text: University of Antwerp, Belgium

text: public

tag: Namespace:University of Antwerp, Belgium

characteristic: Submitter Id

characteristic: collection date

text: Finland

characteristic: geographic location (country and/or sea)

text: not provided

characteristic: host health state

text: house sparrow

characteristic: host scientific name

characteristic: isolate

text: feces

characteristic: isolation source

text: Helicobacter sp. 'CLO3_human'

text: Helicobacter sp. 'CLO3_human'

text: Helicobacter sp.


status: PUBLIC

tag: attribute

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: University of Antwerp, Belgium

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: Finland

text: not provided

text: house sparrow

text: feces

text: Helicobacter sp. 'house sparrow 1'

characteristic: organism

text: Helicobacter sp. 'house sparrow 1'

text: Helicobacter sp.

characteristic: title


text: University of Antwerp, Belgium

text: public

characteristic: Submitter Id

characteristic: collection date

text: Finland

text: not provided

text: human

text: feces

text: Helicobacter sp. 'CLO3_human'

text: Helicobacter sp. 'CLO3_human'

text: Helicobacter species


text: Mycobacterium abscessus

characteristic: ArrayExpress-SPECIES

text: SC

text: public

text: Mycobacterium abscessus

characteristic: common name

text: Mycobacterium abscessus

text: Mycobacterium abscessus

characteristic: subject id


Mouse Escherichia coli 11

text: INSTITUT PASTEUR

text: public

text: Mouse Escherichia coli 11

tag: Namespace:INSTITUT PASTEUR

text: Strain of Escherichia coli isolated from mouse feces

characteristic: description

text: Escherichia coli

text: Escherichia coli

characteristic: strain


Plasmid of strain MEc11

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: INSTITUT PASTEUR

text: public

text: Plasmid of strain MEc11

text: Plasmid from the Escherichia coli strain MEc1

text: Escherichia coli

text: Escherichia coli


E-MTAB-5847:Sample 1

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: IST Austria

text: public

text: E-MTAB-5847:Sample 1

tag: Namespace:IST Austria

unit: day

characteristic: age

text: ArrayExpress

characteristic: broker name

text: Indianmeal moth

text: Protocols: Wild P. interpunctella were caught in Vienna, Austria in the summer of 2015 and kept on a diet of mixed nuts at 21-22°C on a 10:14 hours light:dark cycle. RNA extractions were performed using the Qiagen RNeasy kit (QIAGEN, Hilden, Germany) according to the manufacturer's instructions. Library preparation and sequencing were performed by the VBCF NGS Unit (www.vbcf.ac.at, Vienna, Austria).

text: adult

characteristic: developmental stage

text: Plodia interpunctella

text: Plodia interpunctella

text: head

characteristic: organism part

text: Plodia interpunctella

text: female

characteristic: sex

text: Sample 1

type: has member


E-MTAB-5847:Sample 10

text: IST Austria

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-5847:Sample 10

text: ArrayExpress

text: Indianmeal moth

text: adult

text: Plodia interpunctella

characteristic: organism

text: Plodia interpunctella

text: thoracic segment of trunk

text: Plodia interpunctella

text: female

text: Sample 10

characteristic: title


E-MTAB-5847:Sample 11

text: IST Austria

text: public

text: E-MTAB-5847:Sample 11

characteristic: Submitter Id

text: ArrayExpress

text: Indianmeal moth

characteristic: common name

characteristic: description

text: adult

text: Plodia interpunctella

text: Plodia interpunctella

text: thoracic segment of trunk

text: Plodia interpunctella

text: male

text: Sample 11


E-MTAB-5847:Sample 12

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: IST Austria

text: public

text: E-MTAB-5847:Sample 12

text: ArrayExpress

text: Indianmeal moth

text: adult

text: Plodia interpunctella

text: Plodia interpunctella

text: thoracic segment of trunk

text: Plodia interpunctella

text: male

text: Sample 12


E-MTAB-5847:Sample 13

characteristic: External Id

text: IST Austria

text: public

text: E-MTAB-5847:Sample 13

text: 21 to 29

characteristic: age

text: ArrayExpress

characteristic: broker name

text: Indianmeal moth

text: fifth instar larvae

text: Plodia interpunctella

text: Plodia interpunctella

text: head

text: Plodia interpunctella

text: female

text: Sample 13


E-MTAB-5847:Sample 14

text: IST Austria

text: public

text: E-MTAB-5847:Sample 14

text: 21 to 29

text: ArrayExpress

text: Indianmeal moth

text: fifth instar larvae

characteristic: developmental stage

text: Plodia interpunctella

text: Plodia interpunctella

text: head

characteristic: organism part

text: Plodia interpunctella

text: female

characteristic: sex

text: Sample 14


E-MTAB-5847:Sample 15

text: IST Austria

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: E-MTAB-5847:Sample 15

text: 21 to 29

text: ArrayExpress

text: Indianmeal moth

text: fifth instar larvae

text: Plodia interpunctella

text: Plodia interpunctella

text: head

text: Plodia interpunctella

text: male

text: Sample 15


E-MTAB-5847:Sample 16

text: IST Austria

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-5847:Sample 16

text: 21 to 29

text: ArrayExpress

text: Indianmeal moth

text: fifth instar larvae

text: Plodia interpunctella

characteristic: organism

text: Plodia interpunctella

text: head

text: Plodia interpunctella

text: male

text: Sample 16


E-MTAB-5847:Sample 2

text: IST Austria

text: public

text: E-MTAB-5847:Sample 2

characteristic: Submitter Id

text: ArrayExpress

text: Indianmeal moth

characteristic: common name

text: adult

text: Plodia interpunctella

text: Plodia interpunctella

text: head

text: Plodia interpunctella

text: female

text: Sample 2

characteristic: title


E-MTAB-5847:Sample 3

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: IST Austria

text: public

text: E-MTAB-5847:Sample 3

text: ArrayExpress

text: Indianmeal moth

characteristic: description

text: adult

text: Plodia interpunctella

text: Plodia interpunctella

text: head

text: Plodia interpunctella

text: male

text: Sample 3


E-MTAB-5847:Sample 4

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: IST Austria

text: public

text: E-MTAB-5847:Sample 4

characteristic: age

text: ArrayExpress

text: Indianmeal moth

text: adult

text: Plodia interpunctella

text: Plodia interpunctella

text: head

text: Plodia interpunctella

text: male

text: Sample 4


E-MTAB-5847:Sample 5

text: IST Austria

text: public

text: E-MTAB-5847:Sample 5

text: ArrayExpress

characteristic: broker name

text: Indianmeal moth

text: adult

characteristic: developmental stage

text: Plodia interpunctella

text: Plodia interpunctella

text: animal ovary

characteristic: organism part

text: Plodia interpunctella

text: female

text: Sample 5


E-MTAB-5847:Sample 6

text: IST Austria

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: E-MTAB-5847:Sample 6

text: ArrayExpress

text: Indianmeal moth

text: adult

text: Plodia interpunctella

text: Plodia interpunctella

text: animal ovary

text: Plodia interpunctella

text: female

characteristic: sex

text: Sample 6


E-MTAB-5847:Sample 7

text: IST Austria

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-5847:Sample 7

text: ArrayExpress

text: Indianmeal moth

text: adult

text: Plodia interpunctella

text: Plodia interpunctella

text: testis

text: Plodia interpunctella

text: male

text: Sample 7


E-MTAB-5847:Sample 8

text: IST Austria

text: public

text: E-MTAB-5847:Sample 8

characteristic: Submitter Id

text: ArrayExpress

text: Indianmeal moth

characteristic: common name

text: adult

text: Plodia interpunctella

characteristic: organism

text: Plodia interpunctella

text: testis

text: Plodia interpunctella

text: male

text: Sample 8


E-MTAB-5847:Sample 9

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: IST Austria

text: public

text: E-MTAB-5847:Sample 9

text: ArrayExpress

text: Indianmeal moth

text: adult

text: Plodia interpunctella

text: Plodia interpunctella

text: thoracic segment of trunk

text: Plodia interpunctella

text: female

text: Sample 9

characteristic: title


text: male

characteristic: ArrayExpress-SEX

text: Escherichia coli

characteristic: ArrayExpress-SPECIES

text: EAEC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: SC

text: public

text: Escherichia coli

text: Male

characteristic: gender

text: Escherichia coli

text: Escherichia coli


text: female

text: Escherichia coli

text: EAEC

text: SC

characteristic: INSDC center name

text: public

text: Escherichia coli

text: Female

text: Escherichia coli

text: Escherichia coli


text: female

text: Escherichia coli

text: ETEC

text: SC

characteristic: INSDC first public

text: public

text: Escherichia coli

text: Female

text: Escherichia coli

text: Escherichia coli


text: male

text: Escherichia coli

text: ETEC

text: SC

text: public

text: Escherichia coli

text: Male

text: Escherichia coli

text: Escherichia coli


text: female

text: Escherichia coli

text: EIEC

text: SC

text: public

text: Escherichia coli

text: Female

text: Escherichia coli

text: Escherichia coli


text: male

text: Escherichia coli

text: EIEC

text: SC

text: public

text: Escherichia coli

text: Male

text: Escherichia coli

text: Escherichia coli


text: male

text: Escherichia coli

text: EPEC

text: SC

text: public

text: Escherichia coli

text: Male

text: Escherichia coli

text: Escherichia coli


text: female

text: Escherichia coli

text: EPEC

text: SC

text: public

text: Escherichia coli

text: Female

text: Escherichia coli

text: Escherichia coli


text: female

text: Escherichia coli

text: STEC

text: SC

text: public

text: Escherichia coli

text: Female

text: Escherichia coli

text: Escherichia coli


text: male

text: Escherichia coli

text: STEC

text: SC

text: public

text: Escherichia coli

text: Male

text: Escherichia coli

text: Escherichia coli


text: male

characteristic: ArrayExpress-Sex

text: Escherichia coli

characteristic: ArrayExpress-Species

text: STEC

characteristic: ArrayExpress-StrainOrLine

text: SC

text: public

text: Escherichia coli

text: Escherichia coli

text: Escherichia coli

text: STEC

characteristic: strain


text: male

text: Salmonella enterica

text: SALMONELLA

text: SC

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: Salmonella enterica

text: Male

text: Salmonella enterica

text: Salmonella enterica


text: female

text: Salmonella enterica

text: SALMONELLA

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: SC

text: public

text: Salmonella enterica

characteristic: common name

text: Female

text: Salmonella enterica

characteristic: organism

text: Salmonella enterica


text: female

characteristic: ArrayExpress-SEX

text: Escherichia coli

characteristic: ArrayExpress-SPECIES

characteristic: ENA-LAST-UPDATE

text: SC

text: public

text: Escherichia coli

text: Female

text: Escherichia coli

text: Escherichia coli

characteristic: title


text: male

text: Escherichia coli

characteristic: External Id

text: SC

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: Escherichia coli

text: Male

characteristic: gender

text: Escherichia coli

text: Escherichia coli


text: male

text: Mus musculus

text: SC

text: public

text: house mouse

text: Male

text: Mus musculus

text: Mus musculus

characteristic: subject id


text: WEIZMANN INSTITUE OF SCIENCE

characteristic: INSDC last update

text: public

tag: Namespace:WEIZMANN INSTITUE OF SCIENCE

text: this mutant came from leave-one-out suppressor analysis.

