text: Genomnia srl

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: ArrayExpress

characteristic: broker name

text: human

text: embryonal rhabdomyosarcoma

text: Stage 3

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: trunk

text: Homo sapiens


status: PUBLIC

tag: attribute

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Genomnia srl

characteristic: INSDC center name

text: public

tag: Namespace:Genomnia srl

text: ArrayExpress

text: human

characteristic: common name

text: Protocols: RMS tumour samples were obtained at diagnosis before any treatment from children admitted to the Department of Paediatrics and Infantile Neuropsychiatry at Sapienzu University of Rome, and to the Department of Oncology at Alder Hey Childrens NHS Trust, Liverpool. Histopathological diagnosis was confirmed using immunohistochemistry. Total RNA was extracted using Trizol reagent, according to the manufacturers instructions. Samples were enriched for small RNAs up to 200 bp by size selection using Pure Link miRNA Isolation Kit (LifeTech). Enriched RNA samples were processed using the Small RNA Expression Kit according to the manufacturers protocol (Small RNA expression kit, rev. C, Applied Biosystems). cDNA libraries were barcoded using the Solid RNA barcoding kit and amplified onto beads using emulsion PCR. Templated beads were deposited on slides and analysed using the Applied Biosystems SOLiD 4 Sequencer

characteristic: description

text: alveolar rhabdomyosarcoma

characteristic: disease

text: Stage 3

characteristic: disease staging

text: Homo sapiens

text: Homo sapiens

text: uterus-vagina

characteristic: organism part

text: Homo sapiens

characteristic: title

type: has member


text: Genomnia srl

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: ArrayExpress

text: human

text: embryonal rhabdomyosarcoma

text: Stage 3

text: Homo sapiens

text: Homo sapiens

text: bladder-prostate

text: Homo sapiens


text: Genomnia srl

text: public

characteristic: INSDC status

characteristic: SRA accession

text: ArrayExpress

text: human

text: embryonal rhabdomyosarcoma

text: Stage 3

text: Homo sapiens

text: Homo sapiens

text: retroperitoneum

text: Homo sapiens


text: Genomnia srl

text: public

characteristic: Submitter Id

text: ArrayExpress

characteristic: broker name

text: human

text: alveolar rhabdomyosarcoma

text: Stage 2

text: Homo sapiens

text: Homo sapiens

text: trunk

text: Homo sapiens


characteristic: ENA-CHECKLIST

text: Genomnia srl

text: public

text: ArrayExpress

text: human

text: alveolar rhabdomyosarcoma

text: Stage 3

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: extremity

text: Homo sapiens


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: Genomnia srl

text: public

text: ArrayExpress

text: human

text: alveolar rhabdomyosarcoma

text: Stage 3

text: Homo sapiens

text: Homo sapiens

text: trunk

text: Homo sapiens


characteristic: External Id

text: Maastricht University

characteristic: INSDC center name

text: public

tag: Namespace:Maastricht University

characteristic: biological replicate

text: ArrayExpress

characteristic: cell line

text: hepatocyte

characteristic: cell type

text: human

text: Protocols: Starting from the Total RNA samples, small RNAs were size selected and ligated for sequencing following the TruSeq Small Prep Kit Preparation (Illumina, 15004197 Rev. D).

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens

text: 6 hour

characteristic: time


text: Maastricht University

text: public

text: ArrayExpress

text: hepatocyte

text: human

characteristic: common name

characteristic: description

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens

text: 36 hour

characteristic: title


text: Maastricht University

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: ArrayExpress

text: hepatocyte

text: human

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens

text: 24 hour


text: Maastricht University

text: public

characteristic: SRA accession

characteristic: Submitter Id

text: ArrayExpress

characteristic: broker name

text: hepatocyte

text: human

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens

text: 18 hour


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: Maastricht University

text: public

text: ArrayExpress

text: hepatocyte

text: human

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: Homo sapiens

text: 12 hour


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Maastricht University

characteristic: INSDC center name

text: public

text: ArrayExpress

text: hepatocyte

text: human

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens

text: 48 hour


text: Wellcome Trust Sanger Institute

text: public

tag: Namespace:Wellcome Trust Sanger Institute

text: 8 weeks

characteristic: age

text: ArrayExpress

text: house mouse

text: Protocols: An 8-week-old C57/BL6 mouse purchased from Charles River was sacrificed, from which brain, heart, kidney, liver, lung, muscle (biceps femoris), spleen and testis were dissected. The tissues were homogenised in Trizol and total RNA was extracted. Any remaining DNA was removed with the Qiagen RNase-free DNase kit (ref. 79254) and total RNA was cleaned up with a Qiagen RNeasy mini kit (ref. 74104) column. Then, poly-A+ RNA was extracted from the total RNA using the Qiagen Oligotex mRNA mini kit (ref. 70022). Reverse transcription was performed with the Invitrogen SuperScript III first-strand synthesis kit (ref. 18080-051) using random hexamers for priming. PCR amplifications were performed using 0.2 ng of initial poly A+ RNA (as measured before doing the reverse transcription) in a final volume of 12.5 uL with JumpStart REDTaq ReadyMix (Sigma-Aldrich) and a primer concentration of 0.4 uM. Reactions took place in 384-well plates format on an automatized Evoware platform (TECAN) combined with a Tetrad2 thermocycler (Bio-Rad) that allows processing four plates in parallel. Because monoexonic amplification is sensitive to genomic DNA contaminations, monoexonic models were assessed by amplification of cDNA in which a dNTP analog was incorporated using the mRNA Selective PCR Kit (TAKARA).

text: Mus musculus

text: Mus musculus

text: brain

characteristic: organism part

text: Mus musculus

text: male

characteristic: sex

characteristic: strain


text: Wellcome Trust Sanger Institute

text: public

text: 8 weeks

text: ArrayExpress

text: house mouse

characteristic: common name

characteristic: description

text: Mus musculus

text: Mus musculus

text: spleen

text: Mus musculus

text: male

characteristic: title


text: Wellcome Trust Sanger Institute

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: 8 weeks

text: ArrayExpress

text: house mouse

text: Mus musculus

text: Mus musculus

text: testis

text: Mus musculus

text: male


text: Wellcome Trust Sanger Institute

text: public

characteristic: SRA accession

characteristic: Submitter Id

text: 8 weeks

text: ArrayExpress

characteristic: broker name

text: house mouse

text: Mus musculus

text: Mus musculus

text: heart

text: Mus musculus

text: male


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: Wellcome Trust Sanger Institute

text: public

text: 8 weeks

text: ArrayExpress

text: house mouse

text: Mus musculus

characteristic: organism

text: Mus musculus

text: lung

text: Mus musculus

text: male


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Wellcome Trust Sanger Institute

characteristic: INSDC center name

text: public

text: 8 weeks

text: ArrayExpress

text: house mouse

text: Mus musculus

text: Mus musculus

text: skeletal muscle

text: Mus musculus

text: male


text: Wellcome Trust Sanger Institute

text: public

text: 8 weeks

characteristic: age

text: ArrayExpress

text: house mouse

text: Mus musculus

text: Mus musculus

text: kidney

characteristic: organism part

text: Mus musculus

text: male

characteristic: sex


text: Wellcome Trust Sanger Institute

text: public

text: 8 weeks

text: ArrayExpress

text: house mouse

characteristic: common name

characteristic: description

text: Mus musculus

text: Mus musculus

text: liver

text: Mus musculus

text: male

characteristic: strain


status: KILLED

characteristic: ArrayExpress-Age

characteristic: ArrayExpress-CellType

characteristic: ArrayExpress-Compound

characteristic: ArrayExpress-DevelopmentalStage

characteristic: ArrayExpress-DiseaseState

characteristic: ArrayExpress-Dose

characteristic: ArrayExpress-Genotype

characteristic: ArrayExpress-GrowthCondition

characteristic: ArrayExpress-Immunoprecipitate

characteristic: ArrayExpress-OrganismPart

characteristic: ArrayExpress-Phenotype

text: male

characteristic: ArrayExpress-Sex

text: Homo sapiens

characteristic: ArrayExpress-Species

characteristic: ArrayExpress-TimePoint

characteristic: ArrayExpress-Treatment

text: SC

characteristic: INSDC first public

characteristic: INSDC last update

text: killed

characteristic: Sample Description

characteristic: Strain

text: human

text: Homo sapiens

text: Homo sapiens


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: CGS-GL

characteristic: INSDC center name

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

characteristic: collection date

text: house mouse

characteristic: common name

text: V4-16S sequencing. Colonization of mice with a defined consortia of microbes. This fecal sample was obtained from mouse #1, 1 days afterV4-16S sequencing. Colonization with Enterobacteriaceae and Enterococci. The mouse was fed the Malawi diet. Please see our paper for additional details.

characteristic: description

characteristic: environment (biome)

characteristic: environment (feature)

characteristic: environment (material)

text: USA

characteristic: geographic location (country and/or sea)

unit: DD

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: mimarks-survey

characteristic: investigation type

text: miscellaneous natural or artificial environment

characteristic: miscellaneous environmental package

text: Mus musculus

characteristic: organism

text: Functional characterization of mucosal IgA-targeted members of the gut microbiota of undernourished Malawian children

characteristic: project name

text: Mus musculus

text: illumina

characteristic: sequencing method

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: CGS-GL

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: house mouse

text: V4-16S sequencing. Colonization of mice with a defined consortia of microbes. This fecal sample was obtained from mouse #2, 1 days afterV4-16S sequencing. Colonization with Enterobacteriaceae and Enterococci. The mouse was fed the Malawi diet. Please see our paper for additional details.

