characteristic: ENA-CHECKLIST

characteristic: External Id

text: DTU-GE

text: public

text: DTU-GE

characteristic: broker name

text: Global sewage consortium

characteristic: collected by

characteristic: collection date

text: Yes

characteristic: environmental sample

text: Malta

text: No

text: wastewater

text: wastewater metagenome

text: wastewater metagenome


status: PUBLIC

tag: attribute

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: DTU-GE

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: DTU-GE

text: Global sewage consortium

text: Yes

text: Hungary

characteristic: geographic location (country and/or sea)

unit: DD

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: No

characteristic: is the sequenced pathogen host associated?

characteristic: isolate

text: wastewater

characteristic: isolation source non-host-associated

text: wastewater metagenome

characteristic: organism

text: wastewater metagenome

characteristic: strain


characteristic: ENA-CHECKLIST

characteristic: External Id

text: DTU-GE

text: public

text: DTU-GE

characteristic: broker name

text: Global sewage consortium

characteristic: collected by

characteristic: collection date

text: Yes

characteristic: environmental sample

text: Saudi Arabia

text: No

text: wastewater

text: wastewater metagenome

text: wastewater metagenome


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: DTU-GE

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: DTU-GE

text: Global sewage consortium

text: Yes

text: Saint Lucia

text: No

text: wastewater

text: wastewater metagenome

text: wastewater metagenome


text: DTU-GE

text: public

characteristic: SRA accession

characteristic: Submitter Id

text: DTU-GE

text: Global sewage consortium

text: Yes

text: India

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: No

characteristic: is the sequenced pathogen host associated?

text: wastewater

text: wastewater metagenome

text: wastewater metagenome


characteristic: ENA-CHECKLIST

characteristic: External Id

text: DTU-GE

text: public

text: DTU-GE

text: Global sewage consortium

text: Yes

text: Togo

text: No

characteristic: isolate

text: wastewater

characteristic: isolation source non-host-associated

text: wastewater metagenome

characteristic: organism

text: wastewater metagenome

characteristic: strain


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: DTU-GE

text: public

text: DTU-GE

characteristic: broker name

text: Global sewage consortium

characteristic: collected by

characteristic: collection date

text: Yes

characteristic: environmental sample

text: Cote d'Ivoire

text: No

text: wastewater

text: wastewater metagenome

text: wastewater metagenome


text: DTU-GE

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: DTU-GE

text: Global sewage consortium

text: Yes

text: Nigeria

text: No

text: wastewater

text: wastewater metagenome

text: wastewater metagenome


characteristic: ENA-CHECKLIST

characteristic: External Id

text: DTU-GE

text: public

text: DTU-GE

text: Global sewage consortium

text: Yes

text: Botswana

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: No

characteristic: is the sequenced pathogen host associated?

text: wastewater

text: wastewater metagenome

text: wastewater metagenome


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: DTU-GE

text: public

text: DTU-GE

text: Global sewage consortium

text: Yes

text: Taiwan

text: No

characteristic: isolate

text: wastewater

characteristic: isolation source non-host-associated

text: wastewater metagenome

characteristic: organism

text: wastewater metagenome

characteristic: strain


text: DTU-GE

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: DTU-GE

characteristic: broker name

text: Global sewage consortium

characteristic: collected by

characteristic: collection date

text: Yes

characteristic: environmental sample

text: USA

text: No

text: wastewater

text: wastewater metagenome

text: wastewater metagenome


characteristic: ENA-CHECKLIST

characteristic: External Id

text: DTU-GE

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: DTU-GE

text: Global sewage consortium

text: Yes

text: Ecuador

text: No

text: wastewater

text: wastewater metagenome

text: wastewater metagenome


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: DTU-GE

text: public

text: DTU-GE

text: Global sewage consortium

text: Yes

text: Peru

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: No

characteristic: is the sequenced pathogen host associated?

text: wastewater

text: wastewater metagenome

text: wastewater metagenome


metagenome data1

text: ROBERT KOCH INSTITUT

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: metagenome data1

tag: Namespace:ROBERT KOCH INSTITUT

text: rainbow trout

characteristic: common name

text: Oncorhynchus mykiss

characteristic: isolate

text: Salmon

characteristic: isolation source

text: Oncorhynchus mykiss

characteristic: organism

characteristic: receipt date

text: Oncorhynchus mykiss

text: metagenome data

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: External Id

text: UMC Utrecht

characteristic: INSDC last update

text: public

characteristic: INSDC status

tag: Namespace:UMC Utrecht

characteristic: collection date

text: USA

text: not provided

characteristic: host health state

text: Homo sapiens

characteristic: host scientific name

text: Streptococcus pyogenes 5448

text: Clinical

text: Streptococcus pyogenes

text: Streptococcus pyogenes

text: Tn Seq Streptococcus pyogenes 5448


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: DTU

text: public

characteristic: SRA accession

characteristic: Submitter Id

text: DTU-GE

characteristic: broker name

text: Denmark

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: metagenome

characteristic: investigation type

text: wastewater metagenome

text: Global sewage

characteristic: project name

text: wastewater metagenome

text: metagenomics

characteristic: sequencing method

text: wastewater/sludge

characteristic: wastewater/sludge environmental package


characteristic: ENA-CHECKLIST

characteristic: External Id

text: UNIVERSITY OF LIVERPOOL

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

tag: Namespace:UNIVERSITY OF LIVERPOOL

text: bread wheat

characteristic: common name

text: Triticum aestivum

characteristic: organism

text: Triticum aestivum

text: Chinese Spring

characteristic: strain

text: 21 day seedling

characteristic: tissue type

text: Wheat gene capture for Chinese Spring-technical replicate 1 of 4

characteristic: title


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: UNIVERSITY OF LIVERPOOL

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: bread wheat

text: Triticum aestivum

text: Triticum aestivum

text: Chinese Spring

text: 21 day seedling

text: Wheat gene capture for Chinese Spring-technical replicate 2 of 4


text: UNIVERSITY OF LIVERPOOL

text: public

text: bread wheat

text: Triticum aestivum

text: Triticum aestivum

text: Chinese Spring

text: 21 day seedling

text: Wheat gene capture for Chinese Spring-technical replicate 3 of 4


text: UNIVERSITY OF LIVERPOOL

text: public

text: bread wheat

text: Triticum aestivum

text: Triticum aestivum

text: Chinese Spring

text: 21 day seedling

text: Wheat gene capture for Chinese Spring-technical replicate 4 of 4


text: UNIVERSITY OF LIVERPOOL

text: public

text: bread wheat

text: Triticum aestivum

text: Triticum aestivum

text: Chinese Spring

text: 21 day seedling

text: Wheat promoter capture for Chinese Spring-technical replicate 1 of 4


text: UNIVERSITY OF LIVERPOOL

text: public

text: bread wheat

text: Triticum aestivum

text: Triticum aestivum

text: Chinese Spring

text: 21 day seedling

text: Wheat promoter capture for Chinese Spring-technical replicate 2 of 4


text: UNIVERSITY OF LIVERPOOL

text: public

text: bread wheat

text: Triticum aestivum

text: Triticum aestivum

text: Chinese Spring

text: 21 day seedling

text: Wheat promoter capture for Chinese Spring-technical replicate 3 of 4


text: UNIVERSITY OF LIVERPOOL

text: public

text: bread wheat

text: Triticum aestivum

text: Triticum aestivum

text: Chinese Spring

text: 21 day seedling

text: Wheat promoter capture for Chinese Spring-technical replicate 4 of 4


text: UNIVERSITY OF LIVERPOOL

text: public

text: bread wheat

text: Triticum aestivum

text: Triticum aestivum

text: Chinese Spring

text: 21 day seedling

text: Wheat gene capture for CIMMYT line 5


text: UNIVERSITY OF LIVERPOOL

text: public

text: bread wheat

text: Triticum aestivum

text: Triticum aestivum

text: Chinese Spring

text: 21 day seedling

text: Wheat promoter capture for CIMMYT line 5


text: UNIVERSITY OF LIVERPOOL

text: public

text: bread wheat

text: Triticum aestivum

text: Triticum aestivum

text: Chinese Spring

text: 21 day seedling

text: Wheat gene capture for CIMMYT line 8


text: UNIVERSITY OF LIVERPOOL

text: public

text: bread wheat

text: Triticum aestivum

text: Triticum aestivum

text: Chinese Spring

text: 21 day seedling

text: Wheat promoter capture for CIMMYT line 8


text: UNIVERSITY OF LIVERPOOL

text: public

text: bread wheat

text: Triticum aestivum

text: Triticum aestivum

text: Chinese Spring

text: 21 day seedling

text: Wheat gene capture for CIMMYT line 11


text: UNIVERSITY OF LIVERPOOL

text: public

text: bread wheat

text: Triticum aestivum

text: Triticum aestivum

text: Chinese Spring

text: 21 day seedling

text: Wheat promoter capture for CIMMYT line 11


text: UNIVERSITY OF LIVERPOOL

text: public

text: bread wheat

text: Triticum aestivum

text: Triticum aestivum

text: Chinese Spring

text: 21 day seedling

text: Wheat gene capture for CIMMYT line 15


text: UNIVERSITY OF LIVERPOOL

text: public

text: bread wheat

text: Triticum aestivum

text: Triticum aestivum

text: Chinese Spring

text: 21 day seedling

text: Wheat promoter capture for CIMMYT line 15


text: UNIVERSITY OF LIVERPOOL

text: public

text: bread wheat

text: Triticum aestivum

text: Triticum aestivum

text: Chinese Spring

text: 21 day seedling

text: Wheat gene capture for CIMMYT line 17


text: UNIVERSITY OF LIVERPOOL

text: public

text: bread wheat

text: Triticum aestivum

text: Triticum aestivum

text: Chinese Spring

text: 21 day seedling

text: Wheat promoter capture for CIMMYT line 17


text: UNIVERSITY OF LIVERPOOL

text: public

text: bread wheat

text: Triticum aestivum

text: Triticum aestivum

text: Chinese Spring

text: 21 day seedling

text: Wheat gene capture for CIMMYT line 19


text: UNIVERSITY OF LIVERPOOL

text: public

text: bread wheat

text: Triticum aestivum

text: Triticum aestivum

text: Chinese Spring

text: 21 day seedling

text: Wheat promoter capture for CIMMYT line 19


text: UNIVERSITY OF LIVERPOOL

text: public

text: bread wheat

text: Triticum aestivum

text: Triticum aestivum

text: Chinese Spring

text: 21 day seedling

text: Wheat gene capture for CIMMYT line 23


text: UNIVERSITY OF LIVERPOOL

text: public

text: bread wheat

text: Triticum aestivum

text: Triticum aestivum

text: Chinese Spring

text: 21 day seedling

text: Wheat promoter capture for CIMMYT line 23


text: UNIVERSITY OF LIVERPOOL

text: public

text: bread wheat

text: Triticum aestivum

text: Triticum aestivum

text: Chinese Spring

text: 21 day seedling

text: Wheat gene capture for CIMMYT line 24


text: UNIVERSITY OF LIVERPOOL

text: public

text: bread wheat

text: Triticum aestivum

text: Triticum aestivum

text: Chinese Spring

text: 21 day seedling

text: Wheat promoter capture for CIMMYT line 24


E-MTAB-6992:Control HSC (rep1)

