name: E-MTAB-6576:148-Ribo-tRNA-seq, control for 150

text: RIKEN Brain Science Institute

characteristic: INSDC center name

text: public

characteristic: SRA accession

text: ArrayExpress

text: baker's yeast

text: wild type genotype

text: YPD medium

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

text: 148-Ribo-tRNA-seq, control for 150


name: E-MTAB-6576:151-tRNA-seq, control for 155

status: PUBLIC

tag: attribute

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: RIKEN Brain Science Institute

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

tag: Namespace:RIKEN Brain Science Institute

characteristic: Submitter Id

text: ArrayExpress

characteristic: broker name

text: baker's yeast

characteristic: common name

text: Protocols: Wild-type, BY4741, Yeast cells were treated with or without stresses before a 2-min treatment of cycloheximide. Cells were quickly frozen in liquid nitrogen for at least 5 mins and fragmented with metal beads under frozen condition. The yeast cell was cultured in YPD medium at 30 degree The treatment of the stresses was 1 hour, except amino acid starvation, SD-mini, which the treatment time was 20 mins. 3AT means 3-Amino-1,2,4-triazole, is a competitive inhibitor of the product of the HIS3 gene. The treatment is 100mM for 1hr in histidine depletion medium. The final concentration of 4EGI-1 treatment is 100uM for 1hr. Total RNA was extracted by phenol/chloroform method. tRNA molecular and mRNA fragments were recycling for library generation. Check the details of the protocol in Chen and Tanaka, Cell Reports 2018.

characteristic: description

text: wild type genotype

characteristic: genotype

text: YPD medium

characteristic: growth condition

text: Saccharomyces cerevisiae

characteristic: organism

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

characteristic: strain

text: 151-tRNA-seq, control for 155

characteristic: title


name: E-MTAB-6576:152-Ribo-tRNA-seq, control for 156

text: RIKEN Brain Science Institute

characteristic: INSDC center name

text: public

characteristic: SRA accession

text: ArrayExpress

text: baker's yeast

text: wild type genotype

text: YPD medium

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

text: 152-Ribo-tRNA-seq, control for 156


name: E-MTAB-6576:153-mRNA-seq, control for 157

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: RIKEN Brain Science Institute

text: public

text: ArrayExpress

text: baker's yeast

text: wild type genotype

text: YPD medium

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

text: 153-mRNA-seq, control for 157


name: E-MTAB-6576:154-Ribo-mRNA-seq, control for 158

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: RIKEN Brain Science Institute

text: public

text: ArrayExpress

text: baker's yeast

text: wild type genotype

text: YPD medium

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

text: 154-Ribo-mRNA-seq, control for 158


E-MTAB-6576:19-tRNA-seq, control for 23

text: RIKEN Brain Science Institute

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: E-MTAB-6576:19-tRNA-seq, control for 23

text: ArrayExpress

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text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

text: 19-tRNA-seq, control for 23


name: E-MTAB-6576:2-Ribo-tRNA-seq, control for 4,6

text: RIKEN Brain Science Institute

text: public

characteristic: INSDC status

characteristic: Submitter Id

text: ArrayExpress

text: baker's yeast

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text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

text: 2-Ribo-tRNA-seq, control for 4,6


name: E-MTAB-6576:20-Ribo-tRNA-seq, control for 24, 3 files

text: RIKEN Brain Science Institute

text: public

text: ArrayExpress

characteristic: broker name

text: baker's yeast

characteristic: common name

text: wild type genotype

text: YPD medium

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae


name: E-MTAB-6576:21-mRNA-seq, control for 25, 3 files

text: RIKEN Brain Science Institute

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characteristic: genotype

text: YPD medium

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text: Saccharomyces cerevisiae

text: 21-mRNA-seq, control for 25, 3 files


name: E-MTAB-6576:22-Ribo-mRNA-seq, control for 26, 8 files

text: RIKEN Brain Science Institute

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text: ArrayExpress

text: baker's yeast

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text: YPD medium

characteristic: growth condition

text: Saccharomyces cerevisiae

characteristic: organism

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae


E-MTAB-6576:27-tRNA-seq, 0mM H2O2

text: RIKEN Brain Science Institute

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text: E-MTAB-6576:27-tRNA-seq, 0mM H2O2

text: ArrayExpress

text: baker's yeast

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text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

characteristic: strain

text: 27-tRNA-seq, 0mM H2O2

characteristic: title


E-MTAB-6576:28-Ribo-tRNA-seq, 0mM H2O2

text: RIKEN Brain Science Institute

characteristic: INSDC center name

text: public

characteristic: SRA accession

text: E-MTAB-6576:28-Ribo-tRNA-seq, 0mM H2O2

text: ArrayExpress

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text: YPD medium

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

text: 28-Ribo-tRNA-seq, 0mM H2O2


E-MTAB-6576:29-mRNA-seq, 0mM H2O2

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text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

text: 29-mRNA-seq, 0mM H2O2


E-MTAB-6576:30-Ribo-mRNA-seq, 0mM H2O2

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characteristic: External Id

text: RIKEN Brain Science Institute

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text: YPD medium

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

text: 30-Ribo-mRNA-seq, 0mM H2O2


name: E-MTAB-6576:43-tRNA-seq, control for 47, 49

text: RIKEN Brain Science Institute

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: ArrayExpress

text: baker's yeast

text: wild type genotype

text: YPD medium

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

text: 43-tRNA-seq, control for 47, 49


name: E-MTAB-6576:44-Ribo-tRNA-seq, control for 48, 50

text: RIKEN Brain Science Institute

text: public

characteristic: INSDC status

characteristic: Submitter Id

text: ArrayExpress

text: baker's yeast

text: wild type genotype

text: YPD medium

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

text: 44-Ribo-tRNA-seq, control for 48, 50


E-MTAB-6576:45-mRNA-seq, control for 51

text: RIKEN Brain Science Institute

text: public

text: E-MTAB-6576:45-mRNA-seq, control for 51

text: ArrayExpress

characteristic: broker name

text: baker's yeast

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text: wild type genotype

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text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

text: 45-mRNA-seq, control for 51


name: E-MTAB-6576:46-Ribo-mRNA-seq, control for 52

text: RIKEN Brain Science Institute

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text: ArrayExpress

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characteristic: description

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characteristic: genotype

text: YPD medium

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text: 46-Ribo-mRNA-seq, control for 52


E-MTAB-6576:53-mRNA-seq, control for 55

text: RIKEN Brain Science Institute

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text: E-MTAB-6576:53-mRNA-seq, control for 55

text: ArrayExpress

text: baker's yeast

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characteristic: growth condition

text: Saccharomyces cerevisiae

characteristic: organism

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

text: 53-mRNA-seq, control for 55


name: E-MTAB-6576:54-Ribo-mRNA-seq, control for 56

text: RIKEN Brain Science Institute

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text: ArrayExpress

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text: YPD medium

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

characteristic: strain

text: 54-Ribo-mRNA-seq, control for 56

characteristic: title


E-MTAB-6576:57-mRNA-seq, control for 59

text: RIKEN Brain Science Institute

characteristic: INSDC center name

text: public

characteristic: SRA accession

text: E-MTAB-6576:57-mRNA-seq, control for 59

text: ArrayExpress

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text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

text: 57-mRNA-seq, control for 59


name: E-MTAB-6576:58-Ribo-mRNA-seq, control for 60

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: RIKEN Brain Science Institute

text: public

text: ArrayExpress

text: baker's yeast

text: wild type genotype

text: YPD medium

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

text: 58-Ribo-mRNA-seq, control for 60


E-MTAB-6576:61-tRNA-seq, control for 63

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: RIKEN Brain Science Institute

text: public

text: E-MTAB-6576:61-tRNA-seq, control for 63

text: ArrayExpress

text: baker's yeast

text: wild type genotype

text: YPD medium

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

text: 61-tRNA-seq, control for 63


name: E-MTAB-6576:62-Ribo-tRNA-seq, control for 64

text: RIKEN Brain Science Institute

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: ArrayExpress

text: baker's yeast

text: wild type genotype

text: YPD medium

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

text: 62-Ribo-tRNA-seq, control for 64


E-MTAB-6576:65-tRNA-seq, control for 67

text: RIKEN Brain Science Institute

text: public

characteristic: INSDC status

text: E-MTAB-6576:65-tRNA-seq, control for 67

characteristic: Submitter Id

text: ArrayExpress

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text: wild type genotype

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text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