characteristic: description

text: Escherichia coli BW25113

text: Escherichia coli BW25113

text: The genetic basis for the adaptation of E. coli to sugar synthesis from CO2


text: Strongyloides ratti

text: SC

text: public

characteristic: INSDC status

characteristic: SRA accession

text: Strongyloides ratti

text: Strongyloides ratti

text: Strongyloides ratti


characteristic: ENA-CHECKLIST

text: UNIVERSITY OF MANCHESTER

text: public

tag: Namespace:UNIVERSITY OF MANCHESTER

characteristic: Submitter Id

text: mutT deletant from the Keio collection (1 of 2)

text: Escherichia coli K-12

text: Escherichia coli K-12


characteristic: ENA-FIRST-PUBLIC

text: UNIVERSITY OF MANCHESTER

text: public

text: mutT deletant from the Keio collection (2 of 2)

text: Escherichia coli K-12

text: Escherichia coli K-12


Fungal gut microbiome

text: Institute of Clinical Molecular Biology

text: public

text: Fungal gut microbiome

tag: Namespace:Institute of Clinical Molecular Biology

text: house mouse

characteristic: common name

text: Sequenced ITS1 region of fungal rRNA isolated from fecal samples of WT C57BL6/J and KO NOD2 mice.

text: Germany

characteristic: geographic location (country and/or sea)

text: Schleswig Holstein, Kiel

characteristic: geographic location (region and locality)

text: Mus musculus

characteristic: organism

text: Mus musculus

text: Fungal gut microbiome of WT C57BL6/J and KO NOD2 mice.


text: Homo sapiens

characteristic: ArrayExpress-SPECIES

text: Human Cell line (HEK293)

characteristic: ENA-LAST-UPDATE

text: SC

text: public

text: human

text: Homo sapiens

text: Homo sapiens

characteristic: title


Porphyromonas sp. TG1

characteristic: External Id

text: University Medical Center Groningen

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: Porphyromonas sp. TG1

tag: Namespace:University Medical Center Groningen

characteristic: collection date

text: New Zealand

text: diseased

characteristic: host health state

text: Ovis aries

characteristic: host scientific name

characteristic: isolate

text: subgingival

characteristic: isolation source

text: Porphyromonas sp. TG1

text: Porphyromonas sp. TG1

text: Porphyromonas gingivalis-related species


text: blood

text: male

characteristic: ArrayExpress-SEX

text: Mus musculus

characteristic: ENA-CHECKLIST

text: SC

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: house mouse

text: Male

characteristic: gender

text: Mus musculus

text: Mus musculus

characteristic: subject id


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: UNIMIDIVET

text: public

text: house mouse

characteristic: common name

text: mice microbiome

characteristic: environment (biome)

text: digestive tract

characteristic: environment (feature)

text: feces

characteristic: environment (material)

text: Italy

characteristic: geographic location (country and/or sea)

text: 45.4642° N

unit: DD

characteristic: geographic location (latitude)

text: 9.1900° E

characteristic: geographic location (longitude)

text: host-associated

characteristic: host-associated environmental package

text: metagenome

characteristic: investigation type

text: Mus musculus

characteristic: organism

text: piano di sviluppo unimi

characteristic: project name

text: Mus musculus

text: ILLUMINA

characteristic: sequencing method

text: AgNP

characteristic: title


text: synthetic construct

characteristic: ArrayExpress-SPECIES

characteristic: ENA-CHECKLIST

characteristic: External Id

text: SC

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: synthetic construct

text: synthetic construct

text: synthetic construct


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: GSC

text: public

text: sample_BDQ_310806_Collozoum_PAC37_cDNA_Ovation

text: Collozoum sp. DDM-2005

text: Collozoum sp. DDM-2005


text: GSC

text: public

text: Eucyrtidium acuminatum

text: Eucyrtidium acuminatum


text: GSC

text: public

text: Phaeodaria sp. OSH121

text: Phaeodaria sp. OSH121


text: URMITE

text: public

text: Faecalitalea sp. Marseille-P3755

text: Faecalitalea sp. Marseille-P3755

characteristic: strain

text: Culturomics project


text: CHINESE ACADEMY OF SCIENCES

text: public

tag: Namespace:CHINESE ACADEMY OF SCIENCES

characteristic: collection date

text: cropland

characteristic: environment (biome)

text: long-term fertilization

characteristic: environment (feature)

text: soil

characteristic: environment (material)

text: China

characteristic: geographic location (country and/or sea)

unit: m

characteristic: geographic location (depth)

characteristic: geographic location (elevation)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: metagenome

characteristic: investigation type

text: soil metagenome

text: soil metagenome

text: soil

characteristic: soil environmental package

text: AOA and AOB community in Mengcheng


characteristic: ENA-CHECKLIST

characteristic: External Id

text: University Hospital Galway

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

tag: Namespace:University Hospital Galway

text: Ireland

text: Homo sapiens

characteristic: host scientific name

characteristic: isolate

text: Human

characteristic: isolation source

text: Shigella flexneri 2a

characteristic: organism

text: Shigella flexneri 2a

text: Shigella flexneri 2a

characteristic: serovar

characteristic: title


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: University Hospital Galway

text: public

characteristic: SRA accession

characteristic: Submitter Id

characteristic: collection date

text: Ireland

characteristic: geographic location (country and/or sea)

text: Homo sapiens

text: Human

text: Shigella flexneri

text: Shigella flexneri

text: Shigella flexneri


characteristic: ENA-CHECKLIST

characteristic: External Id

text: University Hospital Galway

text: public

text: Ireland

text: Homo sapiens

text: Human

text: Shigella sonnei

text: Shigella sonnei

text: Shigella sonnei


text: University Hospital Galway

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: Ireland

text: Homo sapiens

text: Human

text: Shigella flexneri 2b

text: Shigella flexneri 2b

text: Shigella flexneri 2b


text: University Hospital Galway

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: Ireland

text: Homo sapiens

text: Human

text: Shigella flexneri 1c

text: Shigella flexneri 1c

text: Shigella flexneri 1c


text: EMBL

text: public

text: ArrayExpress

characteristic: broker name

text: HeLa

characteristic: cell line

text: human

characteristic: common name

text: Protocols: HeLa cells were placed on ice, washed 3x in PBS, subjected to 254 nm UV-crosslinking (150 mJ/cm2), and lysed on the plate in lysis buffer (500mM NaCl, 50mM Tris-HCl pH 7.5, 8.5% glycerol, 1mM EDTA pH 8.0, 0.5% Triton X100, 2mM BME and complete EDTA free protease inhibitor (Roche)). Lysates were sonicated (Branson sonifier) and cleared by centrifugation at 16 000 x g for 10 min at 4C. Lysates were treated with RNase I (10ul 1:25 dilution/extracts from 8.0 x E6 cells; Ambion) to fragment RNA and turbo DNase (2ul/extracts from 8.0x E6 cells, Thermo) for 5minutes at 37C and 1200 rpm shaking. 125ul Dyna G magnetic beads were washed with lysis buffer 2x before coupling 10ug of anti-ZONAB (Bethyl Laboratories, #A303-070A) or total rabbit IgG (Sigma) rotating for 1 hour at 4C, and free antibody was removed by washing the beads 2x with lysis buffer after coupling. RNAse/DNase treated extracts were added to the bead/antibody mixture and the YBX3-RNA complexes were immunoprecipitated for 2 h, 4C with gentle rotation. Samples processed for all subsequent steps following supplementary protocol one described previously (Van Nostrand et al. 2016 PMID: 27018577). Standard eCLIP library preparation was done following supplementary protocol one described previously (Van Nostrand et al. 2016 PMID: 27018577). The SMI samples were amplified using 9 cycles while the IP samples were amplified using 18 cycles. The samples were multiplexed and sequenced on Illumina HiSeq2000 platform (125PE v4 chemistry).

characteristic: description

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens


text: EMBL

text: public

text: ArrayExpress

text: HeLa

text: human

text: Protocols: HeLa cells were placed on ice, washed 3x in PBS, subjected to 254 nm UV-crosslinking (150 mJ/cm2), and lysed on the plate in lysis buffer (500mM NaCl, 50mM Tris-HCl pH 7.5, 8.5% glycerol, 1mM EDTA pH 8.0, 0.5% Triton X100, 2mM BME and complete EDTA free protease inhibitor (Roche)). Lysates were sonicated (Branson sonifier) and cleared by centrifugation at 16 000 x g for 10 min at 4C. Lysates were treated with RNase I (10ul 1:25 dilution/extracts from 8.0 x E6 cells; Ambion) to fragment RNA and turbo DNase (2ul/extracts from 8.0x E6 cells, Thermo) for 5minutes at 37C and 1200 rpm shaking. Samples processed for all subsequent steps following supplementary protocol one described previously (Van Nostrand et al. 2016 PMID: 27018577). Standard eCLIP library preparation was done following supplementary protocol one described previously (Van Nostrand et al. 2016 PMID: 27018577). The SMI samples were amplified using 9 cycles while the IP samples were amplified using 18 cycles. The samples were multiplexed and sequenced on Illumina HiSeq2000 platform (125PE v4 chemistry).

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: Homo sapiens

characteristic: title


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: Discuva

text: public

text: gut metagenome

text: gut metagenome


text: gut metagenome

characteristic: ArrayExpress-SPECIES

text: SC

text: public

characteristic: SRA accession

characteristic: Submitter Id

text: gut metagenome

text: gut metagenome

text: gut metagenome

characteristic: subject id


characteristic: ENA-CHECKLIST

characteristic: External Id

text: WAGENINGEN UR

text: public

tag: Namespace:WAGENINGEN UR

text: western gorilla

text: Gorilla Y chromosome using whole-genome amplifcation, PacBio sequencing and Pacasus read correction

text: Gorilla gorilla

text: Gorilla gorilla

text: Gorilla Y chromosome


text: WAGENINGEN UR

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: thale cress

text: Arabidopsis thaliana

text: Arabidopsis thaliana

text: Arabidopsis thaliana WGA


text: WAGENINGEN UR

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: thale cress

text: Arabidopsis thaliana

text: Arabidopsis thaliana

text: Arabidopsis thaliana


Bacterial gut microbiome

text: Institute of Clinical Molecular Biology

text: public

text: Bacterial gut microbiome

text: house mouse

text: Sequenced 16S rRNA gene isolated from fecal samples of WT C57BL6/J and KO NOD2 mice.

text: Germany

characteristic: geographic location (country and/or sea)

text: Schleswig Holstein, Kiel

characteristic: geographic location (region and locality)

text: Mus musculus

text: Mus musculus

text: Bacterial gut microbiome of WT C57BL6/J and KO NOD2 mice.


