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name: M. tuberculosis H37Rv Gly (TCC) glyV rep

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text: in vitro

characteristic: isolate

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text: FZB

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text: WGS of M. tuberculosis from Kopanyo, Botswana 2012-2016

text: Mycobacterium tuberculosis

text: Mycobacterium tuberculosis


E-MTAB-13007:Sample 1

text: public

text: E-MTAB-13007:Sample 1

tag: Namespace:Universite Paris Cite, Centre de Recherche sur l'Inflammation (CRI), INSERM, U1149, CNRS, ERL 8252, F-75018 Paris, France.

text: ArrayExpress

characteristic: broker name

text: chemo-naive

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characteristic: common name

text: Protocols: Manual microdissection chemo-naive Qiagen RNeasy FFPE Lexogen 3' QuantSeq REV

text: pancreatic ductal adenocarcinoma

characteristic: disease

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: pancreas

characteristic: organism part

text: tumor

characteristic: sampling site

text: Homo sapiens

text: Sample 1

text: not available

characteristic: tumor size


E-MTAB-13007:Sample 10

text: Universite Paris Cite, Centre de Recherche sur l'Inflammation (CRI), INSERM, U1149, CNRS, ERL 8252, F-75018 Paris, France.

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characteristic: title

text: not available


E-MTAB-13007:Sample 11

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text: not available


E-MTAB-13007:Sample 12

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text: ArrayExpress

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text: pancreas

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text: not available


E-MTAB-13007:Sample 13

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text: chemo-naive

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text: not available


E-MTAB-13007:Sample 14

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text: not available

characteristic: tumor size


E-MTAB-13007:Sample 15

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characteristic: title

text: not available


E-MTAB-13007:Sample 16

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text: pancreas

text: tumor

text: Homo sapiens

text: Sample 16

text: not available


E-MTAB-13007:Sample 17

characteristic: External Id

characteristic: INSDC center name

text: public

text: E-MTAB-13007:Sample 17

text: ArrayExpress

characteristic: broker name

text: chemo-naive

characteristic: clinical information

text: human

text: pancreatic ductal adenocarcinoma

text: Homo sapiens

text: Homo sapiens

text: pancreas

text: tumor

text: Homo sapiens

text: Sample 17

text: not available


E-MTAB-13007:Sample 18

text: public

text: E-MTAB-13007:Sample 18

text: ArrayExpress

text: chemo-naive

text: human

characteristic: common name

text: pancreatic ductal adenocarcinoma

characteristic: disease

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: pancreas

characteristic: organism part

text: tumor

text: Homo sapiens

text: Sample 18

text: not available


E-MTAB-13007:Sample 19

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: E-MTAB-13007:Sample 19

text: ArrayExpress

text: chemo-naive

text: human

text: pancreatic ductal adenocarcinoma

text: Homo sapiens

text: Homo sapiens

text: pancreas

text: tumor

characteristic: sampling site

text: Homo sapiens

text: Sample 19

text: not available

characteristic: tumor size


E-MTAB-13007:Sample 2

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-13007:Sample 2

characteristic: Submitter Id

text: ArrayExpress

text: chemo-naive

text: human

text: pancreatic ductal adenocarcinoma

text: Homo sapiens

text: Homo sapiens

text: pancreas

text: tumor

text: Homo sapiens

text: Sample 2

characteristic: title

text: not available


E-MTAB-13007:Sample 20

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: public

text: E-MTAB-13007:Sample 20

text: ArrayExpress

text: chemo-naive

text: human

characteristic: description

text: pancreatic ductal adenocarcinoma

text: Homo sapiens

text: Homo sapiens

text: pancreas

text: tumor

text: Homo sapiens

text: Sample 20

text: not available


E-MTAB-13007:Sample 21

characteristic: External Id

characteristic: INSDC center name

text: public

text: E-MTAB-13007:Sample 21

text: ArrayExpress

characteristic: broker name

text: chemo-naive

characteristic: clinical information

text: human

text: pancreatic ductal adenocarcinoma

text: Homo sapiens

text: Homo sapiens

text: pancreas

text: tumor

text: Homo sapiens

text: Sample 21

text: not available


E-MTAB-13007:Sample 22

text: public

text: E-MTAB-13007:Sample 22

text: ArrayExpress

text: chemo-naive

text: human

characteristic: common name

text: pancreatic ductal adenocarcinoma

characteristic: disease

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: pancreas

characteristic: organism part

text: tumor

text: Homo sapiens

text: Sample 22

text: not available


E-MTAB-13007:Sample 23

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: E-MTAB-13007:Sample 23

text: ArrayExpress

text: chemo-naive

text: human

text: pancreatic ductal adenocarcinoma

text: Homo sapiens

text: Homo sapiens

text: pancreas

text: tumor

characteristic: sampling site

text: Homo sapiens

text: Sample 23

text: not available

characteristic: tumor size


E-MTAB-13007:Sample 24

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-13007:Sample 24

characteristic: Submitter Id

text: ArrayExpress

text: chemo-naive

text: human

text: pancreatic ductal adenocarcinoma

text: Homo sapiens

text: Homo sapiens

text: pancreas

text: tumor

text: Homo sapiens

text: Sample 24

characteristic: title

text: not available


E-MTAB-13007:Sample 25

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: public

text: E-MTAB-13007:Sample 25

text: ArrayExpress

text: chemo-naive

text: human

characteristic: description

text: pancreatic ductal adenocarcinoma

text: Homo sapiens

text: Homo sapiens

text: pancreas

text: tumor

text: Homo sapiens

text: Sample 25

text: not available


E-MTAB-13007:Sample 26

characteristic: External Id

characteristic: INSDC center name

text: public

text: E-MTAB-13007:Sample 26

text: ArrayExpress

characteristic: broker name

text: chemo-naive

characteristic: clinical information

text: human

text: pancreatic ductal adenocarcinoma

text: Homo sapiens

text: Homo sapiens

text: pancreas

text: tumor

text: Homo sapiens

text: Sample 26

text: not available


E-MTAB-13007:Sample 27

text: public

text: E-MTAB-13007:Sample 27

text: ArrayExpress

text: chemo-naive

text: human

characteristic: common name

text: pancreatic ductal adenocarcinoma

characteristic: disease

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: pancreas

characteristic: organism part

text: tumor

text: Homo sapiens

text: Sample 27

text: not available


E-MTAB-13007:Sample 28

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: E-MTAB-13007:Sample 28

text: ArrayExpress

text: chemo-naive

text: human

text: pancreatic ductal adenocarcinoma

text: Homo sapiens

text: Homo sapiens

text: pancreas

text: tumor

characteristic: sampling site

