characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: DTU Biosustain

text: public

text: Pseudomonas aeruginosa

characteristic: common name

text: Whole genome sequening of genomic DNA deriving from a representative clone isolated from sputum sample P77F1_S1 on 18/11/2016 collected from patient P77F1. The clone belongs to the Danish clone type DK01.

text: sputum sample

text: Pseudomonas aeruginosa

characteristic: organism

text: Pseudomonas aeruginosa

text: P77F1 clinical isolate, whole genome sequencing, DK01 clone type

characteristic: title


status: PUBLIC

tag: attribute

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: DTU Biosustain

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

tag: Namespace:DTU Biosustain

characteristic: Submitter Id

characteristic: collection date

text: Pseudomonas aeruginosa

text: Whole genome sequening of genomic DNA deriving from a representative clone isolated from sputum sample P24M1_S2 on 28/11/2016 collected from patient P24M1. The clone belongs to the Danish clone type DK02.

characteristic: description

text: sputum sample

characteristic: isolation source

text: Pseudomonas aeruginosa

text: Pseudomonas aeruginosa

text: P24M1 clinical isolate, whole genome sequencing, DK02 clone type


text: DTU Biosustain

text: public

text: Pseudomonas aeruginosa

text: Whole genome sequening of genomic DNA deriving from a representative clone isolated from sputum sample P24M1_S2 on 28/11/2016 collected from patient P24M1. The clone belongs to a previously uncharacterized clone type (UNK).

text: sputum sample

text: Pseudomonas aeruginosa

text: Pseudomonas aeruginosa

text: P24M1 clinical isolate, whole genome sequencing, UNK clone type


text: DTU Biosustain

text: public

text: Pseudomonas aeruginosa

text: Whole genome sequening of genomic DNA deriving from a representative clone isolated from sputum sample on 07/01/2017 collected from patient P73F1. The clone belongs to the Danish clone type DK02.

text: sputum sample

text: Pseudomonas aeruginosa

text: Pseudomonas aeruginosa

text: P73F1 clinical isolate, whole genome sequencing, DK02 clone type


text: DTU Biosustain

text: public

text: Pseudomonas aeruginosa

text: In vitro RNA-seq of PA-P30M0 isolate. LB medium, shaking (250 rpm), exponential phase. Biological replicate 1

text: laboratory culture

text: Pseudomonas aeruginosa

text: Pseudomonas aeruginosa


text: DTU Biosustain

text: public

text: Pseudomonas aeruginosa

text: In vitro RNA-seq of PA-P30M0 isolate. LB medium, shaking (250 rpm), exponential phase. Biological replicate 2

text: laboratory culture

text: Pseudomonas aeruginosa

text: Pseudomonas aeruginosa


text: DTU Biosustain

text: public

text: Pseudomonas aeruginosa

text: In vitro RNA-seq of PA-P30M0 isolate. LB medium, shaking (250 rpm), stationary phase. Biological replicate 1

text: laboratory culture

text: Pseudomonas aeruginosa

text: Pseudomonas aeruginosa


text: DTU Biosustain

text: public

text: Pseudomonas aeruginosa

text: In vitro RNA-seq of PA-P30M0 isolate. LB medium, shaking (250 rpm), stationary phase. Biological replicate 2

text: laboratory culture

text: Pseudomonas aeruginosa

text: Pseudomonas aeruginosa


text: DTU Biosustain

text: public

text: Pseudomonas aeruginosa

text: In vitro RNA-seq of P. aeruginosa PA14 strain. LB medium, shaking (250 rpm), exponential phase. Biological replicate 1

text: laboratory culture

text: Pseudomonas aeruginosa

text: Pseudomonas aeruginosa


text: DTU Biosustain

text: public

text: Pseudomonas aeruginosa

text: In vitro RNA-seq of P. aeruginosa PA14 strain. LB medium, shaking (250 rpm), exponential phase. Biological replicate 2

text: laboratory culture

text: Pseudomonas aeruginosa

text: Pseudomonas aeruginosa


text: DTU Biosustain

text: public

text: Pseudomonas aeruginosa

text: In vitro RNA-seq of P. aeruginosa PA14 strain. LB medium, shaking (250 rpm), stationary phase. Biological replicate 1

text: laboratory culture

text: Pseudomonas aeruginosa

text: Pseudomonas aeruginosa


text: DTU Biosustain

text: public

text: Pseudomonas aeruginosa

text: In vitro RNA-seq of P. aeruginosa PA14 strain. LB medium, shaking (250 rpm), stationary phase. Biological replicate 2

text: laboratory culture

text: Pseudomonas aeruginosa

text: Pseudomonas aeruginosa


text: DTU Biosustain

text: public

text: Pseudomonas aeruginosa

text: Reads assigned to P. aeruginosa species deriving from in vivo RNA-seq experiment performed on sputum sample of patient P11F2 collected on 16/06/2016

text: sputum sample

text: Pseudomonas aeruginosa

text: Pseudomonas aeruginosa


text: DTU Biosustain

text: public

text: Pseudomonas aeruginosa

text: Reads assigned to P. aeruginosa species deriving from in vivo RNA-seq experiment performed on sputum sample of patient P24M1 collected on 05/12/2016

text: sputum sample

text: Pseudomonas aeruginosa

text: Pseudomonas aeruginosa


text: DTU Biosustain

text: public

text: Pseudomonas aeruginosa

text: Reads assigned to P. aeruginosa species deriving from in vivo RNA-seq experiment performed on sputum sample of patient P24M1 collected on 16/06/16

text: sputum sample

text: Pseudomonas aeruginosa

text: Pseudomonas aeruginosa


text: DTU Biosustain

text: public

text: Pseudomonas aeruginosa

text: Reads assigned to P. aeruginosa species deriving from in vivo RNA-seq experiment performed on sputum sample of patient P24M1 collected on 28/11/16

text: sputum sample

text: Pseudomonas aeruginosa

text: Pseudomonas aeruginosa


text: DTU Biosustain

text: public

text: Pseudomonas aeruginosa

text: Reads assigned to P. aeruginosa species deriving from in vivo RNA-seq experiment performed on sputum sample of patient P30M0 collected on 23/06/2016

text: sputum sample

text: Pseudomonas aeruginosa

text: Pseudomonas aeruginosa


text: DTU Biosustain

text: public

text: Pseudomonas aeruginosa

text: Reads assigned to P. aeruginosa species deriving from in vivo RNA-seq experiment performed on sputum sample of patient P30M0 collected on 25/05/2016

text: sputum sample

text: Pseudomonas aeruginosa

text: Pseudomonas aeruginosa


text: DTU Biosustain

text: public

text: Pseudomonas aeruginosa

text: Reads assigned to P. aeruginosa species deriving from in vivo RNA-seq experiment performed on the first sputum sample of patient P30M0 collected on 28/02/2017. Technical replicate 1

text: sputum sample

text: Pseudomonas aeruginosa

text: Pseudomonas aeruginosa


text: DTU Biosustain

text: public

text: Pseudomonas aeruginosa

text: Reads assigned to P. aeruginosa species deriving from in vivo RNA-seq experiment performed on the first sputum sample of patient P30M0 collected on 28/02/2017. Technical replicate 2

text: sputum sample

text: Pseudomonas aeruginosa

text: Pseudomonas aeruginosa


text: DTU Biosustain

text: public

text: Pseudomonas aeruginosa

text: Reads assigned to P. aeruginosa species deriving from in vivo RNA-seq experiment performed on the second sputum sample of patient P30M0 collected on 28/02/2017. Technical replicate 1

text: sputum sample

text: Pseudomonas aeruginosa

text: Pseudomonas aeruginosa


text: DTU Biosustain

text: public

text: Pseudomonas aeruginosa

text: Reads assigned to P. aeruginosa species deriving from in vivo RNA-seq experiment performed on the second sputum sample of patient P30M0 collected on 28/02/2017. Technical replicate 2

text: sputum sample

text: Pseudomonas aeruginosa

text: Pseudomonas aeruginosa


text: DTU Biosustain

text: public

text: Pseudomonas aeruginosa

text: Reads assigned to P. aeruginosa species deriving from in vivo RNA-seq experiment performed on sputum sample of patient P73F1 collected on 22/02/2017. Technical replicate 1

text: sputum sample

text: Pseudomonas aeruginosa

text: Pseudomonas aeruginosa


text: DTU Biosustain

text: public

text: Pseudomonas aeruginosa

text: Reads assigned to P. aeruginosa species deriving from in vivo RNA-seq experiment performed on sputum sample of patient P73F1 collected on 22/02/2017. Technical replicate 2

text: sputum sample

text: Pseudomonas aeruginosa

text: Pseudomonas aeruginosa


text: DTU Biosustain

text: public

text: Pseudomonas aeruginosa

text: Reads assigned to P. aeruginosa species deriving from in vivo RNA-seq experiment performed on sputum sample of patient P77F1 collected on 02/12/2016

text: sputum sample

text: Pseudomonas aeruginosa

text: Pseudomonas aeruginosa


text: DTU Biosustain

text: public

text: Pseudomonas aeruginosa

text: Reads assigned to P. aeruginosa species deriving from in vivo RNA-seq experiment performed on sputum sample of patient P77F1 collected on 18/11/2016

text: sputum sample

text: Pseudomonas aeruginosa

text: Pseudomonas aeruginosa


text: DTU Biosustain

text: public

text: Pseudomonas aeruginosa

text: Reads assigned to P. aeruginosa species deriving from in vivo RNA-seq experiment performed on sputum sample of patient P77F1 collected on 25/11/2016

text: sputum sample

text: Pseudomonas aeruginosa

text: Pseudomonas aeruginosa


DB21MT 5

text: Genoscope CEA

text: public

text: DB21MT 5

tag: Namespace:Genoscope CEA

text: Moritella yayanosii

text: Moritella yayanosii

text: DB21MT 5

characteristic: strain

text: Moritella yayanosii DB21MT 5 genome


characteristic: ENA-CHECKLIST

text: public

tag: Namespace:Department of Interdisciplinary Genome Science and Cell Metabolism, Institute for Biomedical Science, Shinshu University

text: ArrayExpress

characteristic: broker name

text: Protocols: S. coelicolor A3(2) cells were grown to middle-exponential phase at 30°C in MR5 liquid medium with or without lincomycin (10 µg/mL), then harvested by filtration through filter papers. Total RNA was isolated from cells (approximately 50 mg wet weight) grown in MR5 liquid medium with Sepasol-RNA I super G reagent (Nacalai Tesque, Inc.). After treatment with RNase-free recombinant DNase I (TaKaRa Bio, Inc., Shiga, Japan), each sample was further purified using a High Pure RNA Isolation Kit (Roche Life Science, Penzberg, Germany). Fifty micrograms of total RNA were subjected to rRNA depletion followed by the preparation of cDNA libraries.