text: Faculty of medecine and pharmacy RABAT

text: public

tag: Namespace:Faculty of medecine and pharmacy RABAT

characteristic: description

text: Acinetobacter johnsonii

text: Acinetobacter johnsonii


text: PHE

text: public

text: GAS outbreak paper

text: Streptococcus pyogenes

characteristic: organism

text: Streptococcus pyogenes


text: Mycoplasma gateae

text: SC

text: public

text: Mycoplasma gateae

characteristic: common name

text: Mycoplasma gateae

text: Mycoplasma gateae

characteristic: title


text: Moraxella atlantae

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: SC

text: public

text: Moraxella atlantae

text: Moraxella atlantae

text: Moraxella atlantae


text: Micrococcus luteus

characteristic: ArrayExpress-SPECIES

text: SC

text: public

characteristic: SRA accession

text: Micrococcus luteus

text: Micrococcus luteus

text: Micrococcus luteus


text: Campylobacter jejuni subsp. jejuni

text: SC

text: public

characteristic: Submitter Id

text: Campylobacter jejuni subsp. jejuni

text: Campylobacter jejuni subsp. jejuni

text: Campylobacter jejuni subsp. jejuni

characteristic: subject id


text: [Eubacterium] minutum

characteristic: ENA-CHECKLIST

characteristic: External Id

text: SC

text: public

text: [Eubacterium] minutum

text: [Eubacterium] minutum

text: [Eubacterium] minutum


text: Campylobacter coli

text: SC

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: Campylobacter coli

text: Campylobacter coli

text: Campylobacter coli


text: Mycoplasma cricetuli

text: SC

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: Mycoplasma cricetuli

text: Mycoplasma cricetuli

text: Mycoplasma cricetuli


text: Sphingobacterium thalpophilum

text: SC

text: public

text: Sphingobacterium thalpophilum

text: Sphingobacterium thalpophilum

text: Sphingobacterium thalpophilum


text: Pseudomonas luteola

text: SC

text: public

text: Pseudomonas luteola

text: Pseudomonas luteola

text: Pseudomonas luteola


text: Providencia alcalifaciens

text: SC

text: public

text: Providencia alcalifaciens

text: Providencia alcalifaciens

text: Providencia alcalifaciens


text: Pasteurella stomatis

text: SC

text: public

text: Pasteurella stomatis

text: Pasteurella stomatis

text: Pasteurella stomatis


text: Campylobacter upsaliensis

text: SC

text: public

text: Campylobacter upsaliensis

text: Campylobacter upsaliensis

text: Campylobacter upsaliensis


text: Pasteurella canis

text: SC

text: public

text: Pasteurella canis

text: Pasteurella canis

text: Pasteurella canis


text: UCSDMI

text: public

text: digester

text: TRUE

characteristic: elevation

text: urban biome

characteristic: env biome

text: research facility

characteristic: env feature

text: wastewater/sludge

characteristic: env package

text: anaerobic digester sludge

characteristic: host subject id

characteristic: latitude

characteristic: longitude

text: anaerobic digester metagenome

text: Cornell U

text: TRUE

characteristic: position

characteristic: reactor

text: anaerobic fermenter sludge

characteristic: sample type

text: anaerobic digester metagenome

text: ratio experiment


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: UCSDMI

text: public

characteristic: SRA accession

characteristic: Submitter Id

text: digester

characteristic: description

text: TRUE

text: urban biome

text: research facility

text: wastewater/sludge

text: organic material

text: anaerobic digester metagenome

characteristic: organism

text: Cornell U

text: TRUE

text: anaerobic fermenter sludge

text: anaerobic digester metagenome

text: ratio experiment

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: External Id

text: UCSDMI

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: digester

text: TRUE

characteristic: elevation

text: urban biome

text: research facility

text: wastewater/sludge

text: organic material

text: anaerobic digester metagenome

text: Cornell U

text: TRUE

text: anaerobic fermenter sludge

text: anaerobic digester metagenome

text: ratio experiment


text: IRD, Cirad, Univ. Montpellier, IPME

text: public

text: E-MTAB-5891:Control_Wheat_Leaves_Replicate1

tag: Namespace:IRD, Cirad, Univ. Montpellier, IPME

unit: month

characteristic: age

text: ArrayExpress

characteristic: broker name

text: bread wheat

characteristic: common name

text: Chinese Spring

characteristic: cultivar

text: Protocols: Bacterial strains and plant inoculation The X. translucens type strain CFBP 2054 was used in this study. Bacteria were cultivated at 28°C in Peptone sucrose agar (PSA) medium.. Triticum aestivum cv. Chinese Spring plants were maintained in a growth chamber with cycles of 12 h of light at 21°C and 50% relative humidity (RH) and 12 h of dark at 21°C and 50% RH. Leaves of 49 days-old plants were infiltrated with a bacterial suspension in water with an optical density at 600 nm (OD600) of 0.5 using a needleless syringe. Plants inoculated with water were used as controls. For transcriptomic and proteomic analyses, leaves and root tissues were harvested 1 day post-inoculation (dpi), when symptoms were not visible yet. The infiltrated zone was collected as previously described (Reimers et al., 1991). Three biological replicates per treatment were performed, and each with pooled leaves from two independent plants per replicate. Once pulverized in liquid nitrogen, each sample was split into two aliquots, for protein and RNA extraction respectively. RNA-seq transcriptome sequencing was performed on leaves and roots. Samples were ground to a fine powder in liquid nitrogen and total RNA was isolated (TRI Reagent® (MRC, Cincinnati, OH)) 25. Then, it was treated with DNase and RNA quality was confirmed with Experion™ Automated Electrophoresis System, Nanodrop™ and gel electrophoresis The preparation of mRNA libraries was done using the TrueSeq Stranded mRNA Sample Preparation kit (Illumina Inc., San Diego, CA). The library quality validation (concentration and length of DNA fragments) was performed by Fragment Analyzer using the standard and high sensitivity DNA kits (Agilent Technologies, Santa Clara, CA) and by qPCR (LightCycler 480; Roche Diagnostics, Meylan, France).

text: wild type genotype

characteristic: genotype

text: growth chamber study

characteristic: growth condition

text: Triticum aestivum

text: Triticum aestivum

text: leaf

characteristic: organism part

text: Triticum aestivum


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: IRD, Cirad, Univ. Montpellier, IPME

text: public

characteristic: SRA accession

text: E-MTAB-5891:Control_Wheat_Leaves_Replicate2

characteristic: Submitter Id

text: ArrayExpress

text: bread wheat

text: Chinese Spring

characteristic: description

text: wild type genotype

text: growth chamber study

text: Triticum aestivum

text: Triticum aestivum

text: leaf

text: Triticum aestivum


characteristic: ENA-CHECKLIST

characteristic: External Id

text: IRD, Cirad, Univ. Montpellier, IPME

characteristic: INSDC center name

text: public

text: E-MTAB-5891:Control_Wheat_Leaves_Replicate3

text: ArrayExpress

text: bread wheat

text: Chinese Spring

text: wild type genotype

text: growth chamber study

text: Triticum aestivum

characteristic: organism

text: Triticum aestivum

text: leaf

text: Triticum aestivum

characteristic: title


text: IRD, Cirad, Univ. Montpellier, IPME

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: E-MTAB-5891:Control_Wheat_Roots_Replicate1

characteristic: age

text: ArrayExpress

text: bread wheat

text: Chinese Spring

text: wild type genotype

text: growth chamber study

text: Triticum aestivum

text: Triticum aestivum

text: root

text: Triticum aestivum


text: IRD, Cirad, Univ. Montpellier, IPME

text: public

text: E-MTAB-5891:Control_Wheat_Roots_Replicate2

text: ArrayExpress

characteristic: broker name

text: bread wheat

characteristic: common name

text: Chinese Spring

characteristic: cultivar

text: wild type genotype

characteristic: genotype

text: growth chamber study

text: Triticum aestivum

text: Triticum aestivum

text: root

text: Triticum aestivum


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: IRD, Cirad, Univ. Montpellier, IPME

text: public

text: E-MTAB-5891:Control_Wheat_Roots_Replicate3

text: ArrayExpress

text: bread wheat

text: Chinese Spring

text: wild type genotype

text: growth chamber study

characteristic: growth condition

text: Triticum aestivum

text: Triticum aestivum

text: root

characteristic: organism part

text: Triticum aestivum


characteristic: ENA-CHECKLIST

text: IRD, Cirad, Univ. Montpellier, IPME

text: public

characteristic: SRA accession

characteristic: Submitter Id

text: ArrayExpress

text: bread wheat

text: Chinese Spring

characteristic: description

text: wild type genotype

text: growth chamber study

text: Triticum aestivum

text: Triticum aestivum

text: leaf

text: Triticum aestivum


characteristic: External Id

text: IRD, Cirad, Univ. Montpellier, IPME

characteristic: INSDC center name

text: public

text: ArrayExpress

text: bread wheat

text: Chinese Spring

text: wild type genotype

text: growth chamber study

text: Triticum aestivum

characteristic: organism

text: Triticum aestivum

text: root

text: Triticum aestivum

characteristic: title


text: UCSDMI

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: digester

text: TRUE

characteristic: elevation

characteristic: emp status

text: urban biome

characteristic: env biome

text: research facility

characteristic: env feature

text: wastewater/sludge

characteristic: env package

text: anaerobic digester sludge

characteristic: host subject id

characteristic: latitude

characteristic: longitude

text: anaerobic digester metagenome

text: Ithaca

text: TRUE

characteristic: reactor

text: sequenced

text: anaerobic fermenter sludge

characteristic: sample type

text: anaerobic digester metagenome

text: hydrogen experiment


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: UCSDMI

text: public

characteristic: SRA accession

characteristic: Submitter Id

text: digester

characteristic: description

text: TRUE

text: urban biome

text: research facility

text: wastewater/sludge

text: anaerobic digester sludge

text: anaerobic digester metagenome

text: Ithaca

text: TRUE

text: sequenced

text: anaerobic fermenter sludge

text: anaerobic digester metagenome

text: hydrogen experiment


text: WEIZMANN INSTITUE OF SCIENCE

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: This mutant came form the leave-one-out suppressor analysis.

text: Escherichia coli BW25113

characteristic: organism

text: Escherichia coli BW25113

text: The genetic basis for the adaptation of E.coli to sugar synthesis from CO2

characteristic: title


Leptidea Sinapis

text: Evolutionary Biology Centre

text: public

text: Leptidea Sinapis

tag: Namespace:Evolutionary Biology Centre

text: Leptidea Sinapis genome assembly, assembled using ALLPATHS-LG.

text: Leptidea sinapis

text: Leptidea sinapis

text: Genome assembly


text: EESC/USP

text: public

characteristic: collection date

text: strict methanogenic conditions

text: anaerobic reactor

characteristic: environment (biome)

text: biomass

characteristic: environment (feature)

text: granular biomass

characteristic: environment (material)

