype

text: HU-MCB

text: public

characteristic: Replicate

text: human

text: Homo sapiens

text: Homo sapiens


text: HU-MCB

text: public

text: human

characteristic: description

text: Homo sapiens

characteristic: organism

text: Homo sapiens


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: WT

text: HU-MCB

text: public

text: human

text: Homo sapiens

text: Homo sapiens


text: Vero cells

characteristic: CellLine

text: 4 days post infection

characteristic: DevelopmentalStage

characteristic: External Id

text: SC

text: public

text: Neospora caninum

characteristic: Organism

text: ArrayExpress

characteristic: broker name

text: Protocols: Neospora caninum-Liverpool isolate tachyzoites were maintained as described previously (Cohen et al. 2002). Briefly, parasites were cultured by twice weekly passage into African Green Monkey Kidney Fibroblasts (Vero cells) using Iscove's Modified Dulbecco's Medium (IMDM, Lonza, Walkersville, USA) supplemented with 5 percents (v/v) foetal calf serum (FCS, Labtech international, UK) and 100Uml-1 penicillin/100ugml-1 streptomycin (Sigma-Aldrich). Parasites were harvested 2, 3, 4 or 6 days post-infection in aliquots of 108 tachyzoites and stored at -20oC either resuspended in TRI Reagent (Sigma-Aldrich) for RNA extraction or as pellets for proteomics. RNA was extracted from Trizol with chloroform (as per the Invitrogen protocol), ethanol precipitated and then resuspended in RNAse free water. Poly A+ mRNA was purified from total RNA using oligo dT dyna bead selection followed by metal ion hydrolysis fragmentation with the Ambion RNA fragmentation kit. 1st strand cDNA is synthesized using randomly primed oligos followed by 2nd strand synthesis to produce dscDNA. This was followed by end repair with T4 and Klenow DNA polymerases and T4 polynucleotide kinase to blunt-end the DNA fragments. A single 3' A nucleotide was added to the repaired ends using Klenow exo- and dATP to deter concatemerization of templates, limit adapter dimers and increase the efficiency of adapter ligation. Adapters were then ligated (containing primer sites for sequencing). Ligated fragments were run on an agarose gel, size selected for 200-250bp inserts and DNA extracted as per Qiagen gel extraction kit protocol but with dissolution of gel slices at room temperature (rather than 50oC) to avoid heat induced bias. Libraries were then amplified by PCR to enrich for properly ligated template strands, to generate enough DNA and to add primers for flowcell surface annealing followed by a clean up with AMPure SPRI beads. These libraries were quantified using Agilent Bioanalyser chip and Kapa Illumina SYBR Fast qPCR kit.

text: Neospora caninum

text: Neospora caninum

characteristic: title


text: Vero cells

text: 3 days post infection

text: SC

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: Neospora caninum

text: ArrayExpress

text: Neospora caninum

text: Neospora caninum


text: Vero cells

text: 6 days post infection

text: SC

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: Neospora caninum

text: ArrayExpress

text: Neospora caninum

text: Neospora caninum


text: Vero cells

text: 3 days post infection

text: SC

text: public

text: Neospora caninum

characteristic: SRA accession

characteristic: Submitter Id

text: ArrayExpress

text: Protocols: Neospora caninum-Liverpool isolate tachyzoites were maintained as described previously (Cohen et al. 2002). Briefly, parasites were cultured by twice weekly passage into African Green Monkey Kidney Fibroblasts (Vero cells) using Iscove's Modified Dulbecco's Medium (IMDM, Lonza, Walkersville, USA) supplemented with 5 percents (v/v) foetal calf serum (FCS, Labtech international, UK) and 100Uml-1 penicillin/100ugml-1 streptomycin (Sigma-Aldrich). Parasites were harvested 2, 3, 4 or 6 days post-infection in aliquots of 108 tachyzoites and stored at -20oC either resuspended in TRI Reagent (Sigma-Aldrich) for RNA extraction or as pellets for proteomics. RNA was extracted from Trizol with chloroform (as per the Invitrogen protocol), ethanol precipitated and then resuspended in RNAse free water. mRNA was purified from total RNA using terminator exonuclease to digest RNA species that have 5' phosphate followed by metal ion hydrolysis fragmentation with the Ambion RNA fragmentation kit. 1st strand cDNA is synthesized using randomly primed oligos followed by 2nd strand synthesis to produce dscDNA. This was followed by end repair with T4 and Klenow DNA polymerases and T4 polynucleotide kinase to blunt-end the DNA fragments. A single 3' A nucleotide was added to the repaired ends using Klenow exo- and dATP to deter concatemerization of templates, limit adapter dimers and increase the efficiency of adapter ligation. Adapters were then ligated (containing primer sites for sequencing). Ligated fragments were run on an agarose gel, size selected for 200-250bp inserts and DNA extracted as per Qiagen gel extraction kit protocol but with dissolution of gel slices at room temperature (rather than 50oC) to avoid heat induced bias. Libraries were then amplified by PCR to enrich for properly ligated template strands, to generate enough DNA and to add primers for flowcell surface annealing followed by a clean up with AMPure SPRI beads. These libraries were quantified using Agilent Bioanalyser chip and Kapa Illumina SYBR Fast qPCR kit.

