E-MTAB-13269:Sample 1

characteristic: ENA-FIRST-PUBLIC

text: public

text: E-MTAB-13269:Sample 1

tag: Namespace:Fraunhofer Institute for Molecular Biology and Applied Ecology (IME)

unit: hour

characteristic: age

text: ArrayExpress

characteristic: broker name

text: not collected

text: zebrafish

characteristic: common name

text: Protocols: at the end of exposure, 10 Embryos were euthanized on ice then homogenised in lysis buffer using Lysing Matrix D ceramic beads in FastPrep-24 homogeniser (MP Biomedicals, Irvine, USA) at 5 m/s speed for 45 seconds. Zebrafish embryos were exposed to difenoconazole for 96 hours according to OECD test guidelines No. 236 at 26 ± 1 °C and a light/dark cycle of 14:10 hours three zebrafish embryos replicate groups originating from three different tanks were exposed to each of two sub-lethal concentrations of difenoconazole (high exposure and low exposure concentrations) in addition to untreated control groups. simutaneous RNA and protein extraction was performed from the homogenised samples using Macherey & Nagel RNA/protein extraction kit. RNA libraries were prepared from RNA extracts with RNA integrity number (RIN) values > 8 using poly(A) RNA purification and the TruSeq RNA Library Prep Kit v2 (Illumina, San Diego, USA)

text: embryo

characteristic: developmental stage

text: wild type genotype

characteristic: genotype

text: not collected

text: not applicable

characteristic: isolate

text: Danio rerio

text: Danio rerio

text: whole organism

characteristic: organism part

text: Danio rerio

text: AB

characteristic: strain

characteristic: tank

text: Sample 1


E-MTAB-13269:Sample 2

status: PUBLIC

tag: attribute

characteristic: ENA-CHECKLIST

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Fraunhofer Institute for Molecular Biology and Applied Ecology (IME)

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-13269:Sample 2

characteristic: Submitter Id

text: ArrayExpress

text: not collected

characteristic: collection date

text: zebrafish

characteristic: description

text: embryo

text: wild type genotype

text: not collected

characteristic: geographic location (country and/or sea)

text: not applicable

text: Danio rerio

characteristic: organism

text: Danio rerio

text: whole organism

text: Danio rerio

text: AB

text: Sample 2

characteristic: title


E-MTAB-13269:Sample 3

characteristic: ENA-FIRST-PUBLIC

text: public

text: E-MTAB-13269:Sample 3

characteristic: age

text: ArrayExpress

characteristic: broker name

text: not collected

text: zebrafish

characteristic: common name

text: embryo

characteristic: developmental stage

text: wild type genotype

characteristic: genotype

text: not collected

text: not applicable

characteristic: isolate

text: Danio rerio

text: Danio rerio

text: whole organism

characteristic: organism part

text: Danio rerio

text: AB

text: Sample 3


E-MTAB-13269:Sample 4

characteristic: ENA-CHECKLIST

characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: E-MTAB-13269:Sample 4

text: ArrayExpress

text: not collected

text: zebrafish

text: embryo

text: wild type genotype

text: not collected

text: not applicable

text: Danio rerio

text: Danio rerio

text: whole organism

text: Danio rerio

text: AB

characteristic: strain

characteristic: tank

text: Sample 4


E-MTAB-13269:Sample 5

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-13269:Sample 5

characteristic: Submitter Id

text: ArrayExpress

text: not collected

characteristic: collection date

text: zebrafish

characteristic: description

text: embryo

text: wild type genotype

text: not collected

characteristic: geographic location (country and/or sea)

text: not applicable

text: Danio rerio

characteristic: organism

text: Danio rerio

text: whole organism

text: Danio rerio

text: AB

text: Sample 5

characteristic: title


E-MTAB-13269:Sample 6

characteristic: ENA-FIRST-PUBLIC

text: public

text: E-MTAB-13269:Sample 6

characteristic: age

text: ArrayExpress

characteristic: broker name

text: not collected

text: zebrafish

characteristic: common name

text: embryo

characteristic: developmental stage

text: wild type genotype

characteristic: genotype

text: not collected

text: not applicable

characteristic: isolate

text: Danio rerio

text: Danio rerio

text: whole organism

characteristic: organism part

text: Danio rerio

text: AB

text: Sample 6


E-MTAB-13269:Sample 7

characteristic: ENA-CHECKLIST

characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: E-MTAB-13269:Sample 7

text: ArrayExpress

text: not collected

text: zebrafish

text: embryo

text: wild type genotype

text: not collected

text: not applicable

text: Danio rerio

text: Danio rerio

text: whole organism

text: Danio rerio

text: AB

characteristic: strain

characteristic: tank

text: Sample 7


E-MTAB-13269:Sample 8

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-13269:Sample 8

characteristic: Submitter Id

text: ArrayExpress

text: not collected

characteristic: collection date

text: zebrafish

characteristic: description

text: embryo

text: wild type genotype

text: not collected

characteristic: geographic location (country and/or sea)

text: not applicable

text: Danio rerio

characteristic: organism

text: Danio rerio

text: whole organism

text: Danio rerio

text: AB

text: Sample 8

characteristic: title


E-MTAB-13269:Sample 9

characteristic: ENA-FIRST-PUBLIC

text: public

text: E-MTAB-13269:Sample 9

characteristic: age

text: ArrayExpress

characteristic: broker name

text: not collected

text: zebrafish

characteristic: common name

text: embryo

characteristic: developmental stage

text: wild type genotype

characteristic: genotype

text: not collected

text: not applicable

characteristic: isolate

text: Danio rerio

text: Danio rerio

text: whole organism

characteristic: organism part

text: Danio rerio

text: AB

text: Sample 9


E-MTAB-13270:Sample 1

characteristic: ENA-CHECKLIST

characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: E-MTAB-13270:Sample 1

tag: Namespace:Fraunhofer Institute for Molecular Biology and Aplied Ecology (IME)

text: ArrayExpress

text: not collected

text: zebrafish

text: Protocols: : at the end of exposure, 10 Embryos were euthanized on ice then homogenised in lysis buffer using Lysing Matrix D ceramic beads in FastPrep-24 homogeniser (MP Biomedicals, Irvine, USA) at 5 m/s speed for 45 seconds. Zebrafish embryos were exposed to metalaxyl for 96 hours according to OECD test guidelines No. 236 at 26 ± 1 °C and a light/dark cycle of 14:10 hours. three zebrafish embryos replicate groups originating from three different tanks were exposed to each of two sub-lethal concentrations of metalaxyl (high exposure and low exposure concentrations) in addition to untreated control groups. RNA libraries were prepared from RNA extracts with RNA integrity number (RIN) values > 8 using poly(A) RNA purification and the TruSeq RNA Library Prep Kit v2 (Illumina, San Diego, USA). RNA libraries were prepared from RNA extracts with RNA integrity number (RIN) values > 8 using poly(A) RNA purification and the TruSeq RNA Library Prep Kit v2 (Illumina, San Diego, USA).

text: embryo

text: wild type genotype

text: not collected

text: not applicable

text: Danio rerio

text: Danio rerio

text: whole organism

text: Danio rerio

text: AB

characteristic: strain

characteristic: tank

text: Sample 1


E-MTAB-13270:Sample 2

text: Fraunhofer Institute for Molecular Biology and Aplied Ecology (IME)

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-13270:Sample 2

characteristic: Submitter Id

text: ArrayExpress

text: not collected

characteristic: collection date

text: zebrafish

characteristic: description

text: embryo

text: wild type genotype

text: not collected

characteristic: geographic location (country and/or sea)

text: not applicable

text: Danio rerio

characteristic: organism

text: Danio rerio

text: whole organism

text: Danio rerio

text: AB

text: Sample 2

characteristic: title


E-MTAB-13270:Sample 3

characteristic: ENA-FIRST-PUBLIC

text: public

text: E-MTAB-13270:Sample 3

characteristic: age

text: ArrayExpress

characteristic: broker name

text: not collected

text: zebrafish

characteristic: common name

text: embryo

characteristic: developmental stage

text: wild type genotype

characteristic: genotype

text: not collected

text: not applicable

characteristic: isolate

text: Danio rerio

text: Danio rerio

text: whole organism

characteristic: organism part

text: Danio rerio

text: AB

text: Sample 3


E-MTAB-13270:Sample 4

characteristic: ENA-CHECKLIST

characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: E-MTAB-13270:Sample 4

text: ArrayExpress

text: not collected

text: zebrafish

text: embryo

text: wild type genotype

text: not collected

text: not applicable

text: Danio rerio

text: Danio rerio

text: whole organism

text: Danio rerio

text: AB

characteristic: strain

characteristic: tank

text: Sample 4


E-MTAB-13270:Sample 5

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-13270:Sample 5

characteristic: Submitter Id

text: ArrayExpress

text: not collected

characteristic: collection date

text: zebrafish

characteristic: description

text: embryo

text: wild type genotype

text: not collected

characteristic: geographic location (country and/or sea)

text: not applicable

text: Danio rerio

characteristic: organism

text: Danio rerio

text: whole organism

text: Danio rerio

text: AB

text: Sample 5

characteristic: title


E-MTAB-13270:Sample 6

characteristic: ENA-FIRST-PUBLIC

text: public

text: E-MTAB-13270:Sample 6

characteristic: age

text: ArrayExpress

characteristic: broker name

text: not collected

text: zebrafish

characteristic: common name

text: embryo

characteristic: developmental stage

text: wild type genotype

characteristic: genotype

text: not collected

text: not applicable

characteristic: isolate

text: Danio rerio

text: Danio rerio

text: whole organism

characteristic: organism part

text: Danio rerio

text: AB

text: Sample 6


E-MTAB-13270:Sample 7

characteristic: ENA-CHECKLIST

characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: E-MTAB-13270:Sample 7

text: ArrayExpress

text: not collected

text: zebrafish

text: embryo

text: wild type genotype

text: not collected

text: not applicable

text: Danio rerio

text: Danio rerio

text: whole organism

text: Danio rerio

text: AB

characteristic: strain

characteristic: tank

text: Sample 7


E-MTAB-13270:Sample 8

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-13270:Sample 8

characteristic: Submitter Id

text: ArrayExpress

text: not collected

characteristic: collection date

text: zebrafish

characteristic: description

text: embryo

text: wild type genotype

text: not collected

characteristic: geographic location (country and/or sea)

text: not applicable

text: Danio rerio

characteristic: organism

text: Danio rerio

text: whole organism

text: Danio rerio

text: AB

text: Sample 8

characteristic: title


E-MTAB-13270:Sample 9

characteristic: ENA-FIRST-PUBLIC

text: public

text: E-MTAB-13270:Sample 9

characteristic: age

text: ArrayExpress

characteristic: broker name

text: not collected

text: zebrafish

characteristic: common name

text: embryo

characteristic: developmental stage

text: wild type genotype

characteristic: genotype

text: not collected

text: not applicable

characteristic: isolate

text: Danio rerio

text: Danio rerio

text: whole organism

characteristic: organism part

text: Danio rerio

text: AB

text: Sample 9


characteristic: ENA-CHECKLIST

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: LANGEBIO-CINVESTAV

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: thale cress

text: RNA-Seq library paired-end of the Carpel Margin Meristem (CMM) of Arabidopsis gynoecium_Biological Replica 1