text: Brazil

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: metagenome

characteristic: investigation type

text: wastewater metagenome

text: Anaerobic biodegradation of phenol

characteristic: project name

text: wastewater metagenome

text: platform Illumina MiSeq 2 × 250 bp

characteristic: sequencing method

text: strict methanogenic conditions

text: wastewater/sludge

characteristic: wastewater/sludge environmental package


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: EESC/USP

characteristic: INSDC center name

text: public

characteristic: SRA accession

characteristic: Submitter Id

text: methanogenic and sulfidogenic conditions

characteristic: description

text: anaerobic reactor

text: biomass

text: granular biomass

text: Brazil

text: metagenome

text: wastewater metagenome

text: Anaerobic biodegradation of phenol

text: wastewater metagenome

text: platform Illumina MiSeq 2 × 250 bp

text: wastewater/sludge


text: WEIZMANN INSTITUE OF SCIENCE

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: Escherichia coli BW25113

characteristic: organism

text: Escherichia coli BW25113

characteristic: title


text: ROSWELL PARK CANCER INSTITUTE

text: public

tag: Namespace:ROSWELL PARK CANCER INSTITUTE

text: human

characteristic: common name

text: HEK-293T empty pcDNA 3.1+ vector transfectant, biological replicate 1

text: Homo sapiens

text: Homo sapiens


text: ROSWELL PARK CANCER INSTITUTE

text: public

text: human

text: HEK-293T empty pcDNA 3.1+ vector transfectant, biological replicate 3

text: Homo sapiens

text: Homo sapiens


text: ROSWELL PARK CANCER INSTITUTE

text: public

text: human

text: HEK-293T hAPOBEC3A transfectant, biological replicate 1

text: Homo sapiens

text: Homo sapiens


text: ROSWELL PARK CANCER INSTITUTE

text: public

text: human

text: HEK-293T hAPOBEC3A transfectant, biological replicate 2

text: Homo sapiens

text: Homo sapiens


text: ROSWELL PARK CANCER INSTITUTE

text: public

text: human

text: HEK-293T hAPOBEC3A transfectant, biological replicate 3

text: Homo sapiens

text: Homo sapiens


text: ROSWELL PARK CANCER INSTITUTE

text: public

text: human

text: HEK-293T hAPOBEC3C transfectant, biological replicate 1

text: Homo sapiens

text: Homo sapiens


text: ROSWELL PARK CANCER INSTITUTE

text: public

text: human

text: HEK-293T hAPOBEC3C transfectant, biological replicate 2

text: Homo sapiens

text: Homo sapiens


text: ROSWELL PARK CANCER INSTITUTE

text: public

text: human

text: HEK-293T hAPOBEC3C transfectant, biological replicate 3

text: Homo sapiens

text: Homo sapiens


text: ROSWELL PARK CANCER INSTITUTE

text: public

text: human

text: HEK-293T hAPOBEC3D transfectant, biological replicate 1

text: Homo sapiens

text: Homo sapiens


text: ROSWELL PARK CANCER INSTITUTE

text: public

text: human

text: HEK-293T hAPOBEC3D transfectant, biological replicate 2

text: Homo sapiens

text: Homo sapiens


text: ROSWELL PARK CANCER INSTITUTE

text: public

text: human

text: HEK-293T hAPOBEC3D transfectant, biological replicate 3

text: Homo sapiens

text: Homo sapiens


text: ROSWELL PARK CANCER INSTITUTE

text: public

text: human

text: HEK-293T hAPOBEC3F transfectant, biological replicate 1

text: Homo sapiens

text: Homo sapiens


text: ROSWELL PARK CANCER INSTITUTE

text: public

text: human

text: HEK-293T hAPOBEC3F transfectant, biological replicate 2

text: Homo sapiens

text: Homo sapiens


text: ROSWELL PARK CANCER INSTITUTE

text: public

text: human

text: HEK-293T hAPOBEC3F transfectant, biological replicate 3

text: Homo sapiens

text: Homo sapiens


text: ROSWELL PARK CANCER INSTITUTE

text: public

text: human

text: HEK-293T hAPOBEC3G transfectant, biological replicate 1

text: Homo sapiens

text: Homo sapiens


text: ROSWELL PARK CANCER INSTITUTE

text: public

text: human

text: HEK-293T hAPOBEC3G transfectant, biological replicate 2

text: Homo sapiens

text: Homo sapiens


text: ROSWELL PARK CANCER INSTITUTE

text: public

text: human

text: HEK-293T hAPOBEC3G transfectant, biological replicate 3

text: Homo sapiens

text: Homo sapiens


text: ROSWELL PARK CANCER INSTITUTE

text: public

text: human

text: HEK-293T hAPOBEC3H transfectant, biological replicate 1

text: Homo sapiens

text: Homo sapiens


text: ROSWELL PARK CANCER INSTITUTE

text: public

text: human

text: HEK-293T hAPOBEC3H transfectant, biological replicate 2

text: Homo sapiens

text: Homo sapiens


text: ROSWELL PARK CANCER INSTITUTE

text: public

text: human

text: HEK-293T hAPOBEC3H transfectant, biological replicate 3

text: Homo sapiens

text: Homo sapiens


text: ROSWELL PARK CANCER INSTITUTE

text: public

text: human

text: HEK-293T hAPOBEC3B transfectant, biological replicate 1

text: Homo sapiens

text: Homo sapiens


text: ROSWELL PARK CANCER INSTITUTE

text: public

text: human

text: HEK-293T hAPOBEC3B transfectant, biological replicate 2

text: Homo sapiens

text: Homo sapiens


text: ROSWELL PARK CANCER INSTITUTE

text: public

text: human

text: HEK-293T hAPOBEC3B transfectant, biological replicate 3

text: Homo sapiens

text: Homo sapiens


text: WEIZMANN INSTITUE OF SCIENCE

text: public

text: Escherichia coli BW25113

text: Escherichia coli BW25113

text: The genetic basis for the adaptation of E.coli to sugar synthesis from CO2


text: IRD, Cirad, Univ Montpellier, IPME

text: public

text: E-MTAB-5896:Wheat+Azospirillum_Leaves_Replicate1

tag: Namespace:IRD, Cirad, Univ Montpellier, IPME

characteristic: age

text: ArrayExpress

characteristic: broker name

text: bread wheat

text: Chinese Spring

characteristic: cultivar

text: Protocols: Plant material and plant inoculations. Seeds of Triticum aestivum cv Chinese Srping were disinfected by washing for 40 min in a sodium hypoclorite solution (Hurek et al., 1994) and pregerminated. Experiments were performed under glasshouse conditions under cycles of 12 h of light at 21°C and 50% relative humidity (RH) and 12 h of dark at 21°C and 50% RH. Plants were grown in pots in a 50/50 mix of sand and soil. After 50 days, two plants were pooled per replicate, with 3 biological replicates per treatment. Prior to RNA extraction, samples were removed from the −80°C freezer and ground to a fine powder with liquid nitrogen using a sterilized mortar and pestle. RNA-seq was performed on leaves and roots. Total RNA was isolated from roots and leaves with TRI Reagent® (MRC, Cincinnati, OH) (Chomczynski and Sacchi, 1987) , and after DNase treatment and confirmation of RNA integrity using a triple check, Nanodrop™, Experion™ Automated Electrophoresis System, and gel electrophoresis, the total RNA was used in mRNA preparation, fragmentation and cDNA synthesis. The preparation of mRNA libraries was done by TruSeq Stranded mRNA Sample (Illumina Preparation. The library quality validation (fragment concentration and length) was performed by Fragment Analyzer (kit High Sensitivity NGS and kit Standard sensitivity) and by qPCR (ROCHE Light Cycler 480).

text: wild type genotype

characteristic: genotype

text: green house study

characteristic: growth condition

text: Triticum aestivum

text: Triticum aestivum

text: leaf

characteristic: organism part

text: Triticum aestivum


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: IRD, Cirad, Univ Montpellier, IPME

text: public

text: E-MTAB-5896:Wheat+Azospirillum_Leaves_Replicate2

text: ArrayExpress

text: bread wheat

text: Chinese Spring

text: wild type genotype

text: green house study

text: Triticum aestivum

text: Triticum aestivum

text: leaf

text: Triticum aestivum


text: IRD, Cirad, Univ Montpellier, IPME

characteristic: INSDC center name

text: public

characteristic: SRA accession

text: E-MTAB-5896:Wheat+Azospirillum_Leaves_Replicate3

characteristic: Submitter Id

text: ArrayExpress

text: bread wheat

text: Chinese Spring

characteristic: description

text: wild type genotype

text: green house study

text: Triticum aestivum

text: Triticum aestivum

text: leaf

text: Triticum aestivum


text: IRD, Cirad, Univ Montpellier, IPME

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: E-MTAB-5896:Wheat+Azospirillum_Roots_Replicate1

text: ArrayExpress

text: bread wheat

text: Chinese Spring

text: wild type genotype

text: green house study

text: Triticum aestivum

characteristic: organism

text: Triticum aestivum

text: root

text: Triticum aestivum


text: IRD, Cirad, Univ Montpellier, IPME

text: public

text: E-MTAB-5896:Wheat+Azospirillum_Roots_Replicate2

characteristic: age

text: ArrayExpress

characteristic: broker name

text: bread wheat

characteristic: common name

text: Chinese Spring

text: wild type genotype

text: green house study

text: Triticum aestivum

text: Triticum aestivum

text: root

text: Triticum aestivum

characteristic: title


text: IRD, Cirad, Univ Montpellier, IPME

text: public

text: E-MTAB-5896:Wheat+Azospirillum_Roots_Replicate3

text: ArrayExpress

text: bread wheat

text: Chinese Spring

characteristic: cultivar

text: wild type genotype

characteristic: genotype

text: green house study

characteristic: growth condition

text: Triticum aestivum

text: Triticum aestivum

text: root

characteristic: organism part

text: Triticum aestivum


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: IRD, Cirad, Univ Montpellier, IPME

text: public

text: E-MTAB-5896:Wheat+Burkholderia_Leaves_Replicate1

text: ArrayExpress

text: bread wheat

text: Chinese Spring

text: wild type genotype

text: green house study

text: Triticum aestivum

text: Triticum aestivum

text: leaf

text: Triticum aestivum


text: IRD, Cirad, Univ Montpellier, IPME

characteristic: INSDC center name

text: public

characteristic: SRA accession

text: E-MTAB-5896:Wheat+Burkholderia_Leaves_Replicate2

characteristic: Submitter Id

text: ArrayExpress

text: bread wheat

text: Chinese Spring

characteristic: description

text: wild type genotype

text: green house study

text: Triticum aestivum

text: Triticum aestivum

text: leaf

text: Triticum aestivum


text: IRD, Cirad, Univ Montpellier, IPME

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: E-MTAB-5896:Wheat+Burkholderia_Leaves_Replicate3

text: ArrayExpress

text: bread wheat

text: Chinese Spring

text: wild type genotype

text: green house study

text: Triticum aestivum

characteristic: organism

text: Triticum aestivum

text: leaf

text: Triticum aestivum


text: IRD, Cirad, Univ Montpellier, IPME

text: public

text: E-MTAB-5896:Wheat+Burkholderia_Roots_Replicate1

characteristic: age

text: ArrayExpress

characteristic: broker name

text: bread wheat

characteristic: common name

text: Chinese Spring

text: wild type genotype

text: green house study

text: Triticum aestivum

text: Triticum aestivum

text: root

text: Triticum aestivum

characteristic: title


text: IRD, Cirad, Univ Montpellier, IPME

text: public

text: E-MTAB-5896:Wheat+Burkholderia_Roots_Replicate2

text: ArrayExpress

text: bread wheat

text: Chinese Spring

characteristic: cultivar

text: wild type genotype

characteristic: genotype

text: green house study

characteristic: growth condition

text: Triticum aestivum

text: Triticum aestivum

text: root

characteristic: organism part

text: Triticum aestivum


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: IRD, Cirad, Univ Montpellier, IPME

text: public

text: E-MTAB-5896:Wheat+Burkholderia_Roots_Replicate3

text: ArrayExpress

text: bread wheat

text: Chinese Spring

text: wild type genotype

text: green house study

text: Triticum aestivum

text: Triticum aestivum

text: root

text: Triticum aestivum


characteristic: INSDC center name

text: public

characteristic: SRA accession

tag: Namespace:Centrum Medyczne Ksztalcenia Podyplomowego

characteristic: Submitter Id

text: house mouse

text: sepsis

characteristic: description

text: lungs

characteristic: organ

text: Mus musculus

text: Mus musculus

characteristic: time


text: Centrum Medyczne Ksztalcenia Podyplomowego

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: house mouse

text: sepsis

text: lungs

text: Mus musculus

characteristic: organism

text: Mus musculus


text: public

text: house mouse

characteristic: common name

text: control

text: lungs

text: Mus musculus

text: Mus musculus

characteristic: title


E-MTAB-5884:Sample 1

text: public

text: E-MTAB-5884:Sample 1

tag: Namespace:The Sainsbury Laboratory, University of Cambridge

characteristic: age

text: ArrayExpress

characteristic: broker name

text: thale cress

text: Protocols: Arabidopsis thaliana seeds were surfaced sterilized and sown in petri dishes with agarified (0.8% Bacto Agar) 0.5x MS medium, containing 1% sucrose and 0.05% MES at pH 5.7. After stratification for 3 days at 4°C, plants were grown in a CU-22L growth chamber (Percival) under 21°C and a 12/12 h (day/night) light cycle. For the heat treatment, a pre-chilling step was performed to increase the relative activation of ONSEN. Seedlings were first placed at 4°C for 24 h on a chilling platform built-in within the growth chamber (controlled by an external mini-chiller), but with the chamber temperature set to 6°C. This chilling pre-treatment was followed by 24 h with the chamber set to 37°C for the stressed plants; control plants were moved to 21°C. Pools of seedlings were harvested for RNA extraction. Total RNA was isolated using the the Plant-RNAeasy kit (Invitrogen), following provider's instructions. Strand-specific libraries were prepared with 2 µg of RNA using the TruSeq Stranded mRNA Sample Prep Kit (Illumina); following provider’s instructions.