text: public

text: E-MTAB-6992:Control HSC (rep1)

tag: Namespace:Laboratory of Cellular and Molecular Immunology GIGA-Research Center, Liege University

text: 8 to 12

unit: week

characteristic: age

text: ArrayExpress

characteristic: broker name

text: long term hematopoietic stem cell

characteristic: cell type

text: house mouse

text: Protocols: Bone marrow cells were isolated by flushing femurs, tibias, ilia and humerus with PBS. Cells were filtered through a 70µM cell strainer to obtain single cell suspensions and cell number was assessed by counting with a hemocytometer. Cell suspensions were first enriched for lineage-negative cells by MACS using Mouse Lineage cell depletion kit (Miltenyi Biotec) before staining for cell-surface antigens. Cells were stained for 30 minutes using the following rat anti-mouse monoclonal antibodies: Lineage cocktail (145-2C11, RA3-6B2, RB6-8C5, M1/70 and TER-119)-PE, CD117 (2B8) -PE, CD34 (RAM34) -FITC, CD150 (Q8-480)-BV421, CD150 (mShad150) - PerCP-eFluor710, CD48 (HM48-1) -APC-Cy7, CD127 (SB/199) -V450. All reagents were purchased from ThermoFisher Scientific, BD Bioscience or BioLegend. For RNA-sequencing of long-term hematopoietic stem cells (LT-HSCs), 1500-9000 Elp3HscKO LT-HSCs (Lineage- c-kit+ sca1+ CD34- CD150+ CD48- cells) were FACS-sorted on a FACS Aria 2 (BD Bioscience). MyPs were directly sorted into 1 ml of TRIzol Reagent (ThermoFisher Scientific). RNA was extracted using Direct-zol™ RNA MiniPrep Plus (Zymo Research) and cleaned of potential DNA contamination with RNeasy MinElute Cleanup Kit (Qiagen). LT-HSCs were directly FACS-sorted in 2 µl of Reaction Buffer from SMART-SeqTM v4 UltraTM Low input RNA Kit. For MyPs, cDNA was synthesized with 10 ng of total RNA using the SMART-SeqTM v4 UltraTM Low input RNA Kit for Sequencing (Clontech Laboratories) and amplified by 7 cycles of LD PCR. For LT-HSCs, cDNA was generated directly and amplified through 14 cycles using the SMART-SeqTM v4 UltraTM Low input RNA Kit for Sequencing (Clontech Laboratories).

characteristic: description

characteristic: genotype

text: Mus musculus

text: Mus musculus

text: bone marrow

characteristic: organism part

text: c-kit+ sca1+ CD34- CD150+ CD48-

characteristic: phenotype

text: Mus musculus

text: mixed pool of male and female

characteristic: sex

text: Control HSC (rep1)


E-MTAB-6992:Control HSC (rep2)

characteristic: ENA-CHECKLIST

characteristic: External Id

text: Laboratory of Cellular and Molecular Immunology GIGA-Research Center, Liege University

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: E-MTAB-6992:Control HSC (rep2)

text: 8 to 12

text: ArrayExpress

text: long term hematopoietic stem cell

text: house mouse

characteristic: common name

text: Mus musculus

characteristic: organism

text: Mus musculus

text: bone marrow

text: c-kit+ sca1+ CD34- CD150+ CD48-

text: Mus musculus

text: mixed pool of male and female

text: Control HSC (rep2)


E-MTAB-6992:Control HSC (rep3)

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-6992:Control HSC (rep3)

text: 8 to 12

text: ArrayExpress

text: long term hematopoietic stem cell

text: house mouse

text: Mus musculus

text: Mus musculus

text: bone marrow

text: c-kit+ sca1+ CD34- CD150+ CD48-

text: Mus musculus

text: mixed pool of male and female

characteristic: strain

text: Control HSC (rep3)

characteristic: title


E-MTAB-6992:Elp3HscKO HSC (rep1)

text: public

text: E-MTAB-6992:Elp3HscKO HSC (rep1)

characteristic: Submitter Id

text: 8 to 12

characteristic: age

text: ArrayExpress

characteristic: broker name

text: long term hematopoietic stem cell

characteristic: cell type

text: house mouse

characteristic: description

text: Elp3fl/fl vav-iCreT/+

characteristic: genotype

text: Mus musculus

text: Mus musculus

text: bone marrow

text: c-kit+ sca1+ CD34- CD150+ CD48-

text: Mus musculus

text: mixed pool of male and female

text: Elp3HscKO HSC (rep1)


E-MTAB-6992:Elp3HscKO HSC (rep2)

characteristic: ENA-CHECKLIST

characteristic: External Id

characteristic: INSDC center name

text: public

text: E-MTAB-6992:Elp3HscKO HSC (rep2)

text: 8 to 12

text: ArrayExpress

text: long term hematopoietic stem cell

text: house mouse

text: Elp3fl/fl vav-iCreT/+

text: Mus musculus

text: Mus musculus

text: bone marrow

characteristic: organism part

text: c-kit+ sca1+ CD34- CD150+ CD48-

characteristic: phenotype

text: Mus musculus

text: mixed pool of male and female

characteristic: sex

text: Elp3HscKO HSC (rep2)


name: E-MTAB-6992:Control Myeloid Progenitors (rep1)

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: 8 to 12

text: ArrayExpress

text: myeloid lineage restricted progenitor cell

text: house mouse

characteristic: common name

text: Protocols: Bone marrow cells were isolated by flushing femurs, tibias, ilia and humerus with PBS. Cells were filtered through a 70µM cell strainer to obtain single cell suspensions and cell number was assessed by counting with a hemocytometer. Cell suspensions were first enriched for lineage-negative cells by MACS using Mouse Lineage cell depletion kit (Miltenyi Biotec) before staining for cell-surface antigens. Cells were stained for 30 minutes using the following rat anti-mouse monoclonal antibodies: Lineage cocktail (145-2C11, RA3-6B2, RB6-8C5, M1/70 and TER-119)-PE, CD34 (RAM34) -FITC, CD150 (Q8-480)-BV421, CD150 (mShad150) - PerCP-eFluor710, CD48 (HM48-1) -APC-Cy7, CD127 (SB/199) -V450. All reagents were purchased from ThermoFisher Scientific, BD Bioscience or BioLegend. For RNA-sequencing of Myeloid Progenitors (MyPs), 90000 MyPs (Lineage- CD127- c-kit+ Sca1- cells) were FACS-sorted on a FACS Aria 2 (BD Bioscience). MyPs were directly sorted into 1 ml of TRIzol Reagent (ThermoFisher Scientific). RNA was extracted using Direct-zol™ RNA MiniPrep Plus (Zymo Research) and cleaned of potential DNA contamination with RNeasy MinElute Cleanup Kit (Qiagen). LT-HSCs were directly FACS-sorted in 2 µl of Reaction Buffer from SMART-SeqTM v4 UltraTM Low input RNA Kit. For MyPs, cDNA was synthesized with 10 ng of total RNA using the SMART-SeqTM v4 UltraTM Low input RNA Kit for Sequencing (Clontech Laboratories) and amplified by 7 cycles of LD PCR. For LT-HSCs, cDNA was generated directly and amplified through 14 cycles using the SMART-SeqTM v4 UltraTM Low input RNA Kit for Sequencing (Clontech Laboratories).

text: Mus musculus

characteristic: organism

text: Mus musculus

text: bone marrow

text: CD127- c-kit+ Sca1-

text: Mus musculus

text: mixed pool of male and female

text: Control Myeloid Progenitors (rep1)


name: E-MTAB-6992:Control Myeloid Progenitors (rep2)

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: 8 to 12

characteristic: age

text: ArrayExpress

text: house mouse

text: Mus musculus

text: Mus musculus

text: bone marrow

text: CD127- c-kit+ Sca1-

text: Mus musculus

text: mixed pool of male and female

characteristic: strain

text: Control Myeloid Progenitors (rep2)

characteristic: title


name: E-MTAB-6992:Control Myeloid Progenitors (rep3)

characteristic: ENA-CHECKLIST

characteristic: External Id

text: public

text: 8 to 12

text: ArrayExpress

characteristic: broker name

characteristic: cell type

text: house mouse

characteristic: description

characteristic: genotype

text: Mus musculus

text: Mus musculus

text: bone marrow

text: CD127- c-kit+ Sca1-

text: Mus musculus

text: mixed pool of male and female

text: Control Myeloid Progenitors (rep3)


name: E-MTAB-6992:Elp3/Trp53HscDKO Myeloid Progenitors (rep1)

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: INSDC center name

text: public

text: 8 to 12

text: ArrayExpress

text: house mouse

text: Elp3fl/fl Trp53fl/fl vav-iCreT/+

text: Mus musculus

text: Mus musculus

text: bone marrow

characteristic: organism part

text: CD127- c-kit+ Sca1-

characteristic: phenotype

text: Mus musculus

text: mixed pool of male and female

characteristic: sex


name: E-MTAB-6992:Elp3/Trp53HscDKO Myeloid Progenitors (rep2)

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: 8 to 12

text: ArrayExpress

text: house mouse

characteristic: common name

text: Elp3fl/fl Trp53fl/fl vav-iCreT/+

text: Mus musculus

characteristic: organism

text: Mus musculus

text: bone marrow

text: CD127- c-kit+ Sca1-

text: Mus musculus

text: mixed pool of male and female


name: E-MTAB-6992:Elp3/Trp53HscDKO Myeloid Progenitors (rep3)

characteristic: ENA-CHECKLIST

characteristic: External Id

text: public

characteristic: Submitter Id

text: 8 to 12

characteristic: age

text: ArrayExpress

text: house mouse

text: Elp3fl/fl Trp53fl/fl vav-iCreT/+

text: Mus musculus

text: Mus musculus

text: bone marrow

text: CD127- c-kit+ Sca1-

text: Mus musculus

text: mixed pool of male and female

characteristic: strain

characteristic: title


name: E-MTAB-6992:Elp3HscKO Myeloid Progenitors (rep1)