text: USA

text: mimarks-survey

text: Mus musculus

text: Mus musculus

text: illumina


text: CGS-GL

text: public

characteristic: Submitter Id

characteristic: collection date

text: house mouse

characteristic: common name

text: V4-16S sequencing. Colonization of mice with a defined consortia of microbes. This fecal sample was obtained from mouse #3, 1 days afterV4-16S sequencing. Colonization with Enterobacteriaceae and Enterococci. The mouse was fed the Malawi diet. Please see our paper for additional details.

characteristic: description

characteristic: environment (biome)

characteristic: environment (feature)

characteristic: environment (material)

text: USA

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

text: mimarks-survey

text: Mus musculus

text: Mus musculus

text: illumina


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: CGS-GL

text: public

text: house mouse

text: V4-16S sequencing. Colonization of mice with a defined consortia of microbes. This fecal sample was obtained from mouse #4, 1 days afterV4-16S sequencing. Colonization with Enterobacteriaceae and Enterococci. The mouse was fed the Malawi diet. Please see our paper for additional details.

text: USA

characteristic: geographic location (longitude)

text: mimarks-survey

characteristic: investigation type

characteristic: miscellaneous environmental package

text: Mus musculus

characteristic: organism

characteristic: project name

text: Mus musculus

text: illumina

characteristic: sequencing method

characteristic: title


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: CGS-GL

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

characteristic: collection date

text: house mouse

text: V4-16S sequencing. Colonization of mice with a defined consortia of microbes. This fecal sample was obtained from mouse #5, 1 days afterV4-16S sequencing. Colonization with Enterobacteriaceae and Enterococci. The mouse was fed the Malawi diet. Please see our paper for additional details.

text: USA

text: mimarks-survey

text: Mus musculus

text: Mus musculus

text: illumina


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: CGS-GL

text: public

text: house mouse

characteristic: common name

text: V4-16S sequencing. Colonization of mice with a defined consortia of microbes. This fecal sample was obtained from mouse #6, 1 days afterV4-16S sequencing. Colonization with Enterobacteriaceae and Enterococci. The mouse was fed the Malawi diet. Please see our paper for additional details.

characteristic: description

characteristic: environment (biome)

characteristic: environment (feature)

characteristic: environment (material)

text: USA

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

text: mimarks-survey

text: Mus musculus

text: Mus musculus

text: illumina


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: CGS-GL

text: public

text: house mouse

text: V4-16S sequencing. Colonization of mice with a defined consortia of microbes. This fecal sample was obtained from mouse #7, 1 days afterV4-16S sequencing. Colonization with Enterobacteriaceae and Enterococci. The mouse was fed the Malawi diet. Please see our paper for additional details.

text: USA

characteristic: geographic location (longitude)

text: mimarks-survey

characteristic: investigation type

characteristic: miscellaneous environmental package

text: Mus musculus

characteristic: organism

characteristic: project name

text: Mus musculus

text: illumina

characteristic: sequencing method

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: CGS-GL

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

characteristic: collection date

text: house mouse

text: V4-16S sequencing. Colonization of mice with a defined consortia of microbes. This fecal sample was obtained from mouse #8, 1 days afterV4-16S sequencing. Colonization with Enterobacteriaceae and Enterococci. The mouse was fed the Malawi diet. Please see our paper for additional details.

text: USA

text: mimarks-survey

text: Mus musculus

text: Mus musculus

text: illumina


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: CGS-GL

text: public

text: house mouse

characteristic: common name

text: V4-16S sequencing. Colonization of mice with a defined consortia of microbes. This fecal sample was obtained from mouse #1, 1 days afterV4-16S sequencing. Colonization with Enterobacteriaceae, Bacteroidetes and Enterococci. The mouse was fed the Malawi diet. Please see our paper for additional details.

characteristic: description

characteristic: environment (biome)

characteristic: environment (feature)

characteristic: environment (material)

text: USA

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

text: mimarks-survey

text: Mus musculus

text: Mus musculus

text: illumina


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: CGS-GL

text: public

text: house mouse

text: V4-16S sequencing. Colonization of mice with a defined consortia of microbes. This fecal sample was obtained from mouse #2, 1 days afterV4-16S sequencing. Colonization with Enterobacteriaceae, Bacteroidetes and Enterococci. The mouse was fed the Malawi diet. Please see our paper for additional details.

text: USA

characteristic: geographic location (longitude)

text: mimarks-survey

characteristic: investigation type

characteristic: miscellaneous environmental package

text: Mus musculus

characteristic: organism

characteristic: project name

text: Mus musculus

text: illumina

characteristic: sequencing method

characteristic: title


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: CGS-GL

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

characteristic: collection date

text: house mouse

text: V4-16S sequencing. Colonization of mice with a defined consortia of microbes. This fecal sample was obtained from mouse #3, 1 days afterV4-16S sequencing. Colonization with Enterobacteriaceae, Bacteroidetes and Enterococci. The mouse was fed the Malawi diet. Please see our paper for additional details.

text: USA

text: mimarks-survey

text: Mus musculus

text: Mus musculus

text: illumina


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: CGS-GL

text: public

text: house mouse

characteristic: common name

text: V4-16S sequencing. Colonization of mice with a defined consortia of microbes. This fecal sample was obtained from mouse #4, 1 days afterV4-16S sequencing. Colonization with Enterobacteriaceae, Bacteroidetes and Enterococci. The mouse was fed the Malawi diet. Please see our paper for additional details.

characteristic: description

characteristic: environment (biome)

characteristic: environment (feature)

characteristic: environment (material)

text: USA

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

text: mimarks-survey

text: Mus musculus

text: Mus musculus

text: illumina


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: CGS-GL

text: public

text: house mouse

text: V4-16S sequencing. Colonization of mice with a defined consortia of microbes. This fecal sample was obtained from mouse #5, 1 days afterV4-16S sequencing. Colonization with Enterobacteriaceae, Bacteroidetes and Enterococci. The mouse was fed the Malawi diet. Please see our paper for additional details.

text: USA

characteristic: geographic location (longitude)

text: mimarks-survey

characteristic: investigation type

characteristic: miscellaneous environmental package

text: Mus musculus

characteristic: organism

characteristic: project name

text: Mus musculus

text: illumina

characteristic: sequencing method

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: CGS-GL

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

characteristic: collection date

text: house mouse

text: V4-16S sequencing. Colonization of mice with a defined consortia of microbes. This fecal sample was obtained from mouse #6, 1 days afterV4-16S sequencing. Colonization with Enterobacteriaceae, Bacteroidetes and Enterococci. The mouse was fed the Malawi diet. Please see our paper for additional details.

text: USA

text: mimarks-survey

text: Mus musculus

text: Mus musculus

text: illumina


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: CGS-GL

text: public

text: house mouse

characteristic: common name

text: V4-16S sequencing. Colonization of mice with a defined consortia of microbes. This fecal sample was obtained from mouse #7, 1 days afterV4-16S sequencing. Colonization with Enterobacteriaceae, Bacteroidetes and Enterococci. The mouse was fed the Malawi diet. Please see our paper for additional details.

characteristic: description

characteristic: environment (biome)

characteristic: environment (feature)

characteristic: environment (material)

text: USA

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

text: mimarks-survey

text: Mus musculus

text: Mus musculus

text: illumina


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: CGS-GL

text: public

text: house mouse

text: V4-16S sequencing. Colonization of mice with a defined consortia of microbes. This fecal sample was obtained from mouse #8, 1 days afterV4-16S sequencing. Colonization with Enterobacteriaceae, Bacteroidetes and Enterococci. The mouse was fed the Malawi diet. Please see our paper for additional details.

text: USA

characteristic: geographic location (longitude)

text: mimarks-survey

characteristic: investigation type

characteristic: miscellaneous environmental package

text: Mus musculus

characteristic: organism

characteristic: project name

text: Mus musculus

text: illumina

characteristic: sequencing method

characteristic: title


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: CGS-GL

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

characteristic: collection date

text: house mouse

text: V4-16S sequencing. Colonization of mice with a defined consortia of microbes. This fecal sample was obtained from mouse #9, 1 days afterV4-16S sequencing. Colonization with Enterobacteriaceae, Bacteroidetes and Enterococci. The mouse was fed the Malawi diet. Please see our paper for additional details.

text: USA

text: mimarks-survey

text: miscellaneous natural or artificial environment

text: Mus musculus

text: Mus musculus

text: illumina


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: CGS-GL

text: public

text: house mouse

characteristic: common name

text: V4-16S sequencing. Colonization of mice with a defined consortia of microbes. This fecal sample was obtained from mouse #1, 1 days afterV4-16S sequencing. Colonization with Bacteroidetes and Enterococci. The mouse was fed the Malawi diet. Please see our paper for additional details.

characteristic: description

characteristic: environment (biome)

characteristic: environment (feature)

characteristic: environment (material)

text: USA

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

text: mimarks-survey

text: Mus musculus

text: Functional characterization of mucosal IgA-targeted members of the gut microbiota of undernourished Malawian children

text: Mus musculus

text: illumina


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: CGS-GL

text: public

text: house mouse

text: V4-16S sequencing. Colonization of mice with a defined consortia of microbes. This fecal sample was obtained from mouse #2, 1 days afterV4-16S sequencing. Colonization with Bacteroidetes and Enterococci. The mouse was fed the Malawi diet. Please see our paper for additional details.