text: seedling

characteristic: developmental stage

characteristic: ecotype

characteristic: genotype

text: Arabidopsis thaliana

text: Arabidopsis thaliana

text: Arabidopsis thaliana

text: Sample 1


E-MTAB-5884:Sample 2

tag: attribute

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: The Sainsbury Laboratory, University of Cambridge

characteristic: INSDC center name

text: public

text: E-MTAB-5884:Sample 2

text: ArrayExpress

text: thale cress

text: seedling

text: Arabidopsis thaliana

text: Arabidopsis thaliana

text: Arabidopsis thaliana

text: Sample 2


E-MTAB-5884:Sample 5

text: public

characteristic: SRA accession

text: E-MTAB-5884:Sample 5

characteristic: Submitter Id

text: ArrayExpress

text: thale cress

characteristic: description

text: seedling

text: nrpd1-3 with novel insertions of ONSEN/Copia78 LTR retrotransposon

text: plant 2L

characteristic: individual

text: Arabidopsis thaliana

text: Arabidopsis thaliana

text: Arabidopsis thaliana

text: Sample 5


E-MTAB-5884:Sample 6

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: E-MTAB-5884:Sample 6

text: ArrayExpress

text: thale cress

text: seedling

text: plant 2L

text: Arabidopsis thaliana

characteristic: organism

text: Arabidopsis thaliana

text: Arabidopsis thaliana

text: Sample 6


E-MTAB-5884:Sample 3

text: public

text: E-MTAB-5884:Sample 3

characteristic: age

text: ArrayExpress

characteristic: broker name

text: thale cress

characteristic: common name

text: seedling

text: Arabidopsis thaliana

text: Arabidopsis thaliana

text: Arabidopsis thaliana

text: Sample 3

characteristic: title


E-MTAB-5884:Sample 4

characteristic: ENA-CHECKLIST

text: public

text: E-MTAB-5884:Sample 4

text: ArrayExpress

text: thale cress

text: seedling

characteristic: developmental stage

characteristic: ecotype

characteristic: genotype

text: Arabidopsis thaliana

text: Arabidopsis thaliana

text: Arabidopsis thaliana

text: Sample 4


E-MTAB-5884:Sample 7

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC center name

text: public

text: E-MTAB-5884:Sample 7

text: ArrayExpress

text: thale cress

text: seedling

text: plant 2L

text: Arabidopsis thaliana

text: Arabidopsis thaliana

text: Arabidopsis thaliana

text: Sample 7


E-MTAB-5884:Sample 8

text: public

characteristic: SRA accession

text: E-MTAB-5884:Sample 8

characteristic: Submitter Id

text: ArrayExpress

text: thale cress

characteristic: description

text: seedling

text: plant 2L

characteristic: individual

text: Arabidopsis thaliana

text: Arabidopsis thaliana

text: Arabidopsis thaliana

text: Sample 8


text: Herpetomonas megaseliae

characteristic: ArrayExpress-SPECIES

text: SC

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: Herpetomonas megaseliae

text: Herpetomonas megaseliae

characteristic: organism

text: Herpetomonas megaseliae

characteristic: subject id


characteristic: ENA-CHECKLIST

text: CENTRE FOR GENOMIC RESEARCH (CGR)

text: public

tag: Namespace:CENTRE FOR GENOMIC RESEARCH (CGR)

text: Sodalis glossinidius

text: Sodalis glossinidius

text: Sodalis glossinidius

characteristic: title


text: Normal

characteristic: ArrayExpress-PHENOTYPE

text: Mus musculus

text: SC

text: public

text: house mouse

characteristic: common name

text: Mus musculus

text: Normal

characteristic: phenotype

text: Mus musculus


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: INSTITUT PASTEUR

text: public

tag: Namespace:INSTITUT PASTEUR

text: Population of bacteriophages LF82_P10 at Day 24 from Conventional Mice colonized by LF82

text: Escherichia coli

text: Escherichia coli

text: Bacteriophage LF82_P10

characteristic: strain


text: URMITE

characteristic: INSDC center name

text: public

characteristic: SRA accession

characteristic: Submitter Id

text: Clostridium sp. SN20

text: Clostridium sp. SN20

text: Culturomics study


characteristic: INSDC first public

text: public

tag: Namespace:SWISS FEDERAL INSTITUTE FOR FOREST, SNOW AND LANDSCAPE RESEARCH

characteristic: collection date

text: Scots pine

text: temperate woodland biome

characteristic: environment (biome)

text: plant litter

characteristic: environment (feature)

text: leaf

characteristic: environment (material)

text: Switzerland

characteristic: geographic location (country and/or sea)

text: 5 - 8

characteristic: geographic location (depth)

characteristic: geographic location (elevation)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: mimarks-survey

characteristic: investigation type

text: Pinus sylvestris

text: Improved recovery of ancient DNA from subfossil wood - application to the world’s oldest Late Glacial pine forest

characteristic: project name

text: Pinus sylvestris

text: sediment

characteristic: sediment environmental package

text: Illumina

characteristic: sequencing method

text: Plant DNA metabarcoding data from the uncleaned surface and cleaned wood of subfossil tree trunks


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: SWISS FEDERAL INSTITUTE FOR FOREST, SNOW AND LANDSCAPE RESEARCH

characteristic: INSDC center name

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: Scots pine

characteristic: common name

text: temperate woodland biome

text: plant litter

text: leaf

text: Switzerland

text: 5 - 8

text: mimarks-survey

text: Pinus sylvestris

characteristic: organism

text: Pinus sylvestris

text: sediment

text: Illumina

characteristic: title


characteristic: INSDC first public

text: public

characteristic: SRA accession

characteristic: Submitter Id

characteristic: collection date

text: Scots pine

text: temperate woodland biome

characteristic: environment (biome)

text: plant litter

characteristic: environment (feature)

text: wood

characteristic: environment (material)

text: Switzerland

characteristic: geographic location (country and/or sea)

text: 5 - 8

characteristic: geographic location (depth)

characteristic: geographic location (elevation)

text: mimarks-survey

text: Pinus sylvestris

text: Pinus sylvestris

text: sediment

text: Illumina


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: WEIZMANN INSTITUE OF SCIENCE

text: public

tag: Namespace:WEIZMANN INSTITUE OF SCIENCE

text: Escherichia coli BW25113

text: Escherichia coli BW25113

text: The genetic basis for the adaptation of E.coli to sugar synthesis from CO2


text: URMITE

characteristic: INSDC center name

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: Anaerotruncus sp. AT3

text: Anaerotruncus sp. AT3

characteristic: strain

text: Culturomics study


text: INSTITUT PASTEUR

characteristic: INSDC first public

text: public

characteristic: SRA accession

text: Population of bacteriophages L82_P10 at day 24 from mice colonized with strains LF82 and MG1655

characteristic: description

text: Escherichia coli

characteristic: organism

text: Escherichia coli

text: Bacteriophage LF82_P10_variant_CM_2S

characteristic: title


text: INSTITUT PASTEUR

text: public

characteristic: Submitter Id

text: Population of adapted bacteriophages L82_P10 at day 24 from mice colonized with strains LF82 and MG1655 Exp.A

text: Escherichia coli

text: Escherichia coli

text: Bacteriophage LF82_P10variant_CM_2S_ad_A


text: URMITE

text: public

text: Raoultibacter massiliensis

text: Raoultibacter massiliensis

text: Raoultibacter massiliensis genome


text: INSTITUT PASTEUR

text: public

text: Population of adapted bacteriophages L82_P10 at day 24 from mice colonized with strains LF82 and MG1655 Exp.B

text: Escherichia coli

text: Escherichia coli

text: Bacteriophage LF82_P10_variant_CM_2S_ad_B


text: INSTITUT PASTEUR

text: public

text: Escherichia coli

text: Escherichia coli

text: Bacteriophage LF82_P10_variant_DM_2S


text: INSTITUT PASTEUR

text: public

text: Escherichia coli

text: Escherichia coli

text: Bacteriophage LF82_P10_variant_IV_1S


text: INSTITUT PASTEUR

text: public

text: Population of bacteriophages L82_P10 at day 24 incubated in vitro with strains LF82 and MG1655

text: Escherichia coli

text: Escherichia coli

text: Bacteriophage LF82_P10_variant_IV_2S


text: URMITE

text: public

text: Clostridiales bacterium Marseille-P2846

text: Clostridiales bacterium Marseille-P2846

text: Beduinella massiliensis genome


text: Burkholderia cenocepacia

characteristic: ArrayExpress-SPECIES

text: SC

text: public

text: Burkholderia cenocepacia

characteristic: common name

text: Burkholderia cenocepacia

text: Burkholderia cenocepacia

characteristic: subject id


characteristic: ENA-CHECKLIST

text: public

tag: Namespace:Institute of Medical Microbiology and Hygiene, University Tuebingen

characteristic: collection date

text: clinical isolate

text: Germany

characteristic: geographic location (country and/or sea)

text: human and environmental

characteristic: isolation source

text: Pseudomonas putida

text: Pseudomonas putida

text: Characterization of clinical and environmenatal Pseudomonas putida group isolates and Pseudomonas aeruginosa isolates


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Institute of Medical Microbiology and Hygiene, University Tuebingen

characteristic: INSDC center name

text: public

text: clinical isolate

text: Germany

text: human and environmental

text: Pseudomonas putida

text: Pseudomonas putida


characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: environmental isolate

text: Germany

text: human and environmental

text: Pseudomonas putida

text: Pseudomonas putida


text: public

characteristic: SRA accession

text: clinical isolate

characteristic: description

text: Germany

text: human and environmental

text: Pseudomonas aeruginosa

characteristic: organism

text: Pseudomonas aeruginosa


text: public

characteristic: Submitter Id

text: environmental sample

text: Germany

text: human and environmental

text: Pseudomonas aeruginosa

text: Pseudomonas aeruginosa

characteristic: title


text: NATIONAL FOOD INSTITUTE - DTU

text: public

tag: Namespace:NATIONAL FOOD INSTITUTE - DTU

text: Denmark

text: diseased

characteristic: host health state

text: Homo sapiens

characteristic: host scientific name

characteristic: isolate

text: human eye

text: Enterococcus faecalis

text: Enterococcus faecalis

text: Isolate 7.1 from patient C2


characteristic: ENA-CHECKLIST

text: NATIONAL FOOD INSTITUTE - DTU

text: public

characteristic: collection date

text: Denmark

characteristic: geographic location (country and/or sea)

text: diseased

text: Homo sapiens

text: human eye

text: Enterococcus faecalis

text: Enterococcus faecalis

text: Isolate 7.2 from patient C2


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: NATIONAL FOOD INSTITUTE - DTU

text: public

text: Denmark

text: diseased

text: Homo sapiens

text: human eye

characteristic: isolation source

text: Staphylococcus epidermidis

text: Staphylococcus epidermidis

text: Isolate 10 from patient C3


characteristic: External Id

text: NATIONAL FOOD INSTITUTE - DTU

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: Denmark

text: diseased

text: Homo sapiens

text: human eye

text: Enterococcus faecalis

text: Enterococcus faecalis

text: Isolate 13.1 from patient C6


text: NATIONAL FOOD INSTITUTE - DTU

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: Denmark

text: diseased

text: Homo sapiens

text: human eye

text: Enterococcus faecalis

text: Enterococcus faecalis

text: Isolate 13.2 from patient C6


text: NATIONAL FOOD INSTITUTE - DTU

text: public

characteristic: Submitter Id

text: Denmark

text: diseased

text: Homo sapiens

text: human eye

text: Staphylococcus epidermidis

characteristic: organism

text: Staphylococcus epidermidis

text: Isolate 17 from patient C7


text: NATIONAL FOOD INSTITUTE - DTU

text: public

text: Denmark

text: diseased

characteristic: host health state

text: Homo sapiens

text: human eye

text: Staphylococcus epidermidis

text: Staphylococcus epidermidis

text: Isolate 5 from patient I4

characteristic: title


text: NATIONAL FOOD INSTITUTE - DTU

text: public

text: Denmark

text: diseased

text: Homo sapiens

characteristic: host scientific name

characteristic: isolate

text: human eye

text: Staphylococcus epidermidis

text: Staphylococcus epidermidis

text: Isolate 23.3 from patient I6


characteristic: ENA-CHECKLIST

text: NATIONAL FOOD INSTITUTE - DTU

text: public

characteristic: collection date

text: Denmark

text: diseased

text: Homo sapiens

text: human eye

text: Staphylococcus epidermidis

text: Staphylococcus epidermidis

text: Isolate 23.2 from patient I6


characteristic: ENA-FIRST-PUBLIC

text: NATIONAL FOOD INSTITUTE - DTU

text: public

text: Denmark

characteristic: geographic location (country and/or sea)

text: diseased

text: Homo sapiens

text: human eye

text: Staphylococcus epidermidis

text: Staphylococcus epidermidis

text: Isolate 23.1 from patient I6


E-MTAB-5872:21194 rep1

characteristic: ENA-LAST-UPDATE

text: Animal Health Trust

text: public

text: E-MTAB-5872:21194 rep1

tag: Namespace:Animal Health Trust

text: ArrayExpress

characteristic: broker name

text: Protocols: Strains were grown to OD 0.3 600 nm in Todd Hewitt broth at 37C 5 % CO2, humidified. RNA was extracted using Qiagen RNA kits and rRNA depleted using an epicentre kit for Gram positive bacteria. Libraries were constructed using the NEB Ultra directional RNA library preparation kit for Illumina.