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: public

text: 8 to 12

text: ArrayExpress

characteristic: broker name

characteristic: cell type

text: house mouse

characteristic: description

text: Elp3fl/fl vav-iCreT/+

characteristic: genotype

text: Mus musculus

text: Mus musculus

text: bone marrow

text: CD127- c-kit+ Sca1-

text: Mus musculus

text: mixed pool of male and female

text: Elp3HscKO Myeloid Progenitors (rep1)


name: E-MTAB-6992:Elp3HscKO Myeloid Progenitors (rep2)

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: 8 to 12

text: ArrayExpress

text: house mouse

text: Elp3fl/fl vav-iCreT/+

text: Mus musculus

text: Mus musculus

text: bone marrow

characteristic: organism part

text: CD127- c-kit+ Sca1-

characteristic: phenotype

text: Mus musculus

text: mixed pool of male and female

characteristic: sex

text: Elp3HscKO Myeloid Progenitors (rep2)


name: E-MTAB-6992:Elp3HscKO Myeloid Progenitors (rep3)

characteristic: ENA-CHECKLIST

characteristic: External Id

text: public

characteristic: INSDC status

characteristic: SRA accession

text: 8 to 12

text: ArrayExpress

text: house mouse

characteristic: common name

text: Elp3fl/fl vav-iCreT/+

text: Mus musculus

characteristic: organism

text: Mus musculus

text: bone marrow

text: CD127- c-kit+ Sca1-

text: Mus musculus

text: mixed pool of male and female

text: Elp3HscKO Myeloid Progenitors (rep3)


name: E-MTAB-6992:Trp53HscKO Myeloid Progenitors (rep1)

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: public

characteristic: Submitter Id

text: 8 to 12

characteristic: age

text: ArrayExpress

text: house mouse

text: Trp53fl/fl vav-iCreT/+

text: Mus musculus

text: Mus musculus

text: bone marrow

text: CD127- c-kit+ Sca1-

text: Mus musculus

text: mixed pool of male and female

characteristic: strain

text: Trp53HscKO Myeloid Progenitors (rep1)

characteristic: title


name: E-MTAB-6992:Trp53HscKO Myeloid Progenitors (rep2)

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: 8 to 12

text: ArrayExpress

characteristic: broker name

characteristic: cell type

text: house mouse

characteristic: description

text: Trp53fl/fl vav-iCreT/+

characteristic: genotype

text: Mus musculus

text: Mus musculus

text: bone marrow

text: CD127- c-kit+ Sca1-

text: Mus musculus

text: mixed pool of male and female

text: Trp53HscKO Myeloid Progenitors (rep2)


name: E-MTAB-6992:Trp53HscKO Myeloid Progenitors (rep3)

characteristic: ENA-CHECKLIST

characteristic: External Id

characteristic: INSDC last update

text: public

text: 8 to 12

text: ArrayExpress

text: house mouse

text: Trp53fl/fl vav-iCreT/+

text: Mus musculus

text: Mus musculus

text: bone marrow

characteristic: organism part

text: CD127- c-kit+ Sca1-

characteristic: phenotype

text: Mus musculus

text: mixed pool of male and female

characteristic: sex

text: Trp53HscKO Myeloid Progenitors (rep3)


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: IMEDEA

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: collection date

text: hypersaline environment

characteristic: environment (biome)

text: brines

characteristic: environment (feature)

text: brines

characteristic: environment (material)

text: Spain

characteristic: geographic location (country and/or sea)

unit: m

characteristic: geographic location (depth)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: metagenome

characteristic: investigation type

text: hypersaline lake metagenome

characteristic: organism

text: Metagenomes cristalyzer ponds

characteristic: project name

text: hypersaline lake metagenome

text: Illumina

characteristic: sequencing method

text: Control

text: water

characteristic: water environmental package


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: External Id

text: IMEDEA

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: Submitter Id

text: hypersaline environment

text: brines

text: brines

text: Spain

text: metagenome

text: hypersaline lake metagenome

text: Metagenomes cristalyzer ponds

text: hypersaline lake metagenome

text: Illumina

text: Shaded-Unshaded

characteristic: title

text: water


characteristic: ENA-LAST-UPDATE

text: IMEDEA

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: collection date

text: hypersaline environment

characteristic: environment (biome)

text: brines

characteristic: environment (feature)

text: brines

characteristic: environment (material)

text: Spain

characteristic: geographic location (country and/or sea)

text: metagenome

text: hypersaline lake metagenome

text: Metagenomes cristalyzer ponds

text: hypersaline lake metagenome

text: Illumina

text: Unshaded-Shaded

text: water


Unsha _12_T24h

text: IMEDEA

text: public

text: Unsha _12_T24h

text: hypersaline environment

text: brines

text: brines

text: Spain

characteristic: geographic location (depth)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: metagenome

characteristic: investigation type

text: hypersaline lake metagenome

characteristic: organism

text: Metagenomes cristalyzer ponds

characteristic: project name

text: hypersaline lake metagenome

text: Illumina

characteristic: sequencing method

text: Unshaded-Shaded

text: water

characteristic: water environmental package


Unsha _12_T2d

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: External Id

text: IMEDEA

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: Unsha _12_T2d

characteristic: Submitter Id

text: hypersaline environment

text: brines

text: brines

text: Spain

text: metagenome

text: hypersaline lake metagenome

text: Metagenomes cristalyzer ponds

text: hypersaline lake metagenome

text: Illumina

text: Unshaded-Shaded

characteristic: title

text: water


Unsha _12_T1w

characteristic: ENA-LAST-UPDATE

text: IMEDEA

text: public

characteristic: INSDC status

characteristic: SRA accession

text: Unsha _12_T1w

characteristic: collection date

text: hypersaline environment

characteristic: environment (biome)

text: brines

characteristic: environment (feature)

text: brines

characteristic: environment (material)

text: Spain

characteristic: geographic location (country and/or sea)

text: metagenome

text: hypersaline lake metagenome

text: Metagenomes cristalyzer ponds

text: hypersaline lake metagenome

text: Illumina

text: Unshaded-Shaded

text: water


Unsha _12_T1m

text: IMEDEA

text: public

text: Unsha _12_T1m

text: hypersaline environment

text: brines

text: brines

text: Spain

characteristic: geographic location (depth)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: metagenome

characteristic: investigation type

text: hypersaline lake metagenome

characteristic: organism

text: Metagenomes cristalyzer ponds

characteristic: project name

text: hypersaline lake metagenome

text: Illumina

characteristic: sequencing method

text: Unshaded-Shaded

text: water

characteristic: water environmental package


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: External Id

text: CCMAR

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: Submitter Id

text: Pelvetiopsis arborescens

text: Pelvetiopsis arborescens

text: pelvetiopsis gene expression

characteristic: title


characteristic: ENA-LAST-UPDATE

text: CCMAR

text: public

characteristic: INSDC status

characteristic: SRA accession

text: Hesperophycus californicus

text: Hesperophycus californicus

text: pelvetiopsis gene expression


text: CCMAR

text: public

text: Pelvetiopsis hybrida

text: Pelvetiopsis hybrida

text: pelvetiopsis gene expression


text: CCMAR

text: public

text: Pelvetiopsis limitata

text: Pelvetiopsis limitata

text: pelvetiopsis gene expression


text: UMC Utrecht

text: public

characteristic: collection date

text: not provided

characteristic: geographic location (country and/or sea)

text: not provided

characteristic: host health state

text: Homo sapiens

characteristic: host scientific name

text: Newman

characteristic: isolate

text: Clinical

characteristic: isolation source

text: Staphylococcus aureus

text: Staphylococcus aureus

text: Phage unselected library


characteristic: ENA-CHECKLIST

text: UMC Utrecht

text: public

text: not provided

text: not provided

text: Homo sapiens

text: Newman

text: Clinical

text: Staphylococcus aureus

characteristic: organism

text: Staphylococcus aureus

text: Phage selection library


MinION NA19240

characteristic: ENA-FIRST-PUBLIC

characteristic: External Id

text: VIB-CMN Antwerp

text: public

text: MinION NA19240

tag: Namespace:VIB-CMN Antwerp

text: human

characteristic: common name

text: Homo sapiens

text: Homo sapiens

text: MinION NA19240


E-MTAB-6979:Sample 1

text: Arabian Gulf University

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: E-MTAB-6979:Sample 1

tag: Namespace:Arabian Gulf University

text: ArrayExpress

characteristic: broker name

characteristic: cell line

text: T lymphocyte

characteristic: cell type

text: house mouse

text: Protocols: EL4 (Mus musculus lymphoma, ATCC ID: TIB 39) mouse T-cell lymphoma cells were maintained in Dulbecco’s modified Eagle’s medium (DMEM) (Sigma-Aldrich, St. Louis, MO, USA) supplemented with 10% horse serum (Gibco, Gaithersburg, MD, USA), 0.1 mg/ml streptomycin and 100 U/ml penicillin at 37°C with 5% CO2. Cells were grown to reach a density of 2.5x106 cells/ml. A total of 2x107 cells were mixed with 10 μg of either p-SELECT-zeo-ISRAA expressing N-terminal 6His-tagged ISRAA or p-SELECT-zeo-eGFP. The cell suspension (0.4 ml) was subjected to electroporation using a BTX Electro Cell Manipulator with the following parameters; 140 V, 720 Ohms, and 3175 μF, across a BTX cuvette with a 0.2 cm electrode gap. Pulse lengths varied between 25 and 28 ms. Electroporated cells were incubated at room temperature for 15 minutes, then transferred to complete medium and returned to the cell culture incubator. Zeocin was subsequently added for selection at concentrations ranging from 100 to 200 μg/ml. The electroporation efficiency was assessed by fluorescence microscopy with the p-SELECT-zeo-eGFP electroporated live cells. Ten days after transfection, 2x105 cells were harvested and assayed for recombinant ISRAA expression by Western blotting and total RNA extraction. RNA extraction using Rneasy Mini Kit (QIAGEN) For RNA-seq analysis, 5 μg of total RNA was isolated using an RNeasy Mini kit (QIAGEN) according to the manufacturer’s recommendations. RNA purification, reverse transcription, library construction and sequencing were performed according to the manufacturer’s instructions (Illumina, San Diego, CA). Two RNA-seq transcriptome libraries (ISRAA-expressing EL4 cells and non-electroporated control EL4 cells) were prepared using a modified Illumina TruSeq RNA Sample Preparation protocol. The first step involves the removal of ribosomal RNA (rRNA) using biotinylated, target-specific oligos combined with Ribo-Zero rRNA removal beads. The Ribo-Zero Gold kit (Illumina, San Diego, CA) depletes samples of both cytoplasmic and mitochondrial rRNA. Following purification, the mRNA is fragmented using divalent cations under elevated temperature. Taking these short fragments as templates, double-stranded cDNA was synthesized using a SuperScript double-stranded cDNA synthesis kit (Invitrogen, CA) with random hexamer primers (Illumina, USA). Then, the synthesized cDNA was subjected to end-repair, phosphorylation, ‘A’ base addition and ligation of the adapters according to Illumina’s library construction protocol. Libraries were size- selected for 200-300 bp cDNA target fragments on 2% Low-Range Ultra Agarose followed by PCR amplification using Phusion DNA polymerase (New England Biolabs, Boston, MA).