text: Mexico

unit: DD

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: Plants grown in the growth chamber under long day conditions and tissue collected was with Laser Asisted Microdissection

characteristic: isolation and growth condition

text: Arabidopsis thaliana

text: Stage 7 of Flower and Fruit development

characteristic: plant developmental stage

text: In soil (3:1:1, peat moss:perlite:vermiculite)

characteristic: plant growth medium

text: Carpel Margin Meristem (CMM) of Arabidopsis thaliana gynoecium_Col-0 ecotype

characteristic: plant structure

text: Arabidopsis thaliana


characteristic: ENA-FIRST-PUBLIC

text: LANGEBIO-CINVESTAV

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

characteristic: collection date

text: thale cress

characteristic: common name

text: RNA-Seq library paired-end of the Carpel Margin Meristem (CMM) of Arabidopsis gynoecium_Biological Replica 2

characteristic: description

text: Mexico

characteristic: geographic location (country and/or sea)

text: Arabidopsis thaliana

characteristic: organism

text: Stage 7 of Flower and Fruit development

text: Arabidopsis thaliana

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: LANGEBIO-CINVESTAV

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: thale cress

text: RNA-Seq library paired-end of the Carpel Margin Meristem (CMM) of Arabidopsis gynoecium_Biological Replica 3

text: Mexico

text: Arabidopsis thaliana

text: Stage 7 of Flower and Fruit development

text: Arabidopsis thaliana


text: LANGEBIO-CINVESTAV

text: public

text: thale cress

text: RNA-Seq library paired-end of the presumptive carpel wall (PC) of Arabidopsis gynoecium_Biological Replica 1

text: Mexico

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

characteristic: isolation and growth condition

text: Arabidopsis thaliana

text: Stage 7 of Flower and Fruit development

characteristic: plant developmental stage

characteristic: plant growth medium

text: Presumptive Carpel Wall (PC) of Arabidopsis gynoecium_Col-0 ecotype

characteristic: plant structure

text: Arabidopsis thaliana


characteristic: ENA-FIRST-PUBLIC

text: LANGEBIO-CINVESTAV

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

characteristic: collection date

text: thale cress

characteristic: common name

text: RNA-Seq library paired-end of the presumptive carpel wall (PC) of Arabidopsis gynoecium_Biological Replica 2

text: Mexico

text: Arabidopsis thaliana

text: Stage 7 of Flower and Fruit development

text: Arabidopsis thaliana


characteristic: ENA-CHECKLIST

characteristic: ENA-LAST-UPDATE

text: LANGEBIO-CINVESTAV

text: public

text: thale cress

text: RNA-Seq library paired-end of the presumptive carpel wall (PC) of Arabidopsis gynoecium_Biological Replica 3

characteristic: description

text: Mexico

characteristic: geographic location (country and/or sea)

text: Arabidopsis thaliana

characteristic: organism

text: Stage 7 of Flower and Fruit development

text: Arabidopsis thaliana

characteristic: title


characteristic: External Id

text: LANGEBIO-CINVESTAV

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: thale cress

text: RNA-Seq library paired-end of the Septum (SEP) of Arabidopsis gynoecium_Biological Replica 1

text: Mexico

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: Arabidopsis thaliana

text: Stage 10 of Flower and Fruit development

text: Septum (SEP) of Arabidopsis gynoecium_Col-0 ecotype

text: Arabidopsis thaliana


characteristic: ENA-FIRST-PUBLIC

text: LANGEBIO-CINVESTAV

text: public

characteristic: INSDC status

text: thale cress

text: RNA-Seq library paired-end of the Septum (SEP) of Arabidopsis gynoecium_Biological Replica 2

text: Mexico

characteristic: isolation and growth condition

text: Arabidopsis thaliana

characteristic: plant developmental stage

characteristic: plant growth medium

characteristic: plant structure

text: Arabidopsis thaliana


characteristic: ENA-CHECKLIST

characteristic: ENA-LAST-UPDATE

text: LANGEBIO-CINVESTAV

text: public

characteristic: SRA accession

characteristic: Submitter Id

characteristic: collection date

text: thale cress

characteristic: common name

text: RNA-Seq library paired-end of the Septum (SEP) of Arabidopsis gynoecium_Biological Replica 3

text: Mexico

text: Arabidopsis thaliana

text: Arabidopsis thaliana


characteristic: External Id

text: LANGEBIO-CINVESTAV

characteristic: INSDC center name

text: public

text: thale cress

text: RNA-Seq library paired-end of the Valves (VV) of Arabidopsis gynoecium_Biological Replica 1

characteristic: description

text: Mexico

characteristic: geographic location (country and/or sea)

text: Arabidopsis thaliana

characteristic: organism

text: Valve (VV) of Arabidopsis gyneocium_Col-0 ecotype

text: Arabidopsis thaliana

characteristic: title


characteristic: ENA-FIRST-PUBLIC

text: LANGEBIO-CINVESTAV

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: thale cress

text: RNA-Seq library paired-end of the Valves (VV) of Arabidopsis gynoecium_Biological Replica 2

text: Mexico

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: Arabidopsis thaliana

text: Arabidopsis thaliana


characteristic: ENA-CHECKLIST

characteristic: ENA-LAST-UPDATE

text: LANGEBIO-CINVESTAV

text: public

text: thale cress

text: RNA-Seq library paired-end of the Valves (VV) of Arabidopsis gynoecium_Biological Replica 3

text: Mexico

text: Plants grown in the growth chamber under long day conditions and tissue collected was with Laser Asisted Microdissection

characteristic: isolation and growth condition

text: Arabidopsis thaliana

characteristic: plant developmental stage

characteristic: plant growth medium

characteristic: plant structure

text: Arabidopsis thaliana


characteristic: External Id

characteristic: INSDC center name

text: public

characteristic: SRA accession

tag: Namespace:Laboratory for Molecular Infection Medicine Sweden, Umeå university

characteristic: Submitter Id

text: ArrayExpress

characteristic: broker name

text: not collected

characteristic: collection date

text: Protocols: The animals were collected and rinsed three times with M9 buffer. After washing, the worm pellet was frozen in liquid nitrogen. To obtain RNA samples for RNA-seq, thirty young adult animals were picked to each fresh plate and allowed to lay eggs for 2 hours, after which the adult animals were removed and eggs were allowed to develop into day one adults. Day one animals were subsequently challenged with H2S for three different time points (1 hour, 2 hours and 12 hours). For each time point, five plates of day one animals were exposed to 50ppm H2S, 150ppm H2S or 7% O2 as a control group. Animals were homogenized using Bullet Blender (Next Advance) in the presence of Qiazol Lysis Reagent and 0.5mm Zirconia beads at 4°C. RNA was prepared using RNeasy Plus Universal Mini Kit (Qiagen). Six independent RNA samples were prepared for all different treatments. The 2100 Bioanalyzer instrument (Agilent) was used for the RNA quality control with a microfluidic chip specific for RNA (Agilent RNA 6000 Nano Kit). 1 ug of qualified RNA samples in RNase-free ddH2O was used for library preparation. Library was constructed and sequenced by Novogene.

text: adult

characteristic: developmental stage

text: wild type genotype

characteristic: genotype

text: not collected

text: pool of individuals

characteristic: individual

text: not applicable

characteristic: isolate

text: Caenorhabditis elegans

text: Caenorhabditis elegans

text: whole organism

characteristic: organism part

characteristic: replicate

text: Caenorhabditis elegans

text: mixed

characteristic: sex

characteristic: strain


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: Laboratory for Molecular Infection Medicine Sweden, Umeå university

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: ArrayExpress

text: not collected

characteristic: description

text: adult

text: wild type genotype

text: not collected

characteristic: geographic location (country and/or sea)

text: pool of individuals

text: not applicable

text: Caenorhabditis elegans

characteristic: organism

text: Caenorhabditis elegans

text: whole organism

text: Caenorhabditis elegans

text: mixed

characteristic: title


characteristic: External Id

characteristic: INSDC center name

text: public

characteristic: SRA accession

characteristic: Submitter Id

text: ArrayExpress

characteristic: broker name

text: not collected

characteristic: collection date

text: adult

characteristic: developmental stage

text: wild type genotype

characteristic: genotype

text: not collected

text: pool of individuals

text: not applicable

text: Caenorhabditis elegans

text: Caenorhabditis elegans

text: whole organism

text: d

text: Caenorhabditis elegans

text: mixed


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: public

text: ArrayExpress

text: not collected

text: adult

text: wild type genotype

text: not collected

text: pool of individuals

characteristic: individual

text: not applicable

characteristic: isolate

text: Caenorhabditis elegans

text: Caenorhabditis elegans

text: whole organism

characteristic: organism part

text: a

characteristic: replicate

text: Caenorhabditis elegans

text: mixed

characteristic: sex

characteristic: strain


characteristic: ENA-LAST-UPDATE

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: ArrayExpress

text: not collected

characteristic: description

text: adult

text: wild type genotype

text: not collected

characteristic: geographic location (country and/or sea)

text: pool of individuals

text: not applicable

text: Caenorhabditis elegans

characteristic: organism

text: Caenorhabditis elegans

text: whole organism

text: b

text: Caenorhabditis elegans

text: mixed

characteristic: title


characteristic: External Id

characteristic: INSDC center name

text: public

characteristic: SRA accession

characteristic: Submitter Id

text: ArrayExpress

characteristic: broker name

text: not collected

characteristic: collection date

text: adult

characteristic: developmental stage

text: wild type genotype

characteristic: genotype

text: not collected

text: pool of individuals

text: not applicable

text: Caenorhabditis elegans

text: Caenorhabditis elegans

text: whole organism

text: c

text: Caenorhabditis elegans

text: mixed


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: public

text: ArrayExpress

text: not collected

text: adult

text: wild type genotype

text: not collected

text: pool of individuals

characteristic: individual

text: not applicable

characteristic: isolate

text: Caenorhabditis elegans

text: Caenorhabditis elegans

text: whole organism

characteristic: organism part

text: g

characteristic: replicate

text: Caenorhabditis elegans

text: mixed

characteristic: sex

characteristic: strain


characteristic: ENA-LAST-UPDATE

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: ArrayExpress

text: not collected

characteristic: description

text: adult

text: wild type genotype

text: not collected

characteristic: geographic location (country and/or sea)

text: pool of individuals

text: not applicable

text: Caenorhabditis elegans

characteristic: organism

text: Caenorhabditis elegans

text: whole organism

text: f

text: Caenorhabditis elegans

text: mixed

characteristic: title


characteristic: External Id

characteristic: INSDC center name

text: public

characteristic: SRA accession

characteristic: Submitter Id

text: ArrayExpress

characteristic: broker name

text: not collected

characteristic: collection date

text: adult

characteristic: developmental stage

text: wild type genotype

characteristic: genotype

text: not collected

text: pool of individuals

text: not applicable

text: Caenorhabditis elegans

text: Caenorhabditis elegans

text: whole organism

text: h

text: Caenorhabditis elegans

text: mixed


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: University of Bern

text: public

tag: Namespace:University of Bern

text: Root bacteria isolated from maize

text: Switzerland

text: Morchellaceae sp.