text: 65-tRNA-seq, control for 67


name: E-MTAB-6576:66-Ribo-tRNA-seq, control for 68

text: RIKEN Brain Science Institute

text: public

text: ArrayExpress

characteristic: broker name

text: baker's yeast

characteristic: common name

text: wild type genotype

text: YPD medium

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

text: 66-Ribo-tRNA-seq, control for 68


E-MTAB-6576:69-tRNA-seq, control for 71

text: RIKEN Brain Science Institute

text: public

text: E-MTAB-6576:69-tRNA-seq, control for 71

text: ArrayExpress

text: baker's yeast

characteristic: description

text: wild type genotype

characteristic: genotype

text: YPD medium

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

text: 69-tRNA-seq, control for 71


name: E-MTAB-6576:70-Ribo-tRNA-seq, control for 72

text: RIKEN Brain Science Institute

text: public

text: ArrayExpress

text: baker's yeast

text: wild type genotype

text: YPD medium

characteristic: growth condition

text: Saccharomyces cerevisiae

characteristic: organism

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

text: 70-Ribo-tRNA-seq, control for 72


name: E-MTAB-6576:73-tRNA-seq, control for 77, 81, 85

text: RIKEN Brain Science Institute

text: public

text: ArrayExpress

text: baker's yeast

text: wild type genotype

text: YPD medium

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

characteristic: strain

text: 73-tRNA-seq, control for 77, 81, 85

characteristic: title


name: E-MTAB-6576:74-Ribo-tRNA-seq, control for 78, 82,86

text: RIKEN Brain Science Institute

characteristic: INSDC center name

text: public

characteristic: SRA accession

text: ArrayExpress

text: baker's yeast

text: wild type genotype

text: YPD medium

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

text: 74-Ribo-tRNA-seq, control for 78, 82,86


name: E-MTAB-6576:75-mRNA-seq, control for 79, 83, 87

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: RIKEN Brain Science Institute

text: public

text: ArrayExpress

text: baker's yeast

text: wild type genotype

text: YPD medium

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

text: 75-mRNA-seq, control for 79, 83, 87


name: E-MTAB-6576:76-Ribo-mRNA-seq, control for 80, 84, 88

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: RIKEN Brain Science Institute

text: public

text: ArrayExpress

text: baker's yeast

text: wild type genotype

text: YPD medium

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae


E-MTAB-6576:77-tRNA-seq, pre-CHX

text: RIKEN Brain Science Institute

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: E-MTAB-6576:77-tRNA-seq, pre-CHX

text: ArrayExpress

text: baker's yeast

text: wild type genotype

text: YPD medium

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

text: 77-tRNA-seq, pre-CHX


text: RIKEN Brain Science Institute

text: public

characteristic: INSDC status

text: E-MTAB-6576:78-Ribo-tRNA-seq, post-lysis-CHX

characteristic: Submitter Id

text: ArrayExpress

text: baker's yeast

text: wild type genotype

text: YPD medium

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

text: 78-Ribo-tRNA-seq, post-lysis-CHX


E-MTAB-6576:79-mRNA-seq, post-lysis-CHX

text: RIKEN Brain Science Institute

text: public

text: E-MTAB-6576:79-mRNA-seq, post-lysis-CHX

text: ArrayExpress

characteristic: broker name

text: baker's yeast

characteristic: common name

text: wild type genotype

text: YPD medium

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

text: 79-mRNA-seq, post-lysis-CHX


text: RIKEN Brain Science Institute

text: public

text: E-MTAB-6576:80-Ribo-mRNA-seq, post-lysis-CHX

text: ArrayExpress

text: baker's yeast

characteristic: description

text: wild type genotype

characteristic: genotype

text: YPD medium

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

text: 80-Ribo-mRNA-seq, post-lysis-CHX


E-MTAB-6576:89-tRNA-seq, control for 91

text: RIKEN Brain Science Institute

text: public

text: E-MTAB-6576:89-tRNA-seq, control for 91

text: ArrayExpress

text: baker's yeast

text: wild type genotype

text: YPD medium

characteristic: growth condition

text: Saccharomyces cerevisiae

characteristic: organism

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

text: 89-tRNA-seq, control for 91


name: E-MTAB-6576:9-Ribo-tRNA-seq, control for 10

text: RIKEN Brain Science Institute

text: public

text: ArrayExpress

text: baker's yeast

text: wild type genotype

text: YPD medium

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

characteristic: strain

text: 9-Ribo-tRNA-seq, control for 10

characteristic: title


name: E-MTAB-6576:90-Ribo-tRNA-seq, control for 92

text: RIKEN Brain Science Institute

characteristic: INSDC center name

text: public

characteristic: SRA accession

text: ArrayExpress

text: baker's yeast

text: wild type genotype

text: YPD medium

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

text: 90-Ribo-tRNA-seq, control for 92


E-MTAB-6576:93-tRNA-seq, control for 95

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: RIKEN Brain Science Institute

text: public

text: E-MTAB-6576:93-tRNA-seq, control for 95

text: ArrayExpress

text: baker's yeast

text: wild type genotype

text: YPD medium

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

text: 93-tRNA-seq, control for 95


name: E-MTAB-6576:94-Ribo-tRNA-seq, control for 96

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: RIKEN Brain Science Institute

text: public

text: ArrayExpress

text: baker's yeast

text: wild type genotype

text: YPD medium

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

text: 94-Ribo-tRNA-seq, control for 96


name: E-MTAB-6576:97-tRNA-seq, control for 99, 101, 103

text: RIKEN Brain Science Institute

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: ArrayExpress

text: baker's yeast

text: wild type genotype

text: YPD medium

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

text: 97-tRNA-seq, control for 99, 101, 103


name: E-MTAB-6576:98-Ribo-tRNA-seq, control for 100, 102, 104

text: RIKEN Brain Science Institute

text: public

characteristic: INSDC status

characteristic: Submitter Id

text: ArrayExpress

text: baker's yeast

text: wild type genotype

text: YPD medium

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae


E-MTAB-6576:135-tRNA-seq, dtrm10 rep2

text: RIKEN Brain Science Institute

text: public

text: E-MTAB-6576:135-tRNA-seq, dtrm10 rep2

text: ArrayExpress

characteristic: broker name

text: baker's yeast

characteristic: common name

text: dtrm10 knockout

text: YPD medium

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

text: 135-tRNA-seq, dtrm10 rep2


text: RIKEN Brain Science Institute

text: public

text: E-MTAB-6576:136-Ribo-tRNA-seq, dtrm10 rep2

text: ArrayExpress

text: baker's yeast

characteristic: description

text: dtrm10 knockout

characteristic: genotype

text: YPD medium

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

text: 136-Ribo-tRNA-seq, dtrm10 rep2


E-MTAB-6576:137-tRNA-seq, dabp140 rep2

text: RIKEN Brain Science Institute

text: public

text: E-MTAB-6576:137-tRNA-seq, dabp140 rep2

text: ArrayExpress

text: baker's yeast

text: dtrm10 knockout

text: YPD medium

characteristic: growth condition

text: Saccharomyces cerevisiae

characteristic: organism

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

text: 137-tRNA-seq, dabp140 rep2


text: RIKEN Brain Science Institute

text: public

text: E-MTAB-6576:138-Ribo-tRNA-seq, dabp140 rep2

text: ArrayExpress

text: baker's yeast

text: dabp140 knockout

text: YPD medium

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

characteristic: strain

text: 138-Ribo-tRNA-seq, dabp140 rep2

characteristic: title


E-MTAB-6576:141-tRNA-seq, dtrm1 rep2

text: RIKEN Brain Science Institute

characteristic: INSDC center name

text: public

characteristic: SRA accession

text: E-MTAB-6576:141-tRNA-seq, dtrm1 rep2

text: ArrayExpress

text: baker's yeast

text: dtrm1 knockout

text: YPD medium

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

text: 141-tRNA-seq, dtrm1 rep2


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: RIKEN Brain Science Institute

text: public

text: E-MTAB-6576:142-Ribo-tRNA-seq, dtrm1 rep2

text: ArrayExpress

text: baker's yeast

text: dtrm1 knockout

text: YPD medium

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

text: 142-Ribo-tRNA-seq, dtrm1 rep2


E-MTAB-6576:143-tRNA-seq, dtrm10 rep3

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: RIKEN Brain Science Institute

text: public

text: E-MTAB-6576:143-tRNA-seq, dtrm10 rep3

text: ArrayExpress

text: baker's yeast

text: dtrm10 knockout

text: YPD medium

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

text: 143-tRNA-seq, dtrm10 rep3


text: RIKEN Brain Science Institute

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: E-MTAB-6576:144-Ribo-tRNA-seq, dtrm10 rep3