text: mid-exponential phase

characteristic: developmental stage

text: wild type genotype

characteristic: genotype

text: Modified R5 liquid medium

characteristic: growth condition

text: Streptomyces coelicolor A3(2)

text: Streptomyces coelicolor A3(2)

text: haustorium

characteristic: organism part

text: Streptomyces coelicolor A3(2)

text: Minus-LIN-Control


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Department of Interdisciplinary Genome Science and Cell Metabolism, Institute for Biomedical Science, Shinshu University

text: public

text: ArrayExpress

text: mid-exponential phase

text: wild type genotype

text: Modified R5 liquid medium

text: Streptomyces coelicolor A3(2)

characteristic: organism

text: Streptomyces coelicolor A3(2)

text: haustorium

text: Streptomyces coelicolor A3(2)

text: Plus-LIN

characteristic: title


text: Saccharomyces cerevisiae

characteristic: ArrayExpress-SPECIES

text: SC

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: baker's yeast

characteristic: common name

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

characteristic: subject id


characteristic: ENA-CHECKLIST

text: Technische Universitaet Dresden

text: public

characteristic: Submitter Id

characteristic: collection date

text: freshwater biome

characteristic: environment (biome)

text: wetland

characteristic: environment (feature)

text: detritus

characteristic: environment (material)

text: Yes

characteristic: environmental sample

characteristic: further details

text: Germany

characteristic: geographic location (country and/or sea)

unit: DD

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: uncultured eukaryote

text: EK-565F GCAGTTAAAAAGCTCGTAGT, 18S-EUK-1134-R-UNonMet TTTAAGTTTCAGCCTTGCG

characteristic: pcr primers

text: uncultured eukaryote

characteristic: target gene

characteristic: target subfragment

text: Detritus from wetland and biofilm from freshwater streams


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Technische Universitaet Dresden

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: freshwater biome

text: small stream

text: biofilm

text: Yes

text: Germany

text: uncultured eukaryote

characteristic: organism

text: uncultured eukaryote

characteristic: title


text: Salmonella enterica subsp. enterica serovar Typhimurium

characteristic: ArrayExpress-SPECIES

characteristic: ENA-CHECKLIST

text: SC

text: public

characteristic: Submitter Id

characteristic: common name

characteristic: subject id


text: Klebsiella pneumoniae

text: SC

text: public

text: Klebsiella pneumoniae

text: Klebsiella pneumoniae

text: Klebsiella pneumoniae


text: Escherichia coli

text: SC

text: public

text: Escherichia coli

text: Escherichia coli

text: Escherichia coli


text: Enterobacter cloacae

text: SC

text: public

text: Enterobacter cloacae

text: Enterobacter cloacae

text: Enterobacter cloacae


text: Enterobacter aerogenes

text: SC

text: public

text: Enterobacter aerogenes

text: Klebsiella aerogenes

text: Klebsiella aerogenes


text: Acinetobacter baumannii

text: SC

text: public

text: Acinetobacter baumannii

text: Acinetobacter baumannii

text: Acinetobacter baumannii


text: Citrobacter freundii

text: SC

text: public

text: Citrobacter freundii

text: Citrobacter freundii

text: Citrobacter freundii


text: VHIO

text: public

text: human

text: Normal, FFPE

characteristic: description

text: Homo sapiens

text: Homo sapiens

text: ATC samples


text: VHIO

text: public

text: human

text: Tumor, FFPE

text: Homo sapiens

text: Homo sapiens

text: ATC samples


text: VHIO

text: public

text: human

text: Normal, Blood

text: Homo sapiens

text: Homo sapiens

text: ATC samples


text: VHIO

text: public

text: human

text: Tumor, Fresh tissue

text: Homo sapiens

text: Homo sapiens

text: ATC samples


text: VHIO

text: public

text: human

text: Tumor, Tissue in OCT

text: Homo sapiens

text: Homo sapiens

text: ATC samples


text: VHIO

text: public

text: human

text: Normal, Blood

text: Homo sapiens

text: Homo sapiens

text: Concomitant ATC and PTC components


text: VHIO

text: public

text: human

text: Anaplastic Tumor, Fresh tissue

text: Homo sapiens

text: Homo sapiens

text: Concomitant ATC and PTC components


text: VHIO

text: public

text: human

text: Papillary Tumor, FFPE

text: Homo sapiens

text: Homo sapiens

text: Concomitant ATC and PTC components


text: VHIO

text: public

text: human

text: Normal, Fresh tissue

text: Homo sapiens

text: Homo sapiens

text: Concomitant ATC and PTC components


text: VHIO

text: public

text: human

text: Papillary Tumor, Fresh tissue

text: Homo sapiens

text: Homo sapiens

text: Concomitant ATC and PTC components


text: VHIO

text: public

text: human

text: Normal, FFPE

text: Homo sapiens

text: Homo sapiens

text: Concomitant ATC and PTC components


text: VHIO

text: public

text: human

text: Anaplastic Tumor, FFPE

text: Homo sapiens

text: Homo sapiens

text: Concomitant ATC and PTC components


E-MTAB-6407:Sample 4

text: Linkoping University

text: public

text: E-MTAB-6407:Sample 4

tag: Namespace:Linkoping University

unit: day

characteristic: age

text: ArrayExpress

characteristic: broker name

text: chicken

text: Protocols: Animals were sacrificed at the age of 48 weeks by rapid decapitation. Brains were dissected from the skull and snap frozen in liquid nitrogen within ten minutes, DNA was extracted from hypothalamus using an Allprep RNA/DNA kit (Qiagen), following the manufacturer’s instructions. In short, approximately 20-30 mg tissue was homogenized with 600 µl Buffer RTL Plus using FastPrep® -24 (MP Biomedicals). DNA was separated from the RNA using an AllPrep DNA spin column, and columns were kept on ice whilst RNA was purified for gene expression analysis [38]. 350 µl Buffer AW1 was added to the spin column, which was then centrifuged for 15 s at 17000 g. The supernatant was discarded and a mixture of 20 µl proteinase K (20mg/ml) and 60 µl AW1 was added to each sample, and the samples were then incubated for 5 min at room temperature. The samples were then cleaned with 350 µl AW1, centrifuged at 15 s at full speed 17000 g, followed by centrifugation with 500 µl AW2 for 2min at full speed. Columns were dried via an additional centrifugation at 17000 g for 1 min, then placed in 1.5 ml microcentrifuge tubes. For elution of DNA, 50 µl Buffer EB was added to the spin column, followed by a 10 min incubation at room temperature, then centrifugation for 1 min at 8000 g. DNA concentration and purity was measured using a NanoDrop® ND-2000c (ThermoFisher Scientific). DNA methylation analysis was performed by enrichment of the methylated fraction of the genome by immunoprecipitation with an anti-methyl-cytosine antibody (MeDIP). DNA was fragmented using sonication, and captured with agarose beads.