characteristic: description

text: SNP in csrRS

characteristic: genotype

text: Streptococcus equi

text: Streptococcus equi

text: naturally occuring csrRS SNP compared to wild type strain JKS595A

characteristic: phenotype

text: Streptococcus equi

characteristic: strain

text: 21194 rep1


E-MTAB-5872:21194 rep2

characteristic: External Id

text: Animal Health Trust

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-5872:21194 rep2

text: ArrayExpress

text: SNP in csrRS

text: Streptococcus equi

text: Streptococcus equi

text: Streptococcus equi

text: 21194 rep2


E-MTAB-5872:21194 rep3

text: Animal Health Trust

text: public

text: E-MTAB-5872:21194 rep3

characteristic: Submitter Id

text: ArrayExpress

text: SNP in csrRS

text: Streptococcus equi

characteristic: organism

text: Streptococcus equi

text: Streptococcus equi

text: 21194 rep3

characteristic: title


E-MTAB-5872:Hornline rep1

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: Animal Health Trust

text: public

text: E-MTAB-5872:Hornline rep1

text: ArrayExpress

text: SNP in csrRS

text: Streptococcus equi

text: Streptococcus equi

text: naturally occuring csrRS SNP compared to wild type strain Malisker

text: Streptococcus equi

text: Hornline

text: Hornline rep1


E-MTAB-5872:Hornline rep2

characteristic: ENA-LAST-UPDATE

text: Animal Health Trust

text: public

text: E-MTAB-5872:Hornline rep2

text: ArrayExpress

text: SNP in csrRS

text: Streptococcus equi

text: Streptococcus equi

text: Streptococcus equi

text: Hornline

text: Hornline rep2


E-MTAB-5872:Hornline rep3

text: Animal Health Trust

text: public

text: E-MTAB-5872:Hornline rep3

text: ArrayExpress

characteristic: broker name

text: SNP in csrRS

text: Streptococcus equi

text: Streptococcus equi

text: Streptococcus equi

text: Hornline

text: Hornline rep3


E-MTAB-5872:JKS043 rep1

text: Animal Health Trust

text: public

text: E-MTAB-5872:JKS043 rep1

text: ArrayExpress

characteristic: description

text: wild type genotype

text: Streptococcus equi

text: Streptococcus equi

text: wild type phenotype compared to csrRS SNP strain JKS044B

text: Streptococcus equi

text: JKS043 rep1


E-MTAB-5872:JKS043 rep2

text: Animal Health Trust

text: public

text: E-MTAB-5872:JKS043 rep2

text: ArrayExpress

text: wild type genotype

characteristic: genotype

text: Streptococcus equi

text: Streptococcus equi

text: Streptococcus equi

text: JKS043 rep2


E-MTAB-5872:JKS043 rep3

text: Animal Health Trust

text: public

text: E-MTAB-5872:JKS043 rep3

text: ArrayExpress

text: wild type genotype

text: Streptococcus equi

text: Streptococcus equi

characteristic: phenotype

text: Streptococcus equi

text: JKS043 rep3


E-MTAB-5872:JKS044B rep1

text: Animal Health Trust

text: public

text: E-MTAB-5872:JKS044B rep1

text: ArrayExpress

text: SNP in csrRS

text: Streptococcus equi

text: Streptococcus equi

text: naturally occuring csrRS SNP compared to wild type strain JKS043

text: Streptococcus equi

characteristic: strain

text: JKS044B rep1


E-MTAB-5872:JKS044B rep2

characteristic: External Id

text: Animal Health Trust

text: public

text: E-MTAB-5872:JKS044B rep2

text: ArrayExpress

text: SNP in csrRS

text: Streptococcus equi

text: Streptococcus equi

text: Streptococcus equi

text: JKS044B rep2


E-MTAB-5872:JKS044B rep3

text: Animal Health Trust

characteristic: INSDC center name

text: public

text: E-MTAB-5872:JKS044B rep3

text: ArrayExpress

text: SNP in csrRS

text: Streptococcus equi

text: Streptococcus equi

text: Streptococcus equi

text: JKS044B rep3


E-MTAB-5872:JKS063A rep1

text: Animal Health Trust

characteristic: INSDC first public

text: public

text: E-MTAB-5872:JKS063A rep1

text: ArrayExpress

text: wild type genotype

text: Streptococcus equi

text: Streptococcus equi

text: wild type phenotype compared to csrRS SNP strain JKS063D

text: Streptococcus equi

text: JKS063A rep1


E-MTAB-5872:JKS063A rep2

text: Animal Health Trust

characteristic: INSDC last update

text: public

text: E-MTAB-5872:JKS063A rep2

text: ArrayExpress

text: wild type genotype

text: Streptococcus equi

text: Streptococcus equi

text: Streptococcus equi

text: JKS063A rep2


E-MTAB-5872:JKS063A rep3

text: Animal Health Trust

text: public

characteristic: INSDC status

text: E-MTAB-5872:JKS063A rep3

text: ArrayExpress

text: wild type genotype

text: Streptococcus equi

text: Streptococcus equi

text: Streptococcus equi

text: JKS063A rep3


E-MTAB-5872:JKS063D rep1

text: Animal Health Trust

text: public

characteristic: SRA accession

text: E-MTAB-5872:JKS063D rep1

text: ArrayExpress

text: SNP in csrRS

text: Streptococcus equi

text: Streptococcus equi

text: naturally occuring csrRS SNP compared to wild type strain JKS063A

text: Streptococcus equi

text: JKS063D rep1


E-MTAB-5872:JKS063D rep2

text: Animal Health Trust

text: public

text: E-MTAB-5872:JKS063D rep2

characteristic: Submitter Id

text: ArrayExpress

text: SNP in csrRS

text: Streptococcus equi

text: Streptococcus equi

text: Streptococcus equi

text: JKS063D rep2


E-MTAB-5872:JKS063D rep3

text: Animal Health Trust

text: public

text: E-MTAB-5872:JKS063D rep3

text: ArrayExpress

text: SNP in csrRS

text: Streptococcus equi

characteristic: organism

text: Streptococcus equi

text: Streptococcus equi

text: JKS063D rep3


E-MTAB-5872:JKS595A rep1

text: Animal Health Trust

text: public

text: E-MTAB-5872:JKS595A rep1

text: ArrayExpress

text: wild type genotype

text: Streptococcus equi

text: Streptococcus equi

text: wild type phenotype compared to csrRS SNP strains 21194 and JKS642

text: Streptococcus equi

text: JKS595A rep1

characteristic: title


E-MTAB-5872:JKS595A rep2

characteristic: ENA-CHECKLIST

text: Animal Health Trust

text: public

text: E-MTAB-5872:JKS595A rep2

text: ArrayExpress

text: wild type genotype

text: Streptococcus equi

text: Streptococcus equi

text: Streptococcus equi

text: JKS595A rep2


E-MTAB-5872:JKS595A rep3

characteristic: ENA-FIRST-PUBLIC

text: Animal Health Trust

text: public

text: E-MTAB-5872:JKS595A rep3

text: ArrayExpress

text: wild type genotype

text: Streptococcus equi

text: Streptococcus equi

text: Streptococcus equi

text: JKS595A rep3


E-MTAB-5872:JKS642 rep1

characteristic: ENA-LAST-UPDATE

text: Animal Health Trust

text: public

text: E-MTAB-5872:JKS642 rep1

text: ArrayExpress

text: SNP in csrRS

text: Streptococcus equi

text: Streptococcus equi

text: Streptococcus equi

text: JKS642 rep1


E-MTAB-5872:JKS642 rep2

text: Animal Health Trust

text: public

text: E-MTAB-5872:JKS642 rep2

text: ArrayExpress

characteristic: broker name

text: SNP in csrRS

text: Streptococcus equi

text: Streptococcus equi

text: Streptococcus equi

text: JKS642 rep2


E-MTAB-5872:JKS642 rep3

text: Animal Health Trust

text: public

text: E-MTAB-5872:JKS642 rep3

text: ArrayExpress

characteristic: description

text: SNP in csrRS

text: Streptococcus equi

text: Streptococcus equi

text: Streptococcus equi

text: JKS642 rep3


E-MTAB-5872:JKS750A rep1

text: Animal Health Trust

text: public

text: E-MTAB-5872:JKS750A rep1

text: ArrayExpress

text: wild type genotype

characteristic: genotype

text: Streptococcus equi

text: Streptococcus equi

text: wild type phenotype compared to csrRS SNP strain JSK750B

text: Streptococcus equi

text: JKS750A rep1


E-MTAB-5872:JKS750A rep2

text: Animal Health Trust

text: public

text: E-MTAB-5872:JKS750A rep2

text: ArrayExpress

text: wild type genotype

text: Streptococcus equi

text: Streptococcus equi

characteristic: phenotype

text: Streptococcus equi

text: JKS750A rep2


E-MTAB-5872:JKS750A rep3

text: Animal Health Trust

text: public

text: E-MTAB-5872:JKS750A rep3

text: ArrayExpress

text: wild type genotype

text: Streptococcus equi

text: Streptococcus equi

text: Streptococcus equi

characteristic: strain

text: JKS750A rep3


E-MTAB-5872:JKS750B rep1

characteristic: External Id

text: Animal Health Trust

text: public

text: E-MTAB-5872:JKS750B rep1

text: ArrayExpress

text: SNP in csrRS

text: Streptococcus equi

text: Streptococcus equi

text: naturally occuring csrRS SNP compared to wild type strain JSK750A

text: Streptococcus equi

text: JKS750B rep1


E-MTAB-5872:JKS750B rep2

text: Animal Health Trust

characteristic: INSDC center name

text: public

text: E-MTAB-5872:JKS750B rep2

text: ArrayExpress

text: SNP in csrRS

text: Streptococcus equi

text: Streptococcus equi

text: Streptococcus equi

text: JKS750B rep2


E-MTAB-5872:JKS750B rep3

text: Animal Health Trust

characteristic: INSDC first public

text: public

text: E-MTAB-5872:JKS750B rep3

text: ArrayExpress

text: SNP in csrRS

text: Streptococcus equi

text: Streptococcus equi

text: Streptococcus equi

text: JKS750B rep3


E-MTAB-5872:Malisker rep1

text: Animal Health Trust

characteristic: INSDC last update

text: public

text: E-MTAB-5872:Malisker rep1

text: ArrayExpress

text: wild type genotype

text: Streptococcus equi

text: Streptococcus equi

text: wild type phenotype compared to csrRS SNP strain Hornline

text: Streptococcus equi

text: Malisker

text: Malisker rep1


E-MTAB-5872:Malisker rep2

text: Animal Health Trust

text: public

characteristic: INSDC status

text: E-MTAB-5872:Malisker rep2

text: ArrayExpress

text: wild type genotype

text: Streptococcus equi

text: Streptococcus equi

text: Streptococcus equi

text: Malisker

text: Malisker rep2


E-MTAB-5872:Malisker rep3

text: Animal Health Trust

text: public

characteristic: SRA accession

text: E-MTAB-5872:Malisker rep3

text: ArrayExpress

text: wild type genotype

text: Streptococcus equi

text: Streptococcus equi

text: Streptococcus equi

text: Malisker

text: Malisker rep3


Porphyromonas sp. TT1

text: University Medical Center Groningen

text: public

text: Porphyromonas sp. TT1

tag: Namespace:University Medical Center Groningen

characteristic: Submitter Id

characteristic: collection date

text: New Zealand

characteristic: geographic location (country and/or sea)

text: diseased

characteristic: host health state

text: Ovis aries

characteristic: host scientific name

characteristic: isolate

text: subgingival

characteristic: isolation source

text: Porphyromonas sp. TT1

text: Porphyromonas sp. TT1

text: Porphyromonas gingivalis-related species


text: synthetic construct

characteristic: ArrayExpress-SPECIES

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: SC

text: public

text: synthetic construct

characteristic: common name

text: synthetic construct

characteristic: organism

text: synthetic construct

characteristic: subject id

characteristic: title


characteristic: External Id

text: WEIZMANN INSTITUE OF SCIENCE

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: This mutant came form the leave-one-out suppressor analysis.