text: ArrayExpress

text: baker's yeast

text: dtrm10 knockout

text: YPD medium

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

text: 144-Ribo-tRNA-seq, dtrm10 rep3


E-MTAB-6576:145-tRNA-seq, dabp140 rep3

text: RIKEN Brain Science Institute

text: public

characteristic: INSDC status

text: E-MTAB-6576:145-tRNA-seq, dabp140 rep3

characteristic: Submitter Id

text: ArrayExpress

text: baker's yeast

text: dabp140 knockout

text: YPD medium

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

text: 145-tRNA-seq, dabp140 rep3


text: RIKEN Brain Science Institute

text: public

text: E-MTAB-6576:146-Ribo-tRNA-seq, dabp140 rep3

text: ArrayExpress

characteristic: broker name

text: baker's yeast

characteristic: common name

text: dabp140 knockout

text: YPD medium

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

text: 146-Ribo-tRNA-seq, dabp140 rep3


E-MTAB-6576:5-tRNA-seq, dtrm1 rep1

text: RIKEN Brain Science Institute

text: public

text: E-MTAB-6576:5-tRNA-seq, dtrm1 rep1

text: ArrayExpress

text: baker's yeast

characteristic: description

text: dtrm1 knockout

characteristic: genotype

text: YPD medium

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

text: 5-tRNA-seq, dtrm1 rep1


E-MTAB-6576:6-Ribo-tRNA-seq, dtrm1 rep1

text: RIKEN Brain Science Institute

text: public

text: E-MTAB-6576:6-Ribo-tRNA-seq, dtrm1 rep1

text: ArrayExpress

text: baker's yeast

text: dtrm1 knockout

text: YPD medium

characteristic: growth condition

text: Saccharomyces cerevisiae

characteristic: organism

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

text: 6-Ribo-tRNA-seq, dtrm1 rep1


E-MTAB-6576:7-tRNA-seq, dtrm10 rep1

text: RIKEN Brain Science Institute

text: public

text: E-MTAB-6576:7-tRNA-seq, dtrm10 rep1

text: ArrayExpress

text: baker's yeast

text: dtrm10 knockout

text: YPD medium

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

characteristic: strain

text: 7-tRNA-seq, dtrm10 rep1

characteristic: title


E-MTAB-6576:8-tRNA-seq, dabp140 rep1

text: RIKEN Brain Science Institute

characteristic: INSDC center name

text: public

characteristic: SRA accession

text: E-MTAB-6576:8-tRNA-seq, dabp140 rep1

text: ArrayExpress

text: baker's yeast

text: dabp140 knockout

text: YPD medium

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

text: 8-tRNA-seq, dabp140 rep1


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: UNIVERSITY OF COLOGNE

text: public

tag: Namespace:UNIVERSITY OF COLOGNE

text: not provided

characteristic: collection date

text: Germany, SN, Dresden

characteristic: country

text: Acinetobacter pittii

text: Acinetobacter pittii


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: SC

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: Peptoclostridium difficile R20291

text: Peptoclostridium difficile R20291


text: SC

text: public

characteristic: INSDC status

characteristic: Submitter Id

text: Streptococcus suis

text: Streptococcus suis


text: SC

text: public

characteristic: anonymized name

text: Viet Nam

text: Streptococcus suis

text: Streptococcus suis

characteristic: serovar

text: Homo sapiens

characteristic: specific host


text: Armillaria mellea

characteristic: ArrayExpress-Species

text: SC

text: public

text: Armillaria mellea B497

characteristic: organism

text: Armillaria mellea B497


text: TGAC

characteristic: INSDC center name

text: public

text: durum wheat

characteristic: common name

text: Bulked sample of 14 RSL lines with high grain protein concentration, library size 400 bp

characteristic: description

text: Triticum turgidum subsp. durum

text: Triticum turgidum subsp. durum

type: has member


LDN

text: TGAC

text: public

characteristic: SRA accession

text: LDN

text: durum wheat

text: Durum wheat 'Langdon'

text: Triticum turgidum subsp. durum

text: Triticum turgidum subsp. durum


text: TGAC

text: public

text: durum wheat

text: Bulked sample of 14 RSL lines with high grain protein concentration, library size 250 bp

text: Triticum turgidum subsp. durum

text: Triticum turgidum subsp. durum


text: TGAC

text: public

text: durum wheat

text: Bulked sample of 15 RSL lines with low grain protein concentration, library size 250 bp

text: Triticum turgidum subsp. durum

text: Triticum turgidum subsp. durum


text: TGAC

text: public

text: durum wheat

text: Recombinant substitution line RSL65 from Durum wheat LDN x wild Emmer 6B substitution line LDN (DIC6B)

text: Triticum turgidum subsp. durum

text: Triticum turgidum subsp. durum


text: TGAC

text: public

text: durum wheat

text: Bulked sample of 15 RSL lines with low grain protein concentration, library size 400 bp

text: Triticum turgidum subsp. durum

text: Triticum turgidum subsp. durum


text: Mus musculus

characteristic: ENA-FIRST-PUBLIC

text: SC

text: public

text: SC_MTV5229156-sc-2011-12-06T15:16:12Z-1281389

text: house mouse

text: Mus musculus

text: Mus musculus


text: Mus Musculus

text: SC

text: public

text: 1953STDY5220042-sc-2011-09-02T14:17:11Z-1270062

text: house mouse

text: Mus musculus

text: Mus musculus


text: Mus Musculus

text: SC

text: public

text: 1953STDY5220050-sc-2011-09-02T14:17:11Z-1270070

text: house mouse

text: Mus musculus

text: Mus musculus


text: Mus Musculus

text: SC

text: public

text: 1953STDY5220090-sc-2011-09-02T14:17:14Z-1270110

text: house mouse

text: Mus musculus

text: Mus musculus


text: Mus Musculus

text: SC

text: public

text: 1953STDY5220082-sc-2011-09-02T14:17:14Z-1270102

text: house mouse

text: Mus musculus

text: Mus musculus


text: Mus Musculus

text: SC

text: public

text: 1953STDY5220066-sc-2011-09-02T14:17:12Z-1270086

text: house mouse

text: Mus musculus

text: Mus musculus


text: Mus musculus

text: SC

text: public

text: SC_MTV5229155-sc-2011-12-06T15:16:12Z-1281388

text: house mouse

text: Mus musculus

text: Mus musculus


text: Mus musculus

text: SC

text: public

text: SC_MTV5229157-sc-2011-12-06T15:16:13Z-1281390

text: house mouse

text: Mus musculus

text: Mus musculus


text: Mus Musculus

text: SC

text: public

text: 1953STDY5220034-sc-2011-09-02T14:17:09Z-1270054

text: house mouse

text: Mus musculus

text: Mus musculus


text: Mus Musculus

text: SC

text: public

text: 1953STDY5220058-sc-2011-09-02T14:17:12Z-1270078

text: house mouse

text: Mus musculus

text: Mus musculus


text: Mus Musculus

text: SC

text: public

text: 1953STDY5220074-sc-2011-09-02T14:17:13Z-1270094

text: house mouse

text: Mus musculus

text: Mus musculus


text: CEA/Centre National de Genotypage

text: public

tag: Namespace:CEA/Centre National de Genotypage

text: ArrayExpress

characteristic: broker name

characteristic: cell line

text: embryonic stem cell

characteristic: cell type

text: house mouse

text: Protocols: We used the recombineering technology (Liu, P., Jenkins, N.A. and Copeland, N.G. (2003) Genome Res.) to generate the targeting vectors that introduce the triple affinity tag in the subunits of Pol III, TFIIIB, TFIIIC, and TFIIS. The 46C ES cell line (Ying, Q.L., Stavridis, M., Griffiths, D., Li, M. and Smith, A. (2003) Nat. Biotech.) was transfected by electroporation with each targeting vector. Cells were plated in D15 medium as described (Tessarollo, L. (2001). Methods Mol Biol.) and selected with G418. Individual ES cell colonies were collected seven days after electroporation, amplified and genotyped by Southern blotting, in order to identify the clones that underwent a homologous recombination event. In these clones, a sequence encoding a 6 Histidine-Flag-HA tag followed by a neomycin resistance marker flanked by loxP sites, was inserted just after the last codon of the gene encoding the protein to be tagged. For TCEA1, the tag was inserted just after the start codon. The integration of the cassette at the right loci was verified by Southern blotting using three or four different restriction enzymes and PCR. Transient transfection with a Cre recombinase expression vector was used to remove the selection cassette. The karyotypes of all cell lines were verified. The genes that were modified in the cell lines encoded RPC1 (MGI:2681836), RPC4 (MGI:1914315), BRF1 (MGI:1919558), BRF2 (MGI:1913903), TFIIIC220 (MGI:107887), TFIIIC110 (MGI:1919002), TFIIIC90 (MGI:2138937) and TCEA1 (MGI:1196624) respectively. The expression of the tagged versions of the proteins was verified by western blotting using HA7 anti-HA antibodies (Sigma). Untagged ES cell lines (46C, 46C-2) are used as a negative control for the ChIP-seq experiment. ES cells were cultured on embryonic fibroblast feeder cells blocked with mitomycin C in D15 medium (Dulbecco Modified Eagle Medium High Glucose supplemented with 15% FBS, 2mML-glutamine, 50 units/ml penicillin, 50 ug/ml streptomycin, 0.1 mM nonessential amino acids (all from GIBCO), 0.1 mM 2-mercaptoethanol [Sigma] and 1,000 units/ml LIF). ES cells were maintained at 37C, 5% carbon dioxide, fed with fresh media daily, and transferred to new plates after trypsinization. Typically 150-200 million cells were collected for each ChIP experiment. The cellular proteins and DNA were cross-linked by the addition of formaldehyde (0.4% final concentration) in cell culture media. The plates were incubated for 10 min at room temperature then, the reaction was stopped by the addition of glycine (0.125 M final concentration). The cells were washed twice with 10 ml chilled PBS. Each plate was scraped with 2 ml PBS with protease inhibitors (Roche complete, 10 mM PMSF dissolved in ethanol), pelleted by centrifugation at 2500 rpm and resuspended in 1 ml per dish of FA/SDS buffer (50 mM Tris-HCl pH 7.5, 150 mM NaCl, 1 mM EDTA, 1% Triton X100, 0.1% Na-deoxycholate, 0.1% SDS) with protease inhibitors and incubated on ice for 15 min. The subsequent operations were performed at 4C. Chromatin was collected by centrifugation for 20 min at 12 000 rpm, resuspended in the same amount of FA/SDS and put on a rotating wheel for 1 hr, centrifuged and resuspended in 0.4 volume of FA/SDS with protease inhibitors. 400 ul batches of chromatin were fragmented with a sonicator (Diagenode) to generate DNA fragments of 300-400 bp mean size. The chromatin was collected by centrifugation at 14 000 rpm for 10 min and was kept at -80C until needed. The immunoglobulin-coupled magnetic beads (Dynal) used in the chromatin immunoprecipitation experiments were prepared essentially as described previously (Esnault, C., Ghavi-Helm, Y., Brun, S., Soutourina, J., Van Berkum, N., Boschiero, C., Holstege, F. and Werner, M. (2008) Mol. Cell). Anti-HA antibody was HA7 H-3663 (Sigma) and anti-Flag anti-body was F-1804 (Sigma). For each ChIP experiment, 240 ug DNA (RPC1, RPC4, 46C) or 750 ug DNA (BRF1, BRF2) of sonicated chromatin were incubated with 150 ul beads for 2 hr at room temperature. The beads were magnetically pelleted and the supernatant was removed. The beads were washed with 1 ml of low salt buffer (pH 8.0, 20 mM Tris-HCl, 2 mM EDTA, 150 mM NaCl, 1% Triton X-100, 0.1% SDS), then with the same volume of high salt buffer (pH 8.0, 20 mM Tris-HCl, 2 mM EDTA, 500 mM NaCl, 1% Triton X-100, 0.1% SDS), then with low LiCl buffer (pH 8.0, 10 mM Tris-HCl, 1 mM EDTA, 250 mM LiCl, 1% NP-40, 1% deoxycholate) and finally twice with TE (pH 8.0, 10 mM Tris-HCl, 1 mM EDTA). The first ChIP was performed using the anti-HA antibody. The bound chromatin was eluted using FA/SDS buffer containing the HA peptide (0.5 mg/ml; Ansynth Service) for 4 h at 16C then overnight at 4C. For the second ChIP, the supernatant was incubated with 50 ul beads coupled to anti-Flag antibodies which were treated as above except for the elution that was performed by incubation with a buffer containing 1% SDS and 0.1 M NaHCO3. Reversal of the cross-links and DNA purification were performed as described previously (Kuras, L., Borggrefe, T. and Kornberg, R.D. (2003) Proc. Natl. Acad. Sci. USA).