text: Morchellaceae sp.

text: Maize root bacteria


characteristic: ENA-LAST-UPDATE

text: University of Bern

characteristic: INSDC first public

text: public

text: Root bacteria isolated from maize

text: Switzerland

text: Arthrobacter sp.

text: Arthrobacter sp.

text: Maize root bacteria


text: University of Bern

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: Root bacteria isolated from maize

text: Switzerland

text: Paenarthrobacter sp.

text: Paenarthrobacter sp.

text: Maize root bacteria


text: University of Bern

text: public

text: Root bacteria isolated from maize

characteristic: description

text: Switzerland

characteristic: geographic location (country and/or sea)

text: Bacillus sp. (in: firmicutes)

text: Bacillus sp. (in: firmicutes)

text: Maize root bacteria


text: University of Bern

text: public

text: Root bacteria isolated from maize

text: Switzerland

text: Microbacterium sp.

characteristic: organism

text: Microbacterium sp.

text: Maize root bacteria

characteristic: title


characteristic: External Id

text: University of Bern

characteristic: INSDC center name

text: public

text: Root bacteria isolated from maize

text: Switzerland

text: Pseudomonas sp.

text: Pseudomonas sp.

text: Maize root bacteria


text: University of Bern

text: public

characteristic: SRA accession

characteristic: Submitter Id

text: Root bacteria isolated from maize

text: Switzerland

text: Paenibacillus sp.

text: Paenibacillus sp.

text: Maize root bacteria


text: University of Bern

text: public

characteristic: collection date

text: Root bacteria isolated from maize

text: Switzerland

text: Rhizobium sp.

text: Rhizobium sp.

text: Maize root bacteria


text: University of Bern

text: public

text: Root bacteria isolated from maize

text: Switzerland

text: Sphingobium sp.

text: Sphingobium sp.

text: Maize root bacteria


text: University of Bern

text: public

text: Root bacteria isolated from maize

text: Switzerland

text: Stenotrophomonas sp.

text: Stenotrophomonas sp.

text: Maize root bacteria


text: University of Bern

text: public

text: Root bacteria isolated from maize

text: Switzerland

text: Pantoea sp.

text: Pantoea sp.

text: Maize root bacteria


text: University of Bern

text: public

text: Root bacteria isolated from maize

text: Switzerland

text: Pseudarthrobacter sp.

text: Pseudarthrobacter sp.

text: Maize root bacteria


text: University of Bern

text: public

text: Root bacteria isolated from maize

text: Switzerland

text: Enterobacter sp.

text: Enterobacter sp.

text: Maize root bacteria


text: University of Bern

text: public

text: Root bacteria isolated from maize

text: Switzerland

text: Streptomyces sp.

text: Streptomyces sp.

text: Maize root bacteria


text: University of Bern

text: public

text: Root bacteria isolated from maize

text: Switzerland

text: Nocardioides sp.

text: Nocardioides sp.

text: Maize root bacteria


text: University of Bern

text: public

text: Root bacteria isolated from maize

text: Switzerland

text: Chitinophaga sp.

text: Chitinophaga sp.

text: Maize root bacteria


text: University of Bern

text: public

text: Root bacteria isolated from maize

text: Switzerland

text: Massilia sp.

text: Massilia sp.

text: Maize root bacteria


text: University of Bern

text: public

text: Root bacteria isolated from maize

text: Switzerland

text: Burkholderia sp.

text: Burkholderia sp.

text: Maize root bacteria


text: public

tag: Namespace:Southern University of Science And Technology

text: ArrayExpress

characteristic: broker name

text: mouse embryonic stem cells

text: embryonic stem cell

text: not collected

text: house mouse

characteristic: common name

text: Protocols: Total RNA was purified by RNeasy Minikit (Qiagen) according to the manufacturer’s manual. RNA concentration was determined by Nanodrop, and 500 ng of total RNA was used for library construction using KAPA Stranded mRNA-Seq Kits. Sequencing was performed on Illumina HiSeq 2500 machines with 125 bp pair-end mode. ESCs were cultured in a medium comprising of DMEM (Procell, WH0021U211) supplemented with 10% fetal bovine serum (Labtech, FCS-SA/500), 1% L-Glutamine (Gibco, 25030-081), 1% Penicillin-Streptomycin (Gibco, 15140-122), 0.1% β-Mercaptoethanol (Sigma, M3148), and 103 U/ml mLIF (Genescript, Z03077). For differentiation, ESCs were dissociated using 0.05% Trypsin-EDTA (Gibco, 2072820) and resuspended in ES medium without LIF. Approximately 6~8×105 ESCs were then plated in low-attachment petri dishes and incubated at 37°C with 5% CO2 to induce the formation of embryoid bodies (EBs). To obtain homogeneous AID-tagged Mpp8 ES cells, Rosa26-OsTIR1 ESCs were transfected with the linearized PL-Mpp8-Flag-AID-EGFP vector, the corresponding sgRNA vector, and Cas9-encoding vector using Lipo8000 transfection reagent (Beyotime, C0533FT). Following transfection, colonies were selected using a combination of 250 μg/ml G418 (Sangon Biotech, GDJ958) and 1 μg/ml of Puromycin (Sigma, P8833). Finally, clones were selected for genotyping. To generate inducible Mpp8 overexpressing ESCs, the Mpp8 cDNA was amplified and inserted into the pPBH-TREtight-MLC-EGFP vector. The Mpp8 overexpression vector and PBase vector were then transfected into Mpp8AID ESCs. Colonies were selected for genotyping after being cultured in the selection medium containing 100 μg/ml hygromycin (Invitrogen, 10687010). The culture medium supplemented with 1 μg/ml Doxycycline (Sigma, 3219-99-6) was used to induce the overexpression of Mpp8. Total RNA was extracted using the RNeasy Minikit (Qiagen) based on the manufacturer's instructions. Library was prepared using KAPA Stranded mRNA-Seq Kits based on the manufacturer's instructions.

text: Mpp8 -/-

text: not collected

text: not applicable

characteristic: isolate

text: Mus musculus

text: Mus musculus

text: inner cell mass

characteristic: organism part

text: Mus musculus


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: Southern University of Science And Technology

text: public

text: ArrayExpress

text: mouse embryonic stem cells

text: embryonic stem cell

text: not collected

text: house mouse

text: Mpp8 -/-

characteristic: genotype

text: not collected

text: not applicable

text: Mus musculus

text: Mus musculus

text: inner cell mass

text: Mus musculus


characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: ArrayExpress

text: mouse embryonic stem cells

text: embryonic stem cell

text: not collected

text: house mouse

characteristic: description

text: wild type genotype

text: not collected

text: not applicable

text: Mus musculus

text: Mus musculus

text: inner cell mass

text: Mus musculus


LMG 30234

characteristic: External Id

text: Ghent university

text: public

text: LMG 30234

tag: Namespace:Ghent university

text: Fructobacillus fructosus LMG 30234 isolated from the bumblebee gut (Bombus terrestris)

text: Belgium

characteristic: geographic location (country and/or sea)

text: LMG 30234

text: Fructobacillus fructosus

characteristic: organism

text: Fructobacillus fructosus

text: LMG 30234

characteristic: strain

text: Fructobacillus fructosus LMG 30234

characteristic: title


LMG 30235

text: Ghent university

characteristic: INSDC center name

text: public

characteristic: SRA accession

text: LMG 30235

characteristic: Submitter Id

characteristic: collection date

text: Fructobacillus fructosus LMG 30235 isolated from the bumblebee gut (Bombus lucorum)

text: Belgium

text: LMG 30235

text: Fructobacillus fructosus

text: Fructobacillus fructosus

text: LMG 30235

text: Fructobacillus fructosus LMG 30235


LMG 30237

characteristic: ENA-CHECKLIST

text: Ghent university

text: public

text: LMG 30237

text: Fructobacillus tropaeoli LMG 30237 isolated from the bumblebee gut (Bombus lapidarius)

text: Belgium

text: LMG 30237

characteristic: isolate

text: Fructobacillus tropaeoli

text: Fructobacillus tropaeoli

text: LMG 30237

text: Fructobacillus tropaeoli LMG 30237


LMG 30238

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: Ghent university

text: public

text: LMG 30238

text: Fructobacillus tropaeoli LMG 30238 isolated from the bumblebee gut (Bombus lapidarius)

text: Belgium

text: LMG 30238

text: Fructobacillus tropaeoli

text: Fructobacillus tropaeoli

text: LMG 30238

text: Fructobacillus tropaeoli LMG 30238


text: Ghent university

characteristic: INSDC first public

text: public

text: Fructobacillus tropaeoli R-53137 isolated from the bumblebee gut (Bombus lapidarius)

text: Belgium

text: Fructobacillus tropaeoli

text: Fructobacillus tropaeoli

text: Fructobacillus tropaeoli R-53137


text: Ghent university

characteristic: INSDC last update

text: public

text: Fructobacillus fructosus R-53140 isolated from the bumblebee gut (Bombus lapidarius)

text: Belgium

text: Fructobacillus fructosus

text: Fructobacillus fructosus

text: Fructobacillus fructosus R-53140


text: Ghent university

text: public

characteristic: INSDC status

text: Fructobacillus sp. R-53534 isolated from the bumblebee gut (Bombus hypnorum)

text: Belgium

text: Fructobacillus sp. LMG 32999

text: Fructobacillus sp. LMG 32999

text: Fructobacillus sp. R-53534


text: Ghent university

text: public

text: Fructobacillus cardui R-53653 isolated from the bumblebee gut (Bombus lapidarius)

characteristic: description

text: Belgium

text: Fructobacillus cardui

text: Fructobacillus cardui

text: Fructobacillus cardui R-53653


LMG 32999

characteristic: External Id

text: Ghent university

text: public

text: LMG 32999

text: Fructobacillus sp. LMG 32999 isolated from the bumblebee gut (Bombus lucorum)

text: Belgium

text: LMG 32999

text: Fructobacillus sp. LMG 32999

text: Fructobacillus sp. LMG 32999

text: LMG 32999

text: Fructobacillus sp. LMG 32999


text: Ghent university

text: public

text: Fructobacillus sp. R-54837 isolated from the bumblebee gut (Bombus terrestris)

text: Belgium

characteristic: geographic location (country and/or sea)

text: Fructobacillus sp. LMG 32999

text: Fructobacillus sp. LMG 32999

text: Fructobacillus sp. R-54837


text: Ghent university

text: public

text: Fructobacillus fructosus R-54839 isolated from the bumblebee gut (Bombus terrestris)