characteristic: description

text: lymphoma

characteristic: disease

text: p-SELECT-zeo-ISRAA

characteristic: genotype

text: Mus musculus

text: Mus musculus

text: lymph node

characteristic: organism part

text: overexpression of ISRAA

characteristic: phenotype

text: Mus musculus

characteristic: strain

text: Sample 1


E-MTAB-6979:Sample 2

characteristic: ENA-CHECKLIST

characteristic: ENA-LAST-UPDATE

text: Arabian Gulf University

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-6979:Sample 2

characteristic: Submitter Id

text: ArrayExpress

text: T lymphocyte

text: house mouse

text: lymphoma

text: p-SELECT-zeo-eGFP

text: Mus musculus

text: Mus musculus

text: lymph node

text: wild type phenotype

text: Mus musculus

text: Sample 2

characteristic: title


characteristic: ENA-FIRST-PUBLIC

characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC first public

text: public

tag: Namespace:University of Zurich Department of Microbiology and Plant Biology

unit: day

characteristic: age

text: ArrayExpress

text: thale cress

characteristic: common name

text: Protocols: Entire leaf n°6 of Arabidopsis, 25 days after germination, grown in short day condition (6h light, 18h dark) were harvested, detached and put in the dark for up to 2 days. 0d and 2d samples have been harvested in triplicate for each condition. On soil. 6 h light, 18h dark, 100umol/m2 light, 60% humidity. RNA was extracted using Qiagen RNeays kit with a DNAse removal step. Quality of RNA was controlled by Bioanalyzer. Truseq Stranded Total RNAseq kit from Illumina.

text: rosette growth stage

characteristic: developmental stage

text: Columbia

characteristic: ecotype

text: nye1 mutant

text: Arabidopsis thaliana

characteristic: organism

text: Arabidopsis thaliana

text: leaf

text: leaf 6

characteristic: sampling site

text: Arabidopsis thaliana


text: University of Zurich Department of Microbiology and Plant Biology

characteristic: INSDC last update

text: public

text: ArrayExpress

characteristic: broker name

text: thale cress

characteristic: description

text: rosette growth stage

text: Columbia

text: nye1 mutant

characteristic: genotype

text: Arabidopsis thaliana

text: Arabidopsis thaliana

text: leaf

characteristic: organism part

text: leaf 6

text: Arabidopsis thaliana


characteristic: ENA-CHECKLIST

characteristic: ENA-LAST-UPDATE

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: ArrayExpress

text: thale cress

text: rosette growth stage

text: Columbia

text: continuous dark (no light) regimen

characteristic: environmental stress

text: nye1 mutant

text: Arabidopsis thaliana

text: Arabidopsis thaliana

text: leaf

text: leaf 6

text: Arabidopsis thaliana


characteristic: ENA-FIRST-PUBLIC

characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC first public

text: public

characteristic: age

text: ArrayExpress

text: thale cress

text: rosette growth stage

text: Columbia

text: pao-1 mutant

text: Arabidopsis thaliana

text: Arabidopsis thaliana

text: leaf

text: leaf 6

text: Arabidopsis thaliana

characteristic: title


characteristic: INSDC last update

text: public

text: ArrayExpress

text: thale cress

characteristic: common name

text: rosette growth stage

characteristic: developmental stage

text: Columbia

characteristic: ecotype

text: continuous dark (no light) regimen

text: pao-1 mutant

text: Arabidopsis thaliana

characteristic: organism

text: Arabidopsis thaliana

text: leaf

text: leaf 6

characteristic: sampling site

text: Arabidopsis thaliana


characteristic: ENA-CHECKLIST

characteristic: ENA-LAST-UPDATE

text: public

text: ArrayExpress

characteristic: broker name

text: thale cress

characteristic: description

text: rosette growth stage

text: Columbia

text: pph1 mutant

characteristic: genotype

text: Arabidopsis thaliana

text: Arabidopsis thaliana

text: leaf

characteristic: organism part

text: leaf 6

text: Arabidopsis thaliana


characteristic: ENA-FIRST-PUBLIC

characteristic: External Id

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: ArrayExpress

text: thale cress

text: rosette growth stage

text: Columbia

text: continuous dark (no light) regimen

characteristic: environmental stress

text: pph1 mutant

text: Arabidopsis thaliana

text: Arabidopsis thaliana

text: leaf

text: leaf 6

text: Arabidopsis thaliana


characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: age

text: ArrayExpress

text: thale cress

characteristic: common name

text: rosette growth stage

text: Columbia

text: wild type genotype

text: Arabidopsis thaliana

text: Arabidopsis thaliana

text: leaf

text: leaf 6

text: Arabidopsis thaliana

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-LAST-UPDATE

text: public

text: ArrayExpress

text: thale cress

text: rosette growth stage

characteristic: developmental stage

text: Columbia

characteristic: ecotype

text: continuous dark (no light) regimen

text: wild type genotype

text: Arabidopsis thaliana

characteristic: organism

text: Arabidopsis thaliana

text: leaf

text: leaf 6

characteristic: sampling site

text: Arabidopsis thaliana


characteristic: ENA-FIRST-PUBLIC

characteristic: External Id

text: public

tag: Namespace:OSLO AND AKERSHUS UNIVERSITY COLLEGE OF APPLIED SC

text: Akershus University Hospital

characteristic: collected by

characteristic: collection date

text: No

characteristic: environmental sample

text: Norway

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: diseased

characteristic: host health state

text: human

characteristic: host scientific name

text: Yes

characteristic: is the sequenced pathogen host associated?

text: Escherichia coli stx positive

characteristic: isolate

text: Escherichia coli O145

text: Escherichia coli O145

characteristic: serovar

text: Stx loss from Escherichia


characteristic: ENA-CHECKLIST

characteristic: ENA-LAST-UPDATE

text: OSLO AND AKERSHUS UNIVERSITY COLLEGE OF APPLIED SC

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: Akershus University Hospital

text: No

text: Norway

text: diseased

text: human

text: Yes

text: Escherichia coli stx negative

text: Escherichia coli O145

text: Escherichia coli O145

text: Stx loss from Escherichia

characteristic: title


characteristic: ENA-FIRST-PUBLIC

characteristic: External Id

text: public

text: Akershus University Hospital

characteristic: collected by

characteristic: collection date

text: No

characteristic: environmental sample

text: Norway

characteristic: geographic location (country and/or sea)

text: diseased

text: human

text: Yes

text: Escherichia albertii stx positive

text: Escherichia albertii

characteristic: organism

text: Escherichia albertii

text: Stx loss from Escherichia


text: public

text: Akershus University Hospital

text: No

text: Norway

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: diseased

characteristic: host health state

text: human

characteristic: host scientific name

text: Yes

characteristic: is the sequenced pathogen host associated?

text: Escherichia albertii stx negative

characteristic: isolate

text: Escherichia albertii

text: Escherichia albertii

text: Stx loss from Escherichia


characteristic: ENA-CHECKLIST

characteristic: ENA-LAST-UPDATE

text: FSU-JENA

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: lake

characteristic: environment (biome)

text: humic

characteristic: environment (feature)

text: DNA

characteristic: environment (material)

text: Sweden

characteristic: geographic location (depth)

text: mimarks-survey

characteristic: investigation type

text: metagenome

text: 341r and 805f

characteristic: pcr primers

text: Decreased snow cover stimulates under ice primary producers, but impairs methanotrophic capacity

characteristic: project name

text: metagenome

text: Illumina MiSeq

characteristic: sequencing method

text: DecreasedSnow

text: water

characteristic: water environmental package


characteristic: ENA-FIRST-PUBLIC

characteristic: External Id

text: FSU-JENA

text: public

characteristic: SRA accession

characteristic: Submitter Id

characteristic: collection date

text: lake

text: humic

text: RNA

text: Sweden

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: mimarks-survey

text: metagenome

characteristic: organism

text: 341r and 805f

text: metagenome

text: Illumina MiSeq

text: DecreasedSnow

characteristic: title

text: water


characteristic: # of patient from who tumor was obtained

characteristic: ENA-CHECKLIST

characteristic: ENA-LAST-UPDATE

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

tag: Namespace:Department of Molecular Biology of Cancer, Medical University of Lodz, Poland

text: ArrayExpress

characteristic: broker name

text: human

characteristic: common name

text: Protocols: Melanoma specimens were obtained during surgical intervetions, and grown in vitro in serum-free EGF/bFGF-containing medium as described previously (Sztiller-Sikorska et al., 2012 Melanoma Research. DNA was extracted using DNeasy Blood & Tissue Kit from Qiagen according to manufacturer protocol. DNA samples were subjected to Nextera tagmentation followed by index PCR, first hybridization, capture, washes, elution, second hybridization, capture, washes, elution and enrichment of DNA fragments. The samples were subjected to two rounds of exome enrichment, followed by real-time PCR quantification (KAPA SYBR FAST qPCR Kit) prior to sequencing.

characteristic: description

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens


characteristic: ENA-FIRST-PUBLIC

characteristic: External Id

text: Department of Molecular Biology of Cancer, Medical University of Lodz, Poland

text: public

characteristic: SRA accession

characteristic: Submitter Id

text: ArrayExpress

text: human

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens


text: public

tag: Namespace:Department of Plant Biotechnology and Bioinformatics, Ghent University, Gent, Belgium VIB Center for Plant Systems Biology,VIB, Gent, Belgium

characteristic: age

text: ArrayExpress

text: long-grained rice

text: indica

characteristic: cultivar

text: Protocols: The sample material was 12 pooled fifth leaves of individual plants with three biological replicates for the control line and the epilines LR1, LR2, and LR3, which belongs to the 4th selfing of the EUE selection pedigree. Epilines LR1,LR2, and LR3, and the control line were grown in soil in a growth chamber at 26 C / 21 C (day / night) for 24 days with a 16 h light/8 h dark regime (light intensity was 300 mol m-2 sec-1, the relative humidity was kept at 71%). RNA isolation was performed using the Spectrum™ Plant Total RNA kit (Sigma-Aldrich) according to manufacturer’s instructions. The RNA-seq was done by ServiceXS B.V. (Leiden, The Netherlands). Complementary DNA sequencing libraries were prepared with the Illumina mRNA-seq Sample prep Kit according the Illumina protocol “Preparing Samples for Sequencing of mRNA” (1004898 Rev.D). DNA sequencing using the Illumina HiSeq 2000 (Solexa) was performed according manufacturer’s protocols.