text: Homo sapiens

text: Sample 28

text: not available

characteristic: tumor size


E-MTAB-13007:Sample 29

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-13007:Sample 29

characteristic: Submitter Id

text: ArrayExpress

text: chemo-naive

text: human

text: pancreatic ductal adenocarcinoma

text: Homo sapiens

text: Homo sapiens

text: pancreas

text: tumor

text: Homo sapiens

text: Sample 29

characteristic: title

text: not available


E-MTAB-13007:Sample 3

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: public

text: E-MTAB-13007:Sample 3

text: ArrayExpress

text: chemo-naive

text: human

characteristic: description

text: pancreatic ductal adenocarcinoma

text: Homo sapiens

text: Homo sapiens

text: pancreas

text: tumor

text: Homo sapiens

text: Sample 3

text: not available


E-MTAB-13007:Sample 30

characteristic: External Id

characteristic: INSDC center name

text: public

text: E-MTAB-13007:Sample 30

text: ArrayExpress

characteristic: broker name

text: chemo-naive

characteristic: clinical information

text: human

text: pancreatic ductal adenocarcinoma

text: Homo sapiens

text: Homo sapiens

text: pancreas

text: tumor

text: Homo sapiens

text: Sample 30

text: not available


E-MTAB-13007:Sample 31

text: public

text: E-MTAB-13007:Sample 31

text: ArrayExpress

text: chemo-naive

text: human

characteristic: common name

text: pancreatic ductal adenocarcinoma

characteristic: disease

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: pancreas

characteristic: organism part

text: tumor

text: Homo sapiens

text: Sample 31

text: not available


E-MTAB-13007:Sample 32

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: E-MTAB-13007:Sample 32

text: ArrayExpress

text: chemo-naive

text: human

text: pancreatic ductal adenocarcinoma

text: Homo sapiens

text: Homo sapiens

text: pancreas

text: tumor

characteristic: sampling site

text: Homo sapiens

text: Sample 32

unit: centimeter

characteristic: tumor size


E-MTAB-13007:Sample 33

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-13007:Sample 33

characteristic: Submitter Id

text: ArrayExpress

text: chemo-naive

text: human

text: pancreatic ductal adenocarcinoma

text: Homo sapiens

text: Homo sapiens

text: pancreas

text: tumor

text: Homo sapiens

text: Sample 33

characteristic: title


E-MTAB-13007:Sample 34

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: public

text: E-MTAB-13007:Sample 34

text: ArrayExpress

text: chemo-naive

text: human

characteristic: description

text: pancreatic ductal adenocarcinoma

text: Homo sapiens

text: Homo sapiens

text: pancreas

text: tumor

text: Homo sapiens

text: Sample 34


E-MTAB-13007:Sample 35

characteristic: External Id

characteristic: INSDC center name

text: public

text: E-MTAB-13007:Sample 35

text: ArrayExpress

characteristic: broker name

text: chemo-naive

characteristic: clinical information

text: human

text: pancreatic ductal adenocarcinoma

text: Homo sapiens

text: Homo sapiens

text: pancreas

text: tumor

text: Homo sapiens

text: Sample 35


E-MTAB-13007:Sample 36

text: public

text: E-MTAB-13007:Sample 36

text: ArrayExpress

text: chemo-naive

text: human

characteristic: common name

text: pancreatic ductal adenocarcinoma

characteristic: disease

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: pancreas

characteristic: organism part

text: tumor

text: Homo sapiens

text: Sample 36


E-MTAB-13007:Sample 37

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: E-MTAB-13007:Sample 37

text: ArrayExpress

text: chemo-naive

text: human

text: pancreatic ductal adenocarcinoma

text: Homo sapiens

text: Homo sapiens

text: pancreas

text: tumor

characteristic: sampling site

text: Homo sapiens

text: Sample 37

characteristic: tumor size


E-MTAB-13007:Sample 38

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-13007:Sample 38

characteristic: Submitter Id

text: ArrayExpress

text: chemo-naive

text: human

text: pancreatic ductal adenocarcinoma

text: Homo sapiens

text: Homo sapiens

text: pancreas

text: tumor

text: Homo sapiens

text: Sample 38

characteristic: title


E-MTAB-13007:Sample 39

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: public

text: E-MTAB-13007:Sample 39

text: ArrayExpress

text: chemo-naive

text: human

characteristic: description

text: pancreatic ductal adenocarcinoma

text: Homo sapiens

text: Homo sapiens

text: pancreas

text: tumor

text: Homo sapiens

text: Sample 39


E-MTAB-13007:Sample 4

characteristic: External Id

characteristic: INSDC center name

text: public

text: E-MTAB-13007:Sample 4

text: ArrayExpress

characteristic: broker name

text: chemo-naive

characteristic: clinical information

text: human

text: pancreatic ductal adenocarcinoma

text: Homo sapiens

text: Homo sapiens

text: pancreas

text: tumor

text: Homo sapiens

text: Sample 4

text: not available


E-MTAB-13007:Sample 40

text: public

text: E-MTAB-13007:Sample 40

text: ArrayExpress

text: chemo-naive

text: human

characteristic: common name

text: pancreatic ductal adenocarcinoma

characteristic: disease

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: pancreas

characteristic: organism part

text: tumor

text: Homo sapiens

text: Sample 40


E-MTAB-13007:Sample 41

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: E-MTAB-13007:Sample 41

text: ArrayExpress

text: chemo-naive

text: human

text: pancreatic ductal adenocarcinoma

text: Homo sapiens

text: Homo sapiens

text: pancreas

text: tumor

characteristic: sampling site

text: Homo sapiens

text: Sample 41

characteristic: tumor size


E-MTAB-13007:Sample 42

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-13007:Sample 42

characteristic: Submitter Id

text: ArrayExpress

text: chemo-naive

text: human

text: pancreatic ductal adenocarcinoma

text: Homo sapiens

text: Homo sapiens

text: pancreas

text: tumor

text: Homo sapiens

text: Sample 42

characteristic: title


E-MTAB-13007:Sample 43

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: public

text: E-MTAB-13007:Sample 43

text: ArrayExpress

text: chemo-naive

text: human

characteristic: description

text: pancreatic ductal adenocarcinoma

text: Homo sapiens

text: Homo sapiens

text: pancreas

text: tumor

text: Homo sapiens

text: Sample 43


E-MTAB-13007:Sample 44

characteristic: External Id

characteristic: INSDC center name

text: public

text: E-MTAB-13007:Sample 44

text: ArrayExpress

characteristic: broker name

text: chemo-naive

characteristic: clinical information

text: human

text: pancreatic ductal adenocarcinoma

text: Homo sapiens

text: Homo sapiens

text: pancreas

text: tumor

text: Homo sapiens

text: Sample 44


E-MTAB-13007:Sample 45

text: public

text: E-MTAB-13007:Sample 45

text: ArrayExpress

text: chemo-naive

text: human

characteristic: common name

text: pancreatic ductal adenocarcinoma

characteristic: disease

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: pancreas

characteristic: organism part

text: tumor

text: Homo sapiens

text: Sample 45


E-MTAB-13007:Sample 46

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: E-MTAB-13007:Sample 46

text: ArrayExpress

text: chemo-naive

text: human

text: pancreatic ductal adenocarcinoma