text: transfection

characteristic: geneticmodification

text: BRF2 tagged

characteristic: genotype

text: Mus musculus

text: Mus musculus

text: Mus musculus

text: male

characteristic: sex

characteristic: title


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: CEA/Centre National de Genotypage

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: Submitter Id

text: ArrayExpress

text: embryonic stem cell

text: house mouse

text: Protocols: We used the recombineering technology (Liu, P., Jenkins, N.A. and Copeland, N.G. (2003) Genome Res.) to generate the targeting vectors that introduce the triple affinity tag in the subunits of Pol III, TFIIIB, TFIIIC, and TFIIS. The 46C ES cell line (Ying, Q.L., Stavridis, M., Griffiths, D., Li, M. and Smith, A. (2003) Nat. Biotech.) was transfected by electroporation with each targeting vector. Cells were plated in D15 medium as described (Tessarollo, L. (2001). Methods Mol Biol.) and selected with G418. Individual ES cell colonies were collected seven days after electroporation, amplified and genotyped by Southern blotting, in order to identify the clones that underwent a homologous recombination event. In these clones, a sequence encoding a 6 Histidine-Flag-HA tag followed by a neomycin resistance marker flanked by loxP sites, was inserted just after the last codon of the gene encoding the protein to be tagged. For TCEA1, the tag was inserted just after the start codon. The integration of the cassette at the right loci was verified by Southern blotting using three or four different restriction enzymes and PCR. Transient transfection with a Cre recombinase expression vector was used to remove the selection cassette. The karyotypes of all cell lines were verified. The genes that were modified in the cell lines encoded RPC1 (MGI:2681836), RPC4 (MGI:1914315), BRF1 (MGI:1919558), BRF2 (MGI:1913903), TFIIIC220 (MGI:107887), TFIIIC110 (MGI:1919002), TFIIIC90 (MGI:2138937) and TCEA1 (MGI:1196624) respectively. The expression of the tagged versions of the proteins was verified by western blotting using HA7 anti-HA antibodies (Sigma). Untagged ES cell lines (46C, 46C-2) are used as a negative control for the ChIP-seq experiment. ES cells were cultured on embryonic fibroblast feeder cells blocked with mitomycin C in D15 medium (Dulbecco Modified Eagle Medium High Glucose supplemented with 15% FBS, 2mML-glutamine, 50 units/ml penicillin, 50 ug/ml streptomycin, 0.1 mM nonessential amino acids (all from GIBCO), 0.1 mM 2-mercaptoethanol [Sigma] and 1,000 units/ml LIF). ES cells were maintained at 37C, 5% carbon dioxide, fed with fresh media daily, and transferred to new plates after trypsinization. Typically 150-200 million cells were collected for each ChIP experiment. The cellular proteins and DNA were cross-linked by the addition of formaldehyde (1% final concentration) in cell culture media. The plates were incubated for 10 min at room temperature then, the reaction was stopped by the addition of glycine (0.125 M final concentration). The cells were washed twice with 10 ml chilled PBS. Each plate was scraped with 2 ml PBS with protease inhibitors (Roche complete, 10 mM PMSF dissolved in ethanol). Untagged ES cells (46C-2), TFIIIC subunits and TCEA1 ChIPs were fragmented using MNase I. The protocol will be described in details elsewhere (M. Gerard, manuscript in preparation).

text: transfection

text: TFIIIC110 tagged

text: Mus musculus

text: Mus musculus

text: Mus musculus

text: male


text: CEA/Centre National de Genotypage

characteristic: INSDC center name

text: public

text: ArrayExpress

text: embryonic stem cell

text: house mouse

characteristic: common name

text: transfection

text: RPC4 tagged

text: Mus musculus

characteristic: organism

text: Mus musculus

text: Mus musculus

text: male


characteristic: ENA-FIRST-PUBLIC

text: CEA/Centre National de Genotypage

text: public

characteristic: SRA accession

text: ArrayExpress

text: embryonic stem cell

text: house mouse

characteristic: description

text: transfection

text: BRF1 tagged

text: Mus musculus

text: Mus musculus

text: Mus musculus

text: male


text: CEA/Centre National de Genotypage

text: public

text: ArrayExpress

characteristic: broker name

characteristic: cell line

text: embryonic stem cell

characteristic: cell type

text: house mouse

text: transfection

text: TFIIIC220 tagged

text: Mus musculus

text: Mus musculus

text: Mus musculus

text: male


text: CEA/Centre National de Genotypage

text: public

text: ArrayExpress

text: embryonic stem cell

text: house mouse

text: transfection

characteristic: geneticmodification

text: TCEA1 tagged

characteristic: genotype

text: Mus musculus

text: Mus musculus

text: Mus musculus

text: male

characteristic: sex


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: CEA/Centre National de Genotypage

text: public

text: ArrayExpress

text: embryonic stem cell

text: house mouse

text: Protocols: ES cells were cultured on embryonic fibroblast feeder cells blocked with mitomycin C in D15 medium (Dulbecco Modified Eagle Medium High Glucose supplemented with 15% FBS, 2mML-glutamine, 50 units/ml penicillin, 50 ug/ml streptomycin, 0.1 mM nonessential amino acids (all from GIBCO), 0.1 mM 2-mercaptoethanol [Sigma] and 1,000 units/ml LIF). ES cells were maintained at 37C, 5% carbon dioxide, fed with fresh media daily, and transferred to new plates after trypsinization. Typically 150-200 million cells were collected for each ChIP experiment. The cellular proteins and DNA were cross-linked by the addition of formaldehyde (0.4% final concentration) in cell culture media. The plates were incubated for 10 min at room temperature then, the reaction was stopped by the addition of glycine (0.125 M final concentration). The cells were washed twice with 10 ml chilled PBS. Each plate was scraped with 2 ml PBS with protease inhibitors (Roche complete, 10 mM PMSF dissolved in ethanol), pelleted by centrifugation at 2500 rpm and resuspended in 1 ml per dish of FA/SDS buffer (50 mM Tris-HCl pH 7.5, 150 mM NaCl, 1 mM EDTA, 1% Triton X100, 0.1% Na-deoxycholate, 0.1% SDS) with protease inhibitors and incubated on ice for 15 min. The subsequent operations were performed at 4C. Chromatin was collected by centrifugation for 20 min at 12 000 rpm, resuspended in the same amount of FA/SDS and put on a rotating wheel for 1 hr, centrifuged and resuspended in 0.4 volume of FA/SDS with protease inhibitors. 400 ul batches of chromatin were fragmented with a sonicator (Diagenode) to generate DNA fragments of 300-400 bp mean size. The chromatin was collected by centrifugation at 14 000 rpm for 10 min and was kept at -80C until needed. The immunoglobulin-coupled magnetic beads (Dynal) used in the chromatin immunoprecipitation experiments were prepared essentially as described previously (Esnault, C., Ghavi-Helm, Y., Brun, S., Soutourina, J., Van Berkum, N., Boschiero, C., Holstege, F. and Werner, M. (2008) Mol. Cell). Anti-HA antibody was HA7 H-3663 (Sigma) and anti-Flag anti-body was F-1804 (Sigma). For each ChIP experiment, 240 ug DNA (RPC1, RPC4, 46C) or 750 ug DNA (BRF1, BRF2) of sonicated chromatin were incubated with 150 ul beads for 2 hr at room temperature. The beads were magnetically pelleted and the supernatant was removed. The beads were washed with 1 ml of low salt buffer (pH 8.0, 20 mM Tris-HCl, 2 mM EDTA, 150 mM NaCl, 1% Triton X-100, 0.1% SDS), then with the same volume of high salt buffer (pH 8.0, 20 mM Tris-HCl, 2 mM EDTA, 500 mM NaCl, 1% Triton X-100, 0.1% SDS), then with low LiCl buffer (pH 8.0, 10 mM Tris-HCl, 1 mM EDTA, 250 mM LiCl, 1% NP-40, 1% deoxycholate) and finally twice with TE (pH 8.0, 10 mM Tris-HCl, 1 mM EDTA). The first ChIP was performed using the anti-HA antibody. The bound chromatin was eluted using FA/SDS buffer containing the HA peptide (0.5 mg/ml; Ansynth Service) for 4 h at 16C then overnight at 4C. For the second ChIP, the supernatant was incubated with 50 ul beads coupled to anti-Flag antibodies which were treated as above except for the elution that was performed by incubation with a buffer containing 1% SDS and 0.1 M NaHCO3. Reversal of the cross-links and DNA purification were performed as described previously (Kuras, L., Borggrefe, T. and Kornberg, R.D. (2003) Proc. Natl. Acad. Sci. USA).