text: Neospora caninum

text: Neospora caninum


text: Vero cells

text: 4 days post infection

text: SC

text: public

text: Neospora caninum

text: ArrayExpress

text: Neospora caninum

text: Neospora caninum


text: Vero cells

text: 4 days post infection

text: SC

text: public

text: Neospora caninum

text: ArrayExpress

text: Protocols: Neospora caninum-Liverpool isolate tachyzoites were maintained as described previously (Cohen et al. 2002). Briefly, parasites were cultured by twice weekly passage into African Green Monkey Kidney Fibroblasts (Vero cells) using Iscove's Modified Dulbecco's Medium (IMDM, Lonza, Walkersville, USA) supplemented with 5 percents (v/v) foetal calf serum (FCS, Labtech international, UK) and 100Uml-1 penicillin/100ugml-1 streptomycin (Sigma-Aldrich). Parasites were harvested 2, 3, 4 or 6 days post-infection in aliquots of 108 tachyzoites and stored at -20oC either resuspended in TRI Reagent (Sigma-Aldrich) for RNA extraction or as pellets for proteomics. RNA was extracted from Trizol with chloroform (as per the Invitrogen protocol), ethanol precipitated and then resuspended in RNAse free water. Poly A+ mRNA was purified from total RNA using oligo dT dyna bead selection followed by metal ion hydrolysis fragmentation with the Ambion RNA fragmentation kit. 1st strand cDNA is synthesized using randomly primed oligos followed by 2nd strand synthesis to produce dscDNA. This was followed by end repair with T4 and Klenow DNA polymerases and T4 polynucleotide kinase to blunt-end the DNA fragments. A single 3-prime A nucleotide was added to the repaired ends using Klenow exo- and dATP to deter concatemerization of templates, limit adapter dimers and increase the efficiency of adapter ligation. Adapters were then ligated (containing primer sites for sequencing). Ligated fragments were run on an agarose gel, size selected for 200-250bp inserts and DNA extracted as per Qiagen gel extraction kit protocol but with dissolution of gel slices at room temperature (rather than 50oC) to avoid heat induced bias. Libraries were then amplified by PCR to enrich for properly ligated template strands, to generate enough DNA and to add primers for flowcell surface annealing followed by a clean up with AMPure SPRI beads. These libraries were quantified using Agilent Bioanalyser chip and Kapa Illumina SYBR Fast qPCR kit.

text: Neospora caninum

text: Neospora caninum


Vanstein 191658

text: HMGU

text: public

text: Vanstein 191658

text: cattle

characteristic: common name

text: Fleckvieh bull Vanstein 191658, genomic DNA extracted from peripheral blood sample

text: Bos taurus

text: Bos taurus


name: Galleria larval transcriptome raw 454 data sample

text: Larval

characteristic: Development Stage

text: MPICE

text: public

text: greater wax moth

text: GS/FLX sequence data generated from a normalized cDNA generated from immunized Galleria larvae

characteristic: description

text: Galleria mellonella

text: Galleria mellonella


larvae exposed to atrazine

characteristic: ENA-FIRST-PUBLIC

text: CNRS

text: public

text: larvae exposed to atrazine

text: yellow fever mosquito

text: Aedes aegypti, laboratory strain Bora-Bora, fourth stage 5 days-old larvae of mixed sexes, grown in standard insectary conditions, exposed to 10 ï¿½g/L atrazine for 48h, total RNA isolated from 3 batches of 30 fresh larvae