text: LP.05 five leaves visible stage

characteristic: developmental stage

text: wild type genotype

characteristic: genotype

text: pool of leaves from 12 plants

characteristic: individual

text: Oryza sativa Indica Group

text: Oryza sativa Indica Group

text: leaf

characteristic: organism part

text: Oryza sativa Indica Group


characteristic: ENA-CHECKLIST

characteristic: ENA-LAST-UPDATE

text: Department of Plant Biotechnology and Bioinformatics, Ghent University, Gent, Belgium VIB Center for Plant Systems Biology,VIB, Gent, Belgium

characteristic: INSDC center name

text: public

text: ArrayExpress

text: long-grained rice

text: indica

text: LP.05 five leaves visible stage

text: wild type genotype

text: pool of leaves from 12 plants

text: Oryza sativa Indica Group

characteristic: organism

text: Oryza sativa Indica Group

text: leaf

text: Oryza sativa Indica Group

characteristic: title


characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: ArrayExpress

characteristic: broker name

text: long-grained rice

characteristic: common name

text: indica

text: LP.05 five leaves visible stage

text: pool of leaves from 12 plants

text: Oryza sativa Indica Group

text: Oryza sativa Indica Group

text: leaf

text: Oryza sativa Indica Group


text: Plasmodium falciparum

characteristic: ArrayExpress-SPECIES

characteristic: ENA-FIRST-PUBLIC

characteristic: External Id

text: SC

text: public

characteristic: SRA accession

characteristic: Submitter Id

text: malaria parasite P. falciparum

text: Plasmodium falciparum

text: Plasmodium falciparum

characteristic: subject id


text: THE ROSLIN INSTITUTE

text: public

tag: Namespace:THE ROSLIN INSTITUTE

text: sheep

text: Infected male 66days

characteristic: description

text: Ovis aries

text: Ovis aries


characteristic: ENA-CHECKLIST

text: THE ROSLIN INSTITUTE

text: public

text: sheep

text: Infected female 85days

text: Ovis aries

text: Ovis aries


characteristic: ENA-LAST-UPDATE

text: THE ROSLIN INSTITUTE

text: public

text: sheep

text: Infected male 71days

text: Ovis aries

text: Ovis aries


text: THE ROSLIN INSTITUTE

characteristic: INSDC center name

text: public

text: sheep

text: Infected male 85days

text: Ovis aries

text: Ovis aries


text: THE ROSLIN INSTITUTE

text: public

text: sheep

text: Control male 66days

text: Ovis aries

characteristic: organism

text: Ovis aries


text: THE ROSLIN INSTITUTE

text: public

text: sheep

text: Control male 85days

text: Ovis aries

text: Ovis aries

characteristic: title


text: THE ROSLIN INSTITUTE

characteristic: INSDC first public

text: public

text: sheep

text: Control male 71days

text: Ovis aries

text: Ovis aries


text: THE ROSLIN INSTITUTE

characteristic: INSDC last update

text: public

text: sheep

text: Control female 85days

text: Ovis aries

text: Ovis aries


text: public

characteristic: INSDC status

characteristic: age

text: ArrayExpress

text: long-grained rice

text: indica

characteristic: cultivar

text: Protocols: The sample material was 12 pooled fourth leaves of individual plants of to the 4th selfing of the EUE selection pedigree. Plants were grown in soil in a growth chamber at 26 C / 21 C (day / night) for 24 days with a 16 h light/8 h dark regime (light intensity was 300 mol m-2 sec-1, the relative humidity was kept at 71%) DNA isolation was performed using the CTAB (cetyltrimethyl/ammonium bromide) standard protocol For WGBS, paired-end bisulfite sequencing libraries were constructed by Alpha Biolaboratory, Inc. Saratoga, CA as described previously (Ibarra et al., 2012) with modifications. About 300 ng of genomic DNA was fragmented by sonication, end repaired and ligated to custom-synthesized methylated adapters (Eurofins MWG Operon, Huntsville, AL) according to the manufacturer’s (Illumina, San Diego, CA) instructions for gDNA library construction. Adaptor-ligated libraries were subjected to two successive treatments of sodium bisulfite conversion using the EpiTect Bisulfite kit (Qiagen, Hilden, Germany) as outlined in the manufacturer’s instructions. One quarter of the bisulfite-converted libraries was PCR amplified using the following conditions: 2.5 U of ExTaq DNA polymerase (Takara Bio), 5 µL of 10 x Extaq reaction buffer, 25 µM dNTPs, 1 µL primer 1.1, 1 µl primer 2.1 in a 50 µL reaction. The thermocyling conditions were as follows: 95°C for 3 min, then 12-14 cycles of 95°C for 30 s, 65°C for 30 s and 72°C for 60 s. The enriched libraries were purified twice with solid phase reversible immobilization (SPRI) method using 0.8 x v/v AM-Pure beads (Beckman Coulter, Brea, CA) prior to quantification with a Bioanalyzer (Agilent Technologies, Santa Clara, CA).

text: LP.05 five leaves visible stage

characteristic: developmental stage

characteristic: genotype

text: pool of leaves from 12 plants

characteristic: individual

text: Oryza sativa Indica Group

text: Oryza sativa Indica Group

text: leaf

characteristic: organism part

text: Oryza sativa Indica Group


characteristic: ENA-FIRST-PUBLIC

characteristic: External Id

text: DUNDEE

text: public

characteristic: SRA accession

characteristic: Submitter Id

characteristic: collection date

text: common reed

characteristic: common name

text: 16S rRNA gene amplicon library from rhizoplane, rhizosphere of Phragmites australis and Typha latifolia and water basin controls

text: wetland biome

characteristic: environment (biome)

text: artificial oxbow lake

characteristic: environment (feature)

text: rhizoplane rhizosphere and water

characteristic: environment (material)

text: Italy

characteristic: geographic location (country and/or sea)

text: 41.469834 N

characteristic: geographic location (latitude)

text: 14.090730 E

characteristic: geographic location (longitude)

text: metagenome

characteristic: investigation type

text: Phragmites australis

text: plant-associated

characteristic: plant-associated environmental package

text: Phragmites australis and Typha latifolia microbiota investigation

characteristic: project name

text: Phragmites australis

text: Illumina MiSeq PE

characteristic: sequencing method


characteristic: ENA-CHECKLIST

characteristic: ENA-LAST-UPDATE

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: age

text: ArrayExpress

characteristic: broker name

text: long-grained rice

text: indica

characteristic: cultivar

text: Protocols: The sample material was 12 pooled fifth leaves of individual plants with two biological replicates for the control line and the epiline LR2, which belongs to the 5th selfing of the EUE selection pedigree. LR2 and the control line were grown in soil in a growth chamber at 26 C / 21 C (day / night) for 24 days with a 16 h light/8 h dark regime (light intensity was 300 mol m-2 sec-1, the relative humidity was kept at 71%). Liquid Nitrogen Fixation was performed by means of pre-cooled (-80°C) mortar, pestle, metal spatula, and sample, which are placed on dry ice. Approximately 1 g per sample was grinded to a fine powder, put into the plant fixation buffer (40 ml Plant Cross-linking and Extraction Buffer, 1 ml 37 % formaldehyde, and 400 µl 0.1 M PMSF), mixed in vacuum for 10 min, 1.6 ml 2.5 M glycine added and mixed for 5 min in vacuum. The samples were transferred to a 50 ml conical tube and spun for 10 min at 2,500 rpm at 4 °C. The pellet washed twice in 10 ml ice-cold diH2O, spun for 10 min at 2,500 rpm and 4 °C, and the pellets were frozen on dry ice. Genomic DNA (Input) was prepared by treating aliquots of chromatin with RNase, proteinase K and heat for de-crosslinking, followed by ethanol precipitation. Pellets were resuspended and the resulting DNA was quantified on a NanoDrop spectrophotometer. Extrapolation to the original chromatin volume allowed quantitation of the total chromatin yield. Chromatin was prepared by resuspending each pellet in 5 ml Nuclei isolation buffer, 5 µl protease inhibitor cocktail (PIC), and 50 µl 0.1M PMSF. Samples were incubated on ice for 10 min, homogenized with 20 strokes of bouncing, centrifuged for 10 min at 2,500 rpm and 4 °C, and each pellet was resuspended in 500 µl DOC sonication buffer (5 µL PIC and 5 µl 0.1 M PMSF), incubated on ice for 10 min, and 50 mg of glass beads were added. The samples were sonicated twice with a microtip, 10 min in total, at 30 s pulse and 30 s pause, amplitude at 45 %. The tubes were centrifuged to pellet debris at maximum speed for 10 min at 4 °C. 10 µl supernatant was distributed for two replicates for Input DNA preparations. The assays for histone modification H3K4me3- and PolII-detection were performed and provided by Active Motif, Inc. Illumina sequencing libraries were prepared from the ChIP and Input DNAs by the standard consecutive enzymatic steps of end-polishing, dA-addition, and adaptor ligation. After a final PCR amplification step, the resulting DNA libraries were quantified.