text: transfection

text: untagged cell

text: Mus musculus

text: Mus musculus

text: Mus musculus

text: male

characteristic: title


text: CEA/Centre National de Genotypage

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: ArrayExpress

text: embryonic stem cell

text: house mouse

text: transfection

text: RPC1 tagged

text: Mus musculus

text: Mus musculus

text: Mus musculus

text: male


text: CEA/Centre National de Genotypage

characteristic: INSDC center name

text: public

characteristic: Submitter Id

text: ArrayExpress

text: embryonic stem cell

text: house mouse

characteristic: common name

text: Protocols: ES cells were cultured on embryonic fibroblast feeder cells blocked with mitomycin C in D15 medium (Dulbecco Modified Eagle Medium High Glucose supplemented with 15% FBS, 2mML-glutamine, 50 units/ml penicillin, 50 ug/ml streptomycin, 0.1 mM nonessential amino acids (all from GIBCO), 0.1 mM 2-mercaptoethanol [Sigma] and 1,000 units/ml LIF). ES cells were maintained at 37C, 5% carbon dioxide, fed with fresh media daily, and transferred to new plates after trypsinization. Typically 150-200 million cells were collected for each ChIP experiment. The cellular proteins and DNA were cross-linked by the addition of formaldehyde (1% final concentration) in cell culture media. The plates were incubated for 10 min at room temperature then, the reaction was stopped by the addition of glycine (0.125 M final concentration). The cells were washed twice with 10 ml chilled PBS. Each plate was scraped with 2 ml PBS with protease inhibitors (Roche complete, 10 mM PMSF dissolved in ethanol). Untagged ES cells (46C-2), TFIIIC subunits and TCEA1 ChIPs were fragmented using MNase I. The protocol will be described in details elsewhere (M. Gerard, manuscript in preparation).

text: transfection

text: untagged cell

text: Mus musculus

text: Mus musculus

text: Mus musculus

text: male


characteristic: ENA-FIRST-PUBLIC

text: CEA/Centre National de Genotypage

text: public

characteristic: SRA accession

text: ArrayExpress

text: embryonic stem cell

text: house mouse

text: transfection

text: TFIIIC90 tagged

text: Mus musculus

characteristic: organism

text: Mus musculus

text: Mus musculus

text: male


text: unidentified

characteristic: ArrayExpress-Species

text: SC

text: public

text: unidentified

text: unidentified


text: unidentified

text: SC

text: public

text: E184_B13-sc-2011-09-14T15:57:49Z-1278933

text: unidentified

text: unidentified


text: unidentified

text: SC

text: public

text: E260_L14-sc-2011-09-14T15:57:51Z-1278937

text: unidentified

text: unidentified


text: unidentified

text: SC

text: public

text: E249_B22-sc-2011-09-14T15:57:50Z-1278935

text: unidentified

text: unidentified


text: CRI

text: public

text: ArrayExpress

characteristic: broker name

characteristic: cell line

text: epithelial

characteristic: cell type

text: human

text: Protocols: MCF7 cells were grown in DMEM medium, supplemented with 8% FBS and standard antibiotics. Three days prior to hormonal treatment, cells were switched to phenolred-free DMEM, supplemented with 5% charcoal-treated FBS and standard antibiotics. Medium was replaced daily. Serum-deprived MCF7 cells were treated with 10-7 M Estradiol in 20ml medium for 2 hours and 50 minutes, after which cells were fixed with1% PFA and processed as described (Schmidt et al., Methods 48:3 pp240-2482009). Cell lysis and precipitation procedures were performed as described (Schmidt et al., Methods 48:3 pp240-248 2009).

characteristic: description

text: Homo sapiens

text: Homo sapiens

text: breast

characteristic: organism part

text: Homo sapiens

text: female


A.thaliana-RNA-Seq

characteristic: ENA-LAST-UPDATE

text: SRA-Webin

characteristic: ENA-SUBMISSION-TOOL

characteristic: External Id

text: MPI-TUEBINGEN

text: public

text: A.thaliana-RNA-Seq

text: thale cress

text: A.thaliana RNA-Seq data of mutation accumulation lines, leaf tissue

text: Arabidopsis thaliana

text: Arabidopsis thaliana

text: RNA-Seq


A.thaliana-BS-Seq

text: SRA-Webin

text: MPI-TUEBINGEN

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: A.thaliana-BS-Seq

text: thale cress

text: A.thaliana BS-Seq data of mutation accumulation lines, leaf tissue

text: Arabidopsis thaliana

text: Arabidopsis thaliana

text: BS-Seq

characteristic: title


text: SRA-Webin

characteristic: INSDC center name

text: public

characteristic: INSDC status

characteristic: Submitter Id

text: human

text: Day14 MCF7 cells treated with shRNA pool 2k

text: Homo sapiens

text: Homo sapiens


characteristic: ENA-FIRST-PUBLIC

text: SRA-Webin

text: public

characteristic: SRA accession

text: human

characteristic: common name

text: Time0 MCF7 cells treated with shRNA pool 2k

text: Homo sapiens

text: Homo sapiens


text: SRA-Webin

text: public

text: human

text: Day7 MCF7 cells treated with shRNA pool 10k

text: Homo sapiens

characteristic: organism

text: Homo sapiens


text: SRA-Webin

text: public

text: human

text: Time0 MCF7 cells treated with shRNA pool 5k

text: Homo sapiens

text: Homo sapiens


text: SRA-Webin

text: public

text: human

text: Day7 MCF7 cells treated with shRNA pool 2k

text: Homo sapiens

text: Homo sapiens


text: SRA-Webin

text: public

text: human

text: Day7 MCF7 cells treated with shRNA pool 5k

text: Homo sapiens

text: Homo sapiens


text: SRA-Webin

text: public

text: human

text: Day14 MCF7 cells treated with shRNA pool 5k

text: Homo sapiens

text: Homo sapiens


text: SRA-Webin

text: public

text: human

text: Reference MCF7 cells treated with shRNA pool 201-300

text: Homo sapiens

text: Homo sapiens


text: SRA-Webin

text: public

text: human

text: Day14 MCF7 cells treated with shRNA pool 10k

text: Homo sapiens

text: Homo sapiens


text: SRA-Webin

text: public

text: human

text: Depletion MCF7 cells treated with shRNA pool 201-300

text: Homo sapiens

text: Homo sapiens


text: SRA-Webin

text: public

text: human

text: Time0 MCF7 cells treated with shRNA pool 10k

text: Homo sapiens

text: Homo sapiens


text: SRA-Webin

text: EBI

text: public

text: house mouse

text: Mus musculus

text: Mus musculus

text: DNA derived from BALB/c adult hippocampus tissue digested with McrBC enzyme


text: SRA-Webin

text: EBI

text: public

text: house mouse

text: Mus musculus

text: Mus musculus

text: DNA derived from BALB/cxC57BL/6, cross-fostered to C57BL/6 mother, adult hippocampus tissue digested with methylation-sensitive enzymes


text: SRA-Webin

text: EBI

text: public

text: house mouse

text: Mus musculus

text: Mus musculus

text: DNA derived from BALB/cxC57BL/6 adult hippocampus tissue digested with methylation-sensitive enzymes


text: SRA-Webin

text: EBI

text: public

text: house mouse

text: Mus musculus

text: Mus musculus

text: DNA derived from C57BL/6 adult hippocampus tissue digested with methylation-sensitive enzymes