text: Aedes aegypti

characteristic: organism

text: Aedes aegypti

text: atrazine

characteristic: xenobiotic used for exposure


unexposed larvae

characteristic: ENA-LAST-UPDATE

text: CNRS

text: public

text: unexposed larvae

text: yellow fever mosquito

text: Aedes aegypti, laboratory strain Bora-Bora, fourth stage 5 days-old larvae of mixed sexes, grown in standard insectary conditions, unexposed to any xenobiotic, used as controls for transcription ratios, total RNA isolated from 3 batches of 30 fresh larvae

text: Aedes aegypti

text: Aedes aegypti


larvae exposed to imidacloprid

characteristic: External Id

text: CNRS

text: public

text: larvae exposed to imidacloprid

text: yellow fever mosquito

text: Aedes aegypti, laboratory strain Bora-Bora, fourth stage 5 days-old larvae of mixed sexes, grown in standard insectary conditions, exposed to 40 ï¿½g/L imidacloprid for 48h, total RNA isolated from 3 batches of 30 fresh larvae

text: Aedes aegypti

text: Aedes aegypti

text: imidacloprid


larvae exposed to fluoranthene

text: CNRS

text: public

text: larvae exposed to fluoranthene

text: yellow fever mosquito

text: Aedes aegypti, laboratory strain Bora-Bora, fourth stage 5 days-old larvae of mixed sexes, grown in standard insectary conditions, exposed to 25 ï¿½g/L fluoranthene for 48h, total RNA isolated from 3 batches of 30 fresh larvae

text: Aedes aegypti

text: Aedes aegypti

text: fluoranthene


larvae exposed to copper

text: CNRS

text: public

text: larvae exposed to copper

text: yellow fever mosquito

text: Aedes aegypti, laboratory strain Bora-Bora, fourth stage 5 days-old larvae of mixed sexes, grown in standard insectary conditions, exposed to 2 mg/L copper sulfate for 48h, total RNA isolated from 3 batches of 30 fresh larvae

text: Aedes aegypti

text: Aedes aegypti

text: copper


larvae exposed to permethrin

text: CNRS

text: public

text: larvae exposed to permethrin

text: yellow fever mosquito

text: Aedes aegypti, laboratory strain Bora-Bora, fourth stage 5 days-old larvae of mixed sexes, grown in standard insectary conditions, exposed to 1.5 ï¿½g/L permethrin for 48h, total RNA isolated from 3 batches of 30 fresh larvae

text: Aedes aegypti

text: Aedes aegypti

text: permethrin


larvae exposed to propoxur

text: CNRS

text: public

text: larvae exposed to propoxur

text: yellow fever mosquito

text: Aedes aegypti, laboratory strain Bora-Bora, fourth stage 5 days-old larvae of mixed sexes, grown in standard insectary conditions, exposed to 500 ï¿½g/L propoxur for 48h, total RNA isolated from 3 batches of 30 fresh larvae