text: Homo sapiens

text: Homo sapiens

text: pancreas

text: tumor

characteristic: sampling site

text: Homo sapiens

text: Sample 46

characteristic: tumor size


E-MTAB-13007:Sample 47

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-13007:Sample 47

characteristic: Submitter Id

text: ArrayExpress

text: chemo-naive

text: human

text: pancreatic ductal adenocarcinoma

text: Homo sapiens

text: Homo sapiens

text: pancreas

text: tumor

text: Homo sapiens

text: Sample 47

characteristic: title


E-MTAB-13007:Sample 48

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: public

text: E-MTAB-13007:Sample 48

text: ArrayExpress

text: chemo-naive

text: human

characteristic: description

text: pancreatic ductal adenocarcinoma

text: Homo sapiens

text: Homo sapiens

text: pancreas

text: tumor

text: Homo sapiens

text: Sample 48


E-MTAB-13007:Sample 49

characteristic: External Id

characteristic: INSDC center name

text: public

text: E-MTAB-13007:Sample 49

text: ArrayExpress

characteristic: broker name

text: chemo-naive

characteristic: clinical information

text: human

text: pancreatic ductal adenocarcinoma

text: Homo sapiens

text: Homo sapiens

text: pancreas

text: tumor

text: Homo sapiens

text: Sample 49


E-MTAB-13007:Sample 5

text: public

text: E-MTAB-13007:Sample 5

text: ArrayExpress

text: chemo-naive

text: human

characteristic: common name

text: pancreatic ductal adenocarcinoma

characteristic: disease

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: pancreas

characteristic: organism part

text: tumor

text: Homo sapiens

text: Sample 5

text: not available


E-MTAB-13007:Sample 50

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: E-MTAB-13007:Sample 50

text: ArrayExpress

text: chemo-naive

text: human

text: pancreatic ductal adenocarcinoma

text: Homo sapiens

text: Homo sapiens

text: pancreas

text: tumor

characteristic: sampling site

text: Homo sapiens

text: Sample 50

characteristic: tumor size


E-MTAB-13007:Sample 6

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-13007:Sample 6

characteristic: Submitter Id

text: ArrayExpress

text: chemo-naive

text: human

text: pancreatic ductal adenocarcinoma

text: Homo sapiens

text: Homo sapiens

text: pancreas

text: tumor

text: Homo sapiens

text: Sample 6

characteristic: title

text: not available


E-MTAB-13007:Sample 7

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: public

text: E-MTAB-13007:Sample 7

text: ArrayExpress

text: chemo-naive

text: human

characteristic: description

text: pancreatic ductal adenocarcinoma

text: Homo sapiens

text: Homo sapiens

text: pancreas

text: tumor

text: Homo sapiens

text: Sample 7

text: not available


E-MTAB-13007:Sample 8

characteristic: External Id

characteristic: INSDC center name

text: public

text: E-MTAB-13007:Sample 8

text: ArrayExpress

characteristic: broker name

text: chemo-naive

characteristic: clinical information

text: human

text: pancreatic ductal adenocarcinoma

text: Homo sapiens

text: Homo sapiens

text: pancreas

text: tumor

text: Homo sapiens

text: Sample 8

text: not available


E-MTAB-13007:Sample 9

text: public

text: E-MTAB-13007:Sample 9

text: ArrayExpress

text: chemo-naive

text: human

characteristic: common name

text: pancreatic ductal adenocarcinoma

characteristic: disease

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: pancreas

characteristic: organism part

text: tumor

text: Homo sapiens

text: Sample 9

text: not available


text: UNIVERSITY OF LIVERPOOL

characteristic: INSDC first public

characteristic: INSDC last update

text: public

tag: Namespace:UNIVERSITY OF LIVERPOOL

text: human gut shotgun metagenomics

text: human

characteristic: environment (biome)

text: gut

characteristic: environment (feature)

text: faeces

characteristic: environment (material)

text: United Kingdom

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: human-associated environmental package

characteristic: human-associated environmental package

text: metagenome

characteristic: investigation type

text: England

characteristic: location within the United Kingdom

text: human gut metagenome

text: INTEGRATE

characteristic: project name

text: human gut metagenome

text: Illumina HiSeq

characteristic: sequencing method

characteristic: sequencing run

text: CGR

characteristic: sequencing site


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: UNIVERSITY OF LIVERPOOL

characteristic: INSDC center name

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: human gut shotgun metatranscriptomics

characteristic: description

text: human

text: gut

text: faeces

text: United Kingdom

text: human-associated environmental package

text: metatranscriptome

text: England

text: human gut metagenome

characteristic: organism

text: INTEGRATE

text: human gut metagenome

text: Illumina HiSeq

text: CGR

characteristic: title


text: WEIZMANN INSTITUE OF SCIENCE

characteristic: INSDC first public

characteristic: INSDC last update

text: public

tag: Namespace:WEIZMANN INSTITUE OF SCIENCE

text: Microbiome samples

characteristic: broad-scale environmental context

characteristic: collection date

text: house mouse

characteristic: common name

text: Stool sample KO mouse 1

text: Israel

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: Microbiome samples

characteristic: local environmental context

text: Mus musculus

text: Loss of TET2 and TET3 DNA demethylases results in aberrant differentiation and homeostasis in the small intestine

text: Mus musculus


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: WEIZMANN INSTITUE OF SCIENCE

text: public

text: Microbiome samples

text: house mouse

text: Stool sample KO mouse 2

text: Israel

text: Microbiome samples

text: Mus musculus

characteristic: project name

text: Mus musculus


text: WEIZMANN INSTITUE OF SCIENCE

characteristic: INSDC center name

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: Microbiome samples

text: house mouse

text: Stool sample KO mouse 3

characteristic: description

text: Israel

text: Microbiome samples

text: Mus musculus

text: Mus musculus


text: WEIZMANN INSTITUE OF SCIENCE

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: Microbiome samples

characteristic: broad-scale environmental context

text: house mouse

text: Stool sample KO mouse 4

text: Israel

text: Microbiome samples

text: Mus musculus

characteristic: organism

text: Mus musculus


text: WEIZMANN INSTITUE OF SCIENCE

text: public

text: Microbiome samples

characteristic: collection date

text: house mouse

characteristic: common name

text: Stool sample KO mouse 5

text: Israel

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

text: Microbiome samples

text: Mus musculus

text: Mus musculus


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: WEIZMANN INSTITUE OF SCIENCE

text: public

text: Microbiome samples

text: house mouse

text: Stool sample KO mouse 6

text: Israel

characteristic: geographic location (longitude)

text: Microbiome samples

characteristic: local environmental context

text: Mus musculus

text: Mus musculus


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: WEIZMANN INSTITUE OF SCIENCE