text: Belgium

text: Fructobacillus fructosus

characteristic: organism

text: Fructobacillus fructosus

text: Fructobacillus fructosus R-54839


text: Ghent university

text: public

text: Fructobacillus fructosus R-54866 isolated from the bumblebee gut (Bombus terrestris)

text: Belgium

text: Fructobacillus fructosus

text: Fructobacillus fructosus

characteristic: strain

text: Fructobacillus fructosus R-54866


text: Ghent university

text: public

text: Fructobacillus sp. R-55203 isolated from the bumblebee gut (Bombus lapidarius)

text: Belgium

text: Fructobacillus sp. LMG 32999

text: Fructobacillus sp. LMG 32999

text: Fructobacillus sp. R-55203

characteristic: title


text: Ghent university

characteristic: INSDC center name

text: public

text: Fructobacillus fructosus R-55210 isolated from the bumblebee gut (Bombus hypnorum)

text: Belgium

text: Fructobacillus fructosus

text: Fructobacillus fructosus

text: Fructobacillus fructosus R-55210


text: Ghent university

text: public

characteristic: SRA accession

text: Fructobacillus sp. R-55214 isolated from the bumblebee gut (Bombus terrestris)

text: Belgium

text: Fructobacillus sp. LMG 32999

text: Fructobacillus sp. LMG 32999

text: Fructobacillus sp. R-55214


text: Ghent university

text: public

characteristic: Submitter Id

text: Fructobacillus tropaeoli R-55227 isolated from the bumblebee gut (Bombus pascuorum)

text: Belgium

text: Fructobacillus tropaeoli

text: Fructobacillus tropaeoli

text: Fructobacillus tropaeoli R-55227


text: Ghent university

text: public

characteristic: collection date

text: Fructobacillus sp. R-55234 isolated from the bumblebee gut (Bombus. terrestris)

text: Belgium

text: Fructobacillus sp. LMG 32999

text: Fructobacillus sp. LMG 32999

text: Fructobacillus sp. R-55234


characteristic: ENA-CHECKLIST

text: Ghent university

text: public

text: Fructobacillus sp. R-55250 isolated from the bumblebee gut (Bombus pascuorum)

text: Belgium

text: Fructobacillus sp. LMG 32999

text: Fructobacillus sp. LMG 32999

text: Fructobacillus sp. R-55250


text: Ghent university

text: public

text: Fructobacillus cardui R-82265 isolated from flower Poppies

text: Belgium

characteristic: isolate

text: Fructobacillus cardui

text: Fructobacillus cardui

text: Fructobacillus cardui R-82265


characteristic: ENA-FIRST-PUBLIC

text: Ghent university

text: public

text: Fructobacillus cardui R-82291 isolated from common comfrey flowers

text: Belgium

text: Fructobacillus cardui

text: Fructobacillus cardui

text: Fructobacillus cardui R-82291


characteristic: ENA-LAST-UPDATE

text: Ghent university

text: public

text: Fructobacillus cardui R-82641 Calibrachoa sp. flowers

text: Belgium

text: Fructobacillus cardui

text: Fructobacillus cardui

text: Fructobacillus cardui R-82641


text: INRAE

characteristic: INSDC first public

text: public

characteristic: broad-scale environmental context

text: Flamenko

characteristic: environmental medium

text: France

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

characteristic: local environmental context

text: rhizosphere metagenome

characteristic: project name

text: rhizosphere metagenome


characteristic: External Id

text: INRAE

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: Flamenko-Balltrap

characteristic: description

text: France

characteristic: geographic location (country and/or sea)

text: rhizosphere metagenome

characteristic: organism

text: rhizosphere metagenome


characteristic: ENA-CHECKLIST

text: INRAE

characteristic: INSDC center name

text: public

characteristic: SRA accession

characteristic: Submitter Id

characteristic: collection date

text: Flamenko-Dexter

text: France

text: rhizosphere metagenome

text: rhizosphere metagenome

characteristic: title


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: INRAE

characteristic: INSDC first public

text: public

characteristic: broad-scale environmental context

characteristic: environmental medium

text: France

text: rhizosphere metagenome

text: rhizosphere metagenome


characteristic: External Id

text: INRAE

text: public

text: Flamenko-Enduro

text: France

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

characteristic: local environmental context

text: rhizosphere metagenome

characteristic: project name

text: rhizosphere metagenome


text: INRAE

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: Balltrap

characteristic: description

text: France

characteristic: geographic location (country and/or sea)

text: rhizosphere metagenome

characteristic: organism

text: rhizosphere metagenome


characteristic: ENA-CHECKLIST

text: INRAE

characteristic: INSDC center name

text: public

characteristic: SRA accession

characteristic: Submitter Id

characteristic: collection date

text: Dexter

text: France

text: rhizosphere metagenome

text: rhizosphere metagenome


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: INRAE

characteristic: INSDC first public

text: public

characteristic: broad-scale environmental context

text: Enduro

text: France

text: rhizosphere metagenome

text: rhizosphere metagenome

characteristic: title


characteristic: External Id

text: INRAE

text: public

text: Balltrap-Flamenko

characteristic: environmental medium

text: France

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

characteristic: local environmental context

text: rhizosphere metagenome

text: rhizosphere metagenome


text: INRAE

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: Dexter-Flamenko

characteristic: description

text: France

characteristic: geographic location (country and/or sea)

text: rhizosphere metagenome

characteristic: project name

text: rhizosphere metagenome


characteristic: ENA-CHECKLIST

text: INRAE

characteristic: INSDC center name

text: public

characteristic: SRA accession

characteristic: Submitter Id

text: Enduro-Flamenko

text: France

text: rhizosphere metagenome

characteristic: organism

text: rhizosphere metagenome


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: INRAE

characteristic: INSDC first public

text: public

characteristic: broad-scale environmental context

characteristic: collection date

text: Bulksoil

text: France

text: rhizosphere metagenome

text: rhizosphere metagenome

text: Bulksoil


E-MTAB-13301:Sample 004

characteristic: External Id

text: public

text: E-MTAB-13301:Sample 004

tag: Namespace:Computational Biology Program, Ontario Institute for Cancer Research, Toronto, ON, Canada

text: ArrayExpress

characteristic: broker name

text: Hepatitis C

characteristic: clinical history

text: not collected

text: human

characteristic: common name

text: Protocols: Three liver hepatocellular carcinoma (HCC) samples were collected from male patients on a background of liver disease due to Hepatitis C, who underwent liver transplantation at the Ajmera Transplant Centre of Toronto General Hospital (ON, Canada) in 2016-2019 Approximately 30 mg of HCC tumor sample was used for each ChIP reaction. Frozen HCC tissues were dounce homogenized into single cell suspensions and cross-linked with 1% formaldehyde in Solution A (50 mM Hepes–KOH, 100 mM NaCl, 1 mM EDTA, 0.5 mM EGTA) for 20 min at RT. Fixation was quenched by adding glycine to a final concentration of 125 mM. After two washes with ice cold PBS, cells were filtered through 100 μm cell strainer to remove any connective tissue. Cell lysis and nuclei isolation were carried out in 10 mL of LB1 buffer (Diagenode) by rotating 20 min at 4 C, followed by nuclear lysis in 5 mL of LB2 (Diagenode) and rotating 10 min at 4C. For chromatin shearing, the cell pellet was resuspended in Shearing Buffer (Diagenode) supplemented with complete proteinase inhibitors (Roche), and sonicated for 5 cycles (30 s ON, 30 s OFF) with the Bioruptor Pico sonicator (Diagenode). Chromatin was cleared by centrifugation (13,000 rpm for 10 min at 4 C). For ChIP, chromatin lysates were combined with 5 ug of anti-TOP2B, anti-CTCF, or anti-RAD21 antibodies and incubated overnight in IP buffer (Diagenode) rotating at 4 C, and then with 70 μl of pre-blocked (0.5 mg/mL BSA) Dynabeads protein G (ThermoFisher) for 4 hours. Beads were then washed six times with RIPA buffer (50 mM Hepes–KOH, pH 7.5; 500 Mm LiCl; 1 mM EDTA; 1% NP-40 or Igepal CA-630; 0.7% Na– Deoxycholate), and one time with TBS (20 mM Tris–HCl, pH 7.6; 150 mM NaCl), and resuspended in ChIP Elution buffer (50 mM Tris–HCl, pH 8; 10 mM EDTA; 1% SDS). Cross-linking was reversed by overnight incubation at 65 C. Cellular proteins and RNA were digested with Proteinase K (Invitrogen) and RNaseA (Ambion). ChIP DNA was purified with P:C:I method. ChIP-seq libraries were prepared using NEBNext Ultra II DNA Library preparation Kit following the manufactures instructions (NEB, E7645). Libraries were amplified for 9 cycles using Q5 Hot Start High-Fidelity DNA Polymerase (NEB, M0493L), purified and size-selected with AMPure XP PCR purification beads (Beckman Coulter, A63881), and quantified with 2100 Bioanalyzer (Agilent). Input control DNA extracted from sonicated cell lysates of each sample were processed in parallel.

text: adult

characteristic: developmental stage

text: hepatocellular carcinoma

characteristic: disease

text: not collected

characteristic: individual

text: not applicable

characteristic: isolate

text: Homo sapiens

text: Homo sapiens

text: liver

characteristic: organism part

text: Homo sapiens

text: male

characteristic: sex

text: Sample 004

characteristic: title


E-MTAB-13301:Sample 005

characteristic: ENA-CHECKLIST

text: Computational Biology Program, Ontario Institute for Cancer Research, Toronto, ON, Canada

characteristic: INSDC center name

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-13301:Sample 005

characteristic: Submitter Id

text: ArrayExpress

text: Hepatitis C

text: not collected

text: human

characteristic: description

text: adult

text: hepatocellular carcinoma

text: not collected

characteristic: geographic location (country and/or sea)

text: not applicable

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: liver

text: Homo sapiens

text: male

text: Sample 005


E-MTAB-13301:Sample 006

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC first public

text: public

text: E-MTAB-13301:Sample 006

text: ArrayExpress

characteristic: broker name

text: Hepatitis C

characteristic: clinical history

text: not collected

characteristic: collection date

text: human

characteristic: common name

text: adult

text: hepatocellular carcinoma

text: not collected

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: liver

text: Homo sapiens

text: male

text: Sample 006


E-MTAB-13301:Sample 012

characteristic: ENA-CHECKLIST

text: public

text: E-MTAB-13301:Sample 012

text: ArrayExpress

text: Hepatitis C

text: not collected

text: human

text: adult

characteristic: developmental stage

text: hepatocellular carcinoma

characteristic: disease

text: not collected

characteristic: individual

text: not applicable

characteristic: isolate

text: Homo sapiens

text: Homo sapiens

text: liver

characteristic: organism part

text: Homo sapiens

text: male

characteristic: sex

text: Sample 012

characteristic: title


E-MTAB-13301:Sample 016

characteristic: INSDC center name

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-13301:Sample 016

characteristic: Submitter Id

text: ArrayExpress

text: Hepatitis C

text: not collected

text: human

characteristic: description

text: adult

text: hepatocellular carcinoma

text: not collected

characteristic: geographic location (country and/or sea)