text: Aedes aegypti

text: Aedes aegypti

text: propoxur


text: Gamboa, Panama

characteristic: Habitat

text: BGI

text: public

text: 1 male

characteristic: Sample extracted from

text: DNA

characteristic: Sample type

unit: Year

characteristic: Time of sample collection

text: Panamanian leafcutter ant

text: Genome DNA sample for 500bp and 800bp insert size library

text: Acromyrmex echinatior

text: Acromyrmex echinatior


text: Gamboa, Panama

text: BGI

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: 40 males

text: DNA

text: Panamanian leafcutter ant

text: Genome DNA sample for 5kb insert size library

text: Acromyrmex echinatior

text: Acromyrmex echinatior


text: Gamboa, Panama

text: BGI

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: 1 male

text: DNA

text: Panamanian leafcutter ant

text: Genome DNA sample for 2kb insert size library

text: Acromyrmex echinatior

text: Acromyrmex echinatior


text: Gamboa, Panama

text: BGI

text: public

characteristic: SRA accession

text: 40 males

text: DNA

characteristic: Submitter Id

text: Panamanian leafcutter ant

text: Genome DNA sample for 10kb insert size library

text: Acromyrmex echinatior

text: Acromyrmex echinatior


text: Gamboa, Panama

text: BGI

text: public

text: eggs, larvae, pupae, workers, males,gynes

text: RNA

text: Panamanian leafcutter ant

characteristic: common name

text: Transcriptome RNA sample

text: Acromyrmex echinatior

text: Acromyrmex echinatior


text: MPIMG

text: public

text: human

text: CEU Human MP1

characteristic: description

text: Homo sapiens

text: Homo sapiens

text: Human MP1

characteristic: title


est Pandinus imperator

text: adult

characteristic: Development stage

characteristic: ENA-FIRST-PUBLIC

text: MPIMG

text: public

text: est Pandinus imperator

text: emperor scorpion

text: RNA was extracted from total animal. A Cloneminer cDNA construction was performed from 3 ug poly(A)+ RNA. A plasmid-pool of the cDNA library was used as template for insert amplification using vector specific primers (5'-TTTTATAATGCCAACTTTGTA-3'; 5'-TAATGCCAACTTTGTACAAG-3'). PCR products were sequenced by the 454 FLX technology (Roche, Basel, Switzerland).

text: Pandinus imperator

characteristic: organism

text: Pandinus imperator

text: female

characteristic: sex

text: total animal


text: 1 to 3 hours

characteristic: Age

text: UCSD Drosophila Stock Center

characteristic: BioSourceProvider

characteristic: BioSourceType

text: embryonic stage 5 to 8

characteristic: DevelopmentalStage

characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: Genotype

text: STOWERS INSTITUTE FO

text: public

text: Drosophila simulans

characteristic: Organism

characteristic: Sex

tag: Namespace:STOWERS INSTITUTE FO

text: ArrayExpress

characteristic: broker name

text: Protocols: Flies of all six species were raised at 25C and 60% humidity on corn syrup based food. Two to four days post enclosure flies were moved to a plexiglas cage and fed yeast paste on 150mm apple agar plates. All collections resulted in embryos 2-4 hours in age (For D. pseudoobscura, opuntia powder was also sprinkled on apple agar plates to increase numbers of eggs laid). Plates were left in cages for 2 hours allowing flies to lay eggs on them. Afterwards plates were removed and allowed to incubate for an additional 1.5h at 25C till harvest started, at which point bleach was added to the plate for two minutes to dechorionate embryos. Collection windows for most species were 2-4 hours post egg laying to match D. melanogaster embryonic development. We observed a delay in D. pseudoobscura, and acceleration in D. simulans embryonic development, which are consistent with an earlier study about heterochrony in Drosophila embryonic development (PMID:10618397). Therefore, for these two species, collection windows were adjusted empirically based on two criteria: a. to ensure majority of embryos were within Bownes stage 5-8; b. to obtain optimal signal/noise ratio from ChIP-seq experiments. Collection plates were removed after 2 hours of egg laying and were incubated for additional 0.5, 1.5, or 2.5 hours at 25C until the start of harvest for 1-3, 2-4, or 3-5 hour collections, respectively. Embryos were fixed using a modified protocol from Furlong et.al. Briefly, embryos were transferred to a tube containing PBT (PBS with 0.1% Triton) and allowed to settle. After PBT being removed, embryos were crosslinked by being vortexed in a mixture of fixing buffer (50 mM HEPES, pH 7.5, 1 mM EDTA, 0.5 mM, EGTA, 100 mM NaCl, 1.8% formaldehyde) and heptane for 15 minutes at room temperature. To stop crosslinking, fixing solution and heptane were removed, and 2.5 M glycine in PBT was added to fixed embryos before they were vortexed for 1 minute. Embryos were washed with PBT and either used for preparation of whole cell extract for chromatin immunoprecipitation or rapidly frozen in liquid nitrogen and stored at -80C. For staging embryos, some fixed embryos were vortexed in methanol:heptane (V:V=1:1) for 10 minutes for devitellinization, and washed twice by methanol before being stored in methanol at -20C. ChIPs were done using a modified protocol from Furlong lab (http://furlonglab.embl.de/methods/extras/ChIP-on-chip-Drosophila.pdf). On the day before ChIP, 100 ul protein A-conjugated Dynobeads (Invitrogen 100-02D) were washed three times by block solution (PBS with 5 mg/ml BSA), and incubated with 20 ul affinity purified rabbit polycolonal anti-Drosophila melanogaster Twist antibody (a generous gift from Levine lab and Furlong lab) at 4C overnight. To prepare nuclear extract, embryos cross-linked in 1.8% formaldehyde were resuspended in buffer A1 (15 mM HEPES, pH 7.5, 15 mM NaCl, 60 mM KCl, 4 mM MgCl2, 0.5 % Triton X-100, 0.5 mM DDT, freshly added complete EDTA-free protease inhibitor cocktail (Roche 11873580001)), and homogenized six times by both pestles on ice. Nuclei were precipitated by centrifuge, washed three times by buffer A1, and resuspended in buffer A2 (15mM HEPES, pH 7.5, 140 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 1 % Triton X-100, 0.1% sodium deoxycholate, 0.1% SDS, 0.5% N-lauroylsarcosine, freshly added complete EDTA-free protease inhibitor cocktail (Roche 11873580001)). Chromatin was fragmented by sonication to the average size of 400-500 bp, and the soluble fraction (whole cell extract, WCE) was precipitated by centrifuge. For each ChIP, 300 ul WCE (100-120 mg embryos) was incubated with pre-treated protein A-conjugated Dynobeads overnight at 4C by rotating. Beads were washed four to five times by RIPA buffer (50 mM HEPES, pH 7.5, 1 mM EDTA, 0.7% Na deoxycholate, 1% IGEPAL CA-630, 0.5 M LiCl), and bound chromatin was eluted by 100 ul elution buffer (50 mM Tris + 1% SDS) on a thermomixer at 65C for 20 minutes with agitation. Supernatant was transferred and 100 ul TE was added to each ChIP sample before reverse crosslinking. For control, 50 ul WCE was mixed with 50 ul TE and 100 ul elution buffer. Reverse crosslinking was done by incubating samples at 65C for six hours. Reverse crosslinked DNA was then first treated with RNase A (0.2 ug/ul) and then with proteinase K (0.2 ug/ul) for two hours at 37C and 55C, respectively. DNA was cleaned with phenol (Sigma P4557) and phenol-chloroform-isoamyl alcohol mixture (Sigma 77617). For precipitation, glycogen and NaCl were added to each sample to the final concentration of 0.15 ug/ul and 200 mM, respectively. DNA was precipitated by 2.5 fold (v:v) 100% ethanol at -80C for at least two hours before DNA being precipitated by centrifuge and washed with 70% ethanol at 4C. Precipitated DNA was solved in TE. Level of Twist enrichment was monitored by real-time PCR. For D. melanogaster, regions within the enhancers of brinker and rhomboid genes were chosen as positive controls, while a region in chromosome 2L as negative control (NonG). Similarly, for individual non-melanogaster species, a region upstream of tup gene, and regions within the open reading frame of the othologues of D. melanogaster Dscam gene were chosen as positive control, while orthologous regions of NonG was used as negative control. Sequences for oligos used in PCR are available upon request.