text: SRA-Webin

text: EBI

text: public

text: house mouse

text: Mus musculus

text: Mus musculus

text: DNA derived from BALB/cxC57BL/6 adult hippocampus tissue digested with McrBC enzyme


text: SRA-Webin

text: EBI

text: public

text: house mouse

text: Mus musculus

text: Mus musculus

text: DNA derived from BALB/c adult hippocampus tissue digested with methylation-sensitive enzymes


text: SRA-Webin

text: EBI

text: public

text: house mouse

text: Mus musculus

text: Mus musculus

text: DNA derived from BALB/cxC57BL/6, cross-fostered to C57BL/6 mother, adult hippocampus tissue digested with McrBC enzyme


text: SRA-Webin

text: EBI

text: public

text: house mouse

text: Mus musculus

text: Mus musculus

text: DNA derived from BALB/cxC57BL/6, cross-fostered to BALB/c mother, adult hippocampus tissue digested with McrBC enzyme


text: SRA-Webin

text: EBI

text: public

text: house mouse

text: Mus musculus

text: Mus musculus

text: DNA derived from C57BL/6xBALB/c adult hippocampus tissue digested with methylation-sensitive enzymes


text: SRA-Webin

text: EBI

text: public

text: house mouse

text: Mus musculus

text: Mus musculus

text: DNA derived from C57BL/6xBALB/c adult hippocampus tissue digested with McrBC enzyme


text: SRA-Webin

text: EBI

text: public

text: house mouse

text: Mus musculus

text: Mus musculus

text: DNA derived from BALB/cxC57BL/6, cross-fostered to BALB/c mother, adult hippocampus tissue digested with methylation-sensitive enzymes


characteristic: ENA-CHECKLIST

text: SC

text: public

text: Salmonella_enteritidis_D24793-sc-2011-09-22T14:21:56Z-1280395

characteristic: anonymized name

characteristic: collection date

text: Malawi

characteristic: country

text: disease

characteristic: host status

text: Blood

characteristic: isolation source

text: Salmonella enterica subsp. enterica serovar Enteritidis

text: Enteritidis

characteristic: serovar

text: human

characteristic: specific host

characteristic: strain

text: enterica

characteristic: sub species


text: Salmonella enterica subsp. enterica serovar Typhimurium

characteristic: ArrayExpress-Species

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: SC

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: Salmonella_typhimurium__D25352-sc-2011-09-22T14:22:02Z-1280401


characteristic: ENA-FIRST-PUBLIC

text: SC

text: public

characteristic: INSDC status

characteristic: SRA accession

text: Salmonella_typhimurium__D23005-sc-2011-09-22T14:22:02Z-1280402

characteristic: Submitter Id

characteristic: organism


characteristic: ENA-CHECKLIST

text: SC

text: public

text: Salmonella_enteritidis_D23682-sc-2011-09-22T14:21:57Z-1280396

characteristic: anonymized name

characteristic: collection date

text: Malawi

characteristic: country

text: disease

characteristic: host status

text: Blood

text: Enteritidis

text: human

text: enterica

characteristic: title


characteristic: ArrayExpress-Species

text: SC

text: public

text: Salmonella_enteritidis_D24359-sc-2011-09-22T14:21:58Z-1280398


characteristic: ENA-LAST-UPDATE

text: SC

text: public

text: Salmonella_enteritidis_D21685-sc-2011-09-22T14:21:55Z-1280393


characteristic: External Id

text: SC

text: public

text: Salmonella_typhimurium__D26104-sc-2011-09-22T14:22:03Z-1280403


text: SC

characteristic: INSDC center name

text: public

text: Salmonella_typhimurium_B11430LG-sc-2011-09-22T14:22:07Z-1280407


text: SC

characteristic: INSDC first public

text: public

text: Salmonella_typhimurium_BA583-sc-2011-09-22T14:22:03Z-1280404


text: SC

characteristic: INSDC last update

text: public

text: Salmonella_typhimurium_BA584-sc-2011-09-22T14:22:04Z-1280405


characteristic: ENA-FIRST-PUBLIC

text: SC

text: public

text: Salmonella_typhimurium__D24871-sc-2011-09-22T14:22:01Z-1280400


text: SC

text: public

characteristic: INSDC status

text: Salmonella_enteritidis_D24953-sc-2011-09-22T14:21:58Z-1280397

text: Malawi

text: disease

text: Blood

characteristic: isolation source

text: Enteritidis

characteristic: serovar

text: human

characteristic: specific host

characteristic: strain

text: enterica

characteristic: sub species


text: INRA-CMSE

text: public

unit: mg/kg

characteristic: N (NH4)

characteristic: N (NO3)

unit: g/kg

characteristic: SRA accession

characteristic: Submitter Id

characteristic: clay

text: Rizosphere bacterial communities of Medicago truncatula DZA 045-6 at 934 degree-days after sowing in a silt-clay loam soil (Mas d'Imbert, France)

characteristic: description

characteristic: organic carbon

text: soil metagenome

characteristic: organism

characteristic: ph

characteristic: sand

text: soil metagenome

characteristic: silt

characteristic: total nitrogen


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: BGI-Shenzhen, Shenzhen, China.

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: 4 years

characteristic: age

text: ArrayExpress

characteristic: broker name

text: sika deer

characteristic: common name

text: Protocols: Total RNA was isolated using TRIzol reagent (Invitrogen) according to the manufacturers instructions.

text: Cervus nippon

text: Cervus nippon

text: antler tip

characteristic: organism part

text: Cervus nippon

text: male

characteristic: sex

characteristic: title


text: SRA-Webin

characteristic: ENA-SUBMISSION-TOOL

text: IGIB

text: public

characteristic: SRA accession

characteristic: Submitter Id

text: Japanese encephalitis virus

characteristic: organism

text: Japanese encephalitis virus

text: hologenome


text: female

characteristic: ArrayExpress-Sex

text: Mus musculus

characteristic: ArrayExpress-Species

characteristic: ArrayExpress-StrainOrLine

characteristic: ENA-FIRST-PUBLIC

text: SC

text: public

text: C57BL_6NJ-sc-2012-12-20T14:17:30Z-1278946

text: house mouse

text: Mus musculus

characteristic: sample description

text: Mus musculus

characteristic: strain


text: female

text: Mus musculus

text: WSB/EiJ

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: SC

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: house mouse

text: Mus musculus

text: WSB/EiJ

text: Mus musculus

text: WSB/EiJ


text: female

text: Mus musculus

text: CBA/J

text: SC

text: public

text: house mouse

characteristic: common name

text: Mus musculus

text: CBA/J

text: Mus musculus

text: CBA/J


text: female

text: Mus musculus

text: SC

text: public

text: house mouse

text: Mus musculus

text: Mus musculus


text: female

text: Mus musculus

text: LP/J

text: SC

text: public

text: house mouse

text: Mus musculus

text: LP/J

text: Mus musculus

text: LP/J


text: female

text: Mus musculus

text: SC

text: public

text: Mus_musculus-sc-2012-12-20T11:42:32Z-1278939

text: house mouse

text: Mus musculus

text: Mus musculus


text: GSC

text: public

text: Glomus intraradices (DAOM 197198)

characteristic: description

text: Rhizophagus irregularis DAOM 181602

text: Rhizophagus irregularis DAOM 181602


text: SRA-Webin

characteristic: ENA-SUBMISSION-TOOL

text: DUNDEE

text: public

characteristic: SRA accession

text: Solanum phureja

text: Solanum phureja

text: Solanum phureja doubled monoploid clone, DM1-3 516R44 (CIP801092) selected BAC clones

characteristic: title


text: SRA-Webin

text: DUNDEE

text: public

characteristic: Submitter Id

text: BAC clones from the Lucigen library. Clones were prepared, end-sequence verified and pooled at near equal concentration (by UV absorbance) LuSp205A07 LuSp209M11 LuSp211F06 LuSp212H12 LuSp213B14 LuSp216O18 LuSp218F19 LuSp221E11 LuSp231I22 LuSp234F05 LuSp235H19 LuSp238K20 LuSp255A13 Library info: Vector: pSMART; Solanum phureja doubled monoploid clone, DM1-3 516R44 (CIP801092). Nuclei were isolated and DNA sheared and cloned into the pSMART vector by Lucigen. The official name of the library is LuSpBAC.

text: Solanum phureja

characteristic: organism

text: Solanum phureja


text: SRA-Webin

text: ICMB

text: public

text: 153_M_edulisStressAllTissues_081024_Titration13

text: Animals were sampled in March 2008 in Kiel Fjord (Germany) in front of the Leibniz Institute of Marine Sciences (IFM-GEOMAR). Animals were cleaned from epifauna and kept in a constant temperature room at 10degree celcius with a flow-through of natural unfiltered seawater from Kiel Bay. After 1 week of acclimation, animals were exposed to the different experimental conditions (5 animals each): high temperature (20degree celcius); anoxia: wrapped in a double layer of parafilm at 10degree celcius, injury: cracking the shell, and immune system challenge: injection of 10microgramm lipopolysaccharide. After 5 days animals were taken from each experiment, the different tissues dissected and frozen in liquid nitrogen. From these experiments, digestive gland, gill, foot and adductor muscle was used for sequence generation.