text: not applicable

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: liver

text: Homo sapiens

text: male

text: Sample 016


E-MTAB-13301:Sample 017

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC first public

text: public

text: E-MTAB-13301:Sample 017

text: ArrayExpress

characteristic: broker name

text: Hepatitis C

characteristic: clinical history

text: not collected

characteristic: collection date

text: human

characteristic: common name

text: adult

text: hepatocellular carcinoma

text: not collected

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: liver

text: Homo sapiens

text: male

text: Sample 017


E-MTAB-13301:Sample 018

characteristic: ENA-CHECKLIST

text: public

text: E-MTAB-13301:Sample 018

text: ArrayExpress

text: Hepatitis C

text: not collected

text: human

text: adult

characteristic: developmental stage

text: hepatocellular carcinoma

characteristic: disease

text: not collected

characteristic: individual

text: not applicable

characteristic: isolate

text: Homo sapiens

text: Homo sapiens

text: liver

characteristic: organism part

text: Homo sapiens

text: male

characteristic: sex

text: Sample 018

characteristic: title


E-MTAB-13301:Sample 021

characteristic: INSDC center name

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-13301:Sample 021

characteristic: Submitter Id

text: ArrayExpress

text: Hepatitis C

text: not collected

text: human

characteristic: description

text: adult

text: hepatocellular carcinoma

text: not collected

characteristic: geographic location (country and/or sea)

text: not applicable

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: liver

text: Homo sapiens

text: male

text: Sample 021


E-MTAB-13301:Sample 026

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC first public

text: public

text: E-MTAB-13301:Sample 026

text: ArrayExpress

characteristic: broker name

text: Hepatitis C

characteristic: clinical history

text: not collected

characteristic: collection date

text: human

characteristic: common name

text: adult

text: hepatocellular carcinoma

text: not collected

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: liver

text: Homo sapiens

text: male

text: Sample 026


E-MTAB-13301:Sample 029

characteristic: ENA-CHECKLIST

text: public

text: E-MTAB-13301:Sample 029

text: ArrayExpress

text: Hepatitis C

text: not collected

text: human

text: adult

characteristic: developmental stage

text: hepatocellular carcinoma

characteristic: disease

text: not collected

characteristic: individual

text: not applicable

characteristic: isolate

text: Homo sapiens

text: Homo sapiens

text: liver

characteristic: organism part

text: Homo sapiens

text: male

characteristic: sex

text: Sample 029

characteristic: title


E-MTAB-13301:Sample 030

characteristic: INSDC center name

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-13301:Sample 030

characteristic: Submitter Id

text: ArrayExpress

text: Hepatitis C

text: not collected

text: human

characteristic: description

text: adult

text: hepatocellular carcinoma

text: not collected

characteristic: geographic location (country and/or sea)

text: not applicable

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: liver

text: Homo sapiens

text: male

text: Sample 030


E-MTAB-13301:Sample 031

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC first public

text: public

text: E-MTAB-13301:Sample 031

text: ArrayExpress

characteristic: broker name

text: Hepatitis C

characteristic: clinical history

text: not collected

characteristic: collection date

text: human

characteristic: common name

text: adult

text: hepatocellular carcinoma

text: not collected

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: liver

text: Homo sapiens

text: male

text: Sample 031


characteristic: ENA-CHECKLIST

text: HOMER ION Co., Ltd.

text: public

tag: Namespace:HOMER ION Co., Ltd.

unit: week

characteristic: age

text: ArrayExpress

text: not collected

text: Norway rat

text: Protocols: They were divided into three groups: control (CONT), denervation (DEN), and denervation + electrical stimulation (DEN + ES), and chronic response analysis was performed. For electrical stimulation, chronic responses were performed under isoflurane anesthesia (1 set of 5 min, once every 2 days for 7 days), and 24 h after the last stimulation, the gastrocnemius muscle was collected Ten-week-old male Sprague-Dawley rats were used.The rats were housed in cages at 23 °C with a 12 h/12 h light/dark cycle (dark time 18:00–06:00). All rats received a standard solid diet (CE-7; CLEA Japan) and water ad libitum.All rats were acclimatized by rearing in the environment described above for 1 week prior to the experiment. The right and left ankle joints were shaved under isoflurane anesthesia (anesthetic aspiration rate: 250–300 mL/min, concentration: 2.0–2.2%). The rats were placed on their backs on a table, and belt-type electrodes were attached to both ankle joints. The muscles of the lower extremities were stimulated simultaneously on both sides using electrical stimulation at 60 Hz, eliciting continuous tetanus for 5 min. Stimulation intensity was preliminarily tested with a belt electrode and set to 3.0 mA, which is the minimum current run value at which maximum torque was obtained with 60 Hz stimulation. During contraction, the lower limb was not immobilized, and the exercise was performed in a natural extension position. Data were analyzed using iDEP. Gene expression difference analysis was performed using DEseq2 [false discovery rate (FDR) cutoff: 0.1, minimum fold change: 2]. Pathway analysis was performed on the GO Biological Process gene set using Generally Applicable Gene Set Enrichment for pathway analysis (GAGE; FDR cutoff:0.10). Muscle was homogenized with TRIzol reagent. Chloroform was added, mixed, and allowed to stand for 15 minutes, and the muscle samples were centrifuged at 4°C, 12,000 x g for 15 minutes. The supernatant was collected, ethanol was added and mixed, and total RNA was extracted using RNeasy kit (74106; QIAGEN, Hilden, Germany). Sequencing libraries were prepared using the QuantSeq 30 mRNA-seq LibraryPrep Kit FWD for Illumina (Lexogen, Inc.). After removal of the RNA template, a second strand was synthesized using random primers. The double-stranded cDNA library was purified using magnetic beads after washing, and the library was amplified by PCR using primers containing adapters and i7 index sequences. Libraries were purified with magnetic beads, quantified using an Affluorometer (Qubit 4, Thermo Fisher Scientific), and pooled to equimolar concentrations.

text: not collected

characteristic: injury

text: not applicable

characteristic: isolate

text: Rattus norvegicus

text: Rattus norvegicus

text: skeletal muscle tissue

characteristic: organism part

text: Rattus norvegicus

text: male

characteristic: sex

characteristic: stimulus

text: Sprague-Dawley

characteristic: strain

characteristic: title


characteristic: ENA-FIRST-PUBLIC

text: HOMER ION Co., Ltd.

characteristic: INSDC center name

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: ArrayExpress

text: not collected

text: Norway rat

characteristic: description

text: not collected

characteristic: geographic location (country and/or sea)

text: denervation

text: not applicable

text: Rattus norvegicus

characteristic: organism

text: Rattus norvegicus

text: skeletal muscle tissue

text: Rattus norvegicus

text: male

text: Sprague-Dawley


characteristic: ENA-CHECKLIST

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: HOMER ION Co., Ltd.

characteristic: INSDC first public

text: public

characteristic: age

text: ArrayExpress

characteristic: broker name

text: not collected

characteristic: collection date

text: Norway rat

characteristic: common name

text: not collected

text: denervation

text: not applicable

text: Rattus norvegicus

text: Rattus norvegicus

text: skeletal muscle tissue

text: Rattus norvegicus

text: male

text: electrical

text: Sprague-Dawley


characteristic: ENA-FIRST-PUBLIC

text: Medical Center University of Freiburg

text: public

tag: Namespace:Medical Center University of Freiburg

text: human

text: Preoperative stool sample for v2 chemistry MiSeq 16S sequencing

text: Germany

text: Homo sapiens

text: Homo sapiens

text: Stool sample

characteristic: title


text: Medical Center University of Freiburg

characteristic: INSDC center name

characteristic: INSDC last update

text: public

text: human

text: Postoperative stool sample for v2 chemistry MiSeq ITS2 sequencing

text: Germany

text: Homo sapiens

text: Homo sapiens

text: Stool sample


text: CNRS

text: public

characteristic: INSDC status

characteristic: SRA accession

unit: day

text: ArrayExpress

text: not collected

text: yellow fever mosquito

text: Protocols: pool of 75 females, three days post emergence, not blood fed Gentra Puregene Tissue kit (Qiagen) with 3mL cell lysis bufferr.DNA fragment length was visualized on agarose gels, and concentration was measured with Qubit and adjusted to 150 ng/µl. DNA was size selected with SRE (Short Read Eliminator) kits from Circulomics. A library was prepared using 1 ug DNA and Nanopore SQK-LSK109 kit A library was prepared using 1 ug DNA and Nanopore SQK-LSK109 kit

text: adult

characteristic: developmental stage

text: wild type genotype

characteristic: genotype

text: not collected

text: pool of 75 individuals

characteristic: individual

text: not applicable

characteristic: isolate

text: Aedes aegypti

text: Aedes aegypti

text: whole organism

characteristic: organism part

text: Aedes aegypti

text: female

characteristic: sex

text: IR0F (deltamethrin resistant)

characteristic: strain


characteristic: ENA-CHECKLIST

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: CNRS

characteristic: INSDC first public

text: public

characteristic: Submitter Id

characteristic: age

text: ArrayExpress

text: not collected

text: yellow fever mosquito

characteristic: description

text: adult

text: wild type genotype

text: not collected

characteristic: geographic location (country and/or sea)

text: pool of 75 individuals

text: not applicable

text: Aedes aegypti

characteristic: organism

text: Aedes aegypti

text: whole organism

text: Aedes aegypti

text: female

text: IR13 (deltamethrin sensitive)


characteristic: ENA-FIRST-PUBLIC

text: CNRS

characteristic: INSDC center name

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: ArrayExpress

characteristic: broker name

text: not collected

characteristic: collection date

text: yellow fever mosquito

characteristic: common name

text: Protocols: 2 pools of 50 females, three days post emergence, not blood fed PureGene Core Kit A (Qiagen); gDNA extracts were then pooled in equal proportions A library was prepared using 1 ug DNA and Nanopore SQK-LSK109 kit according to the TruSeq DNA Nano Reference guide for Illumina Paired-end Indexed sequencing (version oct. 2017)

text: adult

text: wild type genotype

text: not collected

text: pool of 50 individuals

text: not applicable

text: Aedes aegypti

text: Aedes aegypti

text: whole organism

text: Aedes aegypti

text: female

text: IR0F (deltamethrin resistant)

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-LAST-UPDATE

text: CNRS

text: public

text: ArrayExpress

text: not collected

text: yellow fever mosquito

text: adult

characteristic: developmental stage

text: wild type genotype

characteristic: genotype

text: not collected

text: pool of 50 individuals

characteristic: individual

text: not applicable

characteristic: isolate

text: Aedes aegypti

text: Aedes aegypti

text: whole organism

characteristic: organism part

text: Aedes aegypti

text: female

characteristic: sex

text: IR13 (deltamethrin sensitive)

characteristic: strain


characteristic: ENA-FIRST-PUBLIC

characteristic: External Id

text: FamilyTreeDNA

characteristic: INSDC center name

characteristic: INSDC first public

text: public

characteristic: Submitter Id

text: Rene Herrera

text: human

text: Ami

characteristic: description

text: Taiwan

characteristic: geographic location (country and/or sea)

text: Hualien County (Coastal East Central Formosa)

characteristic: geographic location (region and locality)