text: Drosophila simulans

text: Drosophila simulans


text: 2 to 4 hours

text: UCSD Drosophila Stock Center

text: embryonic stage 5 to 8

text: STOWERS INSTITUTE FO

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: Drosophila yakuba

characteristic: SRA accession

characteristic: Submitter Id

text: ArrayExpress

text: Drosophila yakuba

text: Drosophila yakuba


text: 3 to 5 hours

text: UCSD Drosophila Stock Center

text: embryonic stage 5 to 8

characteristic: ENA-FIRST-PUBLIC

text: STOWERS INSTITUTE FO

text: public

text: Drosophila pseudoobscura

text: ArrayExpress

characteristic: description

text: Drosophila pseudoobscura

characteristic: organism

text: Drosophila pseudoobscura

characteristic: title


text: 2 to 4 hours

characteristic: Age

text: UCSD Drosophila Stock Center

characteristic: BioSourceProvider

characteristic: BioSourceType

text: embryonic stage 5 to 8

characteristic: DevelopmentalStage

text: STOWERS INSTITUTE FO

text: public

text: Drosophila erecta

text: ArrayExpress

text: Drosophila erecta

text: Drosophila erecta


text: 2 to 4 hours

text: UCSD Drosophila Stock Center

text: embryonic stage 5 to 8

characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: Genotype

text: STOWERS INSTITUTE FO

text: public

text: Drosophila ananassae

characteristic: Organism

text: ArrayExpress

text: Drosophila ananassae

text: Drosophila ananassae


text: SC

characteristic: INSDC center name

characteristic: INSDC first public

text: public

characteristic: collection date

text: Uganda

characteristic: geographic location (country and/or sea)