characteristic: INSDC center name

text: public

text: Microbiome samples

text: house mouse

text: Stool sample KO mouse 7

text: Israel

text: Microbiome samples

text: Mus musculus

characteristic: project name

text: Mus musculus


text: WEIZMANN INSTITUE OF SCIENCE

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: Microbiome samples

text: house mouse

text: Stool sample KO mouse 8

characteristic: description

text: Israel

text: Microbiome samples

text: Mus musculus

text: Mus musculus


text: WEIZMANN INSTITUE OF SCIENCE

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: Microbiome samples

characteristic: broad-scale environmental context

text: house mouse

text: Stool sample KO mouse 9

text: Israel

text: Microbiome samples

text: Mus musculus

characteristic: organism

text: Mus musculus


text: WEIZMANN INSTITUE OF SCIENCE

text: public

text: Microbiome samples

characteristic: collection date

text: house mouse

characteristic: common name

text: Stool sample KO mouse 10

text: Israel

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

text: Microbiome samples

text: Mus musculus

text: Mus musculus


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: WEIZMANN INSTITUE OF SCIENCE

text: public

text: Microbiome samples

text: house mouse

text: Stool sample KO mouse 11

text: Israel

characteristic: geographic location (longitude)

text: Microbiome samples

characteristic: local environmental context

text: Mus musculus

text: Mus musculus


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: WEIZMANN INSTITUE OF SCIENCE

characteristic: INSDC center name

text: public

text: Microbiome samples

text: house mouse

text: Stool sample KO mouse 12

text: Israel

text: Microbiome samples

text: Mus musculus

characteristic: project name

text: Mus musculus


text: WEIZMANN INSTITUE OF SCIENCE

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: Microbiome samples

text: house mouse

text: Stool sample KO mouse 13

characteristic: description

text: Israel

text: Microbiome samples

text: Mus musculus

text: Mus musculus


text: WEIZMANN INSTITUE OF SCIENCE

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: Microbiome samples

characteristic: broad-scale environmental context

text: house mouse

text: Sttol sample WT mouse 1

text: Israel

text: Microbiome samples

text: Mus musculus

characteristic: organism

text: Mus musculus


text: WEIZMANN INSTITUE OF SCIENCE

text: public

text: Microbiome samples

characteristic: collection date

text: house mouse

characteristic: common name

text: Sttol sample WT mouse 2

text: Israel

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

text: Microbiome samples

text: Mus musculus

text: Mus musculus


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: WEIZMANN INSTITUE OF SCIENCE

text: public

text: Microbiome samples

text: house mouse

text: Sttol sample WT mouse 3

text: Israel

characteristic: geographic location (longitude)

text: Microbiome samples

characteristic: local environmental context

text: Mus musculus

text: Mus musculus


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: WEIZMANN INSTITUE OF SCIENCE

characteristic: INSDC center name

text: public

text: Microbiome samples

text: house mouse

text: Sttol sample WT mouse 4

text: Israel

text: Microbiome samples

text: Mus musculus

characteristic: project name

text: Mus musculus


text: WEIZMANN INSTITUE OF SCIENCE

text: public

characteristic: INSDC status

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characteristic: geographic location (latitude)

text: Microbiome samples

text: Mus musculus

text: Mus musculus


characteristic: ENA-CHECKLIST

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text: house mouse

text: Intestinal content sample mouse 19 WT

text: Israel

characteristic: geographic location (longitude)

text: Microbiome samples

characteristic: local environmental context

text: Mus musculus

text: Mus musculus


characteristic: ENA-LAST-UPDATE

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tag: Namespace:Division of Genetics, Wadsworth Center, New York State Department of Health