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: male

text: Saliva

text: Ami


characteristic: ENA-CHECKLIST

characteristic: ENA-LAST-UPDATE

text: FamilyTreeDNA

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: Rene Herrera

characteristic: collection date

text: human

characteristic: common name

text: Micronesian

text: Kiribati

text: Kiritimati

text: Homo sapiens

text: Homo sapiens

text: male

text: Saliva

text: Kiritimati

characteristic: title


characteristic: ENA-FIRST-PUBLIC

text: FamilyTreeDNA

text: public

text: Rene Herrera

text: human

text: Polynesian

text: French Polynesia

text: Marquesas Islands

text: Homo sapiens

text: Homo sapiens

text: male

characteristic: sex

text: Saliva

text: Nuku Hiva


characteristic: External Id

text: Guy's and St Thomas' Trust

characteristic: INSDC center name

text: public

tag: Namespace:Guy's and St Thomas' Trust

text: Performance characteristics

text: United Kingdom

text: metagenome

text: Swabs

text: metagenome


text: Guy's and St Thomas' Trust

characteristic: INSDC first public

text: public

characteristic: Submitter Id

text: Performance characteristics

text: United Kingdom

text: metagenome

text: Sputum

text: metagenome


text: Guy's and St Thomas' Trust

text: public

text: Performance characteristics

characteristic: description

text: United Kingdom

characteristic: geographic location (country and/or sea)

text: metagenome

text: swabs

text: metagenome


text: Guy's and St Thomas' Trust

text: public

text: Performance characteristics

text: United Kingdom

text: metagenome

characteristic: organism

text: swab

text: metagenome


characteristic: ENA-CHECKLIST

text: Guy's and St Thomas' Trust

text: public

text: Performance characteristics

text: United Kingdom

text: metagenome

text: BAL

text: metagenome


characteristic: ENA-LAST-UPDATE

text: Guy's and St Thomas' Trust

text: public

text: Performance characteristics

text: United Kingdom

text: metagenome

text: NT

text: metagenome


text: Guy's and St Thomas' Trust

characteristic: INSDC last update

text: public

text: Performance characteristics

text: United Kingdom

text: metagenome

text: NTS

text: metagenome


text: Guy's and St Thomas' Trust

text: public

characteristic: INSDC status

text: Performance characteristics

text: United Kingdom

text: metagenome

text: PF

text: metagenome


text: Guy's and St Thomas' Trust

text: public

characteristic: SRA accession

text: Performance characteristics

text: United Kingdom

text: metagenome

text: NDL

text: metagenome


text: Guy's and St Thomas' Trust

text: public

characteristic: collection date

text: Performance characteristics

text: United Kingdom

text: metagenome

text: BAL/WS

text: metagenome


text: Guy's and St Thomas' Trust

text: public

text: Performance characteristics

text: United Kingdom

text: metagenome

text: ETT

text: metagenome


text: Guy's and St Thomas' Trust

text: public

text: Limit of detection

text: United Kingdom

text: metagenome

text: BAL

text: metagenome


text: Guy's and St Thomas' Trust

text: public

text: Negative control

text: United Kingdom

text: metagenome

text: NTC

text: metagenome


text: Guy's and St Thomas' Trust

text: public

text: Prospective study

text: United Kingdom

text: metagenome

text: BAL

text: metagenome


text: Guy's and St Thomas' Trust

text: public

text: Prospective study

text: United Kingdom

text: metagenome

text: PF

text: metagenome


text: Guy's and St Thomas' Trust

text: public

text: Prospective study

text: United Kingdom

text: metagenome

text: Sputum

text: metagenome


text: Guy's and St Thomas' Trust

text: public

text: Prospective study

text: United Kingdom

text: metagenome

text: ETT

text: metagenome


text: Guy's and St Thomas' Trust

text: public

text: Prospective study

text: United Kingdom

text: metagenome

text: NBL

text: metagenome


name: SAMIN0003777-ITS of red amaranth grown in chemical fertilizer amended Yamuna soil

text: public

tag: Namespace:Pooja Sharma, Daulat Ram College, University of Delhi

text: IBDC

characteristic: broker name

characteristic: common name

text: Red amaranth

characteristic: cultivar

text: Red Amaranth was grown in the Yamuna soil with addition of chemical fertilizer, DAP. Plantation was done in month of April and harvested in June.

text: Yes

text: India

text: plant metagenome

text: plant metagenome


name: SAMIN0003778-ITS of red amaranth grown in leaf waste compost amended Yamuna soil

characteristic: ENA-FIRST-PUBLIC

text: Pooja Sharma, Daulat Ram College, University of Delhi

text: public

text: IBDC

text: red amaranth

text: Red Amaranth was grown in the Yamuna soil with addition of leaf waste compost. Plantation was done in month of April and harvested in June.

text: Yes

text: India

text: plant metagenome

text: plant metagenome

characteristic: title


name: SAMIN0003784-ITS of red amaranth grown in cow dung manure amended Normal soil

characteristic: External Id

characteristic: INSDC center name

text: public

text: IBDC

text: red amaranth

text: Red Amaranth was grown in the Normal soil with addition of cow dung manure. Plantation was done in month of April and harvested in June.

text: Yes

text: India

text: plant metagenome

text: plant metagenome


name: SAMIN0003785-ITS of red amaranth grown in kitchen waste compost amended Normal soil

characteristic: INSDC first public

text: public

characteristic: Submitter Id

text: IBDC

text: red amaranth

text: Red Amaranth was grown in the Normal soil with addition of kitchen waste compost. Plantation was done in month of April and harvested in June.

text: Yes

text: India

text: plant metagenome

text: plant metagenome


name: SAMIN0003782-ITS of red amaranth grown in chemical fertilizer amended Normal soil

text: public

text: IBDC

text: red amaranth

text: Red Amaranth was grown in the Normal soil with addition of chemical fertilizer. Plantation was done in month of April and harvested in June.

characteristic: description

text: Yes

text: India

characteristic: geographic location (country and/or sea)

text: plant metagenome

text: plant metagenome


name: SAMIN0003783-ITS of red amaranth grown in leaf waste compost amended Normal soil

characteristic: ENA-CHECKLIST

text: public

text: IBDC

text: red amaranth

text: Red Amaranth was grown in the Normal soil with addition of leaf waste compost. Plantation was done in month of April and harvested in June.

text: Yes

text: India

text: plant metagenome

characteristic: organism

text: plant metagenome


name: SAMIN0003780-ITS of red amaranth grown in cow dung manure amended Yamuna soil

characteristic: ENA-LAST-UPDATE

characteristic: INSDC last update

text: public

text: IBDC

text: red amaranth

text: Red Amaranth was grown in the Yamuna soil with addition of Cow Dung manure. Plantation was done in month of April and harvested in June.

text: Yes

text: India

text: plant metagenome

text: plant metagenome


name: SAMIN0003781-ITS of red amaranth grown in vermicompost amended Yamuna soil

text: public

characteristic: INSDC status

characteristic: SRA accession

text: IBDC

text: red amaranth

text: Red Amaranth was grown in the Yamuna soil with addition of vermicompost. Plantation was done in month of April and harvested in June.

text: Yes

text: India

text: plant metagenome

text: plant metagenome


text: GSK

text: public

unit: year

characteristic: age

text: ArrayExpress

characteristic: broker name

text: T cell

text: not collected

characteristic: collection date

text: human

text: Protocols: The human biological samples in this study were sourced ethically and their research use was in accord with the terms of the informed consent under an IRB/EC approved protocol. Briefly, mononuclear cells from circulating blood were removed by apheresis. From these leukopaks, primary human CD4+ T cells were enriched using CliniMACS Prodigy setup and human CD4 MicroBeads (Miltenyi, 130-045-101). Following positive selection, cells were aliquoted and cryopreserved. The screen dataset contains two different scRNAseq runs: the first one (8 channels of a 10X Genomics chip B) was performed with fresh cells at the end of the CRISPRi experiment, 10 days post gRNA library transduction; the second one (32 channels across four 10XGenomics chips B) was performed using cells from the same experiment that were cryopreserved 10 days after gRNA transduction and thawed in puromycin-containing media (2 ug/ml) three days before the 10X Genomics run. To remove dead cells and debris, the cell suspension was treated with Lymphoprep (Axis-Shield, 12HHS09) the day before loading the cells into the 10X Chromium Controller. Primary CD4+ T cell vials were thawed at the time of the experiments and cells cultured in RPMI 1640 (Gibco, 11340892) supplemented with 10% heat-inactivated FBS, 1x Glutamax (Thermo Fisher Scientific, 35050061), 1mM Sodium Pyruvate (Thermo Fisher Scientific, 11360088), 5mM HEPES (Thermo Fisher Scientific, 15630080), 1x non-essential aminoacids (Thermo Fisher Scientific, 11140035), 1x Penicillin/streptomycin (Thermo Fisher Scientific, 15070063), 55 µM 2-mercaptoethanol (Thermo Fisher Scientific, 21985023), and 15 ng/mL of recombinant human interleukin 2 (IL-2) (Peprotech, 200-02). Cells were kept in a humidified 5% CO2 atmosphere at 37°C. Primary human CD4+ T cells expressing CBh-ZIM3-dCas9-Bsd were activated with Dynabeads Human T-Activator CD3/CD28 (Thermo Fisher Scientific, 11131D) at 1:1 cell:bead ratio and, 16-20h later, two million cells were transduced with the pooled CRISPRi CROPseq gRNA library at a <0.3 MOI. The transduction was performed in growth media supplemented with 5mM of HEPES (Thermo Fisher Scientific, 15630080) and spinoculation was carried out at 800 x g for 1h at 37˚C. 48h later, cells were selected with 2 ug/mL puromycin for 4 days, and selection was verified by ZsGreen expression in >95% of the cells by flow cytometry (Cytoflex S, Beckman Coulter). Cells were cultured in growth media for an additional 6 days before processing them for scRNA-seq. 10x Genomics Chromium Single Cell 3' Reagent Kit (v3 chemistry) 3’ gene expression libraries (v3) were prepared following manufacturer’s instructions (10X Genomics, PN-1000075). gRNA amplicon libraries were generated from amplified cDNA following the protocol described in (Alda-Catalinas et al. 2021).

text: adult

characteristic: developmental stage

text: normal

characteristic: disease

characteristic: experiment

text: CRISPR RNAi pool with 4 gRNAs

characteristic: genotype

text: not collected

characteristic: individual

text: not applicable

characteristic: isolate

text: Homo sapiens

text: Homo sapiens

text: blood

characteristic: organism part

text: Homo sapiens

text: male

characteristic: sex


name: SAMIN0003779-ITS of red amaranth grown in municipal waste compost amended Yamuna soil