text: USA

characteristic: geographic location (longitude)

text: mimarks-survey

characteristic: investigation type

characteristic: miscellaneous environmental package

text: Mus musculus

characteristic: organism

characteristic: project name

text: Mus musculus

text: illumina

characteristic: sequencing method

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: CGS-GL

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

characteristic: collection date

text: house mouse

text: V4-16S sequencing. Colonization of mice with a defined consortia of microbes. This fecal sample was obtained from mouse #3, 1 days afterV4-16S sequencing. Colonization with Bacteroidetes and Enterococci. The mouse was fed the Malawi diet. Please see our paper for additional details.

text: USA

text: mimarks-survey

text: Mus musculus

text: Mus musculus

text: illumina


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: CGS-GL

text: public

text: house mouse

characteristic: common name

text: V4-16S sequencing. Colonization of mice with a defined consortia of microbes. This fecal sample was obtained from mouse #4, 1 days afterV4-16S sequencing. Colonization with Bacteroidetes and Enterococci. The mouse was fed the Malawi diet. Please see our paper for additional details.

characteristic: description

characteristic: environment (biome)

characteristic: environment (feature)

characteristic: environment (material)

text: USA

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

text: mimarks-survey

text: Mus musculus

text: Mus musculus

text: illumina


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: CGS-GL

text: public

text: house mouse

text: V4-16S sequencing. Colonization of mice with a defined consortia of microbes. This fecal sample was obtained from mouse #5, 1 days afterV4-16S sequencing. Colonization with Bacteroidetes and Enterococci. The mouse was fed the Malawi diet. Please see our paper for additional details.

text: USA

characteristic: geographic location (longitude)

text: mimarks-survey

characteristic: investigation type

characteristic: miscellaneous environmental package

text: Mus musculus

characteristic: organism

characteristic: project name

text: Mus musculus

text: illumina

characteristic: sequencing method

characteristic: title


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: CGS-GL

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

characteristic: collection date

text: house mouse

text: V4-16S sequencing. Colonization of mice with a defined consortia of microbes. This fecal sample was obtained from mouse #6, 1 days afterV4-16S sequencing. Colonization with Bacteroidetes and Enterococci. The mouse was fed the Malawi diet. Please see our paper for additional details.

text: USA

text: mimarks-survey

text: Mus musculus

text: Mus musculus

text: illumina


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: CGS-GL

text: public

text: house mouse

characteristic: common name

text: V4-16S sequencing. Colonization of mice with a defined consortia of microbes. This fecal sample was obtained from mouse #7, 1 days afterV4-16S sequencing. Colonization with Bacteroidetes and Enterococci. The mouse was fed the Malawi diet. Please see our paper for additional details.

characteristic: description

characteristic: environment (biome)

characteristic: environment (feature)

characteristic: environment (material)

text: USA

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

text: mimarks-survey

text: Mus musculus

text: Mus musculus

text: illumina


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: CGS-GL

text: public

text: house mouse

text: V4-16S sequencing. Colonization of mice with a defined consortia of microbes. This fecal sample was obtained from mouse #8, 1 days afterV4-16S sequencing. Colonization with Bacteroidetes and Enterococci. The mouse was fed the Malawi diet. Please see our paper for additional details.

text: USA

characteristic: geographic location (longitude)

text: mimarks-survey

characteristic: investigation type

characteristic: miscellaneous environmental package

text: Mus musculus

characteristic: organism

characteristic: project name

text: Mus musculus

text: illumina

characteristic: sequencing method

characteristic: title


text: 11.5 weeks

characteristic: ArrayExpress-Age

text: Lin- bone marrow cells

characteristic: ArrayExpress-CellType

text: WT

characteristic: ArrayExpress-Genotype

text: wild type

characteristic: ArrayExpress-Phenotype

text: male

characteristic: ArrayExpress-Sex

text: Mus Musculus

characteristic: ArrayExpress-Species

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: 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: house mouse

text: Mus musculus

text: Lin- bone marrow cells

characteristic: sample description

text: Mus musculus


text: 11.5 weeks

text: Lin- bone marrow cells

text: KO

text: wild type

text: male

text: Mus Musculus

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: SC

text: public

text: house mouse

characteristic: common name

text: Mus musculus

characteristic: organism

text: Lin- bone marrow cells

text: Mus musculus


E-MTAB-3258:Sample 15

text: Genomnia srl

text: public

text: E-MTAB-3258:Sample 15

text: ArrayExpress

characteristic: broker name

text: central

characteristic: cancer site

text: human

text: Protocols: 27 total RNA samples were extracted independently from the core and peritumoral region of 13 glioblastoma tumors and 1 sample of healthy white matter Each library was generated by using the SOLiD SAGE Kit with Barcoding Adaptor Module and a SOLiD RNA Barcoding Kit (Catalog nos. 4452811 and 4427046, Applied Biosystems, Foster City, CA), following the manufacturers instructions.