text: ArrayExpress

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text: Protocols: Cultures were crosslinked by adding formaldehyde to a final concentration of 1%, incubated for 20 minutes at room temperature, and quenched by adding glycine to a final concentration of 0.5 M. Cells were washed once in original culture volume of 1X TBS then washed again in 1 mL of 1X TBS. The supernatant was removed and the pellet was stored at -20 degrees C. P. aeruginosa strains were grown overnight, back-diluted 1:100 in fresh LB media and grown to OD600 nm = 2.0. Extraction and Library construction occur in the same protocol: Pelleted cells were resuspended in FA lysis buffer containing 2 mg/mL of lysozyme. Samples were incubated for 30 minutes at 37 degrees C, chilled on ice for at least 5 minutes, and then sonicated for 30 minutes, with 30 s pulses followed by 30 s off. Samples were spun at maximum speed in a microcentrifuge, the supernatants were removed and diluted to 1 mL lysate per 20 mL original culture volume. Samples were immunoprecipitated according to the following procedure: for every 800 uL of chromatin, 25 uL of protein A beads (50% TBS slurry), and 10 uL anti-RhlR polyclonal antibody were added. Samples were incubated on rotisserie rotater for 90 minutes at room temperature. Samples were then transferred to Spin-X columns (Corning) and washed twice with FA lysis buffer (150 mM NaCl), 3 minutes each wash, rotating at room temperature. The samples were spun at 4000 rpm after each wash. The samples were then washed twice in the same way with 10 mM Tris-HCl, pH 7.5. The immunoprecipitated DNA, still attached to protein A beads, were then treated with Quick Blunting Kit (NEB): The samples were resuspended in the following mixture: 10 ul 10x quick blunting buffer, 10 ul dNTP mix (kit supplied), 80 ul dH2O, 2ul blunt enzyme mix. The samples were incubated at room temperature, while rotating, for 30 minutes. The samples were then washed twice with FA lysis buffer (150 mM NaCl), as described above, and then washed twice with 10 mM Tris-HCl, pH 8.0. The samples were then A tailed, using Klenow (3’->5’exo-), from NEB: The samples were resuspended in the following mixture: 10 ul 10X NEBuffer 2, 2 ul 100mM dATP (NEB), 88 ul dH2O, 2 ul Klenow. The samples were incubated at 37 degrees, while rotating, for 30 minutes. The samples were then washed twice with FA lysis buffer (150 mM NaCl), as described above, and then washed twice with 10 mM Tris-HCl, pH 7.5. Illumina adapters were then ligated to the samples using the NEB Quick Ligation kit. The samples were resuspended in the following mixture: 100 ul 1x ligase buffer (50 ul 2x buffer + 50 ul dH2O), 1 ul bracoded adapter, 4ul quick ligase. The samples were then incubated at room temperature, while rotating for 15 minutes. After incubation, the samples were washed, as decribed above, in the following buffers: FA lysis buffer; FA lysis buffer+500 mM NaCl; ChIP wash buffer; TE (10 mM Tris pH 8.0, 1 mM EDTA). Spin-X columns were transferred to a new microcentrifuge tube and 100 uL of ChIP elution buffer was added. Samples were incubated for 10 minutes at 65 degrees C then spun for 1 min at 1500 x g. Eluted DNA was then transferred to a new microcentrifuge tube and incubated for 10 minutes in a boiling water bath to de-crosslink samples. The samples were phenol extracted and ethanol precipitated. The samples were resuspended in 11ul. To determine cycle numbers for library amplification of each sample, 1ul ChIP DNA was used as a template (diluted 1/8 to fill 3 wells) for Real Time PCR with Illumina primers 1.1 and 2.1 (1 uM ea). The manual ct was set to 0.1 and 3 was added to the cycle number to determine the amount of cycles for library amplification. The ChIP DNA was used as a template, using the determined cycle number of: 95 degrees for 30 seconds, 60 degrees for 30 seconds, 72 degrees for 30 seconds. NEB Q5 high fidelity polymerase was used according to the manufacturer protocol with 8 ul ChIP DNA with ligated adapters as template, 1.0 ul Illumina primer 1.1 (100 uM), 1.0 ul Illumina primer 2.1 (100 uM). The libraries were checked on an 8% non-denaturing acrylamide gel. The smear from 200 bp to 500 bp was cut out and gel purified. The barcoded libraries were quantified using Qubit and pooled at equimolar concentrations. Extraction and Library construction occur in the same protocol: Pelleted cells were resuspended in FA lysis buffer containing 2 mg/mL of lysozyme. Samples were incubated for 30 minutes at 37 degrees C, chilled on ice for at least 5 minutes, and then sonicated for 30 minutes, with 30 s pulses followed by 30 s off. Samples were spun at maximum speed in a microcentrifuge, the supernatants were removed and diluted to 1 mL lysate per 20 mL original culture volume. Samples were immunoprecipitated according to the following procedure: for every 800 uL of chromatin, 25 uL of protein A beads (50% TBS slurry), and 10 uL anti-RhlR polyclonal antibody were added. Samples were incubated on rotisserie rotater for 90 minutes at room temperature. Samples were then transferred to Spin-X columns (Corning) and washed twice with FA lysis buffer (150 mM NaCl), 3 minutes each wash, rotating at room temperature. The samples were spun at 4000 rpm after each wash. The samples were then washed twice in the same way with 10 mM Tris-HCl, pH 7.5. The immunoprecipitated DNA, still attached to protein A beads, were then treated with Quick Blunting Kit (NEB): The samples were resuspended in the following mixture: 10 ul 10x quick blunting buffer, 10 ul dNTP mix (kit supplied), 80 ul dH2O, 2ul blunt enzyme mix. The samples were incubated at room temperature, while rotating, for 30 minutes. The samples were then washed twice with FA lysis buffer (150 mM NaCl), as described above, and then washed twice with 10 mM Tris-HCl, pH 8.0. The samples were then A tailed, using Klenow (3’->5’exo-), from NEB: The samples were resuspended in the following mixture: 10 ul 10X NEBuffer 2, 2 ul 100mM dATP (NEB), 88 ul dH2O, 2 ul Klenow. The samples were incubated at 37 degrees, while rotating, for 30 minutes. The samples were then washed twice with FA lysis buffer (150 mM NaCl), as described above, and then washed twice with 10 mM Tris-HCl, pH 7.5. Illumina adapters were then ligated to the samples using the NEB Quick Ligation kit. The samples were resuspended in the following mixture: 100 ul 1x ligase buffer (50 ul 2x buffer + 50 ul dH2O), 1 ul bracoded adapter, 4ul quick ligase. The samples were then incubated at room temperature, while rotating for 15 minutes. After incubation, the samples were washed, as decribed above, in the following buffers: FA lysis buffer; FA lysis buffer+500 mM NaCl; ChIP wash buffer; TE (10 mM Tris pH 8.0, 1 mM EDTA). Spin-X columns were transferred to a new microcentrifuge tube and 100 uL of ChIP elution buffer was added. Samples were incubated for 10 minutes at 65 degrees C then spun for 1 min at 1500 x g. Eluted DNA was then transferred to a new microcentrifuge tube and incubated for 10 minutes in a boiling water bath to de-crosslink samples. The samples were phenol extracted and ethanol precipitated. The samples were resuspended in 11ul. To determine cycle numbers for library amplification of each sample, 1ul ChIP DNA was used as a template (diluted 1/8 to fill 3 wells) for Real Time PCR with Illumina primers 1.1 and 2.1 (1 uM ea). The manual ct was set to 0.1 and 3 was added to the cycle number to determine the amount of cycles for library amplification. The ChIP DNA was used as a template, using the determined cycle number of: 95 degrees for 30 seconds, 60 degrees for 30 seconds, 72 degrees for 30 seconds. NEB Q5 high fidelity polymerase was used according to the manufacturer protocol with 8 ul ChIP DNA with ligated adapters as template, 1.0 ul Illumina primer 1.1 (100 uM), 1.0 ul Illumina primer 2.1 (100 uM). The libraries were checked on an 8% non-denaturing acrylamide gel. The smear from 200 bp to 500 bp was cut out and gel purified. The barcoded libraries were quantified using Qubit and pooled at equimolar concentrations.

text: pqsE D73A

characteristic: genotype

text: Pseudomonas aeruginosa

text: Pseudomonas aeruginosa

text: whole organism

characteristic: organism part

text: Pseudomonas aeruginosa

characteristic: strain

characteristic: title


text: Division of Genetics, Wadsworth Center, New York State Department of Health

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text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: ArrayExpress

characteristic: description

text: pqsE D73A

text: Pseudomonas aeruginosa

characteristic: organism

text: Pseudomonas aeruginosa

text: whole organism

text: Pseudomonas aeruginosa


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: public

text: ArrayExpress

text: pqsE R243A/R246A/R247A

text: Pseudomonas aeruginosa

text: Pseudomonas aeruginosa

text: whole organism

text: Pseudomonas aeruginosa


characteristic: ENA-LAST-UPDATE

text: public

text: ArrayExpress

text: wild type genotype

text: Pseudomonas aeruginosa

text: Pseudomonas aeruginosa

text: whole organism

text: Pseudomonas aeruginosa


characteristic: External Id

text: public

text: ArrayExpress

text: ΔpqsE

text: Pseudomonas aeruginosa

text: Pseudomonas aeruginosa

text: whole organism

text: Pseudomonas aeruginosa


E-MTAB-12966:ΔrhlI ΔpqsE-1

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text: public

text: E-MTAB-12966:ΔrhlI ΔpqsE-1

text: ArrayExpress

text: ΔrhlI ΔpqsE

text: Pseudomonas aeruginosa

text: Pseudomonas aeruginosa

text: whole organism

text: Pseudomonas aeruginosa

text: ΔrhlI ΔpqsE-1


E-MTAB-12966:ΔrhlI ΔpqsE-2

text: public

text: E-MTAB-12966:ΔrhlI ΔpqsE-2

text: ArrayExpress

characteristic: broker name

text: ΔrhlI ΔpqsE

text: Pseudomonas aeruginosa

text: Pseudomonas aeruginosa

text: whole organism

text: Pseudomonas aeruginosa

text: ΔrhlI ΔpqsE-2


text: public

text: ArrayExpress

text: ΔrhlI

characteristic: genotype

text: Pseudomonas aeruginosa

text: Pseudomonas aeruginosa

text: whole organism

text: Pseudomonas aeruginosa


text: public

text: ArrayExpress

text: ΔrhlR

text: Pseudomonas aeruginosa

text: Pseudomonas aeruginosa

text: whole organism

characteristic: organism part

text: Pseudomonas aeruginosa


text: public

tag: Namespace:Advanced Centre for Treatment Research and Education in Cancer (ACTREC)