characteristic: description

text: LP.05 five leaves visible stage

characteristic: developmental stage

text: wild type genotype

characteristic: genotype

text: pooled leaves from 12 plants

characteristic: individual

text: Oryza sativa Indica Group

characteristic: organism

text: Oryza sativa Indica Group

text: leaf

characteristic: organism part

text: Oryza sativa Indica Group

characteristic: title


characteristic: ENA-FIRST-PUBLIC

characteristic: External Id

text: public

characteristic: SRA accession

characteristic: Submitter Id

text: ArrayExpress

text: long-grained rice

characteristic: common name

text: indica

text: LP.05 five leaves visible stage

text: pooled leaves from 12 plants

text: Oryza sativa Indica Group

text: Oryza sativa Indica Group

text: leaf

text: Oryza sativa Indica Group


HepG2 EV

characteristic: ENA-CHECKLIST

characteristic: ENA-LAST-UPDATE

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: HepG2 EV

tag: Namespace:NATIONAL CANCER INSTITUTE, CENTER FOR CANCER RESEA

text: human

text: Homo sapiens

text: Homo sapiens

text: UCD


HepG2 G03/04 shOTC

text: NATIONAL CANCER INSTITUTE, CENTER FOR CANCER RESEA

text: public

characteristic: INSDC status

text: HepG2 G03/04 shOTC

text: human

text: Homo sapiens

text: Homo sapiens

text: UCD


hepG2 sh OTC F10

text: public

text: hepG2 sh OTC F10

text: human

text: Homo sapiens

text: Homo sapiens

text: UCD


SKOV-3 EV

text: public

text: SKOV-3 EV

text: human

text: Homo sapiens

text: Homo sapiens

text: UCD


SKOV-3 shORNT1

text: public

text: SKOV-3 shORNT1

text: human

text: Homo sapiens

text: Homo sapiens

text: UCD


U2OS EV

text: public

text: U2OS EV

text: human

text: Homo sapiens

text: Homo sapiens

text: UCD


U2OS shASS1

text: public

text: U2OS shASS1

text: human

text: Homo sapiens

text: Homo sapiens

text: UCD


LOX-IMVI EV

text: public

text: LOX-IMVI EV

text: human

text: Homo sapiens

text: Homo sapiens

text: UCD


LOX-IMVI Citrin  OE

text: public

text: LOX-IMVI Citrin OE

text: human

text: Homo sapiens

text: Homo sapiens

text: UCD


text: Massey University

text: public

tag: Namespace:Massey University

characteristic: collection date

text: Norway rat

text: DNA sequences extracted from the stomachs of wild rats, sequenced using oxford nanopore sequencing

characteristic: description

text: primary forest

characteristic: environment (biome)

text: mainland

characteristic: environment (feature)

text: stomach

characteristic: environment (material)

text: New Zealand

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: Rattus norvegicus

characteristic: host common name

text: Omnivore

characteristic: host diet

text: host-associated

characteristic: host-associated environmental package

text: metagenome

characteristic: investigation type

text: Rattus norvegicus

characteristic: project name

text: Rattus norvegicus

text: oxford nanopore

characteristic: sequencing method

text: DNA sequences from rattus stomachs


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Massey University

characteristic: INSDC center name

characteristic: INSDC first public

text: public

characteristic: SRA accession

characteristic: Submitter Id

text: Norway rat

characteristic: common name

text: planted forest

text: estuarine

text: stomach

text: New Zealand

text: Rattus norvegicus

text: Omnivore

text: host-associated

text: metagenome

text: Rattus norvegicus

characteristic: organism

text: Rattus norvegicus

text: oxford nanopore

text: DNA sequences from rattus stomachs

characteristic: title


text: Massey University

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: collection date

text: Norway rat

characteristic: description

text: wetland area

characteristic: environment (biome)

text: estuarine

characteristic: environment (feature)

text: stomach

characteristic: environment (material)

text: New Zealand

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: Rattus norvegicus

characteristic: host common name

text: Omnivore

text: host-associated

text: metagenome

text: Rattus norvegicus

text: Rattus norvegicus

text: oxford nanopore

text: DNA sequences from rattus stomachs


E-MTAB-5613:REP 1 - Plus TET

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: ZMBH

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: E-MTAB-5613:REP 1 - Plus TET

text: ArrayExpress

characteristic: broker name

text: Protocols: Culturing and transfection of trypanosomes (Lister 427 strain expressing the tet repressor from pHD1313 [1313 trypanosomes]) were performed as described in reference 35 (see ref in associated publication. doi 10.1128/EC.00018-14). For the expression of tetracycline-inducible genes, 100 ng ml−1 of tetracycline (Tet) (36) was used. For monitoring the growth, procyclic cells were grown in minimal essential medium-Pros medium at 27°C and were diluted to a density of 5 × 105 cells ml−1. RNA interference against PUF2 was done by making a stem-loop RNAi plasmid as described in reference 36. A 432-bp region (bp 399 to 831 of the ORF) of the PUF2 gene was selected for RNAi (the sequence was verified for its specificity by using the RNAit program [http://trypanofan.path.cam.ac.uk/software/RNAit.html]). The stem-loop PUF2 RNAi vector was referred to as pHD2183, and after digestion with NotI the vector was used to transfect 1313 bloodstream- and procyclic-form cells. Approximately 5 × 108 1313 bloodstream-form cells (density, ≈1 × 106 cells ml−1) were fractionated as described in reference 45. Polysomes were purified from the same number of cells according to the method described in reference 46. The polysomal samples were trichloroacetic acid precipitated and resuspended in 4× Laemmli sample buffer. Trifast follow rRNA depletion by RNAse-H treatment For the RNAi experiment, trypanosomes were grown for 1 day in the presence of tetracycline, and poly(A)+ mRNA was sheared and prepared for sequencing according to the standard Illumina protocol. One PUF2 RNAi batch was sequenced on the GAII and the second with HiSeq. Data analysis, including motif searches and enrichment calculations, were performed as described previously (22, 54). All data were log transformed before the correlation coefficient calculations, in order to reduce the influence of outliers and correct for a nonnormal distribution of the data.

text: Bloodstream form

characteristic: developmental stage

text: polysome

characteristic: fraction

text: PUF2 RNAi vector

characteristic: genotype

text: Trypanosoma brucei

text: Trypanosoma brucei

text: tetracycline-mediated repression of PUF2

characteristic: phenotype

text: Trypanosoma brucei

text: tetracycline; 100 nanogram per milliliter

characteristic: stimulus

text: Lister 427

characteristic: strain

text: REP 1 - Plus TET


E-MTAB-5613:REP 2 - Minus TET

text: ZMBH

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-5613:REP 2 - Minus TET

characteristic: Submitter Id

text: ArrayExpress

characteristic: description

text: Bloodstream form

text: polysome

text: PUF2 RNAi vector

text: Trypanosoma brucei

characteristic: organism

text: Trypanosoma brucei

text: wild type phenotype

text: Trypanosoma brucei

text: Lister 427

text: REP 2 - Minus TET

characteristic: title


E-MTAB-5613:REP 2 - Plus TET

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: ZMBH

text: public

text: E-MTAB-5613:REP 2 - Plus TET

text: ArrayExpress

text: Bloodstream form

text: polysome

text: PUF2 RNAi vector

text: Trypanosoma brucei

text: Trypanosoma brucei

text: Trypanosoma brucei

text: Lister 427

text: REP 2 - Plus TET


text: QMUL

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: James Borrell

characteristic: collected by

characteristic: collection date

text: alpine birch

characteristic: common name

characteristic: geographic location (altitude)

text: Finland

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: Kotilampi

characteristic: geographic location (region and locality)

text: James Borrell

characteristic: identified by

characteristic: isolation and growth condition

text: Betula nana

text: dwarf birch

characteristic: organism common name

text: Adult

characteristic: plant developmental stage

text: soil

characteristic: plant growth medium

text: Cambium

characteristic: plant structure

characteristic: ploidy

text: Betula nana

characteristic: source material identifiers


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: QMUL

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: James Borrell

text: alpine birch

text: Finland

text: Kevojarvi

text: James Borrell

text: Betula nana

characteristic: organism

text: dwarf birch

text: Adult

text: soil

text: Cambium

text: Betula nana

characteristic: title


text: QMUL

text: public

text: James Borrell

characteristic: collected by

characteristic: collection date

text: alpine birch

characteristic: common name

characteristic: geographic location (altitude)

text: Finland

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: Kevo Plateau

characteristic: geographic location (region and locality)

text: James Borrell

characteristic: identified by

characteristic: isolation and growth condition

text: Betula nana

text: dwarf birch

characteristic: organism common name

text: Adult

characteristic: plant developmental stage

text: soil

text: Cambium

text: Betula nana


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: QMUL

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: James Borrell

text: alpine birch

text: Finland

text: Kevo Reserve

text: James Borrell

text: Betula nana

text: dwarf birch

text: Adult

text: soil

characteristic: plant growth medium

text: Cambium

characteristic: plant structure

characteristic: ploidy

text: Betula nana

characteristic: source material identifiers


text: QMUL

text: public

characteristic: SRA accession

characteristic: Submitter Id

text: James Borrell

characteristic: collected by

characteristic: collection date

text: alpine birch

characteristic: common name

characteristic: geographic location (altitude)

text: Norway

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: Nordkapp

characteristic: geographic location (region and locality)

text: James Borrell

text: Betula nana

characteristic: organism

text: dwarf birch

text: Adult

text: soil

text: Cambium

text: Betula nana

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: QMUL

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: James Borrell

text: alpine birch

text: Finland

text: Partakko

text: James Borrell

characteristic: identified by

characteristic: isolation and growth condition

text: Betula nana

text: dwarf birch

characteristic: organism common name

text: Adult

characteristic: plant developmental stage

text: soil

text: Cambium

text: Betula nana


text: QMUL

text: public

characteristic: SRA accession

characteristic: Submitter Id

text: James Borrell

characteristic: collected by

characteristic: collection date

text: alpine birch

characteristic: common name

characteristic: geographic location (altitude)

text: Finland

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

text: Skalluvaara

text: James Borrell

text: Betula nana

text: dwarf birch

text: Adult

text: soil

characteristic: plant growth medium

text: Cambium

characteristic: plant structure

characteristic: ploidy

text: Betula nana

characteristic: source material identifiers


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: QMUL

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: James Borrell

text: alpine birch

text: Finland

characteristic: geographic location (longitude)

text: Sirbma

characteristic: geographic location (region and locality)

text: James Borrell

text: Betula nana

characteristic: organism

text: dwarf birch

text: Adult

text: soil

text: Cambium

text: Betula nana

characteristic: title


text: QMUL

text: public

characteristic: SRA accession

characteristic: Submitter Id

text: James Borrell

characteristic: collected by

characteristic: collection date

text: alpine birch

characteristic: common name

characteristic: geographic location (altitude)

text: Finland

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

text: Tenontie

text: James Borrell

characteristic: identified by

characteristic: isolation and growth condition

text: Betula nana

text: dwarf birch

characteristic: organism common name

text: Adult

characteristic: plant developmental stage

text: soil

text: Cambium

text: Betula nana


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: QMUL

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: James Borrell

text: alpine birch

text: Finland

text: Gearddosjavri

text: James Borrell

text: Betula nana

text: dwarf birch

text: Adult

text: soil

characteristic: plant growth medium

text: Cambium

characteristic: plant structure

characteristic: ploidy

text: Betula nana

characteristic: source material identifiers


text: QMUL

text: public

characteristic: SRA accession

characteristic: Submitter Id

text: James Borrell

characteristic: collected by

characteristic: collection date

text: alpine birch

characteristic: common name

characteristic: geographic location (altitude)