characteristic: description

text: Escherichia coli BW25113

text: Escherichia coli BW25113

text: The genetic basis for the adaptation of E.coli to sugar synthesis from CO2


Reconstructed strain

text: WEIZMANN INSTITUE OF SCIENCE

text: public

characteristic: SRA accession

text: Reconstructed strain

characteristic: Submitter Id

text: Escherichia coli BW25113

text: Escherichia coli BW25113


text: MPI-EVA

text: public

text: Homo sapiens neanderthalensis

text: Homo sapiens neanderthalensis

text: Bone

characteristic: tissue type


text: FRAUNHOFER IGB

text: public

tag: Namespace:FRAUNHOFER IGB

text: human

text: Homo sapiens

text: Homo sapiens

text: classifiedReads


text: University Hospital Galway

text: public

tag: Namespace:University Hospital Galway

characteristic: collection date

text: Ireland

characteristic: geographic location (country and/or sea)

text: Homo sapiens

characteristic: host scientific name

characteristic: isolate

text: Human

characteristic: isolation source

text: Shigella flexneri 5b

text: Shigella flexneri 5b

text: Shigella flexneri 5b

characteristic: sub species


text: Legionella pneumophila

characteristic: ArrayExpress-SPECIES

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: SC

text: public

text: Legionella pneumophila

characteristic: common name

text: Legionella pneumophila

characteristic: organism

text: Legionella pneumophila

characteristic: subject id


characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: E-MTAB-5898:Wheat+MycorhizalFungi+Xanthomonas_Leaves_Replicate1

tag: Namespace:IRD, Cirad, Univ Montpellier, IPME, Montpellier, France

characteristic: age

text: ArrayExpress

characteristic: broker name

text: bread wheat

text: Chinese Spring

characteristic: cultivar

text: Protocols: Plants were grown for 50 days in 3 L pots containing a 50/50 mixture of sand and soil carrier containing Funneliformis mossae (sold by MycAgro Lab, Dijon, France). Three replicates per condition, 2 plants per pot. Plants were grown in a light chamber, and half were treated with Xanthomonas translucens CFPB2054 (by infiltration) at 49 days, and all samples (roots, leaves) were collected at 50 days and frozen in liquid nitrogen. Samples were ground to a fine powder in liquid nitrogen and total RNA was isolated (TRI Reagent® (MRC, Cincinnati, OH)). Then, it was treated with DNase and RNA quality was confirmed with Experion™ Automated Electrophoresis System, Nanodrop™ and gel electrophoresis. Total RNA was used for mRNA preparation, fragmentation and cDNA synthesis The preparation of mRNA libraries was done using the TrueSeq Stranded mRNA Sample Preparation kit (Illumina Inc., San Diego, CA). The library quality validation (concentration and length of DNA fragments) was performed by Fragment Analyzer using the standard and high sensitivity DNA kits (Agilent Technologies, Santa Clara, CA) and by qPCR (LightCycler 480; Roche Diagnostics, Meylan, France)

characteristic: description

text: Funneliformis mossae exposure

characteristic: environmental history

text: wild type genotype

characteristic: genotype

text: Triticum aestivum

text: Triticum aestivum

text: leaf

characteristic: organism part

text: Triticum aestivum

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: IRD, Cirad, Univ Montpellier, IPME, Montpellier, France

text: public

characteristic: SRA accession

text: E-MTAB-5898:Wheat+MycorhizalFungi+Xanthomonas_Leaves_Replicate2

characteristic: Submitter Id

text: ArrayExpress

text: bread wheat

text: Chinese Spring

text: Funneliformis mossae exposure

text: wild type genotype

text: Triticum aestivum

text: Triticum aestivum

text: leaf

text: Triticum aestivum


characteristic: External Id

characteristic: INSDC center name

text: public

text: E-MTAB-5898:Wheat+MycorhizalFungi+Xanthomonas_Leaves_Replicate3

text: ArrayExpress

text: bread wheat

characteristic: common name

text: Chinese Spring

text: Funneliformis mossae exposure

text: wild type genotype

text: Triticum aestivum

characteristic: organism

text: Triticum aestivum

text: leaf

text: Triticum aestivum


characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: E-MTAB-5898:Wheat+MycorhizalFungi+Xanthomonas_Roots_Replicate1

characteristic: age

text: ArrayExpress

text: bread wheat

text: Chinese Spring

text: Funneliformis mossae exposure

text: wild type genotype

text: Triticum aestivum

text: Triticum aestivum

text: root

text: Triticum aestivum


text: public

text: E-MTAB-5898:Wheat+MycorhizalFungi+Xanthomonas_Roots_Replicate2

text: ArrayExpress

characteristic: broker name

text: bread wheat

text: Chinese Spring

characteristic: cultivar

characteristic: description

text: Funneliformis mossae exposure

characteristic: environmental history

text: wild type genotype

text: Triticum aestivum

text: Triticum aestivum

text: root

text: Triticum aestivum


characteristic: ENA-CHECKLIST

text: public

text: E-MTAB-5898:Wheat+MycorhizalFungi+Xanthomonas_Roots_Replicate3

text: ArrayExpress

text: bread wheat

text: Chinese Spring

text: Funneliformis mossae exposure

text: wild type genotype

characteristic: genotype

text: Triticum aestivum

text: Triticum aestivum

text: root

characteristic: organism part

text: Triticum aestivum

characteristic: title


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: public

characteristic: SRA accession

text: E-MTAB-5898:Wheat+MycorhizalFungi_Leaves_Replicate1

characteristic: Submitter Id

text: ArrayExpress

text: bread wheat

text: Chinese Spring

text: Funneliformis mossae exposure

text: wild type genotype

text: Triticum aestivum

text: Triticum aestivum

text: leaf

text: Triticum aestivum


characteristic: External Id

characteristic: INSDC center name

text: public

text: E-MTAB-5898:Wheat+MycorhizalFungi_Leaves_Replicate2

text: ArrayExpress

text: bread wheat

characteristic: common name

text: Chinese Spring

text: Funneliformis mossae exposure

text: wild type genotype

text: Triticum aestivum

characteristic: organism

text: Triticum aestivum

text: leaf

text: Triticum aestivum


characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: E-MTAB-5898:Wheat+MycorhizalFungi_Leaves_Replicate3

characteristic: age

text: ArrayExpress

text: bread wheat

text: Chinese Spring

text: Funneliformis mossae exposure

text: wild type genotype

text: Triticum aestivum

text: Triticum aestivum

text: leaf

text: Triticum aestivum


text: public

text: E-MTAB-5898:Wheat+MycorhizalFungi_Roots_Replicate1

text: ArrayExpress

characteristic: broker name

text: bread wheat

text: Chinese Spring

characteristic: cultivar

characteristic: description

text: Funneliformis mossae exposure

characteristic: environmental history

text: wild type genotype

text: Triticum aestivum

text: Triticum aestivum

text: root

text: Triticum aestivum


characteristic: ENA-CHECKLIST

text: public

text: E-MTAB-5898:Wheat+MycorhizalFungi_Roots_Replicate2

text: ArrayExpress

text: bread wheat

text: Chinese Spring

text: Funneliformis mossae exposure

text: wild type genotype

characteristic: genotype

text: Triticum aestivum

text: Triticum aestivum

text: root

characteristic: organism part

text: Triticum aestivum

characteristic: title


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: public

characteristic: SRA accession

text: E-MTAB-5898:Wheat+MycorhizalFungi_Roots_Replicate3

characteristic: Submitter Id

text: ArrayExpress

text: bread wheat

text: Chinese Spring

text: Funneliformis mossae exposure

text: wild type genotype

text: Triticum aestivum

text: Triticum aestivum

text: root

text: Triticum aestivum


characteristic: External Id

text: MPI-EVA

characteristic: INSDC center name

text: public

text: Homo sapiens neanderthalensis

characteristic: organism

text: Homo sapiens neanderthalensis

text: Tooth

characteristic: tissue type

text: Les_Cottes_Z4-1514 nuclear sequences


text: Klebsiella pneumoniae

characteristic: ArrayExpress-SPECIES

text: SC

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: Klebsiella pneumoniae

characteristic: common name

text: Klebsiella pneumoniae

text: Klebsiella pneumoniae

characteristic: subject id


characteristic: ENA-CHECKLIST

text: MPI-EVA

text: public

text: Homo sapiens neanderthalensis

text: Homo sapiens neanderthalensis

text: Bone

text: Mezmaiskaya 2 nuclear DNA sequences


text: INSTITUT PASTEUR

text: public

text: Genomic sequence of the variant LF82_P10_ad1 that is able to infect both LF82 and MG1655 strains

characteristic: description

text: Escherichia coli

text: Escherichia coli

characteristic: strain


characteristic: ENA-FIRST-PUBLIC

text: INSTITUT PASTEUR

text: public

text: Genomic sequence of bacteriophage LF82_P10_ad2 that is able to infect LF82 and MG1655 strains

text: Escherichia coli

text: Escherichia coli

characteristic: title


characteristic: ENA-LAST-UPDATE

text: MPI-EVA

text: public

characteristic: SRA accession

text: Homo sapiens neanderthalensis

text: Homo sapiens neanderthalensis

text: Bone

text: Vindija87 nuclear DNA sequences


characteristic: External Id

text: MPI-EVA

text: public

characteristic: Submitter Id

text: Homo sapiens neanderthalensis

text: Homo sapiens neanderthalensis

text: Tooth

text: Spy 94a nuclear DNA sequences


text: JUSTUS LIEBIG UNIVERSITY

characteristic: INSDC center name

text: public

tag: Namespace:JUSTUS LIEBIG UNIVERSITY

text: Listeria monocytogenes

characteristic: organism

text: Listeria monocytogenes


text: Plasmodium falciparum

characteristic: ArrayExpress-SPECIES

text: SC

text: public

text: malaria parasite P. falciparum

text: Plasmodium falciparum

text: Plasmodium falciparum


text: Plasmodium falciparum

text: SC

characteristic: INSDC first public

text: public

text: Plasmodium falciparum

text: Plasmodium falciparum CAMP/Malaysia

text: Plasmodium falciparum CAMP/Malaysia


text: Plasmodium falciparum

text: SC

characteristic: INSDC last update

text: public

text: Plasmodium falciparum

text: Plasmodium falciparum CDC/Honduras

text: Plasmodium falciparum CDC/Honduras


text: Plasmodium falciparum

text: SC

text: public

characteristic: INSDC status

text: Plasmodium falciparum

text: Plasmodium falciparum FC27/Papua New Guinea


text: public

tag: Namespace:Division of Cardiovascular Sciences School of Medicine Faculty of Biology Medicine and Health Manchester Academic Health Science Centre The University of Manchester

text: ArrayExpress

characteristic: broker name

text: baker's yeast

characteristic: common name

text: Protocols: Strains were grown at 30°C in synthetic complete dextrose media lacking histidine [SCD-his] grown to A600=~0.6. Harvest cells by rapid centrifugation in a warm centrifuge and resuspend them in pre-warmed SD minimal medium (-aa, for 20 min) Triplicate samples of TAP associated RNA was isolated on M-280 magnetic beads as described above. For RNA target identification, after the final wash, the beads were resuspended in 270 µl Buffer A. A 20 μl aliquot of the sample was set aside for western blot analysis, and RNA was purified from the remaining 250 μl. Total (T) RNA and paired immune precipitated (IP) RNA were isolated using a standard Trizol Reagent (Life Technologies, Carlsbad, CA) protocol and re-suspended in 10 µl diethylpyrocarbonate (DEPC) treated water. RNA was quantified using a Nanodrop 8000 spectrophotometer (Thermo Fisher Scientific, Waltham, MA). rRNA was then depleted from both total and IP RNA samples using the RibominusTM Eukaryote Kit for RNA-Seq (Life Technologies, Carlsbad, CA). Depleted samples were ethanol precipitated, washed twice with 70% ethanol and resuspended in 10 µl DEPC water. rRNA depletion was assessed on a 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA) using a RNA nanochip and the remaining RNA stored at -80°C. Sequencing libraries were generated using the whole Transcriptome Library Preparation protocol provided with the SOLiD® Total RNA-Seq Kit (Life Technologies, Carlsbad, CA) as described by the manufacturer.