text: disease

characteristic: host health state

text: blood

characteristic: isolation source

text: Salmonella enterica subsp. enterica serovar Typhimurium

characteristic: pubmed id

text: Typhimurium

characteristic: serovar

text: Human

characteristic: specific host

characteristic: strain


characteristic: ENA-FIRST-PUBLIC

text: SC

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: Mozambique

text: disease

text: blood

characteristic: organism

text: Typhimurium

text: Human

characteristic: title


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: SC

characteristic: INSDC center name

text: public

text: Mexico

text: disease

text: faeces

text: Typhimurium

text: Human


text: SC

characteristic: INSDC first public

text: public

characteristic: collection date

text: United Kingdom

characteristic: geographic location (country and/or sea)

text: disease

text: faeces

text: Typhimurium

text: Human


text: SC

text: public

text: USA: Colorado

text: disease

characteristic: host health state

text: not known

characteristic: isolation source

characteristic: pubmed id

text: Typhimurium

text: lamb


text: SC

text: public

text: Sweden

text: disease

text: not known

text: Typhimurium

characteristic: serovar

text: pigeon

characteristic: specific host

characteristic: strain


characteristic: ENA-FIRST-PUBLIC

text: SC

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: Switzerland

text: disease

text: not known

text: Typhimurium

text: calf


text: SC

text: public

characteristic: SRA accession

characteristic: Submitter Id

text: Sweden

text: disease

text: not known

characteristic: organism

text: Typhimurium

text: animal


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: SC

text: public

text: Sweden

text: disease

text: faeces

text: Typhimurium

text: Rats

characteristic: title


text: SC

characteristic: INSDC center name

characteristic: INSDC first public

text: public

characteristic: collection date

text: Chile

text: disease

text: faeces

text: Typhimurium

text: Human


text: SC

text: public

text: Denmark

characteristic: geographic location (country and/or sea)

text: disease

characteristic: host health state

text: faeces

characteristic: isolation source

text: Typhimurium

text: goose


text: SC

text: public

text: Denmark

text: disease

text: not known

characteristic: pubmed id

text: Typhimurium

characteristic: serovar

text: mouse

characteristic: specific host


characteristic: ENA-FIRST-PUBLIC

text: SC

characteristic: INSDC last update

text: public

text: United Kingdom

text: disease

text: not known

text: Typhimurium

text: not known

characteristic: strain


text: SC

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: Democratic Republic of Congo

text: disease

text: blood

text: Typhimurium

text: Human


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: SC

text: public

text: Denmark

text: disease

text: faeces

characteristic: organism

text: Typhimurium

text: Human


text: SC

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: Mali

text: disease

text: blood

text: Typhimurium

text: Human

characteristic: title


text: SC

text: public

characteristic: collection date

text: Malawi

characteristic: geographic location (country and/or sea)

text: disease

characteristic: host health state

text: blood

text: Typhimurium

text: Human


text: SC

text: public

text: USA: California

text: disease

text: not known

characteristic: isolation source

characteristic: pubmed id

text: Typhimurium

characteristic: serovar

text: Parrot


characteristic: ENA-FIRST-PUBLIC

text: SC

characteristic: INSDC last update

text: public

text: Thailand

text: disease

text: not known

text: Typhimurium

text: not known

characteristic: specific host


text: SC

text: public

characteristic: INSDC status

characteristic: SRA accession

text: USA: California

text: disease

text: not known

text: Typhimurium

text: opposum

characteristic: strain


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: SC

text: public

characteristic: Submitter Id

text: USA: Rhode Island

text: disease

text: not known

text: Typhimurium

text: Horse


text: SC

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: Mongolia

text: disease

text: not known

characteristic: organism

text: Typhimurium

text: not known


text: SC

text: public

characteristic: collection date

text: Malawi

characteristic: geographic location (country and/or sea)

text: disease

text: blood

text: Typhimurium

text: Human

characteristic: title


text: SC

text: public

text: USA: Indiana

text: disease

characteristic: host health state

text: not known

characteristic: isolation source

characteristic: pubmed id

text: Typhimurium

text: Rabbit


characteristic: ENA-FIRST-PUBLIC

text: SC

characteristic: INSDC last update

text: public

text: Mozambique

text: disease

text: blood

text: Typhimurium

characteristic: serovar

text: Human