text: Gallus gallus

text: Gallus gallus

text: hypothalamus

characteristic: organism part

text: high fear

characteristic: phenotype

text: Gallus gallus

text: female

characteristic: sex

text: Red Junglefowl

characteristic: strain

text: Sample 4


E-MTAB-6407:Sample 7

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Linkoping University

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: E-MTAB-6407:Sample 7

text: ArrayExpress

text: chicken

text: Gallus gallus

text: Gallus gallus

text: hypothalamus

text: low fear

text: Gallus gallus

text: male

text: Red Junglefowl

text: Sample 7


E-MTAB-6407:Sample 5

characteristic: ENA-CHECKLIST

text: Linkoping University

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-6407:Sample 5

text: ArrayExpress

text: chicken

text: Gallus gallus

characteristic: organism

text: Gallus gallus

text: hypothalamus

text: high fear

text: Gallus gallus

text: female

text: Red Junglefowl

text: Sample 5

characteristic: title


E-MTAB-6407:Sample 8

text: Linkoping University

text: public

text: E-MTAB-6407:Sample 8

characteristic: Submitter Id

characteristic: age

text: ArrayExpress

text: chicken

characteristic: common name

characteristic: description

text: Gallus gallus

text: Gallus gallus

text: hypothalamus

text: low fear

text: Gallus gallus

text: male

text: Red Junglefowl

text: Sample 8


E-MTAB-6407:Sample 1

text: Linkoping University

text: public

text: E-MTAB-6407:Sample 1

text: ArrayExpress

characteristic: broker name

text: chicken

text: Gallus gallus

text: Gallus gallus

text: hypothalamus

characteristic: organism part

text: high fear

characteristic: phenotype

text: Gallus gallus

text: male

characteristic: sex

text: Red Junglefowl

text: Sample 1


E-MTAB-6407:Sample 2

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Linkoping University

text: public

text: E-MTAB-6407:Sample 2

text: ArrayExpress

text: chicken

text: Gallus gallus

text: Gallus gallus

text: hypothalamus

text: high fear

text: Gallus gallus

text: male

text: Red Junglefowl

characteristic: strain

text: Sample 2


E-MTAB-6407:Sample 10

characteristic: ENA-CHECKLIST

text: Linkoping University

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: E-MTAB-6407:Sample 10

text: ArrayExpress

text: chicken

text: Gallus gallus

text: Gallus gallus

text: hypothalamus

text: low fear

text: Gallus gallus

text: female

text: Red Junglefowl

text: Sample 10


E-MTAB-6407:Sample 9

text: Linkoping University

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-6407:Sample 9

text: ArrayExpress

text: chicken

text: Gallus gallus

characteristic: organism

text: Gallus gallus

text: hypothalamus

text: low fear

text: Gallus gallus

text: male

text: Red Junglefowl

text: Sample 9

characteristic: title


E-MTAB-6407:Sample 11

text: Linkoping University

text: public

text: E-MTAB-6407:Sample 11

characteristic: Submitter Id

characteristic: age

text: ArrayExpress

text: chicken

characteristic: common name

characteristic: description

text: Gallus gallus

text: Gallus gallus

text: hypothalamus

text: low fear

text: Gallus gallus

text: female

text: Red Junglefowl

text: Sample 11


E-MTAB-6407:Sample 3

text: Linkoping University

text: public

text: E-MTAB-6407:Sample 3

text: ArrayExpress

characteristic: broker name

text: chicken

text: Gallus gallus

text: Gallus gallus

text: hypothalamus

characteristic: organism part

text: high fear

characteristic: phenotype

text: Gallus gallus

text: male

characteristic: sex

text: Red Junglefowl

text: Sample 3


E-MTAB-6407:Sample 12

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Linkoping University

text: public

text: E-MTAB-6407:Sample 12

text: ArrayExpress

text: chicken

text: Gallus gallus

text: Gallus gallus

text: hypothalamus

text: low fear

text: Gallus gallus

text: female

text: Red Junglefowl

characteristic: strain

text: Sample 12


E-MTAB-6407:Sample 6

characteristic: ENA-CHECKLIST

text: Linkoping University

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: E-MTAB-6407:Sample 6

text: ArrayExpress

text: chicken

text: Gallus gallus

text: Gallus gallus

text: hypothalamus

text: high fear

text: Gallus gallus

text: female

text: Red Junglefowl

text: Sample 6


text: public

characteristic: INSDC status

characteristic: SRA accession

tag: Namespace:Laboratory for Functional Genomics, Nutrigenomics and Systems Biology, Scientific Genomics Platforms, Max Delbruck Center for Molecular Medicine (BIMSB/BIH)

text: ArrayExpress

characteristic: cell line

text: macrophage

characteristic: cell type

text: human

text: Protocols: The THP-1 monocytic cell line obtained from ATCC (#TIB-202) was used. Approximately 1 million cells were used for each biological replicate. 3 biological replicates were cultured and stimulated independently. THP-1 cells were cultured in RPMI 1640 medium (Biochrom, #FG1215) supplemented with 10% fetal bovine serum (FBS, Biochrom, #S0615).THP-1 cells were seeded from frozen ATCC stocks (5x106cells/ml), incubated at 37°C in a 5% CO2 atmosphere. Sub culturing was done by adding fresh medium to reach a cell concentration of 2x105 cells/ml. Medium was completely renewed every week. All treatment compounds were added to the standard growth medium. THP-1 monocytes were differentiated to macrophages with 10 nM phorbol-12-myristate-13-acetate (PMA, Sigma, #P8139-5MG) for 48 hours. Following differentiation, cell were stimulated with 0.06 mM BSA (BSA, Sigma-Aldrich, #A7030) and 0.4mM NaOH (Sigma Aldrich, #72068) for 24 hours in the presence of 10 nM PMA or left unstimulated. Unstimulated macrophages were incubated in renewed growth medium with 10nM PMA. RNA extraction was performed using RNeasy Mini Kit from Qiagen (#74106) using the standard procedure with 30 min on-column DNase digestion. RNA concentration and quality was controlled using NanoDrop 2000 (Thermo Fisher Scientific) and Bioanalyser 2100 (Agilent). Sequencing libraries were prepared using TruSeq Stranded mRNA Library Prep Kit (Illumina, #RS-122-2001) according to the standard procedure.

text: acute monocytic leukemia

characteristic: disease

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: blood

text: monocyte

characteristic: progenitor cell type

text: Homo sapiens

text: phorbol 13-acetate 12-myristate (10 nanomolar)

characteristic: stimulus

characteristic: title


characteristic: ENA-FIRST-PUBLIC

text: Laboratory for Functional Genomics, Nutrigenomics and Systems Biology, Scientific Genomics Platforms, Max Delbruck Center for Molecular Medicine (BIMSB/BIH)