text: ArrayExpress

text: human

characteristic: common name

text: Protocols: The samples AD2881 and AD2882 are primary tongue tumor and paired adjacent tongue tissue normal, respectively, from a clinically early stage (T2N0M0) tongue cancer patient. The samples were collected from a male patient, aged 38 at the time of sample collection. The patient has a habit of tobacco chewing and alcohol consumption. NT8E cell line was established within the Tata Memorial Centre (Mulherkar et al., Cancer Letters, 1997) and was acquired from the Tata Memorial Hospital, Mumbai, India. NT8E is an epithelial cell line established from the surgical specimen of an untreated, upper aero-digestive tract tumor, diagnosed as a squamous carcinoma of the pyriform fossa. The sex and age of the donor are not available. Also, the NT8E cell line is not deposited in the cell line repositories, such as ATCC, and hence, there is no catalogue number. Each sample was collected by scrapping the cells from a 10cm cell culture dish. Pellet was stored at -20 degrees. NT8E cells were cultured in DMEM medium. The media was supplemented with 10% FBS, 2.5 mg/ml Amphotericin-B (Abbott) and 1.25 μl/ml Gentamycin (Abbott). The cells were cultured at 37 °C in a 5% CO2 incubator. Genomic DNA extraction from the tissue samples was performed using AllPrep DNA/RNA/miRNA Universal Kit (Cat No. 80224, QIAGEN). About 20-30mg tissue sections were cut into small pieces and subjected to bead-based homogenization in 600µL lysis buffer using FastPrep homogenizer (MP Biomedicals, USA) and further processed for genomic DNA extraction as per manufacturer’s protocol. Genomic DNA from the cell lines were extracted using DNeasy Blood and tissue DNA extraction kit (Cat No. 69506, QIAGEN) according to manufacturer’s instructions. Whole genome sequencing (WGS) library was prepared with Illumina-compatible NEXTFlex Rapid DNA Sequencing Bundle (5144-02, NEXTFlex, BIOO Scientific, Inc. USA). Briefly, 300 ng of Qubit quantified DNA was sheared in Covaris microTUBE AFA (520045, Life Technologies) using Covaris S220 sonicator (4465653, Life Technologies, Covaris, Inc. USA) to generate specific fragments with size range of 300-400 bp. The fragment size distribution was verified on Agilent 2100 Bioanalyzer and subsequently purified using HighPrep magnetic beads (AC-60050, MagBio Genomics, Inc, USA). Purified fragments were end-repaired, adenylated and ligated to Illumina multiplex barcode adaptors as per NEXTFlex Rapid DNA sequencing bundle kit protocol. Adapter-ligated DNA was purified using HighPrep beads. Resultant fragments were amplified for 5 cycles of PCR using Illumina-compatible primers provided in the NEXTflex Rapid DNA sequencing Bundle. Final PCR product (sequencing library) was purified with HighPrep beads, followed by library quality control. Sequencing library was quantified by Qubit fluorometer (Thermo Fisher Scientific, MA, USA) and its fragment size distribution was analyzed on Agilent 2100 Bioanalyzer (5067-4626, Agilent High Sensitivity DNA Bioanalyzer Kit).

text: adult

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text: head and neck squamous cell carcinoma

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text: wild type genotype

characteristic: individual

text: Homo sapiens

text: Homo sapiens

text: oropharynx

text: neoplasm

characteristic: sampling site

text: Homo sapiens


text: Advanced Centre for Treatment Research and Education in Cancer (ACTREC)

characteristic: INSDC first public

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characteristic: SRA accession

unit: year

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text: human

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characteristic: sex

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characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

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text: public

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text: ArrayExpress

text: human

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text: Homo sapiens

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text: Homo sapiens

text: male


text: UKHSA

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text: ena-SAMPLE-TAB-22-05-2023-15:57:03:878-15561

characteristic: collection date

text: PVL+

text: United Kingdom

characteristic: geographic location (country and/or sea)

text: diseased

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text: Homo sapien

characteristic: host scientific name

characteristic: isolate

text: Infected person

text: Staphylococcus aureus

text: Staphylococcus aureus


text: UKHSA

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characteristic: INSDC last update

text: public

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characteristic: SRA accession

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text: Staphylococcus aureus


characteristic: ENA-CHECKLIST

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characteristic: title


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text: Staphylococcus aureus

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text: UKHSA

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text: diseased

characteristic: host health state

text: Homo sapien

text: Infected person

text: Staphylococcus aureus

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text: UKHSA

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text: Infected person

text: Staphylococcus aureus

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text: UKHSA

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characteristic: SRA accession

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text: Staphylococcus aureus

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characteristic: ENA-CHECKLIST

text: CEA-MIRCEN

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text: Round 4 of SELEX

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characteristic: ENA-FIRST-PUBLIC

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text: CEA-MIRCEN

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characteristic: External Id

text: CEA-MIRCEN

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text: Round 6 of SELEX

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text: SELEX Round 06


text: CEA-MIRCEN

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text: synthetic construct

text: SELEX Round 07


text: CEA-MIRCEN

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text: public

characteristic: collection date

text: Round 8 of SELEX

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text: SELEX Round 08


text: CEA-MIRCEN

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text: Round 9 of SELEX

text: France

characteristic: geographic location (country and/or sea)