characteristic: description

text: glioblastoma multiforme

characteristic: disease

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens

text: short term

characteristic: survival probability

text: Sample 15

characteristic: title


E-MTAB-3258:Sample 18

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: Genomnia srl

characteristic: INSDC center name

text: public

text: E-MTAB-3258:Sample 18

text: ArrayExpress

text: Peritumoral

text: human

text: glioblastoma multiforme

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens

text: long term

text: Sample 18


E-MTAB-3258:Sample 16

text: Genomnia srl

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: E-MTAB-3258:Sample 16

text: ArrayExpress

text: Peritumoral

text: human

text: glioblastoma multiforme

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens

text: short term

text: Sample 16


E-MTAB-3258:Sample 6

text: Genomnia srl

text: public

characteristic: SRA accession

text: E-MTAB-3258:Sample 6

characteristic: Submitter Id

text: ArrayExpress

text: Peritumoral

text: human

text: glioblastoma multiforme

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens

text: short term

text: Sample 6


E-MTAB-3258:Sample 26

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Genomnia srl

text: public

text: E-MTAB-3258:Sample 26

text: ArrayExpress

text: Peritumoral

text: human

text: glioblastoma multiforme

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens

text: short term

text: Sample 26


E-MTAB-3258:Sample 3

text: Genomnia srl

text: public

text: E-MTAB-3258:Sample 3

text: ArrayExpress

text: central

text: human

characteristic: common name

text: glioblastoma multiforme

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: Homo sapiens

text: short term

text: Sample 3


E-MTAB-3258:Sample 2

text: Genomnia srl

text: public

text: E-MTAB-3258:Sample 2

text: ArrayExpress

characteristic: broker name

text: Peritumoral

characteristic: cancer site

text: human

text: glioblastoma multiforme

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens

text: long term

text: Sample 2


E-MTAB-3258:Sample 21

text: Genomnia srl

text: public

text: E-MTAB-3258:Sample 21

text: ArrayExpress

text: central

text: human

characteristic: description

text: glioblastoma multiforme

characteristic: disease

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens

text: short term

text: Sample 21


E-MTAB-3258:Sample 24

text: Genomnia srl

text: public

text: E-MTAB-3258:Sample 24

text: ArrayExpress

text: Peritumoral

text: human

text: glioblastoma multiforme

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens

text: short term

characteristic: survival probability

text: Sample 24

characteristic: title


E-MTAB-3258:Sample 19

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: Genomnia srl

text: public

text: E-MTAB-3258:Sample 19

text: ArrayExpress

text: central

text: human

text: glioblastoma multiforme

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens

text: short term

text: Sample 19


E-MTAB-3258:Sample 27

text: Genomnia srl

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: E-MTAB-3258:Sample 27

text: ArrayExpress

text: healthy control

text: human

text: healthy control

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens

text: White Matter

text: Sample 27


E-MTAB-3258:Sample 1

text: Genomnia srl

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: E-MTAB-3258:Sample 1

text: ArrayExpress

text: central

text: human

text: glioblastoma multiforme

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens

text: long term

text: Sample 1


E-MTAB-3258:Sample 10

text: Genomnia srl

text: public

characteristic: SRA accession

text: E-MTAB-3258:Sample 10

characteristic: Submitter Id

text: ArrayExpress

text: Peritumoral

text: human

text: glioblastoma multiforme

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens

text: long term

text: Sample 10


E-MTAB-3258:Sample 4

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Genomnia srl

text: public

text: E-MTAB-3258:Sample 4

text: ArrayExpress

text: Peritumoral

text: human

text: glioblastoma multiforme

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens

text: short term

text: Sample 4


E-MTAB-3258:Sample 13

text: Genomnia srl

text: public

text: E-MTAB-3258:Sample 13

text: ArrayExpress

text: central

text: human

characteristic: common name

text: glioblastoma multiforme

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: Homo sapiens

text: short term

text: Sample 13


E-MTAB-3258:Sample 22

text: Genomnia srl

text: public

text: E-MTAB-3258:Sample 22

text: ArrayExpress

characteristic: broker name

text: Peritumoral

characteristic: cancer site

text: human

text: glioblastoma multiforme

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens

text: short term

text: Sample 22


E-MTAB-3258:Sample 5

text: Genomnia srl

text: public

text: E-MTAB-3258:Sample 5

text: ArrayExpress

text: central

text: human

characteristic: description

text: glioblastoma multiforme

characteristic: disease

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens

text: short term

text: Sample 5


E-MTAB-3258:Sample 12

text: Genomnia srl

text: public

text: E-MTAB-3258:Sample 12

text: ArrayExpress

text: Peritumoral

text: human

text: glioblastoma multiforme

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens

text: short term

characteristic: survival probability

text: Sample 12

characteristic: title


E-MTAB-3258:Sample 23

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: Genomnia srl

text: public

text: E-MTAB-3258:Sample 23

text: ArrayExpress

text: central

text: human

text: glioblastoma multiforme

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens

text: short term

text: Sample 23


E-MTAB-3258:Sample 7

text: Genomnia srl

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: E-MTAB-3258:Sample 7

text: ArrayExpress

text: central

text: human

text: glioblastoma multiforme

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens

text: long term

text: Sample 7


E-MTAB-3258:Sample 8

text: Genomnia srl

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: E-MTAB-3258:Sample 8

text: ArrayExpress

text: Peritumoral

text: human

text: glioblastoma multiforme

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens

text: long term

text: Sample 8


E-MTAB-3258:Sample 17

text: Genomnia srl

text: public

characteristic: SRA accession

text: E-MTAB-3258:Sample 17

characteristic: Submitter Id

text: ArrayExpress

text: central

text: human

text: glioblastoma multiforme

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens

text: long term

text: Sample 17


E-MTAB-3258:Sample 9

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Genomnia srl

text: public

text: E-MTAB-3258:Sample 9

text: ArrayExpress

text: central

text: human

text: glioblastoma multiforme

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens

text: long term

text: Sample 9


E-MTAB-3258:Sample 11

text: Genomnia srl

text: public

text: E-MTAB-3258:Sample 11

text: ArrayExpress

text: central

text: human

characteristic: common name

text: glioblastoma multiforme

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: Homo sapiens

text: short term

text: Sample 11


E-MTAB-3258:Sample 20

text: Genomnia srl

text: public

text: E-MTAB-3258:Sample 20

text: ArrayExpress

characteristic: broker name

text: Peritumoral

characteristic: cancer site

text: human

text: glioblastoma multiforme

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens

text: short term

text: Sample 20


E-MTAB-3258:Sample 14

text: Genomnia srl

text: public

text: E-MTAB-3258:Sample 14

text: ArrayExpress

text: Peritumoral

text: human

characteristic: description

text: glioblastoma multiforme

characteristic: disease

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens

text: short term

text: Sample 14


E-MTAB-3258:Sample 25

text: Genomnia srl

text: public

text: E-MTAB-3258:Sample 25

text: ArrayExpress

text: central

text: human

text: glioblastoma multiforme

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens

text: short term

characteristic: survival probability

text: Sample 25

characteristic: title


name: E-MTAB-3272:Cells from pool of 7 E15.5 InsMIP-EGFP/+ [het] embryos (2 litters)

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: Vanderbilt University

text: public

tag: Namespace:Vanderbilt University

text: ArrayExpress

text: Ins-expressing cell

characteristic: cell type

text: house mouse

text: Protocols: Manual dissection was employed to remove as much non-pancreatic tissue as possible. Tissues were dissociated with 0.025% trypsin to mostly single cells. Then the following steps were perfomed: (i) neutralize with 5% FBS, (ii) spin to remove solution, (iii) resuspend and sort cells into 2%FBS in PBS. Purity was visually inspected to verify EGFP fluorescence and viability and it was estimated by by cytospin. Total RNA was isolated using TRIzol LS (Invitrogen) and column purification (Zymo Research), according to manufacturer's instructions. RNA was DNase-treated (Ambion) and integrity was assessed on the Bioanalyzer (Agilent). Total RNA was amplified (0.5-10ng) using the Ovation RNA-Seq system (NuGEN). The transcriptional sequencing methods were performed essentially as previously described (Mortazavi 2008), which is a modification of the standard Illumina methods (Bentley 2008). Median fragment length=700, amount amplified = 5 ng.

text: embryonic day 15.5 (E15.5)

characteristic: developmental stage

text: Mus musculus

text: Mus musculus

text: Mus musculus

characteristic: strain


name: E-MTAB-3272:Cells from pool of 15 E15.5 Ngn3EGFP/EPFP [null] embryos

text: Vanderbilt University

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: ArrayExpress

text: Ngn3-null cell

text: house mouse

text: embryonic day 15.5 (E15.5)

text: Mus musculus

text: Mus musculus

text: Mus musculus


name: E-MTAB-3272:Cells from pool of 12 E10.5 Ngn3EGFP/EPFP [null] embryos (7 litters)

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Vanderbilt University

text: public

characteristic: Submitter Id

text: ArrayExpress

text: Ngn3-null cell

text: house mouse

characteristic: common name

text: embryonic day 10.5 (E10.5)

text: Mus musculus

characteristic: organism

text: Mus musculus

text: Mus musculus


name: E-MTAB-3272:Cells from pool of 9 E10.5 Ngn3EGFP/EPFP [null] embryos (6 litters)

text: Vanderbilt University

text: public

text: ArrayExpress

characteristic: broker name

text: Ngn3-null cell

text: house mouse

characteristic: description

text: embryonic day 10.5 (E10.5)

text: Mus musculus

text: Mus musculus

text: Mus musculus


name: E-MTAB-3272:Cells from pool of 23 E15.5 Ngn3EGFP/+ [het] embryos

characteristic: ENA-CHECKLIST

text: Vanderbilt University

text: public

text: ArrayExpress

text: Ngn3-expressing cell

text: house mouse

text: embryonic day 15.5 (E15.5)

text: Mus musculus

text: Mus musculus

text: Mus musculus

characteristic: title


name: E-MTAB-3272:Cells from pool of 46 E10.5 Ngn3EGFP/+ [het] embryos (13 litters)

characteristic: ENA-FIRST-PUBLIC

text: Vanderbilt University

text: public

text: ArrayExpress

text: Ngn3-expressing cell

characteristic: cell type

text: house mouse

text: embryonic day 10.5 (E10.5)

text: Mus musculus

text: Mus musculus

text: Mus musculus


E-MTAB-3264:Sample 1

text: The Pirbright Institute

text: public

text: E-MTAB-3264:Sample 1

tag: Namespace:The Pirbright Institute

text: ArrayExpress

text: African malaria mosquito

text: Protocols: Testes were dissected under a stereomicroscope using sharpened entomological pins size 000. Care was taken to collect only the gonads with a fragment of vas efferens, but occasionally clumps of fat body cells tightly attached to the apical part of the testis were also taken. In total, testes were dissected from approximately 200 3rd instar and early 4th instar larvae and from 2000 early (up to 4 h old) pupae. An. gambiae G3 strain mosquitoes used in the study were kept in the insectary conditions at 27 °C, 80% RH, and 12h light/12h dark cycle. Larvae were reared in pans with de-ionized water and fed daily with ground fish food (Tetramin). Pans containing fully grown 4th instar larvae were inspected every hour and newly pupated individuals were transferred into clean de-ionized water, and dissected within four hours after collection. Similarly, 3rd and early 4th instar larvae were collected, rinsed in clean water, and used for dissection. Dissected tissues were transferred immediately into RNAlater (Ambion) and stored at -20 °C until RNA isolation. Total RNA was isolated using RNeasy Mini kit (Qiagen) and treated with TURBO DNase (Ambion) according to manufacturers’ protocols. Then, polyA+ mRNA was isolated using Oligotex mRNA Mini kit (Qiagen) and its integrity evaluated using the Agilent 2100 Bioanalyzer. The mRNA was used to synthesize double-stranded cDNA using the SMARTer™ PCR cDNA synthesis kit (Clontech) according to the manufacturer’s recommendation. Fragmentation of 1 μg of double-stranded cDNA by nebulization, fragment ends polishing, adaptor ligation, isolation and estimation of the single-stranded template library concentration, emulsion PCR with library beads, and loading on the 454 plate was performed according to the published protocol (Margulies M, et al. 2005. Nature 437: 376-380).

text: 3rd instar larva, 4th instar larva, pupa

characteristic: developmental stage

text: Anopheles gambiae

text: Anopheles gambiae

text: testis

characteristic: organism part

text: Anopheles gambiae

text: male

characteristic: sex

text: Sample 1


text: Genomnia srl

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: 28 year

characteristic: age

text: ArrayExpress

text: peripheral blood mononuclear cell

text: human

text: Protocols: We enrolled 18 idiopathic PAH (IPAH) patients and 18 healthy subjects, age- and sex-matched. All patients were naive for specific PAH therapy and wild type for BMPR2 mutation. Based upon vasoreactivity test, we distinguished between 12 IPAH non-responder subjects (IPAH-nRes) and 6 responders (IPAH-Res). Seven IPAH patients and 8 healthy subjects underwent to SAGE. Total RNA was isolated from PBMCs with RNeasy Micro kit (Qiagen) following the manufacturers instructions. The concentration and purity (O.D. 260/280 ratio between 1.8 to 2.0) of eluted total RNA was determined spectrophotometrically using ND-1000 V3.3.0 (NanoDrop Technologies, Inc. Wilmington, DE) . The integrity of RNA was assessed using a microfluidics-based platform, Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA). All samples with RIN >8.00 were used for subsequent investigations. The SOLiD SAGE system 15, a modified version of the original protocol 17, was used to generate library of 27 base pairs (bp) tags for all the transcripts in a cell, followed by Sequencing by Oligonucleotide Ligation and Detection (SOLiD) sequencing of the tags and downstream mapping to RefSeq mRNA and genome databases. To this purpose SOLiD-SAGE kit (Life Technologies Corporation) was used and all passages have been performed following manufacturers instructions. Briefly, polyA RNA is captured using oligo-dT coated beads and converted to cDNA. A frequently cutting anchoring enzyme, NlaIII, is used to cleave cDNA molecules, leaving the 3 prime end of the cDNA attached to the beads. Linkers are ligated to the immobilized cDNA fragments containing a site for a type III restriction enzyme EcoP15I used as the tagging enzyme. EcoP15I binds to a recognition sequence in the adapter adjacent to the CATG site and cleaves the cDNA 27 bp downstream from the adapter.