text: public

characteristic: Submitter Id

text: ArrayExpress

characteristic: broker name

text: macrophage

text: human

characteristic: common name

characteristic: description

text: acute monocytic leukemia

text: Homo sapiens

text: Homo sapiens

text: blood

characteristic: organism part

text: monocyte

text: Homo sapiens


characteristic: ENA-CHECKLIST

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: DTU

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: human

text: single cell whole genome

text: Homo sapiens

text: Homo sapiens

text: Cellomatic COM-82


text: DTU

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: human

text: single cell whole genome

text: Homo sapiens

text: Homo sapiens

text: Cellomatic COM-87


text: DTU

text: public

text: human

text: single cell whole genome

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: Cellomatic COM-88


text: DTU

text: public

text: human

text: single cell whole genome

text: Homo sapiens

text: Homo sapiens

text: Cellomatic COM-89


text: DTU

text: public

text: human

text: single cell whole genome

text: Homo sapiens

text: Homo sapiens

text: Cellomatic COM-99


text: DTU

text: public

text: human

text: single cell whole genome

text: Homo sapiens

text: Homo sapiens

text: Cellomatic COM-100


text: DTU

text: public

text: human

text: single cell whole genome

text: Homo sapiens

text: Homo sapiens

text: Cellomatic COM-101


text: DTU

text: public

text: human

text: single cell whole genome

text: Homo sapiens

text: Homo sapiens

text: Cellomatic COM-143


text: DTU

text: public

text: human

text: single cell whole genome

text: Homo sapiens

text: Homo sapiens

text: Cellomatic COM-144


text: DTU

text: public

text: human

text: single cell whole genome

text: Homo sapiens

text: Homo sapiens

text: Cellomatic COM-145


text: DTU

text: public

text: human

text: single cell whole genome

text: Homo sapiens

text: Homo sapiens

text: Cellomatic COM-146


text: DTU

text: public

text: human

text: single cell whole genome

text: Homo sapiens

text: Homo sapiens

text: Cellomatic COM-147


text: DTU

text: public

text: human

text: single cell whole genome

text: Homo sapiens

text: Homo sapiens

text: Cellomatic COM-153


text: DTU

text: public

text: human

text: single cell whole genome

text: Homo sapiens

text: Homo sapiens

text: Cellomatic COM-154


text: DTU

text: public

text: human

text: single cell whole genome

text: Homo sapiens

text: Homo sapiens

text: Cellomatic COM-155


text: DTU

text: public

text: human

text: single cell whole genome

text: Homo sapiens

text: Homo sapiens

text: Cellomatic COM-156


text: DTU

text: public

text: human

text: single cell whole genome

text: Homo sapiens

text: Homo sapiens

text: Cellomatic COM-157


text: DTU

text: public

text: human

text: single cell whole genome

text: Homo sapiens

text: Homo sapiens

text: Cellomatic COM-176


text: DTU

text: public

text: human

text: single cell whole genome

text: Homo sapiens

text: Homo sapiens

text: Cellomatic COM-177


text: DTU

text: public

text: human

text: single cell whole genome

text: Homo sapiens

text: Homo sapiens

text: Cellomatic COM-178


text: DTU

text: public

text: human

text: single cell whole genome

text: Homo sapiens

text: Homo sapiens

text: Cellomatic COM-179


text: DTU

text: public

text: human

text: single cell whole genome

text: Homo sapiens

text: Homo sapiens

text: Cellomatic COM-180


text: DTU

text: public

text: human

text: single cell whole genome

text: Homo sapiens

text: Homo sapiens

text: Cellomatic COM-181


text: DTU

text: public

text: human

text: single cell whole genome

text: Homo sapiens

text: Homo sapiens

text: Cellomatic COM-182


text: DTU

text: public

text: human

text: single cell whole genome

text: Homo sapiens

text: Homo sapiens

text: Cellomatic COM-183


text: DTU

text: public

text: human

text: single cell whole genome

text: Homo sapiens

text: Homo sapiens

text: Cellomatic COM-205


text: DTU

text: public

text: human

text: single cell whole genome

text: Homo sapiens

text: Homo sapiens

text: Cellomatic COM-206


text: DTU

text: public

text: human

text: single cell whole genome

text: Homo sapiens

text: Homo sapiens

text: Cellomatic COM-207


text: DTU

text: public

text: human

text: single cell whole genome

text: Homo sapiens

text: Homo sapiens

text: Cellomatic COM-208


text: DTU

text: public

text: human

text: single cell whole genome

text: Homo sapiens

text: Homo sapiens

text: Cellomatic COM-256


text: DTU

text: public

text: human

text: single cell whole genome

text: Homo sapiens

text: Homo sapiens

text: Cellomatic COM-257


text: DTU

text: public

text: human

text: single cell whole genome

text: Homo sapiens

text: Homo sapiens

text: Cellomatic COM-258


text: DTU

text: public

text: human

text: single cell whole genome

text: Homo sapiens

text: Homo sapiens

text: Cellomatic COM-259


text: DTU

text: public

text: human

text: single cell whole genome

text: Homo sapiens

text: Homo sapiens

text: Cellomatic COM-260


text: DTU

text: public

text: human

text: single cell whole genome

text: Homo sapiens

text: Homo sapiens

text: Cellomatic COM-261


text: DTU

text: public

text: human

text: single cell whole genome

text: Homo sapiens

text: Homo sapiens

text: Cellomatic COM-262


text: DTU

text: public

text: human

text: single cell whole genome

text: Homo sapiens

text: Homo sapiens

text: Cellomatic COM-271


text: DTU

text: public

text: human

text: single cell whole genome

text: Homo sapiens

text: Homo sapiens

text: Cellomatic COM-272


text: DTU

text: public

text: human

text: single cell whole genome

text: Homo sapiens

text: Homo sapiens

text: Cellomatic COM-273


text: RIVM

text: public

text: Staphylococcus aureus

text: Netherlands

characteristic: geographic location (country and/or sea)

text: Staphylococcus aureus

text: Staphylococcus aureus


text: RIVM

text: public

text: Staphylococcus aureus

text: HCW 2012

text: Netherlands

text: Staphylococcus aureus

text: Staphylococcus aureus

text: HCW 2012

characteristic: title


characteristic: ENA-FIRST-PUBLIC

text: RIVM

text: public

text: Staphylococcus aureus

text: HWC 2014

text: Netherlands

text: Staphylococcus aureus

text: Staphylococcus aureus

text: HWC 2014


text: RIVM

text: public

characteristic: Submitter Id

text: Staphylococcus aureus

text: husband

text: Netherlands

text: Staphylococcus aureus

text: Staphylococcus aureus

text: husband


text: public

tag: Namespace:European Research Institute for the Biology of Ageing, University of Groningen, UMC Groningen, The Netherlands

unit: month

characteristic: age

text: ArrayExpress

characteristic: broker name

text: house mouse

text: Protocols: Knock-in in the Cebpb locus that replaces the wt Cebpb-mRNA sequence for a mutated version that contains a mutation in the AUG-initiation codon of the cis-regulatory upstream open reading frame (uORF), abrogating uORF function. The exact mutation is wt AGCATGCCT -> delta-uORF AGAATTCCT (introducing EcoRI site). This mutation results in deficiency of uORF-dependent translation into the C/EBPbeta-LIP protein isoform, leaving translation into the C/EBPbeta-LAP protein isoforms unaffected. Liver tissue from young (5 months) and old (20 months) wt and C/EBPβΔuORF mice (from six individuals per group) was homogenized on ice with a motor driven pellet pestle (Kontes) in the presence of QIAzol reagent (Qiagen) and total RNA was isolated as described in Zidek et al., 2015. RNA was isolated from tissue samples using the RNeasy® Lipid Tissue Mini Kit (QIAGEN). After incubation for 30 min at 37°C with RQ1 RNase‐Free DNase (Promega), the RNA was further purified with the RNeasy® Plus Mini Kit (QIAGEN) according to the manufacture's protocol starting at step 4. Preparation of the sequencing libraries was performed using the TruSeq Sample Preparation V2 Kit (Illumina) according to the manufacturer’s instructions.

text: C/EBP uORF expression

characteristic: genotype

text: Mus musculus

text: Mus musculus

text: liver

text: Mus musculus

text: female

characteristic: sex

characteristic: strain


characteristic: ENA-CHECKLIST

characteristic: ENA-LAST-UPDATE

text: European Research Institute for the Biology of Ageing, University of Groningen, UMC Groningen, The Netherlands

text: public

text: ArrayExpress

text: house mouse

characteristic: common name

characteristic: description

text: C/EBP uORF expression

text: Mus musculus

text: Mus musculus

text: liver

characteristic: organism part

text: Mus musculus

text: female


characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: ArrayExpress

text: house mouse

text: Protocols: Liver tissue from young (5 months) and old (20 months) wt and C/EBPβΔuORF mice (from six individuals per group) was homogenized on ice with a motor driven pellet pestle (Kontes) in the presence of QIAzol reagent (Qiagen) and total RNA was isolated as described in Zidek et al., 2015. RNA was isolated from tissue samples using the RNeasy® Lipid Tissue Mini Kit (QIAGEN). After incubation for 30 min at 37°C with RQ1 RNase‐Free DNase (Promega), the RNA was further purified with the RNeasy® Plus Mini Kit (QIAGEN) according to the manufacture's protocol starting at step 4. Preparation of the sequencing libraries was performed using the TruSeq Sample Preparation V2 Kit (Illumina) according to the manufacturer’s instructions.

text: wild type genotype

text: Mus musculus

text: Mus musculus

text: liver

text: Mus musculus

text: female


text: H3K14ac pAb

characteristic: ArrayExpress-IMMUNOPRECIPITATE

text: male

characteristic: ArrayExpress-SEX

text: Homo sapiens

characteristic: ArrayExpress-SPECIES

characteristic: ENA-FIRST-PUBLIC

text: SC

text: public

characteristic: SRA accession

text: human

text: Male

characteristic: gender

text: Homo sapiens

characteristic: organism

text: Homo sapiens

characteristic: subject id

characteristic: title


text: IgG control

text: male

text: Homo sapiens

characteristic: ENA-CHECKLIST

characteristic: ENA-LAST-UPDATE

text: SC

text: public

characteristic: Submitter Id

text: human

characteristic: common name

text: Male

text: Homo sapiens

text: Homo sapiens


text: male

text: Homo sapiens

characteristic: External Id

text: SC

characteristic: INSDC center name

text: public

text: human

text: Male

text: Homo sapiens

text: Homo sapiens


text: University of Lubeck

characteristic: INSDC first public

characteristic: INSDC last update

text: public

tag: Namespace:University of Lubeck

text: fruit fly

text: Control

characteristic: description

text: Drosophila melanogaster

text: Drosophila melanogaster

text: D. melanogaster microbiome


text: University of Lubeck

text: public

characteristic: INSDC status

text: fruit fly

text: LC treated

text: Drosophila melanogaster

text: Drosophila melanogaster

text: D. melanogaster microbiome


text: public

tag: Namespace:European Bioinformatics Institute (EMBL-EBI)

text: The Pirbright Institute

characteristic: collected by

text: United Kingdom

characteristic: geographic location (country and/or sea)

text: Culicoides sonorensis

text: Culicoides sonorensis

text: Female & Male

characteristic: sex

text: The nuclear genome of culicoidies sonorensis to study gene expression vector competence for Bluetongue virus


E-MTAB-6437:HH24 a

characteristic: ENA-FIRST-PUBLIC

text: The University of Sheffield

text: public

characteristic: SRA accession

text: E-MTAB-6437:HH24 a

tag: Namespace:The University of Sheffield

text: ArrayExpress

characteristic: broker name

text: mesenchymal stem cell

characteristic: cell type

text: chicken

text: Protocols: Workspace and dissection tools were thoroughly cleaned using RNaseZap (Ambion), then rinsed in diethyl pyrocarbonate (depc, SIGMA) treated water. Embryos at the desired stage were dissected into fresh depc treated 1xPBS (Phosphate buffered saline). Distal limb tips (250μm in length) were cut out from the embryo using micro-dissection scissors and placed in RNAlater and stored at -20°C (Ambion). Each sample consists of 10 distal tips pooled together. Distal limb mesenchyme cells were collected from embryonic chickens at Hamburger Hamilton (HH) stages HH24, HH27, and HH29, and also from samples that had been grafted from HH27 to HH20 and left to develop for 24 hours (equivalent to HH24). Samples were collected in triplicate (with 10 distal tips pooled per replicate). Homogenisation: Add 1ml of Trizol and homogenise in an eppendorf. Sample incubated at room temperature for 5 minutes. 0.2 ml chloroform added, and sample shaken vigorously by hand for 15 seconds. Incubate at room temperature for 2 - 3 minutes and centrifuge samples at 12000 x g for 15 minutes at 4 °C. Transfer aqueous (upper) phase to a new tube. Add 1 volume of 70% Ethanol, and then follow protocol as per the PureLink RNA Mini kit (Ambion). Resuspend in 30μl RNAse free water. TruSeq Stranded Total RNA and Ribo-Zero. Enzymatic fragmentation by Illumina Elute, Fragment, Prime mix

text: Hamburger Hamilton Stage 24

characteristic: developmental stage

text: normal

characteristic: disease

text: wild type genotype

characteristic: genotype

text: Gallus gallus

text: Gallus gallus

text: distal limb tip

characteristic: organism part

text: Gallus gallus

text: HH24 a


E-MTAB-6437:HH24 b

characteristic: ENA-CHECKLIST

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: The University of Sheffield