text: United Kingdom

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: An Suidhe

characteristic: geographic location (region and locality)

text: James Borrell

text: Betula nana

characteristic: organism

text: dwarf birch

text: Adult

text: soil

text: Cambium

text: Betula nana

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: QMUL

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: James Borrell

text: alpine birch

text: United Kingdom

text: River Avon

text: James Borrell

characteristic: identified by

characteristic: isolation and growth condition

text: Betula nana

text: dwarf birch

characteristic: organism common name

text: Adult

characteristic: plant developmental stage

text: soil

text: Cambium

text: Betula nana


text: QMUL

text: public

characteristic: SRA accession

characteristic: Submitter Id

text: James Borrell

characteristic: collected by

characteristic: collection date

text: alpine birch

characteristic: common name

characteristic: geographic location (altitude)

text: United Kingdom

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

text: Beinn Bhreac

text: James Borrell

text: Betula nana

text: dwarf birch

text: Adult

text: soil

characteristic: plant growth medium

text: Cambium

characteristic: plant structure

characteristic: ploidy

text: Betula nana

characteristic: source material identifiers


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: QMUL

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: James Borrell

text: alpine birch

text: United Kingdom

characteristic: geographic location (longitude)

text: Beinn Enaiglair

characteristic: geographic location (region and locality)

text: James Borrell

text: Betula nana

characteristic: organism

text: dwarf birch

text: Adult

text: soil

text: Cambium

text: Betula nana

characteristic: title


text: QMUL

text: public

characteristic: SRA accession

characteristic: Submitter Id

text: James Borrell

characteristic: collected by

characteristic: collection date

text: alpine birch

characteristic: common name

characteristic: geographic location (altitude)

text: United Kingdom

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

text: Ben Gullabin

text: James Borrell

characteristic: identified by

characteristic: isolation and growth condition

text: Betula nana

text: dwarf birch

characteristic: organism common name

text: Adult

characteristic: plant developmental stage

text: soil

text: Cambium

text: Betula nana


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: QMUL

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: James Borrell

text: alpine birch

text: United Kingdom

text: Ben Loyal

text: James Borrell

text: Betula nana

text: dwarf birch

text: Adult

text: soil

characteristic: plant growth medium

text: Cambium

characteristic: plant structure

characteristic: ploidy

text: Betula nana

characteristic: source material identifiers


text: QMUL

text: public

characteristic: SRA accession

characteristic: Submitter Id

text: James Borrell

characteristic: collected by

characteristic: collection date

text: alpine birch

characteristic: common name

characteristic: geographic location (altitude)

text: United Kingdom

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: Ben Wyvis W

characteristic: geographic location (region and locality)

text: James Borrell

text: Betula nana

characteristic: organism

text: dwarf birch

text: Adult

text: soil

text: Cambium

text: Betula nana

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: QMUL

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: James Borrell

text: alpine birch

text: United Kingdom

text: Dundreggan

text: James Borrell

characteristic: identified by

characteristic: isolation and growth condition

text: Betula nana

text: dwarf birch

characteristic: organism common name

text: Adult

characteristic: plant developmental stage

text: soil

text: Cambium

text: Betula nana


text: QMUL

text: public

characteristic: SRA accession

characteristic: Submitter Id

text: James Borrell

characteristic: collected by

characteristic: collection date

text: alpine birch

characteristic: common name

characteristic: geographic location (altitude)

text: United Kingdom

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

text: Emblehope

text: James Borrell

text: Betula nana

text: dwarf birch

text: Adult

text: soil

characteristic: plant growth medium

text: Cambium

characteristic: plant structure

characteristic: ploidy

text: Betula nana

characteristic: source material identifiers


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: QMUL

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: James Borrell

text: alpine birch

text: United Kingdom

characteristic: geographic location (longitude)

text: Glen Cannich

characteristic: geographic location (region and locality)

text: James Borrell

text: Betula nana

characteristic: organism

text: dwarf birch

text: Adult

text: soil

text: Cambium

text: Betula nana

characteristic: title


text: QMUL

text: public

characteristic: SRA accession

characteristic: Submitter Id

text: James Borrell

characteristic: collected by

characteristic: collection date

text: alpine birch

characteristic: common name

characteristic: geographic location (altitude)

text: United Kingdom

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

text: Loch Laggan

text: James Borrell

characteristic: identified by

characteristic: isolation and growth condition

text: Betula nana

text: dwarf birch

characteristic: organism common name

text: Adult

characteristic: plant developmental stage

text: soil

text: Cambium

text: Betula nana


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: QMUL

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: James Borrell

text: alpine birch

text: United Kingdom

text: Luichart

text: James Borrell

text: Betula nana

text: dwarf birch

text: Adult

text: soil

characteristic: plant growth medium

text: Cambium

characteristic: plant structure

characteristic: ploidy

text: Betula nana

characteristic: source material identifiers


text: QMUL

text: public

characteristic: SRA accession

characteristic: Submitter Id

text: James Borrell

characteristic: collected by

characteristic: collection date

text: alpine birch

characteristic: common name

characteristic: geographic location (altitude)

text: United Kingdom

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: Loch Loch

characteristic: geographic location (region and locality)

text: James Borrell

text: Betula nana

characteristic: organism

text: dwarf birch

text: Adult

text: soil

text: Cambium

text: Betula nana

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: QMUL

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: James Borrell

text: alpine birch

text: United Kingdom

text: Loch Rannoch

text: James Borrell

characteristic: identified by

characteristic: isolation and growth condition

text: Betula nana

text: dwarf birch

characteristic: organism common name

text: Adult

characteristic: plant developmental stage

text: soil

text: Cambium

text: Betula nana


text: QMUL

text: public

characteristic: SRA accession

characteristic: Submitter Id

text: James Borrell

characteristic: collected by

characteristic: collection date

text: alpine birch

characteristic: common name

characteristic: geographic location (altitude)

text: United Kingdom

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

text: Lennox

text: James Borrell

text: Betula nana

text: dwarf birch

text: Adult

text: soil

characteristic: plant growth medium

text: Cambium

characteristic: plant structure

characteristic: ploidy

text: Betula nana

characteristic: source material identifiers


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: QMUL

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: James Borrell

text: alpine birch

text: United Kingdom

characteristic: geographic location (longitude)

text: Monadhliaths

characteristic: geographic location (region and locality)

text: James Borrell

text: Betula nana

characteristic: organism

text: dwarf birch

text: Adult

text: soil

text: Cambium

text: Betula nana

characteristic: title


text: QMUL

text: public

characteristic: SRA accession

characteristic: Submitter Id

text: James Borrell

characteristic: collected by

characteristic: collection date

text: alpine birch

characteristic: common name

characteristic: geographic location (altitude)

text: United Kingdom

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

text: Loch Meig

text: James Borrell

characteristic: identified by

characteristic: isolation and growth condition

text: Betula nana

text: dwarf birch

characteristic: organism common name

text: Adult

characteristic: plant developmental stage

text: soil

text: Cambium

text: Betula nana


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: QMUL

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: James Borrell

text: alpine birch

text: United Kingdom

text: Meall Odhar

text: James Borrell

text: Betula nana

text: dwarf birch

text: Adult

text: soil

characteristic: plant growth medium

text: Cambium

characteristic: plant structure

characteristic: ploidy

text: Betula nana

characteristic: source material identifiers


text: QMUL

text: public

characteristic: SRA accession

characteristic: Submitter Id

text: James Borrell

characteristic: collected by

characteristic: collection date

text: alpine birch

characteristic: common name

characteristic: geographic location (altitude)

text: United Kingdom

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: Loch Muick E

characteristic: geographic location (region and locality)

text: James Borrell

text: Betula nana

characteristic: organism

text: dwarf birch

text: Adult

text: soil

text: Cambium

text: Betula nana

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: QMUL

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: James Borrell

text: alpine birch

text: United Kingdom

text: Loch Muick W

text: James Borrell

characteristic: identified by

characteristic: isolation and growth condition

text: Betula nana

text: dwarf birch

characteristic: organism common name

text: Adult

characteristic: plant developmental stage

text: soil

text: Cambium

text: Betula nana


text: QMUL

text: public

characteristic: SRA accession

characteristic: Submitter Id

text: James Borrell

characteristic: collected by

characteristic: collection date

text: alpine birch

characteristic: common name

characteristic: geographic location (altitude)

text: United Kingdom

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

text: Portclair

text: James Borrell

text: Betula nana

text: dwarf birch

text: Adult

text: soil

characteristic: plant growth medium

text: Cambium

characteristic: plant structure

characteristic: ploidy

text: Betula nana

characteristic: source material identifiers


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: QMUL

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: James Borrell

text: alpine birch

text: United Kingdom

characteristic: geographic location (longitude)

text: Rannoch Moor B

characteristic: geographic location (region and locality)

text: James Borrell

text: Betula nana

characteristic: organism

text: dwarf birch

text: Adult

text: soil

text: Cambium

text: Betula nana

characteristic: title


text: QMUL

text: public

characteristic: SRA accession

characteristic: Submitter Id

text: James Borrell

characteristic: collected by

characteristic: collection date

text: alpine birch

characteristic: common name

characteristic: geographic location (altitude)

text: United Kingdom

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

text: Rannoch West

text: James Borrell

characteristic: identified by

characteristic: isolation and growth condition

text: Betula nana

text: dwarf birch

characteristic: organism common name

text: Adult

characteristic: plant developmental stage

text: soil

text: Cambium

text: Betula nana


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: QMUL

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: James Borrell

text: alpine birch

text: United Kingdom

text: Spadeadam

text: James Borrell

text: Betula nana

text: dwarf birch

text: Adult

text: soil

characteristic: plant growth medium

text: Cambium

characteristic: plant structure

characteristic: ploidy

text: Betula nana

characteristic: source material identifiers


text: QMUL

text: public

characteristic: SRA accession

characteristic: Submitter Id

text: James Borrell

characteristic: collected by

characteristic: collection date

text: alpine birch

characteristic: common name

characteristic: geographic location (altitude)

text: United Kingdom

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: Meall an t'slugain

characteristic: geographic location (region and locality)

text: James Borrell

text: Betula nana

characteristic: organism

text: dwarf birch

text: Adult

text: soil

text: Cambium

text: Betula nana

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: QMUL

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: James Borrell

text: alpine birch

text: United Kingdom

text: Teesdale

text: James Borrell

characteristic: identified by

characteristic: isolation and growth condition

text: Betula nana

text: dwarf birch

characteristic: organism common name

text: Adult

characteristic: plant developmental stage

text: soil

text: Cambium

text: Betula nana


text: public

characteristic: SRA accession

tag: Namespace:CIIMAR - Interdisciplinary Centre of Marine and Environmental Research

characteristic: Submitter Id

characteristic: collection date

text: Development of an autonomous biosampler to capture in situ aquatic microbiomes

characteristic: description

characteristic: environment (biome)

characteristic: environment (feature)

characteristic: environment (material)

text: Atlantic Ocean

characteristic: geographic location (country and/or sea)

characteristic: geographic location (depth)

characteristic: geographic location (latitude)

text: metagenome

characteristic: investigation type

text: marine plankton metagenome

text: marine prokaryotic (16S rDNA) and eukaryotic (18S rDNA) diversity detected by autonomous biosamples

characteristic: project name

text: marine plankton metagenome

text: Illumina MiSeq - V3 chemistry

characteristic: sequencing method

text: Biosampler to capture aquatic microbiomes

text: water

characteristic: water environmental package


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: CIIMAR - Interdisciplinary Centre of Marine and Environmental Research