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC first public

text: public

characteristic: Submitter Id

text: IBDC

characteristic: common name

text: red amaranth

characteristic: cultivar

text: Red Amaranth was grown in the Yamuna soil with addition of municipal waste compost. Plantation was done in month of April and harvested in June.

characteristic: description

text: Yes

text: India

characteristic: geographic location (country and/or sea)

text: plant metagenome

text: plant metagenome

characteristic: title


characteristic: ENA-LAST-UPDATE

text: LECA

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: age

text: ArrayExpress

characteristic: broker name

text: not collected

characteristic: collection date

text: yellow fever mosquito

text: Protocols: For each line, four RNA-seq libraries were prepared from four batches of 25 calibrated three-day-old non-blood-fed females not exposed to insecticide. Total RNA was extracted using TRIzol® (Thermo Fisher Scientific) following manufacturer's instructions. RNA samples were then treated with RNase-free DNase set (Qiagen) to remove gDNA contamination, purified on RNeasy mini columns (Qiagen) and QC checked using Qubit (Thermo Fisher Scientific) and bioanalyzer (Agilent). RNA-seq libraries were prepared from 500 ng total RNA using the NEBNext® Ultra™ II directional RNA library Prep Kit for Illumina (New England Biolabs) following manufacturer's instructions. Briefly, mRNAs were captured using oligodT magnetic beads and fragmented before being reverse transcribed using random primers. Double-stranded cDNAs were synthesised, end-repaired, and adaptors were incorporated at both ends. Libraries were then amplified by PCR for 10 cycles and purified before QC check using Qubit and Bioanalyzer.

text: adult

characteristic: developmental stage

text: lab strain

text: not collected

text: pool of 25 individuals

text: not applicable

text: Aedes aegypti

characteristic: organism

text: Aedes aegypti

text: whole organism

text: deltamethrin sensitive

characteristic: phenotype

text: Aedes aegypti

text: female

text: Bora

characteristic: strain

text: BORA


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: External Id

text: LECA

characteristic: INSDC center name

characteristic: INSDC first public

text: public

characteristic: Submitter Id

text: ArrayExpress

text: not collected

text: yellow fever mosquito

text: adult

text: isofemale line

characteristic: genotype

text: not collected

text: pool of 25 individuals

characteristic: individual

text: not applicable

characteristic: isolate

text: Aedes aegypti

text: Aedes aegypti

text: whole organism

characteristic: organism part

text: deltamethrin resistant

text: Aedes aegypti

text: female

characteristic: sex


characteristic: ENA-LAST-UPDATE

text: LECA

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: age

text: ArrayExpress

characteristic: broker name

text: not collected

text: yellow fever mosquito

characteristic: common name

characteristic: description

text: adult

text: subline derived from IR03, free from kdr1534 mutation

text: not collected

characteristic: geographic location (country and/or sea)

text: pool of 25 individuals

text: not applicable

text: Aedes aegypti

text: Aedes aegypti

text: whole organism

text: deltamethrin resistant

text: Aedes aegypti

text: female

text: subline derived from IR03

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: External Id

text: LECA

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: ArrayExpress

text: not collected

characteristic: collection date

text: yellow fever mosquito

text: adult

characteristic: developmental stage

text: isofemale line

text: not collected

text: pool of 25 individuals

text: not applicable

text: Aedes aegypti

characteristic: organism

text: Aedes aegypti

text: whole organism

text: weak deltamethrin resistance

characteristic: phenotype

text: Aedes aegypti

text: female

characteristic: strain


characteristic: ENA-LAST-UPDATE

text: Genomix4Life s.r.l.

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

tag: Namespace:Genomix4Life s.r.l.

characteristic: Submitter Id

text: ArrayExpress

text: not collected

text: human

text: Protocols: Human midbrain samples were provided by the Parkinson's UK Brain Bank (Imperial College London, London, England). RNA was extracted starting from 5 µm FFPE slide-mounted sections using RecoverAll Total Nucleic Acid Isolation Protocol (ThermoFischer Scientific), according to the manufacturer’s instructions. The RNA was stored at -80° C until further processing. RNA sequencing and data analysis were performed by Genomix4Life Srl (Baronissi, Italy). The yield and quality of RNA were evaluated by Qubit fluorometer (Thermo Fisher Scientific), and TapeStation 4200 (Agilent Technologies 5301 Stevens Creek Blvd Santa Clara, CA USA), respectively. Indexed libraries were prepared from 50ng/ea purified RNA with Illumina Stranded Total RNA with Ribo-Zero Plus (Illumina) Kit according to the manufacturer’s instructions. For library quantifications, TapeStation 4200 (Agilent Technologies) and Qubit (Thermo Fischer) was used. Indexed libraries were pooled in equimolar amounts with a final concentration of 2 nM.

text: normal

characteristic: disease

text: not collected

text: not applicable

characteristic: isolate

text: Homo sapiens

text: Homo sapiens

text: midbrain

characteristic: organism part

text: Homo sapiens


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: Genomix4Life s.r.l.

text: public

text: ArrayExpress

characteristic: broker name

text: not collected

text: human

characteristic: common name

characteristic: description

text: Parkinson disease

text: not collected

characteristic: geographic location (country and/or sea)

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: midbrain

text: Homo sapiens

characteristic: title


characteristic: External Id

text: Earth Hologenome Iniatiative

characteristic: INSDC center name

characteristic: INSDC first public

text: public

tag: Namespace:Earth Hologenome Iniatiative

text: laboratory

characteristic: broad-scale environmental context

characteristic: collection date

text: faeces

characteristic: environmental medium

text: Spain

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: laboratory

characteristic: local environmental context

text: mouse gut metagenome

characteristic: organism

characteristic: project name

text: mouse gut metagenome


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: JIC

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: Coccomyxa viridis isolated from a thallus of Xanthoria parietina

text: United Kingdom

text: Xanthoria parietina

characteristic: host scientific name

text: Coccomyxa viridis

text: Coccomyxa viridis

text: Coccomyxa viridis


characteristic: External Id

text: John Innes Centre

characteristic: INSDC center name

characteristic: INSDC first public

text: public

tag: Namespace:John Innes Centre

text: rape

characteristic: common name

text: Semi winter oilseed rape Ningyou1, is responsive to Necrosis and Ethylene-inducing peptide 1-like proteins (NLPs)

characteristic: description

text: United Kingdom

characteristic: geographic location (country and/or sea)

text: Brassica napus

text: Brassica napus

characteristic: title

characteristic: variety


text: John Innes Centre

text: public

characteristic: collection date

text: rape

text: Semi winter oilseed rape Ningyou7, is non-responsive to Necrosis and Ethylene-inducing peptide 1-like proteins (NLPs)

text: United Kingdom

text: Brassica napus

characteristic: organism

text: Brassica napus


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: John Innes Centre

text: public

text: rape

text: Semi winter oilseed rape, cross between Ningyou1 and Ningyou7; pool1 is non-responsive to NLP

text: United Kingdom

text: Brassica napus

text: Brassica napus

text: F2-cross between Ningyou1 and Ningyou7


characteristic: ENA-LAST-UPDATE

text: John Innes Centre

characteristic: INSDC last update

text: public

text: rape

text: Semi winter oilseed rape, cross between Ningyou1 and Ningyou7; pool2 is non-responsive to NLP

text: United Kingdom

text: Brassica napus

text: Brassica napus

text: F2-cross between Ningyou1 and Ningyou7


text: John Innes Centre

text: public

characteristic: INSDC status

characteristic: SRA accession

text: rape

text: Semi winter oilseed rape, cross between Ningyou1 and Ningyou7; pool3 is responsive to NLP

text: United Kingdom

text: Brassica napus

text: Brassica napus

text: F2-cross between Ningyou1 and Ningyou7


text: John Innes Centre

text: public

characteristic: Submitter Id

text: rape

text: Semi winter oilseed rape, cross between Ningyou1 and Ningyou7; pool4 is responsive to NLP

text: United Kingdom

text: Brassica napus

text: Brassica napus

text: F2-cross between Ningyou1 and Ningyou7


characteristic: External Id

text: UNIVERSITE DE LIMOGES

text: public

tag: Namespace:UNIVERSITE DE LIMOGES

text: house mouse

text: Chromatin Accessibility in WT1 R

text: France

text: Mus musculus

text: Mus musculus


text: UNIVERSITE DE LIMOGES

characteristic: INSDC center name

text: public

text: house mouse

text: Chromatin Accessibility in WT2 R

text: France

text: Mus musculus

text: Mus musculus


text: UNIVERSITE DE LIMOGES

characteristic: INSDC first public

text: public

text: house mouse

text: Chromatin Accessibility in 3RRKO1 R

text: France

text: Mus musculus

text: Mus musculus


text: UNIVERSITE DE LIMOGES

text: public

text: house mouse

characteristic: common name

text: Chromatin Accessibility in 3RRKO2 R

text: France

text: Mus musculus

text: Mus musculus


text: UNIVERSITE DE LIMOGES

text: public

text: house mouse

text: Chromatin Accessibility in c3RR1 R

characteristic: description

text: France

text: Mus musculus

text: Mus musculus


text: UNIVERSITE DE LIMOGES

text: public

text: house mouse

text: Chromatin Accessibility in c3RR2 R

text: France

characteristic: geographic location (country and/or sea)

text: Mus musculus

text: Mus musculus


text: UNIVERSITE DE LIMOGES

text: public

text: house mouse

text: Chromatin Accessibility in WT1 LPS

text: France

text: Mus musculus

text: Mus musculus

characteristic: title


text: UNIVERSITE DE LIMOGES

text: public

text: house mouse

text: Chromatin Accessibility in WT2 LPS

text: France

text: Mus musculus

text: Mus musculus


text: UNIVERSITE DE LIMOGES

text: public

text: house mouse

text: Chromatin Accessibility in 3RRKO1 LPS

text: France

text: Mus musculus

text: Mus musculus


text: UNIVERSITE DE LIMOGES

text: public

text: house mouse

text: Chromatin Accessibility in c3RR1 LPS

text: France

text: Mus musculus

text: Mus musculus


text: UNIVERSITE DE LIMOGES

text: public

text: house mouse

text: Chromatin Accessibility in c3RR2 LPS

text: France

text: Mus musculus

text: Mus musculus


text: ETH Zurich

text: public

tag: Namespace:ETH Zurich

text: Tetraploid generated from a cross between neo-4X and TBG, genotyped for ACA8 (DDDD) AGC1.5 (DDDD). T refers to derived tetraploid alleles and D refers to ancestral diploid allele.

text: not applicable

text: not collected

characteristic: geographic location (latitude)

text: not collected

characteristic: geographic location (longitude)

text: in vitro pollen germination

characteristic: isolation and growth condition

text: Arabidopsis arenosa

text: flowering stage (PO:0007616)

characteristic: plant developmental stage

text: 50% soil, 50% sand

characteristic: plant growth medium

text: pollen tube cell (PO:0025195)

characteristic: plant structure

text: tetraploid

characteristic: ploidy

text: Arabidopsis arenosa


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: ETH Zurich

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: collection date

text: Tetraploid generated from a cross between neo-4X and TBG, genotyped for ACA8 (TTTT) AGC1.5 (TTTT). T refers to derived tetraploid alleles and D refers to ancestral diploid allele.