text: public

text: E-MTAB-6437:HH24 b

characteristic: Submitter Id

text: ArrayExpress

text: mesenchymal stem cell

text: chicken

characteristic: common name

text: Hamburger Hamilton Stage 24

text: normal

text: wild type genotype

text: Gallus gallus

characteristic: organism

text: Gallus gallus

text: distal limb tip

text: Gallus gallus

text: HH24 b

characteristic: title


E-MTAB-6437:HH24 c

text: The University of Sheffield

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: E-MTAB-6437:HH24 c

text: ArrayExpress

text: mesenchymal stem cell

text: chicken

characteristic: description

text: Hamburger Hamilton Stage 24

text: normal

text: wild type genotype

text: Gallus gallus

text: Gallus gallus

text: distal limb tip

text: Gallus gallus

text: HH24 c


E-MTAB-6437:HH27 a

characteristic: ENA-FIRST-PUBLIC

text: The University of Sheffield

text: public

characteristic: SRA accession

text: E-MTAB-6437:HH27 a

text: ArrayExpress

characteristic: broker name

text: mesenchymal stem cell

characteristic: cell type

text: chicken

text: Hamburger Hamilton Stage 27

text: normal

text: wild type genotype

text: Gallus gallus

text: Gallus gallus

text: distal limb tip

text: Gallus gallus

text: HH27 a


E-MTAB-6437:HH27 b

text: The University of Sheffield

text: public

text: E-MTAB-6437:HH27 b

text: ArrayExpress

text: mesenchymal stem cell

text: chicken

text: Hamburger Hamilton Stage 27

characteristic: developmental stage

text: normal

characteristic: disease

text: wild type genotype

characteristic: genotype

text: Gallus gallus

text: Gallus gallus

text: distal limb tip

characteristic: organism part

text: Gallus gallus

text: HH27 b


E-MTAB-6437:HH27 c

characteristic: ENA-CHECKLIST

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: The University of Sheffield

text: public

text: E-MTAB-6437:HH27 c

characteristic: Submitter Id

text: ArrayExpress

text: mesenchymal stem cell

text: chicken

text: Hamburger Hamilton Stage 27

text: normal

text: wild type genotype

text: Gallus gallus

text: Gallus gallus

text: distal limb tip

text: Gallus gallus

text: HH27 c


E-MTAB-6437:HH27-20 +24h a

text: The University of Sheffield

characteristic: INSDC center name

text: public

text: E-MTAB-6437:HH27-20 +24h a

text: ArrayExpress

text: mesenchymal stem cell

text: chicken

characteristic: common name

text: Hamburger Hamilton Stage 27

text: normal

text: wild type genotype

text: grafted onto Hamburger Hamilton Stage 20 embryo for 24 hours

characteristic: growth condition

text: Gallus gallus

characteristic: organism

text: Gallus gallus

text: distal limb tip

text: Gallus gallus

text: HH27-20 +24h a

characteristic: title


E-MTAB-6437:HH27-20 +24h b

characteristic: ENA-FIRST-PUBLIC

text: The University of Sheffield

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: E-MTAB-6437:HH27-20 +24h b

text: ArrayExpress

text: mesenchymal stem cell

text: chicken

characteristic: description

text: Hamburger Hamilton Stage 27

text: normal

text: wild type genotype

text: Gallus gallus

text: Gallus gallus

text: distal limb tip

text: Gallus gallus

text: HH27-20 +24h b


E-MTAB-6437:HH27-20 +24h c

text: The University of Sheffield

text: public

characteristic: SRA accession

text: E-MTAB-6437:HH27-20 +24h c

text: ArrayExpress

characteristic: broker name

text: mesenchymal stem cell

characteristic: cell type

text: chicken

text: Hamburger Hamilton Stage 27

characteristic: developmental stage

text: normal

characteristic: disease

text: wild type genotype

text: Gallus gallus

text: Gallus gallus

text: distal limb tip

text: Gallus gallus

text: HH27-20 +24h c


E-MTAB-6437:HH29 a

characteristic: ENA-CHECKLIST

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: The University of Sheffield

text: public

text: E-MTAB-6437:HH29 a

text: ArrayExpress

text: mesenchymal stem cell

text: chicken

text: Hamburger Hamilton Stage 29

text: normal

text: wild type genotype

characteristic: genotype

text: Gallus gallus

text: Gallus gallus

text: distal limb tip

characteristic: organism part

text: Gallus gallus

text: HH29 a


E-MTAB-6437:HH29 b

text: The University of Sheffield

characteristic: INSDC center name

text: public

text: E-MTAB-6437:HH29 b

characteristic: Submitter Id

text: ArrayExpress

text: mesenchymal stem cell

text: chicken

characteristic: common name

text: Hamburger Hamilton Stage 29

text: normal

text: wild type genotype

text: Gallus gallus

characteristic: organism

text: Gallus gallus

text: distal limb tip

text: Gallus gallus

text: HH29 b


E-MTAB-6437:HH29 c

characteristic: ENA-FIRST-PUBLIC

text: The University of Sheffield

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: E-MTAB-6437:HH29 c

text: ArrayExpress

text: mesenchymal stem cell

text: chicken

text: Hamburger Hamilton Stage 29

text: normal

text: wild type genotype

text: Gallus gallus

text: Gallus gallus

text: distal limb tip

text: Gallus gallus

text: HH29 c

characteristic: title


TRIP AH-1

text: Genoscope CEA

text: public

characteristic: INSDC status

characteristic: SRA accession

text: TRIP AH-1

text: TRIP AH-1

characteristic: isolate

text: Asphalt lake (Pitch Lake, Trinidad and Tobago)

characteristic: isolation source

text: uncultured Desulfobacterium sp.

text: uncultured Desulfobacterium sp.

text: TRIP AH-1


E-MTAB-6441:GFP-positive SVF progenitor

characteristic: ENA-CHECKLIST

text: PostDoc in UCSF

text: public

text: E-MTAB-6441:GFP-positive SVF progenitor

tag: Namespace:PostDoc in UCSF

text: ArrayExpress

characteristic: broker name

text: progenitor cell

characteristic: cell type

text: house mouse

text: Protocols: FACS sorting Qiagen RNeasy mini-kit and Qiagen RNeasy MinElute cleanup kit TruSeq Stranded Total RNA Sample Protocol

characteristic: description

text: Myod-Cre; mTmG reporter

text: Mus musculus

text: Mus musculus

text: white adipose tissue

text: GFP positive

characteristic: phenotype

text: Mus musculus

characteristic: strain

text: GFP-positive SVF progenitor


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: PostDoc in UCSF

characteristic: INSDC center name

text: public

text: E-MTAB-6441:Tomato-positive SVF progenitor

characteristic: Submitter Id

text: ArrayExpress

text: progenitor cell

text: house mouse

text: Myod-Cre; mTmG reporter

characteristic: genotype

text: Mus musculus

text: Mus musculus

text: white adipose tissue

characteristic: organism part

text: Tomato positive

text: Mus musculus

text: Tomato-positive SVF progenitor


characteristic: ENA-FIRST-PUBLIC

text: URMITE

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: Anaerococcus sp. Marseille-P3915

characteristic: organism

text: Anaerococcus sp. Marseille-P3915

text: Anaerococcus mediannikovii genome

characteristic: title


characteristic: ENA-CHECKLIST

text: URMITE

text: public

characteristic: INSDC status

characteristic: SRA accession

text: stool

characteristic: isolation source

text: Blautia marasmi

text: Blautia marasmi

text: Blautia marasmiensis genome


E-MTAB-6444:Sample 1

text: IP

text: public

text: E-MTAB-6444:Sample 1

text: ArrayExpress

characteristic: broker name

text: Protocols: 12 mosquitoes per pool, in each of two biological replicate pools, were collected 3 d after infection by oral feeding with ONNV and homogenized in TriReagent (Sigma). The A. coluzzii Ngousso strain was originally initiated with mosquitoes collected in Cameroon in January 2006, and belongs to the M molecular and Forest chromosomal forms (Harris et al., 2010). Mosquitoes were reared under standard conditions at 26°C and 80% relative humidity, with a 12 h light/dark cycle as previously described (Mitri et al., 2015). The 10- to 30-nt RNA fragments were purified from the small RNA fraction (<200nt) on a 15% urea PAGE (BioRad). Small RNA libraries were then prepared using TruSeq Small RNA Library reagents (Illumina). 15-30nt RNA extracted from polyacrylamide gel were ligated with 3'- and 5'- TruSeq adapters, as described in the original protocol. Synthesis of cDNA was performed by reverse transcription. The cDNA product was then specifically amplified by 11 cycles of PCR and products purified on Agencourt AMPure XP beads (Beckman Coulter Genomics, # A63881).

characteristic: description

text: Anopheles coluzzii

text: Anopheles coluzzii

text: whole organism

characteristic: replicate

text: Anopheles coluzzii

text: female

characteristic: sex

text: M

text: Sample 1


E-MTAB-6444:Sample 10

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: IP

characteristic: INSDC center name

text: public

text: E-MTAB-6444:Sample 10

text: ArrayExpress

text: Protocols: 12 mosquitoes per pool, in each of two biological replicate pools, were collected 3 d after infection by oral feeding with ONNV and homogenized in TriReagent (Sigma). The A. coluzzii Ngousso strain was originally initiated with mosquitoes collected in Cameroon in January 2006, and belongs to the M molecular and Forest chromosomal forms (Harris et al., 2010). Mosquitoes were reared under standard conditions at 26°C and 80% relative humidity, with a 12 h light/dark cycle as previously described (Mitri et al., 2015). Double-stranded RNAs were synthesized from PCR amplicons using the T7 Megascript Kit (Ambion) as described (Carissimo et al., 2015). For each targeted gene, 500 ng of dsRNA was injected using glass capillary needles into the thorax of cold-anesthetized 1-2 d-old A. coluzzii females using a nano-injector (Nanoject II, Drummond Scientific). The 10- to 30-nt RNA fragments were purified from the small RNA fraction (<200nt) on a 15% urea PAGE (BioRad). Small RNA libraries were then prepared using TruSeq Small RNA Library reagents (Illumina). 15-30nt RNA extracted from polyacrylamide gel were ligated with 3'- and 5'- TruSeq adapters, as described in the original protocol. Synthesis of cDNA was performed by reverse transcription. The cDNA product was then specifically amplified by 11 cycles of PCR and products purified on Agencourt AMPure XP beads (Beckman Coulter Genomics, # A63881).