text: pulmonary arterial hypertension

characteristic: disease

text: Homo sapiens

text: Homo sapiens

text: idiopathic pulmonary arterial hypertension responder

characteristic: phenotype

text: Homo sapiens

text: female

text: GV


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Genomnia srl

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: 29 year

text: ArrayExpress

text: peripheral blood mononuclear cell

text: human

characteristic: common name

text: pulmonary arterial hypertension

text: Homo sapiens

text: Homo sapiens

text: idiopathic pulmonary arterial hypertension non responder

text: Homo sapiens

text: female

text: EM


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: Genomnia srl

text: public

text: 37 year

text: ArrayExpress

characteristic: broker name

text: peripheral blood mononuclear cell

text: human

characteristic: description

text: pulmonary arterial hypertension

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: Healthy

text: Homo sapiens

text: male

text: LR

characteristic: title


text: Genomnia srl

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: 48 year

text: ArrayExpress

text: peripheral blood mononuclear cell

characteristic: cell type

text: human

text: pulmonary arterial hypertension

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens

text: female

characteristic: sex

text: BEZ


text: Genomnia srl

characteristic: INSDC last update

text: public

text: 32 year

characteristic: age

text: ArrayExpress

text: peripheral blood mononuclear cell

text: human

text: pulmonary arterial hypertension

characteristic: disease

text: Homo sapiens

text: Homo sapiens

text: Healthy

characteristic: phenotype

text: Homo sapiens

text: female

text: MG


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Genomnia srl

text: public

characteristic: INSDC status

characteristic: SRA accession

text: 40 year

text: ArrayExpress

text: peripheral blood mononuclear cell

text: human

text: pulmonary arterial hypertension

text: Homo sapiens

text: Homo sapiens

text: Healthy

text: Homo sapiens

text: female

text: CB


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: Genomnia srl

text: public

characteristic: Submitter Id

text: 27 year

text: ArrayExpress

text: peripheral blood mononuclear cell

text: human

characteristic: common name

text: pulmonary arterial hypertension

text: Homo sapiens

text: Homo sapiens

text: Healthy

text: Homo sapiens

text: female


text: Genomnia srl

text: public

text: 54 year

text: ArrayExpress

characteristic: broker name

text: peripheral blood mononuclear cell

text: human

characteristic: description

text: pulmonary arterial hypertension

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: Healthy

text: Homo sapiens

text: male

text: NG

characteristic: title


text: Genomnia srl

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: 41 year

text: ArrayExpress

text: peripheral blood mononuclear cell

characteristic: cell type

text: human

text: pulmonary arterial hypertension

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens

text: male

characteristic: sex

text: AR


text: Genomnia srl

characteristic: INSDC last update

text: public

text: 59 year

characteristic: age

text: ArrayExpress

text: peripheral blood mononuclear cell

text: human

text: pulmonary arterial hypertension

characteristic: disease

text: Homo sapiens

text: Homo sapiens

characteristic: phenotype

text: Homo sapiens

text: male

text: FDP


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Genomnia srl

text: public

characteristic: INSDC status

characteristic: SRA accession

text: 57 year

text: ArrayExpress

text: peripheral blood mononuclear cell

text: human

text: pulmonary arterial hypertension

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens

text: male

text: ED


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: Genomnia srl

text: public

characteristic: Submitter Id

text: 27 year

text: ArrayExpress

text: peripheral blood mononuclear cell

text: human

characteristic: common name

text: pulmonary arterial hypertension

text: Homo sapiens

text: Homo sapiens

text: Healthy

text: Homo sapiens

text: male

text: RT


text: Genomnia srl

text: public

text: 60 year

text: ArrayExpress

characteristic: broker name

text: peripheral blood mononuclear cell

text: human

characteristic: description

text: pulmonary arterial hypertension

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: Healthy

text: Homo sapiens

text: male

text: LF

characteristic: title


text: Genomnia srl

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: 26 year

text: ArrayExpress

text: peripheral blood mononuclear cell

characteristic: cell type

text: human

text: pulmonary arterial hypertension

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens

text: female

characteristic: sex

text: SL


text: Genomnia srl

characteristic: INSDC last update

text: public

text: 44 year

characteristic: age

text: ArrayExpress

text: peripheral blood mononuclear cell

text: human

text: pulmonary arterial hypertension

characteristic: disease

text: Homo sapiens

text: Homo sapiens

text: Healthy

characteristic: phenotype

text: Homo sapiens

text: male

text: MD


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Osaka University

text: public

characteristic: INSDC status

characteristic: SRA accession

tag: Namespace:Osaka University

text: 8 week

text: ArrayExpress

text: house mouse

text: Protocols: Mice were grown under the following condition: temperature 23.5 degree centigrade +/-2 degree , humidity 50 +/-10 % and 12 hour illumination (light period 8:00-20:00) The mouse tail was treated with Protease K and RNase A. The equal amount of Phenol/Chloroform solution was added. After centrifugation, the sup was harvested and then the equal amount of isopropanol was addicted. The DNA pellet was centrifugated and washed with 70% ethanol. The genomic DNAs were dried up at 55 degree centigrade. The DNAs were dilluted with TE. The extracted DNAs were fragmented to a length of 150 -200 nt by Covaris. These DNAs were amplified and concentrated with SureSelect XT Target Enrichment System (Agilent technologies) according to the manufacture's protocol. The bait RNAs corresponding to Miwi2 Promoter sequence were synthesized by Hokkaido System Science.

text: adult

characteristic: developmental stage

characteristic: genotype

text: Mus musculus

text: Mus musculus

text: tail

characteristic: organism part

text: Mus musculus

text: BDF1 background

characteristic: strain


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: Osaka University

text: public

characteristic: Submitter Id

text: ArrayExpress

characteristic: broker name

text: house mouse

characteristic: common name

text: Protocols: Mice were grown under the following condition: temperature 23.5 degree centigrade +/- 2 degree centigrade, humidity 50 +/- 10 % and 12 hour illumination (light period 8:00-20:00) Total RNAs were extracted by ISOGEN (Nippon Gene), according to the manufacture's protocol. The library construction was carried out according to the manufacturers standard protocol

characteristic: description

text: embryonic day 16.5

text: Mus musculus

characteristic: organism

text: Mus musculus

text: testis

text: Mus musculus

characteristic: title


E-MTAB-3248:WT (no Tg)

text: Osaka University

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: E-MTAB-3248:WT (no Tg)

text: ArrayExpress

text: house mouse

text: embryonic day 16.5

text: wild type

text: Mus musculus

text: Mus musculus

text: testis

text: Mus musculus

text: WT (no Tg)


text: male

characteristic: ArrayExpress-Sex

text: Mus Musculus

characteristic: ArrayExpress-Species

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: SC

text: public

characteristic: INSDC status

text: house mouse

text: Mus musculus

text: ESC

characteristic: sample description

text: Mus musculus


text: Plasmodium falciparum

characteristic: ENA-CHECKLIST

text: SC

text: public

characteristic: SRA accession

text: malaria parasite P. falciparum

text: Plasmodium falciparum

text: Plasmodium falciparum


characteristic: ENA-FIRST-PUBLIC

text: public

tag: Namespace:Laboratory of Molecular Medicine and Genomics, Department of Medicine and Surgery, University of Salerno, Baronissi, Italy.

characteristic: Submitter Id

text: ArrayExpress

text: platelet

characteristic: cell type

text: human

text: Protocols: Blood has been processed within 15 minutes from sampling and platelets isolated by differential centrifugation. Platelets were activated with ADP (20uM), Collagen (60ug/mL) or Thrombin Receptor Activating Peptide (TRAP, 25uM) for 120 minutes, under continuous stirring. Total RNA was extracted using RNA was extracted using mirVana Paris kit (life technologies) according to the manufacturer instructions. 1ug of total RNA was used in a library preparation according to the Illumina TruSeq small RNA sample preparation protocol (Illumina, USA). Libraries were multiplexed, by using Illumina indices set A, with indices 36 (RPI36), 38 (RPI38), 39 (RPI39) and 40 (RPI40) for T0 (control), ADP, TRAP and COLL treatment respectively.