text: amino acid deprivation

characteristic: environmental stress

text: MATa his3-1 leu20 met150 ura30 CDC33::TAP-HIS3

characteristic: genotype

text: SD minus amino acids

characteristic: growth condition

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

text: expression of TAP-His-tagged eIF4E

characteristic: phenotype

characteristic: replicate

text: Saccharomyces cerevisiae

text: Mat a

characteristic: sex

text: fresh specimen

characteristic: specimen with known storage state


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Division of Cardiovascular Sciences School of Medicine Faculty of Biology Medicine and Health Manchester Academic Health Science Centre The University of Manchester

text: public

characteristic: SRA accession

text: ArrayExpress

text: baker's yeast

characteristic: description

text: amino acid deprivation

text: MATa his3-1 leu20 met150 ura30 TIF4632::TAP-HIS3

text: SD minus amino acids

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

text: expression of TAP-His-tagged eIF4G2

text: Saccharomyces cerevisiae

text: Mat a

text: fresh specimen

characteristic: strain

characteristic: title


characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: Submitter Id

text: ArrayExpress

characteristic: broker name

text: baker's yeast

text: Protocols: Strains were grown at 30°C in synthetic complete dextrose media lacking histidine [SCD-his] grown to A600=~0.6. Harvest cells by rapid centrifugation in a warm centrifuge and resuspend them in pre-warmed SD minimal medium (-aa, for 20 min) Yeast cultures were grown to A600=~0.6, pelleted, snap frozen in liquid nitrogen and ground in Buffer A (20 mM Tris-HCl [pH 8], 140 mM NaCl, 1 mM MgCl2, 0.5% NP40, 0.5 mM DTT, 1 mM PMSF, EDTA free Protease Inhibitor cocktail tablet (Roche), 100 µM NaV3O4, 5 mM NaF and 40 units/ml RNAsin) using liquid nitrogen and a 6870 Freezer Mill (Spex). Lysates were cleared through two centrifugation steps (15,000 x g at 4°C) and quantified using Bradford Reagent. 10 mg total protein was loaded onto Rabbit IgG coupled Tosyl-activated Dynabeads M-280 magnetic beads (Dynal) to ensure maximum depletion of the tagged protein from each extract. After the final wash, the beads were re-suspended in 270 µl Buffer A. A 20 µl aliquot of the sample was set aside for western blot analysis, and RNA was purified from the remaining 250 µl for RNAseq. Triplicate samples of TAP associated RNA was isolated on M-280 magnetic beads as described above. For RNA target identification, after the final wash, the beads were resuspended in 270 µl Buffer A. A 20 μl aliquot of the sample was set aside for western blot analysis, and RNA was purified from the remaining 250 μl. Total (T) RNA and paired immune precipitated (IP) RNA were isolated using a standard Trizol Reagent (Life Technologies, Carlsbad, CA) protocol and re-suspended in 10 µl diethylpyrocarbonate (DEPC) treated water. RNA was quantified using a Nanodrop 8000 spectrophotometer (Thermo Fisher Scientific, Waltham, MA). rRNA was then depleted from both total and IP RNA samples using the RibominusTM Eukaryote Kit for RNA-Seq (Life Technologies, Carlsbad, CA). Depleted samples were ethanol precipitated, washed twice with 70% ethanol and resuspended in 10 µl DEPC water. rRNA depletion was assessed on a 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA) using a RNA nanochip and the remaining RNA stored at -80°C. Sequencing libraries were generated using the whole Transcriptome Library Preparation protocol provided with the SOLiD® Total RNA-Seq Kit (Life Technologies, Carlsbad, CA) as described by the manufacturer.

text: amino acid deprivation

text: SD minus amino acids

text: Saccharomyces cerevisiae

characteristic: organism

text: Saccharomyces cerevisiae

text: expression of TAP-His-tagged eIF4G2

text: Saccharomyces cerevisiae

text: Mat a

text: fresh specimen


text: public

text: ArrayExpress

text: baker's yeast

characteristic: common name

text: amino acid deprivation

characteristic: environmental stress

characteristic: genotype

text: SD minus amino acids

characteristic: growth condition

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

text: expression of TAP-His-tagged eIF4E

characteristic: phenotype

characteristic: replicate

text: Saccharomyces cerevisiae

text: Mat a

characteristic: sex

text: fresh specimen


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: public

characteristic: SRA accession

text: ArrayExpress

text: baker's yeast

characteristic: description

text: amino acid deprivation

text: SD minus amino acids

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

text: expression of TAP-His-tagged eIF4E

text: Saccharomyces cerevisiae

text: Mat a

text: fresh specimen

characteristic: specimen with known storage state


characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: Submitter Id

text: ArrayExpress

text: baker's yeast

text: amino acid deprivation

text: MATa his3-1 leu20 met150 ura30 TIF4631::TAP-HIS3

text: SD minus amino acids

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

text: expression of TAP-His-tagged eIF4G1

text: Saccharomyces cerevisiae

text: Mat a

text: fresh specimen

characteristic: strain

characteristic: title


text: public

text: ArrayExpress

characteristic: broker name

text: baker's yeast

characteristic: common name

text: amino acid deprivation

characteristic: environmental stress

characteristic: genotype

text: SD minus amino acids

characteristic: growth condition

text: Saccharomyces cerevisiae

characteristic: organism

text: Saccharomyces cerevisiae

text: expression of TAP-His-tagged eIF4G1

characteristic: phenotype

text: Saccharomyces cerevisiae

text: Mat a

text: fresh specimen


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: public

characteristic: SRA accession

text: ArrayExpress

text: baker's yeast

text: Protocols: Strains were grown at 30°C in synthetic complete dextrose media lacking histidine [SCD-his] grown to A600=~0.6. Harvest cells by rapid centrifugation in a warm centrifuge and resuspend them in pre-warmed SC-his medium lacking glucose (-glu for 10 min). Triplicate samples of TAP associated RNA was isolated on M-280 magnetic beads as described above. For RNA target identification, after the final wash, the beads were resuspended in 270 µl Buffer A. A 20 μl aliquot of the sample was set aside for western blot analysis, and RNA was purified from the remaining 250 μl. Total (T) RNA and paired immune precipitated (IP) RNA were isolated using a standard Trizol Reagent (Life Technologies, Carlsbad, CA) protocol and re-suspended in 10 µl diethylpyrocarbonate (DEPC) treated water. RNA was quantified using a Nanodrop 8000 spectrophotometer (Thermo Fisher Scientific, Waltham, MA). rRNA was then depleted from both total and IP RNA samples using the RibominusTM Eukaryote Kit for RNA-Seq (Life Technologies, Carlsbad, CA). Depleted samples were ethanol precipitated, washed twice with 70% ethanol and resuspended in 10 µl DEPC water. rRNA depletion was assessed on a 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA) using a RNA nanochip and the remaining RNA stored at -80°C. Sequencing libraries were generated using the whole Transcriptome Library Preparation protocol provided with the SOLiD® Total RNA-Seq Kit (Life Technologies, Carlsbad, CA) as described by the manufacturer.

text: glucose deprivation

text: SC-his minus glucose

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

text: expression of TAP-His-tagged eIF4G2

characteristic: replicate

text: Saccharomyces cerevisiae

text: Mat a

characteristic: sex

text: fresh specimen


characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: Submitter Id

text: ArrayExpress

text: baker's yeast

text: Protocols: Strains were grown at 30°C in synthetic complete dextrose media lacking histidine [SCD-his] grown to A600=~0.6. Harvest cells by rapid centrifugation in a warm centrifuge and resuspend them in pre-warmed SC-his medium lacking glucose (-glu for 10 min). Yeast cultures were grown to A600=~0.6, pelleted, snap frozen in liquid nitrogen and ground in Buffer A (20 mM Tris-HCl [pH 8], 140 mM NaCl, 1 mM MgCl2, 0.5% NP40, 0.5 mM DTT, 1 mM PMSF, EDTA free Protease Inhibitor cocktail tablet (Roche), 100 µM NaV3O4, 5 mM NaF and 40 units/ml RNAsin) using liquid nitrogen and a 6870 Freezer Mill (Spex). Lysates were cleared through two centrifugation steps (15,000 x g at 4°C) and quantified using Bradford Reagent. 10 mg total protein was loaded onto Rabbit IgG coupled Tosyl-activated Dynabeads M-280 magnetic beads (Dynal) to ensure maximum depletion of the tagged protein from each extract. After the final wash, the beads were re-suspended in 270 µl Buffer A. A 20 µl aliquot of the sample was set aside for western blot analysis, and RNA was purified from the remaining 250 µl for RNAseq. Triplicate samples of TAP associated RNA was isolated on M-280 magnetic beads as described above. For RNA target identification, after the final wash, the beads were resuspended in 270 µl Buffer A. A 20 μl aliquot of the sample was set aside for western blot analysis, and RNA was purified from the remaining 250 μl. Total (T) RNA and paired immune precipitated (IP) RNA were isolated using a standard Trizol Reagent (Life Technologies, Carlsbad, CA) protocol and re-suspended in 10 µl diethylpyrocarbonate (DEPC) treated water. RNA was quantified using a Nanodrop 8000 spectrophotometer (Thermo Fisher Scientific, Waltham, MA). rRNA was then depleted from both total and IP RNA samples using the RibominusTM Eukaryote Kit for RNA-Seq (Life Technologies, Carlsbad, CA). Depleted samples were ethanol precipitated, washed twice with 70% ethanol and resuspended in 10 µl DEPC water. rRNA depletion was assessed on a 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA) using a RNA nanochip and the remaining RNA stored at -80°C. Sequencing libraries were generated using the whole Transcriptome Library Preparation protocol provided with the SOLiD® Total RNA-Seq Kit (Life Technologies, Carlsbad, CA) as described by the manufacturer.

characteristic: description

text: glucose deprivation

text: SC-his minus glucose

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

text: expression of TAP-His-tagged eIF4G2

text: Saccharomyces cerevisiae

text: Mat a

text: fresh specimen

characteristic: specimen with known storage state


text: public

text: ArrayExpress

characteristic: broker name

text: baker's yeast

characteristic: common name

text: glucose deprivation

characteristic: environmental stress

characteristic: genotype

text: SC-his minus glucose

characteristic: growth condition

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

text: expression of TAP-His-tagged eIF4E

text: Saccharomyces cerevisiae

text: Mat a

text: fresh specimen

characteristic: strain

characteristic: title