text: Anopheles coluzzii

text: Anopheles coluzzii

text: whole organism

text: Anopheles coluzzii

text: female

text: M

characteristic: strain

text: Sample 10


E-MTAB-6444:Sample 11

characteristic: ENA-FIRST-PUBLIC

text: IP

text: public

text: E-MTAB-6444:Sample 11

characteristic: Submitter Id

text: ArrayExpress

text: Protocols: 12 mosquitoes per pool, in each of two biological replicate pools, were collected 3 d after infection by oral feeding with ONNV and homogenized in TriReagent (Sigma). The A. coluzzii Ngousso strain was originally initiated with mosquitoes collected in Cameroon in January 2006, and belongs to the M molecular and Forest chromosomal forms (Harris et al., 2010). Mosquitoes were reared under standard conditions at 26°C and 80% relative humidity, with a 12 h light/dark cycle as previously described (Mitri et al., 2015). Double-stranded RNAs were synthesized from PCR amplicons using the T7 Megascript Kit (Ambion) as described (Carissimo et al., 2015). For each targeted gene, 500 ng of dsRNA was injected using glass capillary needles into the thorax of cold-anesthetized 1-2 d-old A. coluzzii females using a nano-injector (Nanoject II, Drummond Scientific). Mosquitoes were infected on an infectious bloodmeal containing physiologically natural viral titers O'Nyong-Nyong strain SG650. The 10- to 30-nt RNA fragments were purified from the small RNA fraction (<200nt) on a 15% urea PAGE (BioRad). Small RNA libraries were then prepared using TruSeq Small RNA Library reagents (Illumina). 15-30nt RNA extracted from polyacrylamide gel were ligated with 3'- and 5'- TruSeq adapters, as described in the original protocol. Synthesis of cDNA was performed by reverse transcription. The cDNA product was then specifically amplified by 11 cycles of PCR and products purified on Agencourt AMPure XP beads (Beckman Coulter Genomics, # A63881).

text: Anopheles coluzzii

text: Anopheles coluzzii

text: whole organism

characteristic: organism part

text: Anopheles coluzzii

text: female

text: M

text: Sample 11


E-MTAB-6444:Sample 12

text: IP

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: E-MTAB-6444:Sample 12

text: ArrayExpress

text: Anopheles coluzzii

characteristic: organism

text: Anopheles coluzzii

text: whole organism

text: Anopheles coluzzii

text: female

text: M

text: Sample 12


E-MTAB-6444:Sample 13

characteristic: ENA-CHECKLIST

text: IP

text: public

characteristic: INSDC status

text: E-MTAB-6444:Sample 13

text: ArrayExpress

text: Anopheles coluzzii

text: Anopheles coluzzii

text: whole organism

text: Anopheles coluzzii

text: female

text: M

text: Sample 13

characteristic: title


E-MTAB-6444:Sample 14

text: IP

text: public

characteristic: SRA accession

text: E-MTAB-6444:Sample 14

text: ArrayExpress

characteristic: broker name

text: Anopheles coluzzii

text: Anopheles coluzzii

text: whole organism

text: Anopheles coluzzii

text: female

text: M

text: Sample 14


E-MTAB-6444:Sample 15

text: IP

text: public

text: E-MTAB-6444:Sample 15

text: ArrayExpress

characteristic: description

text: Anopheles coluzzii

text: Anopheles coluzzii

text: whole organism

characteristic: replicate

text: Anopheles coluzzii

text: female

text: M

text: Sample 15


E-MTAB-6444:Sample 16

characteristic: ENA-LAST-UPDATE

text: IP

text: public

text: E-MTAB-6444:Sample 16

text: ArrayExpress

text: Anopheles coluzzii

text: Anopheles coluzzii

text: whole organism

text: Anopheles coluzzii

text: female

characteristic: sex

text: M

text: Sample 16


E-MTAB-6444:Sample 2

characteristic: External Id

text: IP

characteristic: INSDC center name

text: public

text: E-MTAB-6444:Sample 2

text: ArrayExpress

text: Anopheles coluzzii

text: Anopheles coluzzii

text: whole organism

text: Anopheles coluzzii

text: female

text: M

text: Sample 2


E-MTAB-6444:Sample 3

characteristic: ENA-FIRST-PUBLIC

text: IP

text: public

text: E-MTAB-6444:Sample 3

text: ArrayExpress

text: Protocols: 12 mosquitoes per pool, in each of two biological replicate pools, were collected 3 d after infection by oral feeding with ONNV and homogenized in TriReagent (Sigma). The A. coluzzii Ngousso strain was originally initiated with mosquitoes collected in Cameroon in January 2006, and belongs to the M molecular and Forest chromosomal forms (Harris et al., 2010). Mosquitoes were reared under standard conditions at 26°C and 80% relative humidity, with a 12 h light/dark cycle as previously described (Mitri et al., 2015). Mosquitoes were infected on an infectious bloodmeal containing physiologically natural viral titers O'Nyong-Nyong strain SG650. The 10- to 30-nt RNA fragments were purified from the small RNA fraction (<200nt) on a 15% urea PAGE (BioRad). Small RNA libraries were then prepared using TruSeq Small RNA Library reagents (Illumina). 15-30nt RNA extracted from polyacrylamide gel were ligated with 3'- and 5'- TruSeq adapters, as described in the original protocol. Synthesis of cDNA was performed by reverse transcription. The cDNA product was then specifically amplified by 11 cycles of PCR and products purified on Agencourt AMPure XP beads (Beckman Coulter Genomics, # A63881).

text: Anopheles coluzzii

text: Anopheles coluzzii

text: whole organism

text: Anopheles coluzzii

text: female

text: M

characteristic: strain

text: Sample 3


E-MTAB-6444:Sample 4

text: IP

text: public

text: E-MTAB-6444:Sample 4

characteristic: Submitter Id

text: ArrayExpress

text: Anopheles coluzzii

text: Anopheles coluzzii

text: whole organism

characteristic: organism part

text: Anopheles coluzzii

text: female

text: M

text: Sample 4


E-MTAB-6444:Sample 5

text: IP

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: E-MTAB-6444:Sample 5

text: ArrayExpress

text: Anopheles coluzzii

text: Anopheles coluzzii

text: whole organism

text: Anopheles coluzzii

text: female

text: M

text: Sample 5


E-MTAB-6444:Sample 6

characteristic: ENA-CHECKLIST

text: IP

text: public

text: E-MTAB-6444:Sample 6

text: ArrayExpress

text: Anopheles coluzzii

characteristic: organism

text: Anopheles coluzzii

text: whole organism

text: Anopheles coluzzii

text: female

text: M

text: Sample 6


E-MTAB-6444:Sample 7

text: IP

text: public

characteristic: INSDC status

text: E-MTAB-6444:Sample 7

text: ArrayExpress

text: Anopheles coluzzii

text: Anopheles coluzzii

text: whole organism

text: Anopheles coluzzii

text: female

text: M

text: Sample 7

characteristic: title


E-MTAB-6444:Sample 8

text: IP

text: public

characteristic: SRA accession

text: E-MTAB-6444:Sample 8

text: ArrayExpress

characteristic: broker name

text: Anopheles coluzzii

text: Anopheles coluzzii

text: whole organism

text: Anopheles coluzzii

text: female

text: M

text: Sample 8


E-MTAB-6444:Sample 9

text: IP

text: public

text: E-MTAB-6444:Sample 9

text: ArrayExpress

characteristic: description

text: Anopheles coluzzii

text: Anopheles coluzzii

text: whole organism

characteristic: replicate

text: Anopheles coluzzii

text: female

text: M

text: Sample 9


characteristic: ENA-LAST-UPDATE

text: URMITE

text: public

text: sputum

characteristic: isolation source

text: Brachybacterium sp. Marseille-P4339

text: Brachybacterium sp. Marseille-P4339

text: Brachybacterium timonensis genome


E-MTAB-6443:Sample 1

characteristic: External Id

text: IP

characteristic: INSDC center name

text: public

text: E-MTAB-6443:Sample 1

text: ArrayExpress

text: Protocols: 12 mosquitoes per pool, in each of two biological replicate pools, were collected 3 d after infection by oral feeding with ONNV and homogenized in TriReagent (Sigma). The A. coluzzii Ngousso strain was originally initiated with mosquitoes collected in Cameroon in January 2006, and belongs to the M molecular and Forest chromosomal forms (Harris et al., 2010). Mosquitoes were reared under standard conditions at 26°C and 80% relative humidity, with a 12 h light/dark cycle as previously described (Mitri et al., 2015). 10ug of RNA (>200nt fraction) was used to prepare directional libraries using the TruSeq SmallRNA sample prep kit, set A and B (Illumina). Chemical fragmentation of polyA RNA was made with Ambion reagent (AM8740), followed by purification on RNeasy columns (Qiagen, #74204). Phosphatase and PNK treatments were performed and followed by purification on RNeasy columns (Qiagen, #74204). The fragmented RNA was ligated with 3'- and 5'- TruSeq adapters, as described in the original protocol. Synthesis of cDNA was performed by reverse transcription. The cDNA product was then specifically amplified by 11 cycles of PCR and products purified on Agencourt AMPure XP beads (Beckman Coulter Genomics, # A63881).