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens

text: NS


text: NCGR

text: public

text: Japanese rice

characteristic: common name

text: ssRNA-seq of polyA selected sample from rice leaf

characteristic: description

text: Oryza sativa Japonica Group

text: Oryza sativa Japonica Group


text: NCGR

text: public

text: Japanese rice

text: ssRNA-seq of polyA selected sample from rice panicle

text: Oryza sativa Japonica Group

characteristic: organism

text: Oryza sativa Japonica Group

characteristic: title


text: NCGR

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: Japanese rice

text: ssRNA-seq of polyA depleted sample from rice leaf

text: Oryza sativa Japonica Group

text: Oryza sativa Japonica Group


text: NCGR

characteristic: INSDC last update

text: public

text: Japanese rice

text: ssRNA-seq of polyA depleted sample from rice panicle

text: Oryza sativa Japonica Group

text: Oryza sativa Japonica Group


text: Mus musculus

characteristic: ArrayExpress-Species

text: SC

text: public

text: house mouse

text: Mus musculus

text: Mus musculus


E-MTAB-3037_2:Sample 87

characteristic: ENA-LAST-UPDATE

text: public

text: E-MTAB-3037_2:Sample 87

tag: Namespace:Laboratory of Genetics - Gage The Salk Institute for Biological Studies

text: 1 year

characteristic: age

text: ArrayExpress

characteristic: broker name

text: Primary human fibroblasts

text: human

text: X1yr_O6__F_shRanBP17 Protocols: Trizol-LS and RNeasy mini TruSeq stranded mRNA (Illumina)

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens

text: Sample 87


characteristic: External Id

text: public

characteristic: INSDC status

tag: Namespace:Translational Bioinformatics Group NIHR GSTFT/KCL Comprehensive Biomedical Research Centre

text: ArrayExpress

text: house mouse

text: Protocols: female offspring (3 to 6 individuals per genotype and cross direction were sacrificed at the age of 11 to 13 weeks to prepare the HYP, the VNO, and the LIV from the same individuals. All dissections were done by the same person following personal instructions and standardized protocols designed by Valery Grinevich (MPI for Medical Research Heidelberg for HYP) and Masayo Omura (MPI for Biophysics, Frankfurt for VNO). For the HYP, brains were removed and further dissection was performed on wet ice using gross anatomical borders (i.e., optic chiasm arms, optic tracts, and mammillary body) as markers to remove the HYP. For the VNO, we followed the first steps of the procedure described in Meeks and Holy (2009). Prepared tissues were immediately frozen on dry ice and kept at minus 70 degree centigrade until RNA preparation Using TRIzol Reagent with the PureLink RNA Mini Kit, invitrogen/ambion With On-Column PureLink DNase Treatment during Purification Illumina TruSeq RNA Sample Preparation Kit v2

text: PWD/PhJ

characteristic: genotype

characteristic: individual

text: Mus musculus

text: Mus musculus

text: hypothalamus

characteristic: organism part

text: Mus musculus

text: PWD/PhJ

characteristic: strain


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: Translational Bioinformatics Group NIHR GSTFT/KCL Comprehensive Biomedical Research Centre

text: public

characteristic: SRA accession

characteristic: Submitter Id

text: ArrayExpress

text: house mouse

characteristic: common name

text: PWD/PhJ mother, WSB/EiJ father

text: Mus musculus

text: Mus musculus

text: hypothalamus

text: Mus musculus

text: cross M.m musulus (PWD/PhJ) and M. m. domesticus (WSB/EiJ)


characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: ArrayExpress

text: house mouse

characteristic: description

text: PWD/PhJ mother, WSB/EiJ father

text: Mus musculus

characteristic: organism

text: Mus musculus

text: vomeronasal organ

text: Mus musculus

characteristic: title


characteristic: ENA-LAST-UPDATE

characteristic: INSDC last update

text: public

text: ArrayExpress

characteristic: broker name

text: house mouse

text: WSB/EiJ mother, PWD/PhJ father

text: Mus musculus

text: Mus musculus

text: liver

text: Mus musculus


characteristic: External Id

text: public

characteristic: INSDC status

text: ArrayExpress

text: house mouse

text: PWD/PhJ

characteristic: genotype

text: Mus musculus

text: Mus musculus

text: vomeronasal organ

text: Mus musculus

text: PWD/PhJ


text: public

text: ArrayExpress

text: house mouse

text: WSB/EiJ mother, PWD/PhJ father

characteristic: individual

text: Mus musculus

text: Mus musculus

text: hypothalamus

characteristic: organism part

text: Mus musculus

characteristic: strain


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: public

characteristic: SRA accession

text: ArrayExpress

text: house mouse

text: PWD/PhJ

text: Mus musculus

text: Mus musculus

text: hypothalamus

text: Mus musculus

text: PWD/PhJ


characteristic: INSDC center name

text: public

characteristic: Submitter Id

text: ArrayExpress

text: house mouse

characteristic: common name

text: WSB/EiJ mother, PWD/PhJ father

text: Mus musculus

text: Mus musculus

text: vomeronasal organ

text: Mus musculus


characteristic: INSDC first public

text: public

text: ArrayExpress

text: house mouse

characteristic: description

text: PWD/PhJ

text: Mus musculus

characteristic: organism

text: Mus musculus

text: liver

text: Mus musculus

text: PWD/PhJ


characteristic: ENA-LAST-UPDATE

characteristic: INSDC last update

text: public

text: ArrayExpress

text: house mouse

text: PWD/PhJ mother, WSB/EiJ father

text: Mus musculus

text: Mus musculus

text: liver

text: Mus musculus

characteristic: title


text: Dracunculus medinensis

characteristic: ArrayExpress-Species

characteristic: External Id

text: SC

text: public

characteristic: INSDC status

text: Guinea worm

text: Dracunculus medinensis

text: Dracunculus medinensis


text: adult

characteristic: ArrayExpress-DevelopmentalStage

text: whole organism

characteristic: ArrayExpress-OrganismPart

text: mixed

characteristic: ArrayExpress-Sex

text: Haemonchus contortus

characteristic: ArrayExpress-StrainOrLine

text: SC

text: public

text: barber pole worm

text: Haemonchus contortus

text: genomic DNA from approximately 100 adults (male and female)

characteristic: sample description

text: Haemonchus contortus


text: Mus musculus

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: SC

characteristic: INSDC center name

text: public

characteristic: SRA accession

text: house mouse

text: Mus musculus

text: Mus musculus


text: Danio rerio

text: SC

characteristic: INSDC first public

text: public

characteristic: Submitter Id

text: zebrafish

characteristic: common name

text: Danio rerio

text: DNA libraries made by the addition of tailed oligos in a second round of PCR.

text: Danio rerio


text: Homo Sapien

characteristic: ENA-LAST-UPDATE

text: SC

characteristic: INSDC last update

text: public

text: human

text: Homo sapiens

characteristic: organism

text: Homo sapiens


characteristic: External Id

text: UPPSALA UNIVERSITET

text: public

tag: Namespace:UPPSALA UNIVERSITET

text: Bjorn Brunstrom

characteristic: collected by

text: chicken

text: Female1Brain White Leghorn chicken embryo

characteristic: description

text: 18 day embryo

characteristic: dev stage

text: Sweden

characteristic: geographic location (country and/or sea)

text: Gallus gallus

text: Gallus gallus

text: female

characteristic: sex

text: White Leghorn

characteristic: strain

text: brain

characteristic: tissue type

characteristic: title

text: White Leghorn

characteristic: variety


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: UPPSALA UNIVERSITET

characteristic: INSDC center name

text: public

characteristic: INSDC status

characteristic: SRA accession

text: Bjorn Brunstrom

text: chicken

text: Female1Bursa White Leghorn chicken embryo

text: 18 day embryo

text: Sweden

text: Gallus gallus

text: Gallus gallus

text: female

text: White Leghorn

text: bursa

text: White Leghorn


characteristic: ENA-LAST-UPDATE

text: UPPSALA UNIVERSITET

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: Submitter Id

text: Bjorn Brunstrom

text: chicken

characteristic: common name

text: Female1Heart White Leghorn chicken embryo

text: 18 day embryo

text: Sweden

text: Gallus gallus

text: Gallus gallus

text: female

text: White Leghorn

text: heart

text: White Leghorn


characteristic: External Id

text: UPPSALA UNIVERSITET

text: public

text: Bjorn Brunstrom

characteristic: collected by

text: chicken

text: Female1Kidney White Leghorn chicken embryo

characteristic: description

text: 18 day embryo

characteristic: dev stage

text: Sweden

text: Gallus gallus

characteristic: organism

text: Gallus gallus

text: female

text: White Leghorn

text: kidney

text: White Leghorn


text: UPPSALA UNIVERSITET

text: public

text: Bjorn Brunstrom

text: chicken

text: Female1Liver White Leghorn chicken embryo

text: 18 day embryo

text: Sweden

characteristic: geographic location (country and/or sea)

text: Gallus gallus

text: Gallus gallus

text: female

characteristic: sex

text: White Leghorn

characteristic: strain

text: liver

characteristic: tissue type

characteristic: title

text: White Leghorn


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: UPPSALA UNIVERSITET

characteristic: INSDC center name

text: public

characteristic: INSDC status

text: Bjorn Brunstrom

text: chicken

text: Female1Lung White Leghorn chicken embryo

text: 18 day embryo

text: Sweden

text: Gallus gallus

text: Gallus gallus

text: female

text: White Leghorn

text: lung

text: White Leghorn

characteristic: variety


characteristic: ENA-LAST-UPDATE

text: UPPSALA UNIVERSITET

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: SRA accession

characteristic: Submitter Id

text: Bjorn Brunstrom

text: chicken

text: Female1Muscle White Leghorn chicken embryo

text: 18 day embryo

text: Sweden

text: Gallus gallus

text: Gallus gallus

text: female

text: White Leghorn

text: muscle

text: White Leghorn


characteristic: External Id

text: UPPSALA UNIVERSITET

text: public

text: Bjorn Brunstrom

characteristic: collected by

text: chicken

characteristic: common name

text: Female1Ovarium White Leghorn chicken embryo

characteristic: description

text: 18 day embryo

characteristic: dev stage

text: Sweden

text: Gallus gallus

text: Gallus gallus

text: female

text: White Leghorn

text: ovary

text: White Leghorn


text: UPPSALA UNIVERSITET

text: public

text: Bjorn Brunstrom

text: chicken

text: Female1Spleen White Leghorn chicken embryo

text: 18 day embryo

text: Sweden

characteristic: geographic location (country and/or sea)