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: Atlantic Ocean

characteristic: geographic location (longitude)

text: metagenome

text: marine plankton metagenome

characteristic: organism

text: marine plankton metagenome

text: Illumina MiSeq - V3 chemistry

characteristic: title

text: water


E-MTAB-6984:SCRB-Seq (BAY, rep 1)

text: public

characteristic: SRA accession

text: E-MTAB-6984:SCRB-Seq (BAY, rep 1)

tag: Namespace:Institute of Bioengineering, Ecole Polytechnique Federale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland

characteristic: Submitter Id

text: ArrayExpress

characteristic: broker name

characteristic: cell line

text: B cell

characteristic: cell type

text: human

characteristic: common name

text: Protocols: We used GM12878 cells (LCL) The lymphoblastoid cell line GM12878 was cultured using RPMI 1640 medium supplemented with 10% fetal bovine serum and 1x penicillin/streptomycin. One million cells were treated with DMSO (Applichem #A3672,0250) or 3 µM BAY11-7082 (SignalChem, # C51-900) during 24 hours prior to harvesting for RNA isolation Cells were treated with either DMSO or IKK inhibitor (BAY 11-7082) to induce gene expression differences. Total RNA was isolated using TRI Reagent (Molecular Research Center, #TR118) followed by double precipitation with ethanol. The RNA concentration was determined using the Qubit RNA HS Assay Kit (Invitrogen, #Q32852) and integrity was assessed using a Fragment Analyzer (Advanced Analytical). The RNA from each differentiation time point was used in two technical replicates, resulting in four samples pooled per library. Libraries were prepared with the BRB-seq protocol using total RNA amounts ranging from 1 ng to 2 µg per sample. RNA fragmentation was done using the NEBNext Magnesium RNA Fragmentation Module (NEB, #E6150S) with incubation time at 94°C for one or two minutes. This resulted in RNA with a variable extent of degradation and corresponding RQN values. TruSeq libraries were prepared with 1 µg of total RNA using the TruSeq Stranded mRNA Library Prep Kit (Illumina, #RS-122-2101) and following the manufacturer's instructions. Four libraries were paired-end sequenced (75 nt each) with the NextSeq 500 using the Mid Output v2 kit (150 cycles) (Illumina, #FC-404-2001).

characteristic: description

text: normal

characteristic: disease

text: Homo sapiens

text: Homo sapiens

text: blood

characteristic: organism part

text: Homo sapiens

text: SCRB-Seq (BAY, rep 1)


E-MTAB-6984:SCRB-Seq (BAY, rep 2)

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Institute of Bioengineering, Ecole Polytechnique Federale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland

text: public

text: E-MTAB-6984:SCRB-Seq (BAY, rep 2)

text: ArrayExpress

text: B cell

text: human

text: normal

text: Homo sapiens

text: Homo sapiens

text: blood

text: Homo sapiens

text: SCRB-Seq (BAY, rep 2)


E-MTAB-6984:SCRB-Seq (BAY, rep 3)

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: E-MTAB-6984:SCRB-Seq (BAY, rep 3)

text: ArrayExpress

text: B cell

text: human

text: normal

text: Homo sapiens

text: Homo sapiens

text: blood

text: Homo sapiens

text: SCRB-Seq (BAY, rep 3)


E-MTAB-6984:SCRB-Seq (DMSO, rep 1)

text: public

characteristic: SRA accession

text: E-MTAB-6984:SCRB-Seq (DMSO, rep 1)

text: ArrayExpress

text: B cell

text: human

text: normal

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: blood

text: Homo sapiens

text: SCRB-Seq (DMSO, rep 1)

characteristic: title


E-MTAB-6984:SCRB-Seq (DMSO, rep 2)

text: public

text: E-MTAB-6984:SCRB-Seq (DMSO, rep 2)

characteristic: Submitter Id

text: ArrayExpress

characteristic: broker name

characteristic: cell line

text: B cell

text: human

text: normal

text: Homo sapiens

text: Homo sapiens

text: blood

text: Homo sapiens

text: SCRB-Seq (DMSO, rep 2)


E-MTAB-6984:SCRB-Seq (DMSO, rep 3)

text: public

text: E-MTAB-6984:SCRB-Seq (DMSO, rep 3)

text: ArrayExpress

text: B cell

characteristic: cell type

text: human

characteristic: common name

characteristic: description

text: normal

text: Homo sapiens

text: Homo sapiens

text: blood

text: Homo sapiens

text: SCRB-Seq (DMSO, rep 3)


E-MTAB-6984:TruSeq (BAY, rep 1)

characteristic: ENA-CHECKLIST

text: public

text: E-MTAB-6984:TruSeq (BAY, rep 1)

text: ArrayExpress

text: B cell

text: human

text: normal

characteristic: disease

text: Homo sapiens

text: Homo sapiens

text: blood

characteristic: organism part

text: Homo sapiens

text: TruSeq (BAY, rep 1)


E-MTAB-6984:TruSeq (BAY, rep 2)

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: public

text: E-MTAB-6984:TruSeq (BAY, rep 2)

text: ArrayExpress

text: B cell

text: human

text: normal

text: Homo sapiens

text: Homo sapiens

text: blood

text: Homo sapiens

text: TruSeq (BAY, rep 2)


E-MTAB-6984:TruSeq (BAY, rep 3)

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: E-MTAB-6984:TruSeq (BAY, rep 3)

text: ArrayExpress

text: B cell

text: human

text: normal

text: Homo sapiens

text: Homo sapiens

text: blood

text: Homo sapiens

text: TruSeq (BAY, rep 3)


E-MTAB-6984:TruSeq (DMSO, rep 1)

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-6984:TruSeq (DMSO, rep 1)

text: ArrayExpress

text: B cell

text: human

text: normal

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: blood

text: Homo sapiens

text: TruSeq (DMSO, rep 1)


E-MTAB-6984:TruSeq (DMSO, rep 2)

text: public

text: E-MTAB-6984:TruSeq (DMSO, rep 2)

characteristic: Submitter Id

text: ArrayExpress

characteristic: broker name

text: B cell

text: human

text: normal

text: Homo sapiens

text: Homo sapiens

text: blood

text: Homo sapiens

text: TruSeq (DMSO, rep 2)

characteristic: title


E-MTAB-6984:TruSeq (DMSO, rep 3)

text: public

text: E-MTAB-6984:TruSeq (DMSO, rep 3)

text: ArrayExpress

characteristic: cell line

text: B cell

characteristic: cell type

text: human

characteristic: common name

text: normal

text: Homo sapiens

text: Homo sapiens

text: blood

text: Homo sapiens

text: TruSeq (DMSO, rep 3)


characteristic: ENA-CHECKLIST

text: University Vienna

text: public

tag: Namespace:University Vienna

text: Dumeril's clam worm

text: Platynereis dumerilii

text: Platynereis dumerilii


tag: attribute

text: Animal and Plant Health Agency (APHA)

text: public

tag: Namespace:Animal and Plant Health Agency (APHA)

text: Atlantic salmon

text: Salmo salar

text: Salmo salar

text: Spiked smoked salmon sample for metagenomics ring trial


text: Klebsiella pneumoniae

characteristic: ArrayExpress-SPECIES

text: SC

text: public

text: Klebsiella pneumoniae

text: Klebsiella pneumoniae

text: Klebsiella pneumoniae

characteristic: subject id


text: Plasmodium vivax

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: SC

text: public

text: malaria parasite P. vivax

text: Plasmodium vivax

text: Plasmodium vivax


text: Mus musculus

characteristic: External Id

text: SC

characteristic: INSDC center name

text: public

text: house mouse

text: Mus musculus

text: Mus musculus


text: STOCKHOLM UNIVERSITY

characteristic: INSDC first public

characteristic: INSDC last update

text: public

tag: Namespace:STOCKHOLM UNIVERSITY

text: human

text: Homo sapiens

text: Homo sapiens

text: Ancient Human Genome


text: public

characteristic: INSDC status

characteristic: SRA accession

tag: Namespace:UMR 1095 INRA/UCA, Genetics, Diversity and Ecophysiology of Cereals

text: UMR INRA/UCA 1095 GDEC

characteristic: collected by

characteristic: collection date

text: France

characteristic: geographic location (country and/or sea)

text: wheat

characteristic: host scientific name

text: Triticum aestivum L. spikes

characteristic: isolation source

text: Fusarium graminearum

text: Fusarium graminearum

characteristic: strain

text: Fusarium graminearum MDC_Fg1


control 1

characteristic: ENA-CHECKLIST

text: ED

text: public

text: control 1

characteristic: Submitter Id

text: myelinating cultures

characteristic: cell type

text: house mouse

characteristic: common name

text: 25 days in vitro

characteristic: description

text: Mus musculus

characteristic: organism

text: Mus musculus

text: untreated

characteristic: title


treated 1

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: ED

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: treated 1

text: myelinating cultures

text: house mouse

text: 24h GM-CSF treatment (100 ng/ml) at 24 days in vitro

text: Mus musculus

text: Mus musculus

text: GM-CSF treated


control 2

text: ED

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: control 2

text: myelinating cultures

text: house mouse

text: 25 days in vitro

text: Mus musculus

text: Mus musculus

text: untreated


treated 2

text: ED

text: public

text: treated 2

text: myelinating cultures

text: house mouse

text: Mus musculus

text: Mus musculus

text: GM-CSF treated


control 3

text: ED

text: public

text: control 3

text: myelinating cultures

text: house mouse

text: 25 days in vitro

text: Mus musculus

text: Mus musculus

text: untreated


treated 3

text: ED

text: public

text: treated 3

text: myelinating cultures

text: house mouse

text: Mus musculus

text: Mus musculus

text: GM-CSF treated