text: synthetic construct

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text: SELEX Round 09


text: CEA-MIRCEN

text: public

text: Round 10 of SELEX

text: France

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text: SELEX Round 10


text: CEA-MIRCEN

text: public

text: Round 11 of SELEX

text: France

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text: synthetic construct

text: SELEX Round 11


text: CEA-MIRCEN

text: public

text: Round 12 of SELEX

text: France

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text: SELEX Round 12


text: CEA-MIRCEN

text: public

text: Round 09 of control SELEX

text: France

text: synthetic construct

text: synthetic construct

text: SELEX Round c09


text: CEA-MIRCEN

text: public

text: Round 11 of control SELEX

text: France

text: synthetic construct

text: synthetic construct

text: SELEX Round c11


text: CEA-MIRCEN

text: public

text: Round 12 of control SELEX

text: France

text: synthetic construct

text: synthetic construct

text: SELEX Round c12


text: Wellcome Sanger Institute

text: public

tag: Namespace:Wellcome Sanger Institute

text: 45 to 50

characteristic: age

text: ArrayExpress

characteristic: broker name

text: human

characteristic: common name

text: Protocols: Hearts were acquired after circulatory death (DCD) or after brain death (DBD). For DCD donors after confirmation of death there was a mandatory five-minute stand-off prior to sternotomy. In all cases the aorta was cross-clamped and cold cardioplegia solution was administered to the aortic root prior to cardiotomy. AV1, AV3, AV10, AV13 and AV14 were procured in the standard fashion and then immediately preserved with and transported on a hypothermic perfusion machine. AH2 was similarly preserved, but with immediate normothermic perfusion. It then underwent 4 hours of normothermic perfusion before samples were taken. For spatial transcriptomics, ventricle regions, whose thickness were larger than one side of the Visium frame (6 mm), were separated into epicardial and endocardial portions. Samples used for single nuclei isolation and spatial transcriptomics were flash-frozen or frozen in OCT and stored at −80 °C, or formalin-fixed and subsequently embedded in paraffin blocks. All tissues were stored and transported on ice at all times until freezing or tissue dissociation to minimise any transcriptional degradation. Fresh-frozen (FF) samples: Fresh samples were frozen and embedded in optimal cutting temperature medium (OCT) using a dry ice-cooled bath of isopentane at -45°C. OCT-embedded samples were sectioned using a cryostat (Leica CX3050S) and were cut at 10 μm. Samples of the microanatomical regions of interest were selected on the basis of morphology with expert review (SYH), orientation (based on HE) and RNA integrity number was obtained using Agilent 2100 Bioanalyzer. The Tissue Optimization protocol from 10x Genomics was performed to obtain a permeabilisation time of 45 min, and the FF Visium Spatial Gene Expression experiment (v1 chemistry) was performed as per the manufacturer’s protocol (10x Genomics). H&E stained Visium Gene Expression slides were imaged at 40× on Hamamatsu NanoZoomer S60. cDNA library preparation was were carried out according to the manufacturer’s protocol.

text: adult

characteristic: developmental stage

text: normal

characteristic: disease

characteristic: individual

text: Homo sapiens

text: Homo sapiens

text: right cardiac atrium

characteristic: organism part

text: Homo sapiens

text: male

characteristic: sex


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: Wellcome Sanger Institute

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: 45 to 50

text: ArrayExpress

text: human

text: adult

text: normal

text: Homo sapiens

text: Homo sapiens

text: left cardiac atrium

text: Homo sapiens

text: male

characteristic: title


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Wellcome Sanger Institute

characteristic: INSDC center name

text: public

characteristic: Submitter Id

text: 45 to 50

text: ArrayExpress

text: human

characteristic: description

text: adult

text: normal

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: apical region of left ventricle

text: Homo sapiens

text: male


text: Wellcome Sanger Institute

text: public

text: 55 to 60

characteristic: age

text: ArrayExpress

characteristic: broker name

text: human

characteristic: common name

text: adult

characteristic: developmental stage

text: normal

characteristic: disease

text: Homo sapiens

text: Homo sapiens

text: heart right ventricle

text: Homo sapiens

text: male


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: Wellcome Sanger Institute

text: public

text: 55 to 60

text: ArrayExpress

text: human

text: adult

text: normal

characteristic: individual

text: Homo sapiens

text: Homo sapiens

text: interventricular septum

characteristic: organism part

text: Homo sapiens

text: male

characteristic: sex


text: Wellcome Sanger Institute

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: 45 to 50

text: ArrayExpress

text: human

text: adult

text: normal

text: Homo sapiens

text: Homo sapiens

text: sinoatrial node

text: Homo sapiens

text: female

characteristic: title


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Wellcome Sanger Institute

characteristic: INSDC center name

text: public

characteristic: Submitter Id

text: 70 to 75

text: ArrayExpress

text: human

characteristic: description

text: adult

text: normal

text: Homo sapiens

text: Homo sapiens

text: atrioventricular node

text: Homo sapiens

text: female


text: Wellcome Sanger Institute

text: public

text: 45 to 50

characteristic: age

text: ArrayExpress

characteristic: broker name

text: human

characteristic: common name

text: adult

characteristic: developmental stage

text: normal

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: interventricular septum

text: Homo sapiens

text: female


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: Wellcome Sanger Institute

text: public

text: 45 to 50

text: ArrayExpress

text: human

text: adult

text: normal

characteristic: disease

characteristic: individual

text: Homo sapiens

text: Homo sapiens

text: atrioventricular node

characteristic: organism part

text: Homo sapiens

text: female


text: Wellcome Sanger Institute

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: 45 to 50

text: ArrayExpress

text: human

text: Protocols: Hearts were acquired after circulatory death (DCD) or after brain death (DBD). For DCD donors after confirmation of death there was a mandatory five-minute stand-off prior to sternotomy. In all cases the aorta was cross-clamped and cold cardioplegia solution was administered to the aortic root prior to cardiotomy. AV1, AV3, AV10, AV13 and AV14 were procured in the standard fashion and then immediately preserved with and transported on a hypothermic perfusion machine. AH2 was similarly preserved, but with immediate normothermic perfusion. It then underwent 4 hours of normothermic perfusion before samples were taken. For spatial transcriptomics, ventricle regions, whose thickness were larger than one side of the Visium frame (6 mm), were separated into epicardial and endocardial portions. Samples used for single nuclei isolation and spatial transcriptomics were flash-frozen or frozen in OCT and stored at −80 °C, or formalin-fixed and subsequently embedded in paraffin blocks. All tissues were stored and transported on ice at all times until freezing or tissue dissociation to minimise any transcriptional degradation. Formalin-fixed paraffin-embedded (FFPE) samples: Fresh samples were fixed in >5 times their volume of 4% v/v formalin at ambient temperature for 24 hours before processing to paraffin on a Tissue-Tek Vacuum Infiltration Processor 5 (Sakura Finetek). FFPE blocks were sectioned at 5 μm using a microtome (Leica RM2125RT). Samples of the microanatomical regions of interest were selected on the basis of morphology with expert review (SYH), orientation (based on HE) and DV200 was obtained using Agilent 2100 Bioanalyzer. In addition, FFPE tissues were checked for possible detachment issues using the 10x Genomics Adhesion test slides. FFPE Visium Spatial Gene Expression (v1 chemistry) was performed following the manufacturer’s protocol (10x genomics). H&E stained Visium Gene Expression slides were imaged at 40× on Hamamatsu NanoZoomer S60. cDNA library preparation was were carried out according to the manufacturer’s protocol.