text: Anopheles coluzzii

text: Anopheles coluzzii

text: whole organism

text: Anopheles coluzzii

text: female

characteristic: sex

text: M

text: Sample 1


E-MTAB-6443:Sample 10

characteristic: ENA-FIRST-PUBLIC

text: IP

text: public

text: E-MTAB-6443:Sample 10

characteristic: Submitter Id

text: ArrayExpress

text: Protocols: 12 mosquitoes per pool, in each of two biological replicate pools, were collected 3 d after infection by oral feeding with ONNV and homogenized in TriReagent (Sigma). The A. coluzzii Ngousso strain was originally initiated with mosquitoes collected in Cameroon in January 2006, and belongs to the M molecular and Forest chromosomal forms (Harris et al., 2010). Mosquitoes were reared under standard conditions at 26°C and 80% relative humidity, with a 12 h light/dark cycle as previously described (Mitri et al., 2015). Double-stranded RNAs were synthesized from PCR amplicons using the T7 Megascript Kit (Ambion) as described (Carissimo et al., 2015). For each targeted gene, 500 ng of dsRNA was injected using glass capillary needles into the thorax of cold-anesthetized 1-2 d-old A. coluzzii females using a nano-injector (Nanoject II, Drummond Scientific). 10ug of RNA (>200nt fraction) was used to prepare directional libraries using the TruSeq SmallRNA sample prep kit, set A and B (Illumina). Chemical fragmentation of polyA RNA was made with Ambion reagent (AM8740), followed by purification on RNeasy columns (Qiagen, #74204). Phosphatase and PNK treatments were performed and followed by purification on RNeasy columns (Qiagen, #74204). The fragmented RNA was ligated with 3'- and 5'- TruSeq adapters, as described in the original protocol. Synthesis of cDNA was performed by reverse transcription. The cDNA product was then specifically amplified by 11 cycles of PCR and products purified on Agencourt AMPure XP beads (Beckman Coulter Genomics, # A63881).

text: Anopheles coluzzii

text: Anopheles coluzzii

text: whole organism

text: Anopheles coluzzii

text: female

text: M

characteristic: strain

text: Sample 10


E-MTAB-6443:Sample 11

text: IP

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: E-MTAB-6443:Sample 11

text: ArrayExpress

text: Protocols: 12 mosquitoes per pool, in each of two biological replicate pools, were collected 3 d after infection by oral feeding with ONNV and homogenized in TriReagent (Sigma). The A. coluzzii Ngousso strain was originally initiated with mosquitoes collected in Cameroon in January 2006, and belongs to the M molecular and Forest chromosomal forms (Harris et al., 2010). Mosquitoes were reared under standard conditions at 26°C and 80% relative humidity, with a 12 h light/dark cycle as previously described (Mitri et al., 2015). Double-stranded RNAs were synthesized from PCR amplicons using the T7 Megascript Kit (Ambion) as described (Carissimo et al., 2015). For each targeted gene, 500 ng of dsRNA was injected using glass capillary needles into the thorax of cold-anesthetized 1-2 d-old A. coluzzii females using a nano-injector (Nanoject II, Drummond Scientific). Mosquitoes were infected on an infectious bloodmeal containing physiologically natural viral titers O'Nyong-Nyong strain SG650. 10ug of RNA (>200nt fraction) was used to prepare directional libraries using the TruSeq SmallRNA sample prep kit, set A and B (Illumina). Chemical fragmentation of polyA RNA was made with Ambion reagent (AM8740), followed by purification on RNeasy columns (Qiagen, #74204). Phosphatase and PNK treatments were performed and followed by purification on RNeasy columns (Qiagen, #74204). The fragmented RNA was ligated with 3'- and 5'- TruSeq adapters, as described in the original protocol. Synthesis of cDNA was performed by reverse transcription. The cDNA product was then specifically amplified by 11 cycles of PCR and products purified on Agencourt AMPure XP beads (Beckman Coulter Genomics, # A63881).

text: Anopheles coluzzii

text: Anopheles coluzzii

text: whole organism

characteristic: organism part

text: Anopheles coluzzii

text: female

text: M

text: Sample 11


E-MTAB-6443:Sample 12

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text: IP

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text: E-MTAB-6443:Sample 12

text: ArrayExpress

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characteristic: organism

text: Anopheles coluzzii

text: whole organism

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text: female

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text: Sample 12


E-MTAB-6443:Sample 13

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text: E-MTAB-6443:Sample 13

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text: Anopheles coluzzii

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text: whole organism

text: Anopheles coluzzii

text: female

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text: Sample 13

characteristic: title


E-MTAB-6443:Sample 14

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text: ArrayExpress

characteristic: description

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text: whole organism

characteristic: replicate

text: Anopheles coluzzii

text: female

text: M

text: Sample 14


E-MTAB-6443:Sample 15

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text: IP

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text: ArrayExpress

text: Anopheles coluzzii

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text: whole organism

text: Anopheles coluzzii

text: female

text: M

text: Sample 15


E-MTAB-6443:Sample 16

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text: ArrayExpress

text: Anopheles coluzzii

text: Anopheles coluzzii

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text: Anopheles coluzzii

text: female

characteristic: sex

text: M

text: Sample 16


E-MTAB-6443:Sample 2

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characteristic: Submitter Id

text: ArrayExpress

text: Anopheles coluzzii

text: Anopheles coluzzii

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text: Sample 2


E-MTAB-6443:Sample 3

text: IP

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characteristic: INSDC last update

text: public

text: E-MTAB-6443:Sample 3

text: ArrayExpress

text: Protocols: 12 mosquitoes per pool, in each of two biological replicate pools, were collected 3 d after infection by oral feeding with ONNV and homogenized in TriReagent (Sigma). The A. coluzzii Ngousso strain was originally initiated with mosquitoes collected in Cameroon in January 2006, and belongs to the M molecular and Forest chromosomal forms (Harris et al., 2010). Mosquitoes were reared under standard conditions at 26°C and 80% relative humidity, with a 12 h light/dark cycle as previously described (Mitri et al., 2015). Mosquitoes were infected on an infectious bloodmeal containing physiologically natural viral titers O'Nyong-Nyong strain SG650. 10ug of RNA (>200nt fraction) was used to prepare directional libraries using the TruSeq SmallRNA sample prep kit, set A and B (Illumina). Chemical fragmentation of polyA RNA was made with Ambion reagent (AM8740), followed by purification on RNeasy columns (Qiagen, #74204). Phosphatase and PNK treatments were performed and followed by purification on RNeasy columns (Qiagen, #74204). The fragmented RNA was ligated with 3'- and 5'- TruSeq adapters, as described in the original protocol. Synthesis of cDNA was performed by reverse transcription. The cDNA product was then specifically amplified by 11 cycles of PCR and products purified on Agencourt AMPure XP beads (Beckman Coulter Genomics, # A63881).

text: Anopheles coluzzii

text: Anopheles coluzzii

text: whole organism

text: Anopheles coluzzii

text: female

text: M

text: Sample 3


E-MTAB-6443:Sample 4

characteristic: ENA-CHECKLIST

text: IP

text: public

text: E-MTAB-6443:Sample 4

text: ArrayExpress

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characteristic: organism part

text: Anopheles coluzzii

text: female

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text: Sample 4


E-MTAB-6443:Sample 5

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text: female

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E-MTAB-6443:Sample 6

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text: whole organism

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text: ArrayExpress

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text: Sample 7

characteristic: title


E-MTAB-6443:Sample 8

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text: ArrayExpress

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text: public

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text: Day 290 vertical flow filter sample

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characteristic: organism

text: biofilter metagenome

text: Illumina HiSeq2000

text: VF 290 I

characteristic: title


characteristic: ENA-FIRST-PUBLIC

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text: UNIVERSITY OF TARTU

characteristic: INSDC center name

text: public

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text: biofilter metagenome

text: Illumina HiSeq2000

text: VF 290 II


characteristic: ENA-CHECKLIST

text: UNIVERSITY OF TARTU

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text: anthropogenic environmental material

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characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: metagenome

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characteristic: project name