text: Gallus gallus

characteristic: organism

text: Gallus gallus

text: female

characteristic: sex

text: White Leghorn

characteristic: strain

text: spleen

characteristic: tissue type

text: White Leghorn


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: UPPSALA UNIVERSITET

characteristic: INSDC center name

text: public

characteristic: INSDC status

text: Bjorn Brunstrom

text: chicken

text: Female2Brain White Leghorn chicken embryo

text: 18 day embryo

text: Sweden

text: Gallus gallus

text: Gallus gallus

text: female

text: White Leghorn

text: brain

characteristic: title

text: White Leghorn


characteristic: ENA-LAST-UPDATE

text: UPPSALA UNIVERSITET

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: SRA accession

text: Bjorn Brunstrom

text: chicken

text: Female2Bursa White Leghorn chicken embryo

text: 18 day embryo

text: Sweden

text: Gallus gallus

text: Gallus gallus

text: female

text: White Leghorn

text: bursa

text: White Leghorn

characteristic: variety


characteristic: External Id

text: UPPSALA UNIVERSITET

text: public

characteristic: Submitter Id

text: Bjorn Brunstrom

characteristic: collected by

text: chicken

characteristic: common name

text: Female2Heart White Leghorn chicken embryo

characteristic: description

text: 18 day embryo

text: Sweden

text: Gallus gallus

text: Gallus gallus

text: female

text: White Leghorn

text: heart

text: White Leghorn


text: UPPSALA UNIVERSITET

text: public

text: Bjorn Brunstrom

text: chicken

text: Female2Kidney White Leghorn chicken embryo

text: 18 day embryo

characteristic: dev stage

text: Sweden

characteristic: geographic location (country and/or sea)

text: Gallus gallus

characteristic: organism

text: Gallus gallus

text: female

characteristic: sex

text: White Leghorn

characteristic: strain

text: kidney

text: White Leghorn


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: UPPSALA UNIVERSITET

characteristic: INSDC center name

text: public

characteristic: INSDC status

text: Bjorn Brunstrom

text: chicken

text: Female2Lung White Leghorn chicken embryo

text: 18 day embryo

text: Sweden

text: Gallus gallus

text: Gallus gallus

text: female

text: White Leghorn

text: lung

characteristic: tissue type

text: White Leghorn


characteristic: ENA-LAST-UPDATE

text: UPPSALA UNIVERSITET

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: SRA accession

text: Bjorn Brunstrom

text: chicken

text: Female2Muscle White Leghorn chicken embryo

text: 18 day embryo

text: Sweden

text: Gallus gallus

text: Gallus gallus

text: female

text: White Leghorn

text: muscle

characteristic: title

text: White Leghorn


characteristic: External Id

text: UPPSALA UNIVERSITET

text: public

characteristic: Submitter Id

text: Bjorn Brunstrom

characteristic: collected by

text: chicken

characteristic: common name

text: Female2Ovarium White Leghorn chicken embryo

text: 18 day embryo

text: Sweden

text: Gallus gallus

text: Gallus gallus

text: female

text: White Leghorn

text: ovary

text: White Leghorn

characteristic: variety


text: UPPSALA UNIVERSITET

text: public

text: Bjorn Brunstrom

text: chicken

text: Female5Bursa White Leghorn chicken embryo

characteristic: description

text: 18 day embryo

characteristic: dev stage

text: Sweden

characteristic: geographic location (country and/or sea)

text: Gallus gallus

characteristic: organism

text: Gallus gallus

text: female

characteristic: sex

text: White Leghorn

text: bursa

text: White Leghorn


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: UPPSALA UNIVERSITET

characteristic: INSDC center name

text: public

characteristic: INSDC status

text: Bjorn Brunstrom

text: chicken

text: Female5Heart White Leghorn chicken embryo

text: 18 day embryo

text: Sweden

text: Gallus gallus

text: Gallus gallus

text: female

text: White Leghorn

characteristic: strain

text: heart

text: White Leghorn


characteristic: ENA-LAST-UPDATE

text: UPPSALA UNIVERSITET

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: SRA accession

text: Bjorn Brunstrom

text: chicken

text: Female5Kidney White Leghorn chicken embryo

text: 18 day embryo

text: Sweden

text: Gallus gallus

text: Gallus gallus

text: female

text: White Leghorn

text: kidney

characteristic: tissue type

text: White Leghorn


characteristic: External Id

text: UPPSALA UNIVERSITET

text: public

characteristic: Submitter Id

text: Bjorn Brunstrom

characteristic: collected by

text: chicken

characteristic: common name

text: Female5Lung White Leghorn chicken embryo

text: 18 day embryo

text: Sweden

text: Gallus gallus

text: Gallus gallus

text: female

text: White Leghorn

text: lung

characteristic: title

text: White Leghorn


text: UPPSALA UNIVERSITET

text: public

text: Bjorn Brunstrom

text: chicken

text: Female5Muscle White Leghorn chicken embryo

characteristic: description

text: 18 day embryo

characteristic: dev stage

text: Sweden

characteristic: geographic location (country and/or sea)

text: Gallus gallus

characteristic: organism

text: Gallus gallus

text: female

text: White Leghorn

text: muscle

text: White Leghorn

characteristic: variety


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: UPPSALA UNIVERSITET

characteristic: INSDC center name

text: public

characteristic: INSDC status

text: Bjorn Brunstrom

text: chicken

text: Female5Ovarium White Leghorn chicken embryo

text: 18 day embryo

text: Sweden

text: Gallus gallus

text: Gallus gallus

text: female

characteristic: sex

text: White Leghorn

text: ovary

text: White Leghorn


characteristic: ENA-LAST-UPDATE

text: UPPSALA UNIVERSITET

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: SRA accession

text: Bjorn Brunstrom

text: chicken

text: Female5Spleen White Leghorn chicken embryo

text: 18 day embryo

text: Sweden

text: Gallus gallus

text: Gallus gallus

text: female

text: White Leghorn

characteristic: strain

text: spleen

text: White Leghorn


characteristic: External Id

text: UPPSALA UNIVERSITET

text: public

characteristic: Submitter Id

text: Bjorn Brunstrom

characteristic: collected by

text: chicken

characteristic: common name

text: Male1Brain White Leghorn chicken embryo

text: 18 day embryo

text: Sweden

text: Gallus gallus

text: Gallus gallus

text: male

text: White Leghorn

text: brain

characteristic: tissue type

text: White Leghorn


text: UPPSALA UNIVERSITET

text: public

text: Bjorn Brunstrom

text: chicken

text: Male1Bursa White Leghorn chicken embryo

characteristic: description

text: 18 day embryo

characteristic: dev stage

text: Sweden

characteristic: geographic location (country and/or sea)

text: Gallus gallus

characteristic: organism

text: Gallus gallus

text: male

text: White Leghorn

text: bursa

characteristic: title

text: White Leghorn


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: UPPSALA UNIVERSITET

characteristic: INSDC center name

text: public

characteristic: INSDC status

text: Bjorn Brunstrom

text: chicken

text: Male1Heart White Leghorn chicken embryo

text: 18 day embryo

text: Sweden

text: Gallus gallus

text: Gallus gallus

text: male

text: White Leghorn

text: heart

text: White Leghorn

characteristic: variety


characteristic: ENA-LAST-UPDATE

text: UPPSALA UNIVERSITET

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: SRA accession

text: Bjorn Brunstrom

text: chicken

text: Male1Kidney White Leghorn chicken embryo

text: 18 day embryo

text: Sweden

text: Gallus gallus

text: Gallus gallus

text: male

characteristic: sex

text: White Leghorn

text: kidney

text: White Leghorn


characteristic: External Id

text: UPPSALA UNIVERSITET

text: public

characteristic: Submitter Id

text: Bjorn Brunstrom

characteristic: collected by

text: chicken

characteristic: common name

text: Male1Liver White Leghorn chicken embryo

text: 18 day embryo

text: Sweden

text: Gallus gallus

text: Gallus gallus

text: male

text: White Leghorn

characteristic: strain

text: liver

text: White Leghorn


text: UPPSALA UNIVERSITET

text: public

text: Bjorn Brunstrom

text: chicken

text: Male1Lung White Leghorn chicken embryo

characteristic: description

text: 18 day embryo

characteristic: dev stage

text: Sweden

characteristic: geographic location (country and/or sea)