text: Mytilus edulis

text: Mytilus edulis

text: cDNA sample of gill, foot , adductor muscle, digestive gland tissue of heat, anoxia, injury and LPS treated individuals


text: SRA-Webin

text: ICMB

text: public

text: M. edulis were sampled in Kiel Fjord (Germany) in front of the Leibniz Institute of Marine Sciences (IFM-GEOMAR). Animals were cleaned from epifauna and kept for 2 weeks in a constant temperature room at 10degree celcius with a flow-through of natural unfiltered seawater from Kiel Bay.

text: Mytilus edulis

text: Mytilus edulis

text: digestive gland tissue of control individuals


text: SRA-Webin

text: ICMB

text: public

text: M. edulis were sampled in Kiel Fjord (Germany) in front of the Leibniz Institute of Marine Sciences (IFM-GEOMAR). Animals were cleaned from epifauna and kept for 2 weeks in a constant temperature room at 10degree celcius with a flow-through of natural unfiltered seawater from Kiel Bay before treatment. For cDNA generation digestive gland tissues of Mytilus edulis individuals in which inflammation was chemically induced by dextran sodium sulfate (4%, 5days; TdB Consultancy, Uppsala, Sweden) was used.

text: Mytilus edulis

text: Mytilus edulis

text: digestive gland tissue of DSS treated individuals


text: SRA-Webin

text: ICMB

text: public

text: M. edulis were sampled in Kiel Fjord (Germany) in front of the Leibniz Institute of Marine Sciences (IFM-GEOMAR). For cDNA generation hemocytes were withdrawn from the adductor muscle and treated for 4h in vitro at 16degree celcius with 2.5microgramm/ml flagellin.

text: Mytilus edulis

text: Mytilus edulis

text: hemocytes of flagellin treated individuals


text: SRA-Webin

text: ICMB

text: public

text: Animals were sampled in March 2008 in Kiel Fjord (Germany) in front of the Leibniz Institute of Marine Sciences (IFM-GEOMAR). Animals were cleaned from epifauna and kept in a constant temperature room at 10degree celcius with a flow-through of natural unfiltered seawater from Kiel Bay. After 1 week of acclimation, animals were injected with 10microgramm lipopolysaccharide in the adductor muscle and digestive gland samples taken after 5 days for RNA extraction and cDNA generation.

text: Mytilus edulis

text: Mytilus edulis

text: digestive gland tissue of LPS stimulated individuals


text: SRA-Webin

text: ICMB

text: public

text: M. edulis were sampled in Kiel Fjord (Germany) in front of the Leibniz Institute of Marine Sciences (IFM-GEOMAR). For cDNA generation tissue of the mantle rim was used.

text: Mytilus edulis

text: Mytilus edulis

text: mantle rim tissue


text: SRA-Webin

text: ICMB

text: public

text: Animals were sampled in March 2008 in Kiel Fjord (Germany) in front of the Leibniz Institute of Marine Sciences (IFM-GEOMAR). Animals were cleaned from epifauna and kept for 12days at 10degree celcius and a salinity of 17 in flow-through seawater from Kiel Bay

text: Mytilus edulis

text: Mytilus edulis


text: SRA-Webin

text: ICMB

text: public

text: Mytilus edulis

text: Mytilus edulis

text: generated from digestive gland tissue of control individuals


text: SRA-Webin

text: ICMB

text: public

text: Animals were sampled in March 2008 in Kiel Fjord (Germany) in front of the Leibniz Institute of Marine Sciences (IFM-GEOMAR). Animals were cleaned from epifauna and kept for 12days at 10degree celcius and a salinity of 17 in flow-through seawater from Kiel Bay. For cDNA generation gill, foot, adductor muscle, digestive gland tissue was used

text: Mytilus edulis

text: Mytilus edulis

text: cDNA sample of gill, foot , adductor muscle, digestive gland tissue of control individuals


text: SRA-Webin

text: ICMB

text: public

text: M. edulis were sampled in Kiel Fjord (Germany) in front of the Leibniz Institute of Marine Sciences (IFM-GEOMAR). For cDNA generation tissue of the inner mantle was used.

text: Mytilus edulis

text: Mytilus edulis

text: inner mantle tissue


text: SRA-Webin

text: ICMB

text: public

text: Mytilus edulis

text: Mytilus edulis


text: SRA-Webin

text: ICMB

text: public

text: 153_M_edulisStressAllTissues_081024_Titration14

text: Mytilus edulis

text: Mytilus edulis


text: SRA-Webin

text: ICMB

text: public

text: M. edulis were sampled in Kiel Fjord (Germany) in front of the Leibniz Institute of Marine Sciences (IFM-GEOMAR). For cDNA generation hemocytes were withdrawn from the adductor muscle and kept for 4h in vitro at 16degree celcius for controls.

text: Mytilus edulis

text: Mytilus edulis

text: hemocytes of control individuals


text: SRA-Webin

text: ICMB

text: public

text: 153_M_edulisStressAllTissues_081024_Titration15

text: Animals were sampled in March 2008 in Kiel Fjord (Germany) in front of the Leibniz Institute of Marine Sciences (IFM-GEOMAR). Animals were cleaned from epifauna and kept in a constant temperature room at 10degree celcius with a flow-through of natural unfiltered seawater from Kiel Bay. After 1 week of acclimation, animals were exposed to the different experimental conditions (5 animals each): high temperature (20degree celcius); anoxia: wrapped in a double layer of parafilm at 10degree celcius, injury: cracking the shell, and immune system challenge: injection of 10microgramm lipopolysaccharide. After 5 days animals were taken from each experiment, the different tissues dissected and frozen in liquid nitrogen. From these experiments, digestive gland, gill, foot and adductor muscle was used for sequence generation.

text: Mytilus edulis

text: Mytilus edulis

text: cDNA sample of gill, foot , adductor muscle, digestive gland tissue of heat, anoxia, injury and LPS treated individuals


text: SRA-Webin

text: JHI

text: public

text: Leaf buds were sampled from four-year old blackcurrant plants grown in the field at Invergowrie, Dundee (latitude 56.45, longitude -3.06) of both parents (S10 and S36) of the reference mapping population SCRI 9328 in February 2008, immediately prior to dormancy break, ie. as the buds began to swell. Buds were flash frozen in liquid nitrogen and stored at -80oC

text: Ribes nigrum

text: Ribes nigrum

text: S10 bud material collected just prior to dormancy break


text: SRA-Webin

text: JHI

text: public

text: Ribes nigrum

text: Ribes nigrum

text: S36 bud material collected just prior to dormancy break


text: SRA-Webin

text: UNIVERSITY OF LAUSANNE, SWITZERLAND

text: public

tag: Namespace:UNIVERSITY OF LAUSANNE, SWITZERLAND

text: amplified DNA from Broncho alveolar lavage

text: Pneumocystis jirovecii

text: Pneumocystis jirovecii

text: BBroncho alveolar lavage


text: SRA-Webin

text: SBL-UK

text: public

text: ecoli_tagmentation_10_picogram_and_enzyme_AcuI

text: unspecified

text: Escherichia coli

text: Escherichia coli

text: E. coli gDNA, Tagmentation method for NGS DNA library preparation, using 10 picogram of input DNA, and using enzyme AcuI


text: SRA-Webin

text: SBL-UK

text: public

text: ecoli_tagmentation_100_picogram_and_enzymes_AcuI_BsgI_BpmI_BpeUI

text: unspecified

text: Escherichia coli

text: Escherichia coli

text: E. coli gDNA, Tagmentation method for NGS DNA library preparation, using 100 picogram of input DNA, and using four enzymes (AcuI, BsgI, BpmI, BpeUI)


text: SRA-Webin

text: SBL-UK

text: public

text: ecoli_tagmentation_1_nanogram_and_enzyme_AcuI

text: unspecified

text: Escherichia coli

text: Escherichia coli

text: E. coli gDNA, Tagmentation method for NGS DNA library preparation, using 1 nanogram of input DNA, and using enzyme AcuI


text: SRA-Webin

text: SBL-UK

text: public

text: unspecified

text: Escherichia coli

text: Escherichia coli

text: E. coli gDNA, standard Illumina method for NGS DNA library preparation, using 1 microgram of input DNA


text: SRA-Webin

text: SBL-UK

text: public

text: ecoli_tagmentation_10_picogram_and_enzymes_BsgI_BpmI

text: unspecified

text: Escherichia coli

text: Escherichia coli

text: E. coli gDNA, Tagmentation method for NGS DNA library preparation, using 10 picogram of input DNA, and using two enzymes (BsgI, BpmI)


text: SRA-Webin

text: SBL-UK

text: public

text: ecoli_tagmentation_1_nanogram_and_enzyme_BpeUI

text: unspecified

text: Escherichia coli

text: Escherichia coli

text: E. coli gDNA, Tagmentation method for NGS DNA library preparation, using 1 nanogram of input DNA, and using enzyme BpeUI


text: SRA-Webin

text: SBL-UK

text: public

text: ecoli_tagmentation_1_nanogram_and_enzyme_BpmI

text: unspecified

text: Escherichia coli

text: Escherichia coli

text: E. coli gDNA, Tagmentation method for NGS DNA library preparation, using 1 nanogram of input DNA, and using enzyme BpmI