text: adult

text: normal

text: Homo sapiens

text: Homo sapiens

text: sinoatrial node

text: Homo sapiens

text: female

characteristic: sex


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Wellcome Sanger Institute

characteristic: INSDC center name

text: public

characteristic: Submitter Id

text: 40 to 45

text: ArrayExpress

text: human

text: adult

text: normal

text: Homo sapiens

text: Homo sapiens

text: sinoatrial node

text: Homo sapiens

text: male

characteristic: title


text: Wellcome Sanger Institute

text: public

text: 40 to 45

characteristic: age

text: ArrayExpress

characteristic: broker name

text: human

characteristic: common name

characteristic: description

text: adult

characteristic: developmental stage

text: normal

text: Homo sapiens

text: Homo sapiens

text: atrioventricular node

text: Homo sapiens

text: male


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: Wellcome Sanger Institute

text: public

text: 50 to 55

text: ArrayExpress

text: human

text: adult

text: normal

characteristic: disease

characteristic: individual

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: atrioventricular node

text: Homo sapiens

text: female


text: Wellcome Sanger Institute

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: 45 to 50

text: ArrayExpress

text: human

text: adult

text: normal

text: Homo sapiens

text: Homo sapiens

text: sinoatrial node

characteristic: organism part

text: Homo sapiens

text: male


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Wellcome Sanger Institute

characteristic: INSDC center name

text: public

characteristic: Submitter Id

text: 20 to 25

text: ArrayExpress

text: human

text: adult

text: normal

text: Homo sapiens

text: Homo sapiens

text: sinoatrial node

text: Homo sapiens

text: female

characteristic: sex


text: Wellcome Sanger Institute

text: public

text: 65 to 70

characteristic: age

text: ArrayExpress

characteristic: broker name

text: human

characteristic: common name

characteristic: description

text: adult

text: normal

text: Homo sapiens

text: Homo sapiens

text: heart left ventricle

text: Homo sapiens

text: female

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: Wellcome Sanger Institute

text: public

text: 65 to 70

text: ArrayExpress

text: human

text: adult

characteristic: developmental stage

text: normal

characteristic: disease

characteristic: individual

text: Homo sapiens

text: Homo sapiens

text: left cardiac atrium

text: Homo sapiens

text: female


text: Wellcome Sanger Institute

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: 65 to 70

text: ArrayExpress

text: human

text: adult

text: normal

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: apical region of left ventricle

text: Homo sapiens

text: female


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Wellcome Sanger Institute

characteristic: INSDC center name

text: public

characteristic: Submitter Id

text: 65 to 70

text: ArrayExpress

text: human

text: adult

text: normal

text: Homo sapiens

text: Homo sapiens

text: right cardiac atrium

characteristic: organism part

text: Homo sapiens

text: female


text: Wellcome Sanger Institute

text: public

text: 65 to 70

characteristic: age

text: ArrayExpress

characteristic: broker name

text: human

characteristic: common name

characteristic: description

text: adult

text: normal

text: Homo sapiens

text: Homo sapiens

text: interventricular septum

text: Homo sapiens

text: female

characteristic: sex


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: Wellcome Sanger Institute

text: public

text: 65 to 70

text: ArrayExpress

text: human

text: adult

characteristic: developmental stage

text: normal

characteristic: disease

text: Homo sapiens

text: Homo sapiens

text: heart right ventricle

text: Homo sapiens

text: female

characteristic: title


text: Wellcome Sanger Institute

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: 65 to 70

text: ArrayExpress

text: human

text: adult

text: normal

characteristic: individual

text: Homo sapiens

text: Homo sapiens

text: heart right ventricle

text: Homo sapiens

text: male


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Wellcome Sanger Institute

characteristic: INSDC center name

text: public

characteristic: Submitter Id

text: 65 to 70

text: ArrayExpress

text: human

text: adult

text: normal

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: left cardiac atrium

text: Homo sapiens

text: male


text: Wellcome Sanger Institute

text: public

text: 65 to 70

characteristic: age

text: ArrayExpress

characteristic: broker name

text: human

characteristic: common name

characteristic: description

text: adult

text: normal

text: Homo sapiens

text: Homo sapiens

text: apical region of left ventricle

characteristic: organism part

text: Homo sapiens

text: male


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: Wellcome Sanger Institute

text: public

text: 65 to 70

text: ArrayExpress

text: human

text: adult

characteristic: developmental stage

text: normal

characteristic: disease

text: Homo sapiens

text: Homo sapiens

text: heart left ventricle

text: Homo sapiens

text: male

characteristic: sex


text: Wellcome Sanger Institute

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: 65 to 70

text: ArrayExpress

text: human

text: adult

text: normal

text: Homo sapiens

text: Homo sapiens

text: right cardiac atrium

text: Homo sapiens

text: male

characteristic: title


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Wellcome Sanger Institute

characteristic: INSDC center name

text: public

characteristic: Submitter Id

text: 60 to 65

text: ArrayExpress

text: human

text: adult

text: normal

characteristic: individual

text: Homo sapiens

text: Homo sapiens

text: right cardiac atrium

text: Homo sapiens

text: male


text: Wellcome Sanger Institute

text: public

text: 60 to 65

characteristic: age

text: ArrayExpress

characteristic: broker name

text: human

characteristic: common name

characteristic: description

text: adult

text: normal

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: heart left ventricle

text: Homo sapiens

text: male


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: Anthony Smith, NICD

text: public

tag: Namespace:Anthony Smith, NICD

text: EnteroBase

text: EnteroBase

text: A. Smith, National Institute for Communicable Diseases

characteristic: collection date

text: Whole genome sequencing data uploaded by EnteroBase user

text: South Africa, Mpumalanga

characteristic: geographic location

text: Human, Stool

text: Salmonella enterica

text: Salmonella enterica

text: Enteritidis

characteristic: serovar

characteristic: strain


text: Anthony Smith, NICD

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: EnteroBase

text: EnteroBase

text: South Africa, Free State

text: Human, Stool

text: Salmonella enterica

text: Salmonella enterica

text: Enteritidis

characteristic: title


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Anthony Smith, NICD

characteristic: INSDC center name

text: public

characteristic: Submitter Id

text: EnteroBase

text: EnteroBase

text: South Africa, Gauteng

text: Human, Blood culture

text: Salmonella enterica

text: Salmonella enterica

text: Enteritidis


text: ERIBA, RUG , UMC GRONINGEN

text: public

tag: Namespace:ERIBA, RUG , UMC GRONINGEN

text: human

characteristic: common name

text: HAP1 cells with sgLUC and siSCR

characteristic: description

text: Homo sapiens

text: Homo sapiens

text: HAP1 cells sgLUC+siSCR


characteristic: ENA-CHECKLIST

text: ERIBA, RUG , UMC GRONINGEN

text: public

text: human

text: HAP1 cells with sgLUC and siBLM

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: HAP1 cells sgLUC+siBLM


characteristic: ENA-FIRST-PUBLIC

text: ERIBA, RUG , UMC GRONINGEN

text: public

text: human

text: HAP1 cells with sgFIGNL1 and siSCR

text: Homo sapiens

text: Homo sapiens

text: HAP1 cells sgFIGNL1+siSCR


text: ERIBA, RUG , UMC GRONINGEN

text: public

text: human

text: HAP1 cells with sgFIGNL1 and siBLM

text: Homo sapiens

text: Homo sapiens

text: HAP1 cells sgFIGNL1+siBLM


text: ERIBA, RUG , UMC GRONINGEN

text: public

text: human

text: HAP1 cells with sgC1ORF112 and siSCR

text: Homo sapiens

text: Homo sapiens

text: HAP1 cells sgC1ORF112+siSCR


text: ERIBA, RUG , UMC GRONINGEN

text: public

text: human

text: HAP1 cells with sgC1ORF112 and siBLM

text: Homo sapiens

text: Homo sapiens

text: HAP1 cells sgC1ORF112+siBLM