text: Gallus gallus

characteristic: organism

text: Gallus gallus

text: male

text: White Leghorn

text: lung

characteristic: tissue type

text: White Leghorn


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: UPPSALA UNIVERSITET

characteristic: INSDC center name

text: public

characteristic: INSDC status

text: Bjorn Brunstrom

text: chicken

text: Male1Muscle White Leghorn chicken embryo

text: 18 day embryo

text: Sweden

text: Gallus gallus

text: Gallus gallus

text: male

text: White Leghorn

text: muscle

characteristic: title

text: White Leghorn


characteristic: ENA-LAST-UPDATE

text: UPPSALA UNIVERSITET

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: SRA accession

text: Bjorn Brunstrom

text: chicken

text: Male1Spleen White Leghorn chicken embryo

text: 18 day embryo

text: Sweden

text: Gallus gallus

text: Gallus gallus

text: male

text: White Leghorn

text: spleen

text: White Leghorn

characteristic: variety


characteristic: External Id

text: UPPSALA UNIVERSITET

text: public

characteristic: Submitter Id

text: Bjorn Brunstrom

characteristic: collected by

text: chicken

characteristic: common name

text: Male1Testes White Leghorn chicken embryo

text: 18 day embryo

text: Sweden

text: Gallus gallus

text: Gallus gallus

text: male

characteristic: sex

text: White Leghorn

text: testis

text: White Leghorn


text: UPPSALA UNIVERSITET

text: public

text: Bjorn Brunstrom

text: chicken

text: Male2Brain White Leghorn chicken embryo

characteristic: description

text: 18 day embryo

characteristic: dev stage

text: Sweden

characteristic: geographic location (country and/or sea)

text: Gallus gallus

characteristic: organism

text: Gallus gallus

text: male

text: White Leghorn

characteristic: strain

text: brain

text: White Leghorn


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: UPPSALA UNIVERSITET

characteristic: INSDC center name

text: public

characteristic: INSDC status

text: Bjorn Brunstrom

text: chicken

text: Male2Bursa White Leghorn chicken embryo

text: 18 day embryo

text: Sweden

text: Gallus gallus

text: Gallus gallus

text: male

text: White Leghorn

text: bursa

characteristic: tissue type

text: White Leghorn


characteristic: ENA-LAST-UPDATE

text: UPPSALA UNIVERSITET

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: SRA accession

text: Bjorn Brunstrom

text: chicken

text: Male2Heart White Leghorn chicken embryo

text: 18 day embryo

text: Sweden

text: Gallus gallus

text: Gallus gallus

text: male

text: White Leghorn

text: heart

characteristic: title

text: White Leghorn


characteristic: External Id

text: UPPSALA UNIVERSITET

text: public

characteristic: Submitter Id

text: Bjorn Brunstrom

characteristic: collected by

text: chicken

characteristic: common name

text: Male2Kidney White Leghorn chicken embryo

text: 18 day embryo

text: Sweden

text: Gallus gallus

text: Gallus gallus

text: male

text: White Leghorn

text: kidney

text: White Leghorn

characteristic: variety


text: UPPSALA UNIVERSITET

text: public

text: Bjorn Brunstrom

text: chicken

text: Male2Liver White Leghorn chicken embryo

characteristic: description

text: 18 day embryo

characteristic: dev stage

text: Sweden

characteristic: geographic location (country and/or sea)

text: Gallus gallus

characteristic: organism

text: Gallus gallus

text: male

characteristic: sex

text: White Leghorn

text: liver

text: White Leghorn


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: UPPSALA UNIVERSITET

characteristic: INSDC center name

text: public

characteristic: INSDC status

text: Bjorn Brunstrom

text: chicken

text: Male2Lung White Leghorn chicken embryo

text: 18 day embryo

text: Sweden

text: Gallus gallus

text: Gallus gallus

text: male

text: White Leghorn

characteristic: strain

text: lung

text: White Leghorn


characteristic: ENA-LAST-UPDATE

text: UPPSALA UNIVERSITET

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: SRA accession

text: Bjorn Brunstrom

text: chicken

text: Male2Muscle White Leghorn chicken embryo

text: 18 day embryo

text: Sweden

text: Gallus gallus

text: Gallus gallus

text: male

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text: Bjorn Brunstrom

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characteristic: strain

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text: Bjorn Brunstrom

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

characteristic: Submitter Id

text: C

characteristic: batch

text: ArrayExpress

characteristic: broker name

text: thale cress

characteristic: common name

text: Protocols: Seeds of Blh-1 were provided by Olivier Loudet (INRA, Versailles). Other accessions were obtained from NASC (N22660). Plants were flash-frozen in liquid nitrogen immediately upon harvest. RNAlater-ICE (Ambion), which prevents RNA from degrading, was cooled at -70 degree centigrade, added to the samples and was allowed to penetrate the tissue at -20 degree centigrade for 5 days. The third leaf was collected by microdissection under a microscope. Samples were microdissected in a Petri dish on dry ice to keep the samples below room temperature. Six Arabidopsis thaliana (L.) Heynh accessions (An-1, Blh-1, Col-0, Cvi-0, Oy-0 and Sha) were grown in a growth chamber under controlled environmental conditions (21 degree centigrade, 55% relative humidity, 16 h day/ 8 h night, 110-120 micromol m-2 s-1 light intensity). Plants were germinated in soil-filled 96-well plates after four days of stratification at 4 degreee centigrade in the dark. Seedlings were transferred to pots at four days after stratification (DAS). The 54 average-sized seedlings were selected (Fig. 1A) using an in-house developed image algorithm in order to reduce seedling size effects at the beginning of the experiment. Before transfer, the relative water content of the pots was set at 1.2 g H2O/g dry soil for the mild drought treatment, the control condition was set at 2.2 g H2O/g dry soil (Fig. 1D). Once the seedlings were transferred to pots (Fig. 1B), they were placed on the automated phenotyping platform WIWAM (Skirycz et al., 2011b). The water content of the soil was kept constant until 10 DAS, after which it was lowered daily to target 0.7 g H2O/g dry soil for the mild drought treated plants (Fig. 1D). Pictures of the rosette of each plant were taken daily until 21 DAS and analyzed for the projected rosette area (PRA) (Skirycz et al., 2011b). Dissected leaves were ground with a Retsch machine (Retsch) and 3-mm metal balls. Samples were obtained from 3 independent biological repeats. RNA was extracted with TriZol (Invitrogen) according to the manufacturers instructions. RNA samples were subjected to DNA digestion with RNase-free DNase I kit (Qiagen), and subsequently, impurities were removed with the RNeasy mini kit (Qiagen). Library preparation was done using the TruSeq RNA Sample Preparation Kit v2 (Illumina). In brief, polyA containing mRNA molecules are reverse transcribed, double-stranded cDNA is generated and adapters are ligated. After quality control using 2100 Bioanalyzer (Agilent), clusters are generated through amplification using the TruSeq PE Cluster Kit v3-cBot-HS kit (Illumina) followed by sequencing on a Illumina HiSeq2000 with the TruSeq SBS Kit v3-HS (Illumina).

text: Proliferative tissue

characteristic: developmental stage

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text: Mild drought

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text: Arabidopsis thaliana

text: Arabidopsis thaliana

text: rosette leaf

characteristic: organism part

text: Arabidopsis thaliana


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

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

characteristic: INSDC center name

text: public

text: A

text: ArrayExpress

text: thale cress

text: Protocols: Seeds of Blh-1 were provided by Olivier Loudet (INRA, Versailles). Other accessions were obtained from NASC (N22660). Plants were flash-frozen in liquid nitrogen immediately upon harvest. RNAlater-ICE (Ambion), which prevents RNA from degrading, was cooled at -70 degree centigrade, added to the samples and was allowed to penetrate the tissue at -20 degree centigrade for 5 days. The third leaf was collected by microdissection under a microscope. Samples were microdissected in a Petri dish on dry ice to keep the samples below room temperature. Six Arabidopsis thaliana (L.) Heynh accessions (An-1, Blh-1, Col-0, Cvi-0, Oy-0 and Sha) were grown in a growth chamber under controlled environmental conditions (21 degree centigrade, 55% relative humidity, 16 h day/ 8 h night, 110-120 micromol m-2 s-1 light intensity). Plants were germinated in soil-filled 96-well plates after four days of stratification at 4 degree centigrade in the dark. Seedlings were transferred to pots at four days after stratification (DAS). The 54 average-sized seedlings were selected (Fig. 1A) using an in-house developed image algorithm in order to reduce seedling size effects at the beginning of the experiment. Before transfer, the relative water content of the pots was set at 1.2 g H2O/g dry soil for the mild drought treatment, the control condition was set at 2.2 g H2O/g dry soil (Fig. 1D). Once the seedlings were transferred to pots (Fig. 1B), they were placed on the automated phenotyping platform WIWAM (Skirycz et al., 2011b). The water content of the soil was kept constant until 10 DAS, after which it was lowered daily to target 0.7 g H2O/g dry soil for the mild drought treated plants (Fig. 1D). Pictures of the rosette of each plant were taken daily until 21 DAS and analyzed for the projected rosette area (PRA) (Skirycz et al., 2011b). Dissected leaves were ground with a Retsch machine (Retsch) and 3-mm metal balls. Samples were obtained from 3 independent biological repeats. RNA was extracted with TriZol (Invitrogen) according to the manufacturers instructions. RNA samples were subjected to DNA digestion with RNase-free DNase I kit (Qiagen), and subsequently, impurities were removed with the RNeasy mini kit (Qiagen). Library preparation was done using the TruSeq RNA Sample Preparation Kit v2 (Illumina). In brief, polyA containing mRNA molecules are reverse transcribed, double-stranded cDNA is generated and adapters are ligated. After quality control using 2100 Bioanalyzer (Agilent), clusters are generated through amplification using the TruSeq PE Cluster Kit v3-cBot-HS kit (Illumina) followed by sequencing on a Illumina HiSeq2000 with the TruSeq SBS Kit v3-HS (Illumina).

characteristic: description

text: Proliferative tissue

text: Control

text: Arabidopsis thaliana

characteristic: organism

text: Arabidopsis thaliana

text: rosette leaf

text: Arabidopsis thaliana

characteristic: title