text: not applicable

text: not collected

text: not collected

text: in vitro pollen germination

text: Arabidopsis arenosa

characteristic: organism

text: flowering stage (PO:0007616)

text: 50% soil, 50% sand

text: pollen tube cell (PO:0025195)

text: tetraploid

text: Arabidopsis arenosa


characteristic: External Id

text: ETH Zurich

characteristic: INSDC center name

characteristic: INSDC first public

text: public

characteristic: SRA accession

characteristic: Submitter Id

text: Tetraploid generated from a cross between neo-4X and TBG, genotyped for ACA8 (DDDD) AGC1.5 (TTTT). T refers to derived tetraploid alleles and D refers to ancestral diploid allele.

characteristic: description

text: not applicable

text: not collected

text: not collected

text: in vitro pollen germination

text: Arabidopsis arenosa

text: flowering stage (PO:0007616)

text: 50% soil, 50% sand

text: pollen tube cell (PO:0025195)

text: tetraploid

text: Arabidopsis arenosa


text: ETH Zurich

text: public

text: Tetraploid generated from a cross between neo-4X and TBG, genotyped for ACA8 (TTTT) AGC1.5 (DDDD). T refers to derived tetraploid alleles and D refers to ancestral diploid allele.

text: not applicable

characteristic: geographic location (country and/or sea)

text: not collected

characteristic: geographic location (latitude)

text: not collected

characteristic: geographic location (longitude)

text: in vitro pollen germination

characteristic: isolation and growth condition

text: Arabidopsis arenosa

text: flowering stage (PO:0007616)

characteristic: plant developmental stage

text: 50% soil, 50% sand

text: pollen tube cell (PO:0025195)

text: tetraploid

text: Arabidopsis arenosa

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: ETH Zurich

text: public

text: SNO

text: Slovakia

text: in vitro pollen germination

text: Arabidopsis arenosa

text: flowering stage (PO:0007616)

text: 50% soil, 50% sand

characteristic: plant growth medium

text: pollen tube cell (PO:0025195)

characteristic: plant structure

text: diploid

characteristic: ploidy

text: Arabidopsis arenosa


characteristic: External Id

text: ETH Zurich

characteristic: INSDC center name

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: collection date

text: TBG

text: Germany

text: in vitro pollen germination

text: Arabidopsis arenosa

characteristic: organism

text: flowering stage (PO:0007616)

text: 50% soil, 50% sand

text: pollen tube cell (PO:0025195)

text: autotetraploid

text: Arabidopsis arenosa


text: ETH Zurich

characteristic: INSDC first public

text: public

characteristic: SRA accession

characteristic: Submitter Id

text: second generation neotetraploid (F1 of Neo-4X x Neo-4X, where Neo-4X are colchicine-treated SNO diploids).

characteristic: description

text: not applicable

characteristic: geographic location (country and/or sea)

text: not collected

characteristic: geographic location (latitude)

text: not collected

text: in vitro pollen germination

text: Arabidopsis arenosa

text: flowering stage (PO:0007616)

text: 50% soil, 50% sand

text: pollen tube cell (PO:0025195)

text: tetraploid

text: Arabidopsis arenosa


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: ETH Zurich

text: public

text: second generation neotetraploid (F1 of Neo-4X x Neo-4X, where Neo-4X are colchicine-treated SNO diploids). T refers to derived tetraploid alleles and D refers to ancestral diploid allele.

text: not applicable

text: not collected

text: not collected

characteristic: geographic location (longitude)

text: in vitro pollen germination

characteristic: isolation and growth condition

text: Arabidopsis arenosa

text: flowering stage (PO:0007616)

characteristic: plant developmental stage

text: 50% soil, 50% sand

text: pollen tube cell (PO:0025195)

text: tetraploid

text: Arabidopsis arenosa

characteristic: title


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Guinet Benjamin

characteristic: INSDC center name

text: public

tag: Namespace:Guinet Benjamin

text: N.E. Beckage,L M.Riddiford

text: Filamentous Virus isolated from Cotesia congregata subspecies specialized on Manduca sexta

text: USA

text: Cotesia congregata filamentous virus 1

text: Cotesia congregata filamentous virus 1

text: Cotesia congregata Filamentous Virus


text: Anopheles gambiae

tag: attribute

characteristic: ArrayExpress-SPECIES

text: SC

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: not provided

characteristic: collection date

text: African malaria mosquito

characteristic: common name

text: not provided

text: Anopheles gambiae

text: Anopheles gambiae


text: University of Oulu

characteristic: INSDC first public

text: public

characteristic: SRA accession

tag: Namespace:University of Oulu

characteristic: Submitter Id

text: boreal forest

characteristic: broad-scale environmental context

unit: m

characteristic: depth

text: Area A surface water (round 2) DNA-derived 16S rRNA amplicon sequencing library

characteristic: description

text: surface water

characteristic: environmental medium

text: Finland

text: river

characteristic: local environmental context

text: uncultured bacterium

characteristic: organism

text: Assessing the influence of surface water intrusion on shallow groundwater wells using water quality measurements, stable water isotopes, and microbial community analysis

characteristic: project name

text: uncultured bacterium


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: University of Oulu

text: public

text: boreal forest

text: Area C surface water (round 2) DNA-derived 16S rRNA amplicon sequencing library

text: surface water

text: Finland

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: lake

text: uncultured bacterium

text: uncultured bacterium

characteristic: title


text: University of Oulu

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: boreal forest

characteristic: collection date

text: Area B surface water (round 2) DNA-derived 16S rRNA amplicon sequencing library

text: surface water

text: Finland

text: gravel pit pond

text: uncultured bacterium

text: uncultured bacterium


text: University of Oulu

text: public

characteristic: Submitter Id

text: boreal forest

characteristic: broad-scale environmental context

characteristic: depth

text: Area B comparison well (round 2) DNA-derived 16S rRNA amplicon sequencing library

characteristic: description

text: groundwater

characteristic: environmental medium

text: Finland

text: groundwater well

characteristic: local environmental context

text: uncultured bacterium

text: uncultured bacterium


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: University of Oulu

text: public

text: boreal forest

text: Area C comparison well (round 2) DNA-derived 16S rRNA amplicon sequencing library

text: groundwater

text: Finland

text: groundwater well

text: uncultured bacterium

characteristic: organism

characteristic: project name

text: uncultured bacterium


text: University of Oulu

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: boreal forest

text: Area C study well (round 2) DNA-derived 16S rRNA amplicon sequencing library

text: groundwater

text: Finland

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: groundwater well

text: uncultured bacterium

text: uncultured bacterium

characteristic: title


text: University of Oulu

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: boreal forest

characteristic: broad-scale environmental context

characteristic: collection date

text: Area A surface water (round 3) DNA-derived 16S rRNA amplicon sequencing library

text: surface water

text: Finland

text: river

text: uncultured bacterium

text: uncultured bacterium


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: University of Oulu

text: public

text: boreal forest

characteristic: depth

text: Area C surface water (round 3) DNA-derived 16S rRNA amplicon sequencing library

characteristic: description

text: surface water

characteristic: environmental medium

text: Finland

text: lake

characteristic: local environmental context

text: uncultured bacterium

text: uncultured bacterium


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: University of Oulu

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: boreal forest

text: Area B surface water (round 3) DNA-derived 16S rRNA amplicon sequencing library

text: surface water

text: Finland

text: gravel pit pond

text: uncultured bacterium

characteristic: organism

characteristic: project name

text: uncultured bacterium


text: University of Oulu

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: boreal forest

text: Area B study well (round 3) DNA-derived 16S rRNA amplicon sequencing library

text: groundwater

text: Finland

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: groundwater well

text: uncultured bacterium

text: uncultured bacterium

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: University of Oulu

text: public

characteristic: SRA accession

characteristic: Submitter Id

text: boreal forest

characteristic: broad-scale environmental context

characteristic: collection date

text: Area C comparison well (round 3) DNA-derived 16S rRNA amplicon sequencing library

text: groundwater

text: Finland

text: groundwater well

text: uncultured bacterium

text: uncultured bacterium


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: University of Oulu

text: public

text: boreal forest

characteristic: depth

text: Area A comparison well (round 3) DNA-derived 16S rRNA amplicon sequencing library

characteristic: description

text: groundwater

characteristic: environmental medium

text: Finland

text: groundwater well

characteristic: local environmental context

text: uncultured bacterium

text: uncultured bacterium


text: University of Oulu

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: boreal forest

text: Area A surface water (round 4) DNA-derived 16S rRNA amplicon sequencing library

text: surface water

text: Finland

text: river

text: uncultured bacterium

characteristic: organism

characteristic: project name

text: uncultured bacterium


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: University of Oulu

text: public

text: boreal forest

text: Area C surface water (round 4) DNA-derived 16S rRNA amplicon sequencing library

text: surface water

text: Finland

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: lake

text: uncultured bacterium

text: uncultured bacterium

characteristic: title


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: University of Oulu

text: public

characteristic: SRA accession

characteristic: Submitter Id

text: boreal forest

characteristic: broad-scale environmental context

characteristic: collection date

text: Area B surface water (round 4) DNA-derived 16S rRNA amplicon sequencing library

text: surface water

text: Finland

text: gravel pit pond

text: uncultured bacterium

text: uncultured bacterium


text: University of Oulu

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: boreal forest

characteristic: depth

text: Area B comparison well (round 4) DNA-derived 16S rRNA amplicon sequencing library

characteristic: description

text: groundwater

characteristic: environmental medium

text: Finland

text: groundwater well

characteristic: local environmental context

text: uncultured bacterium

text: uncultured bacterium


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: University of Oulu

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: boreal forest

text: Area B study well (round 4) DNA-derived 16S rRNA amplicon sequencing library

text: groundwater

text: Finland

text: groundwater well

text: uncultured bacterium

characteristic: organism

characteristic: project name

text: uncultured bacterium


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: University of Oulu

text: public

text: boreal forest

text: Area A study well (round 4) DNA-derived 16S rRNA amplicon sequencing library

text: groundwater

text: Finland

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: groundwater well

text: uncultured bacterium

text: Assessing the influence of surface water intrusion on shallow groundwater wells using water quality measurements, stable water isotopes, and microbial community analysis

text: uncultured bacterium

characteristic: title


text: University of Oulu

characteristic: INSDC center name

characteristic: INSDC first public

text: public

characteristic: SRA accession

characteristic: Submitter Id

text: boreal forest

characteristic: broad-scale environmental context

characteristic: collection date

text: Area C comparison well (round 4) DNA-derived 16S rRNA amplicon sequencing library

text: groundwater

text: Finland

text: groundwater well

text: uncultured bacterium

text: uncultured bacterium