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text: Illumina HiSeq2000

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text: VF 290 III


characteristic: ENA-LAST-UPDATE

text: UNIVERSITY OF TARTU

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: Raw LECA of horizontal flow filter

text: biofilter

text: biofilm

text: anthropogenic environmental material

text: Estonia

text: metagenome

text: biofilter metagenome

characteristic: organism

text: biofilter metagenome

text: Illumina HiSeq2000

text: HF LECA

characteristic: title


characteristic: ENA-FIRST-PUBLIC

characteristic: External Id

text: UNIVERSITY OF TARTU

characteristic: INSDC center name

text: public

characteristic: collection date

text: Day 15 horizontal flow filter sample

characteristic: description

text: biofilter

characteristic: environment (biome)

text: biofilm

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text: anthropogenic environmental material

characteristic: environment (material)

text: Estonia

text: metagenome

text: biofilter metagenome

text: biofilter metagenome

text: Illumina HiSeq2000

text: HF 15


characteristic: ENA-CHECKLIST

text: UNIVERSITY OF TARTU

text: public

text: Day 43 horizontal flow filter sample

text: biofilter

text: biofilm

text: anthropogenic environmental material

text: Estonia

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: metagenome

characteristic: investigation type

characteristic: miscellaneous environmental package

text: biofilter metagenome

characteristic: project name

text: biofilter metagenome

text: Illumina HiSeq2000

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text: HF 43


characteristic: ENA-LAST-UPDATE

text: UNIVERSITY OF TARTU

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: Day 78 horizontal flow filter sample

text: biofilter

text: biofilm

text: anthropogenic environmental material

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text: metagenome

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characteristic: organism

text: biofilter metagenome

text: Illumina HiSeq2000

text: HF 78

characteristic: title


characteristic: ENA-FIRST-PUBLIC

characteristic: External Id

text: UNIVERSITY OF TARTU

characteristic: INSDC center name

text: public

characteristic: collection date

text: Day 106 horizontal flow filter sample

characteristic: description

text: biofilter

characteristic: environment (biome)

text: biofilm

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text: anthropogenic environmental material

characteristic: environment (material)

text: Estonia

text: metagenome

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text: biofilter metagenome

text: Illumina HiSeq2000

text: HF 106


characteristic: ENA-CHECKLIST

text: UNIVERSITY OF TARTU

text: public

text: Day 134 horizontal flow filter sample

text: biofilter

text: biofilm

text: anthropogenic environmental material

text: Estonia

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: metagenome

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text: biofilter metagenome

characteristic: project name

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text: Illumina HiSeq2000

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text: HF 134


characteristic: ENA-LAST-UPDATE

text: UNIVERSITY OF TARTU

characteristic: INSDC first public

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text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: Day 162 horizontal flow filter sample

text: biofilter

text: biofilm

text: anthropogenic environmental material

text: Estonia

text: metagenome

text: biofilter metagenome

characteristic: organism

text: biofilter metagenome

text: Illumina HiSeq2000

text: HF 162

characteristic: title


characteristic: ENA-FIRST-PUBLIC

characteristic: External Id

text: UNIVERSITY OF TARTU

characteristic: INSDC center name

text: public

characteristic: collection date

text: Day 190 horizontal flow filter sample

characteristic: description

text: biofilter

characteristic: environment (biome)

text: biofilm

characteristic: environment (feature)

text: anthropogenic environmental material

characteristic: environment (material)

text: Estonia

text: metagenome

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text: biofilter metagenome

text: Illumina HiSeq2000

text: HF 190


characteristic: ENA-CHECKLIST

text: UNIVERSITY OF TARTU

text: public

text: Day 225 horizontal flow filter sample

text: biofilter

text: biofilm

text: anthropogenic environmental material

text: Estonia

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: metagenome

characteristic: investigation type

characteristic: miscellaneous environmental package

text: biofilter metagenome

characteristic: project name

text: biofilter metagenome

text: Illumina HiSeq2000

characteristic: sequencing method

text: HF 225


characteristic: ENA-LAST-UPDATE

text: UNIVERSITY OF TARTU

characteristic: INSDC first public

characteristic: INSDC last update

text: public

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characteristic: SRA accession

characteristic: Submitter Id

text: Day 290 horizontal flow filter sample

text: biofilter

text: biofilm

text: anthropogenic environmental material

text: Estonia

text: metagenome

text: biofilter metagenome

characteristic: organism

text: biofilter metagenome

text: Illumina HiSeq2000

text: HF 290

characteristic: title


characteristic: ENA-FIRST-PUBLIC

characteristic: External Id

text: URMITE

characteristic: INSDC center name

text: public

text: vagin

characteristic: isolation source

text: Helcococcus sp. Marseille-P4590

text: Helcococcus sp. Marseille-P4590

characteristic: strain

text: Helcococcus massiliensis genome


characteristic: ENA-CHECKLIST

text: URMITE

text: public

text: stool

text: Lentibacillus sp. Marseille-P4043

text: Lentibacillus sp. Marseille-P4043

text: Lentibacillus timonensis genome


text: Mycobacterium bovis

characteristic: ArrayExpress-SPECIES

text: SC

text: public

text: Mycobacterium bovis

characteristic: common name

text: Mycobacterium bovis

text: Mycobacterium bovis

characteristic: subject id


text: Mouse

characteristic: ArrayExpress-PHENOTYPE

text: male

characteristic: ArrayExpress-SEX

text: Mus musculus

characteristic: ENA-LAST-UPDATE

text: SC

text: public

text: house mouse

text: Male

characteristic: gender

text: Mus musculus

text: Mouse

characteristic: phenotype

text: Mus musculus


text: OREGON STATE UNIVERS

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-6445:Seedling-shoot-2-days-light-replicate-1

tag: Namespace:OREGON STATE UNIVERS

characteristic: Submitter Id

characteristic: age

text: ArrayExpress

characteristic: broker name

text: stiff brome

text: Protocols: Samples harvested after growing them in continuous dark for 8 days (8DD) including germination and followed by 48hrs (48LL) of continuous exposure to light (120µmol/m2/sec at soil surface). The growth chamber was set to cycle between 20C for 12 hours and 18C for the next 12 hours, and the soil was kept moist by gently spraying with water every 72 hours. For continuous dark (no light) regimen samples, sampling was done at 7.30 pm after green light. For samples with 8 days continuous dark followed by 2 days continous light, sampling was done at 10am under light. Continuous light (2-Days): Samples harvested after growing them in continuous dark for 8 days including germination followed by 48hrs (48LL) of continuous exposure to light (120µmol/m2/sec at soil surface). Total RNA from frozen seedling shoot samples was extracted as per manufacturer's protocol for RNA Plant reagent (Invitrogen Inc., USA), RNeasy kits (Qiagen Inc., USA), and RNase-free DNase (Life Technologies Inc., USA). True-Seq kit (Illumina Inc.) was used to prepare RNA-seq libraries, according to the manufacturer’s protocol.

characteristic: description

text: LP.02 two leaves visible stage

characteristic: developmental stage

characteristic: ecotype

text: continuous light regimen

characteristic: environmental stress

text: wild type genotype

characteristic: genotype

text: 48 hours continuous light regimen after 8 days continuous dark (no light) regimen

characteristic: growth condition

text: Brachypodium distachyon

text: Brachypodium distachyon

text: shoot

characteristic: organism part

text: Brachypodium distachyon


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: OREGON STATE UNIVERS

characteristic: INSDC center name

text: public

text: E-MTAB-6445:Seedling-shoot-2-days-light-replicate-2

text: ArrayExpress

text: stiff brome

characteristic: common name

text: LP.02 two leaves visible stage

text: continuous light regimen

text: wild type genotype

text: Brachypodium distachyon

characteristic: organism

text: Brachypodium distachyon

text: shoot

text: Brachypodium distachyon

characteristic: title


text: OREGON STATE UNIVERS

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-6445:Seedling-shoot-2-days-light-replicate-3

characteristic: Submitter Id

characteristic: age

text: ArrayExpress

text: stiff brome

text: LP.02 two leaves visible stage

text: continuous light regimen

text: wild type genotype

text: Brachypodium distachyon

text: Brachypodium distachyon

text: shoot

text: Brachypodium distachyon


text: OREGON STATE UNIVERS

text: public

text: E-MTAB-6445:Seedling-shoot-8-days-dark-replicate-1

text: ArrayExpress

characteristic: broker name

text: stiff brome

text: Protocols: Samples harvested after growing them in continuous dark for 8 days (8DD) including germination and followed by 48hrs (48LL) of continuous exposure to light (120µmol/m2/sec at soil surface). The growth chamber was set to cycle between 20C for 12 hours and 18C for the next 12 hours, and the soil was kept moist by gently spraying with water every 72 hours. For continuous dark (no light) regimen samples, sampling was done at 7.30 pm after green light. For samples with 8 days continuous dark followed by 2 days continous light, sampling was done at 10am under light. Continuous dark (8-Days): Samples harvested after growing them in continuous dark for 8 days (8DD) including germination. Total RNA from frozen seedling shoot samples was extracted as per manufacturer's protocol for RNA Plant reagent (Invitrogen Inc., USA), RNeasy kits (Qiagen Inc., USA), and RNase-free DNase (Life Technologies Inc., USA). True-Seq kit (Illumina Inc.) was used to prepare RNA-seq libraries, according to the manufacturer’s protocol.

characteristic: description

text: LP.02 two leaves visible stage

characteristic: developmental stage

characteristic: ecotype

text: continuous dark (no light) regimen

characteristic: environmental stress

text: wild type genotype

characteristic: genotype

text: 8 days continuous dark (no light) regimen

text: Brachypodium distachyon

text: Brachypodium distachyon

text: shoot

text: Brachypodium distachyon


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: OREGON STATE UNIVERS

text: public

text: E-MTAB-6445:Seedling-shoot-8-days-dark-replicate-2

text: ArrayExpress

text: stiff brome

text: LP.02 two leaves visible stage

text: continuous dark (no light) regimen

text: wild type genotype

characteristic: growth condition

text: Brachypodium distachyon

text: Brachypodium distachyon

text: shoot

characteristic: organism part

text: Brachypodium distachyon


text: OREGON STATE UNIVERS

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: E-MTAB-6445:Seedling-shoot-8-days-dark-replicate-3

text: ArrayExpress

text: stiff brome

characteristic: common name

text: LP.02 two leaves visible stage

text: continuous dark (no light) regimen

text: wild type genotype

text: Brachypodium distachyon

characteristic: organism

text: Brachypodium distachyon

text: shoot

text: Brachypodium distachyon

characteristic: title


text: synthetic construct

characteristic: ArrayExpress-SPECIES

text: SC

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: synthetic construct

text: synthetic construct

text: synthetic construct

characteristic: subject id