text: SRA-Webin

text: SBL-UK

text: public

text: ecoli_tagmentation_100_picogram_and_enzyme_AcuI

text: unspecified

text: Escherichia coli

text: Escherichia coli

text: E. coli gDNA, Tagmentation method for NGS DNA library preparation, using 100 picogram of input DNA, and using enzyme AcuI


text: SRA-Webin

text: SBL-UK

text: public

text: ecoli_tagmentation_100_picogram_and_enzymes_BsgI_BpmI

text: unspecified

text: Escherichia coli

text: Escherichia coli

text: E. coli gDNA, Tagmentation method for NGS DNA library preparation, using 100 picogram of input DNA, and using two enzymes (BsgI, BpmI)


text: SRA-Webin

text: CIMR

text: public

text: sugar beet

text: Beta vulgaris subsp. vulgaris

text: Beta vulgaris subsp. vulgaris

text: a sugar beet reference transcriptome by de novo assembly of 6.6Gb sequence generated from shoot apex mRNA


text: Chlamydophila abortus

characteristic: ArrayExpress-Species

text: SC

text: public

text: Chlamydophila abortus

text: Chlamydophila abortus


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: SC

text: public

text: 10240482-sc-2011-10-18T11:26:16Z-1290023

characteristic: anonymized name

characteristic: collection date

text: United Kingdom

characteristic: country

text: Diseased

characteristic: host status

text: Invasive

characteristic: isolation source

text: Neisseria meningitidis

text: Neisseria meningitidis

text: Not Known

characteristic: serovar

text: Homo Sapien

characteristic: specific host

text: M10 240482

text: M10 240482


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: SC

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: 10240480-sc-2011-10-18T11:26:15Z-1290021

text: United Kingdom

text: Diseased

text: Invasive

text: Neisseria meningitidis

text: Neisseria meningitidis

text: Not Known

text: Homo Sapien

text: M10 240480

characteristic: strain

text: M10 240480


text: SC

text: public

characteristic: SRA accession

text: 10240474-sc-2011-10-18T11:26:13Z-1290019

characteristic: Submitter Id

text: United Kingdom

text: Diseased

text: Invasive

text: Neisseria meningitidis

characteristic: organism

text: Neisseria meningitidis

text: Not Known

text: Homo Sapien

text: M10 240474

text: M10 240474

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: SC

text: public

text: 10240484-sc-2011-10-18T11:26:17Z-1290024

characteristic: anonymized name

characteristic: collection date

text: United Kingdom

text: Diseased

text: Invasive

text: Neisseria meningitidis

text: Neisseria meningitidis

text: Not Known

text: Homo Sapien

text: M10 240484

text: M10 240484


text: SC

text: public

text: 10240487-sc-2011-10-18T11:26:19Z-1290026

text: United Kingdom

characteristic: country

text: Diseased

characteristic: host status

text: Invasive

characteristic: isolation source

text: Neisseria meningitidis

text: Neisseria meningitidis

text: Not Known

characteristic: serovar

text: Homo Sapien

text: M10 240487

text: M10 240487


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: SC

characteristic: INSDC center name

text: public

text: 10240498-sc-2011-10-18T11:26:21Z-1290029

text: United Kingdom

text: Diseased

text: Invasive

text: Neisseria meningitidis

text: Neisseria meningitidis

text: Not Known

text: Homo Sapien

characteristic: specific host

text: M10 240498

text: M10 240498


text: SC

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: 10240485-sc-2011-10-18T11:26:18Z-1290025

text: United Kingdom

text: Diseased

text: Invasive

text: Neisseria meningitidis

text: Neisseria meningitidis

text: Not Known

text: Homo Sapien

text: M10 240485

characteristic: strain

text: M10 240485


text: SC

text: public

characteristic: SRA accession

text: 10240473-sc-2011-10-18T11:26:10Z-1290018

characteristic: Submitter Id

text: United Kingdom

text: Diseased

text: Invasive

text: Neisseria meningitidis

characteristic: organism

text: Neisseria meningitidis

text: Not Known

text: Homo Sapien

text: M10 240473

text: M10 240473

characteristic: title


characteristic: ENA-FIRST-PUBLIC

text: Karolinska High-Throughput center

text: public

text: ArrayExpress

characteristic: broker name

characteristic: cell line

text: fruit fly

characteristic: common name

text: Protocols: Drosophila S2 cells were cultured at +23.5 C in a cooling incubator (Binder KB) in Invitrogen SFM medium supplemented with 10% fetal bovine serum, 10% insect medium supplement, Sigma), 2 mM glutamine, and antibiotics. Cells (1 million cells per one well of a 6-well plate seeded the previous day in 2 ml medium) were transfected with dsGFP by Effectene (Qiagen) transfection reagent according to the manufacturers instructions, except that 1.1 ug of dsRNA, 8.8 ul of enhancer and 5ul of Effectene in EC buffer (125 ul final volume) was used per well. RNA was extracted with Qiagen RNeasy kits according to manufacturers instructions with DNase treatment. Total RNA was fragmented with hydrolysis by 3 min incubation at 70C in 1x RNA fragmentation buffer (Ambion). The reaction was terminated as instructed by manufacturer. The cDNA synthesis was performed according to the SMART protocol18 with addition of adapters for massively-parallel sequencing using an oligo-dT containing adapter (CAAGCAGAAGACGGCATACGAGCTCTTCCGATCTTTTTTTTTTTTTTTTTTTTTVN; Eurofins MWG Operon). For absolute molecule counting, a random ten base DNA sequence label (N) was added to the 5 prime adapter (ACACTCTTTCCCTACACGACGCTCTTCCGATCT(NNN)dU(NNNN)dU(NNN)[GACTT]rGrGrGrG; Integrated DNA technologies). Sequences in square brackets and parentheses represent an index sequence that was used to enable multiplexed sequencing, and a random ten base DNA sequence label, respectively. dU and rG represent deoxyuridine and guanine ribonucleotide, respectively. To denature RNA and anneal the 3 prime adapter, 12 pmol of both adapters were incubated at 72C for 2 min with 3 ml of the unpurified solution containing 50 ng of fragmented total RNA. RNA was then reverse transcribed with SuperScriptIII (Invitrogen; 200 U) in 15 ml volume with the provided buffer, dNTPs (1 mM), DTT (2 mM) and excess MgCl2 (added to 15 mM). The reaction was carried out at 55 C for 1 h and enzyme was inactivated by incubation at 70 C for 15 min. Uracil-specific excision reagent was used to degrade the random label sequence in the template-switch oligonucleotide (5 U of USER per 50 ng of total RNA at 37 C for 30 min; New England Biolabs). The libraries were amplified using Phusion High-Fidelity DNA polymerase (Finnzymes) from 2 ml of unpurified cDNA reaction mixture with 300 nM Illumina single-read sequencing library primers. PCR was performed according to manufacturers instructions. 20% trehalose was included in the 50 ml reactions, and the following cycle settings were used: denaturation: 1 min at 98 C, followed by 15 to 25 cycles of 10 s at 98 C, 30 s at 64C, and 1 min at 72C. Final extension was 11 min. In the PCR cycle experiment, half of the reaction volume was extracted at cycle 15 and replaced with fresh master mix. PCR products were purified with one volume of Agencourt XP beads (Beckman). Samples with RNA amounts corresponding to 10, 100 or 1000 Drosophila S2 cells were prepared with ca. 0.07, 0.7 or 7 ng of fragmented RNA, the same GFP treated total RNA that was used in mRNA-seq experiments shown in Figure 3. RNA was synthesized to cDNA using paired-end compatible oligo-dT adapter (12 pmol;CTCGGCATTCCTGCTGAACCGCTCTTCCGATCTTTTTTTTTTTTTTTTTTTTTVN; Integrated DNA technologies) with the labeled 5 prime adapter described above (12 pmol) and SuperScriptIII (Invitrogen; 300 U) in 30 ul volume with the provided buffer, dNTPs (0.8 mM), DTT (2.9 mM) and excess MgCl2 (added to 17 mM). The cDNA was treated with 60 U of Exonuclease I (New England Biolabs) prior to uracil-specific excision reagent. The whole volume of treated cDNA was included in a 100 ul PCR reaction, samples were amplified as described above. Due to library preparation, all sequences begin with NNNTNNNNTNNNGACTTGGGG, where N represents the molecular label (file 25c_repeat1_lane2.fastq contains also sequences with a distinct barcode from another sample).

characteristic: description

text: transfection

characteristic: geneticmodification

text: Drosophila melanogaster

text: Drosophila melanogaster

text: Drosophila melanogaster


characteristic: External Id

text: TGAC

text: public

text: rape

text: Brassica napus 2 replicate 3, doubled haploid progeny from B. oleracea A12DH x B. rapa Ro18 cross (B. oleracea maternal)

text: Brassica napus

text: Brassica napus


text: TGAC

characteristic: INSDC center name

text: public

text: rape

text: Brassica napus 1 replicate 1, doubled haploid progeny from B. rapa Ro18 X B.oleracea A12DH cross (B. rapa maternal)

text: Brassica napus

text: Brassica napus


text: TGAC

text: public

text: rape

text: Aphid resistant rape

text: Brassica napus

text: Brassica napus


text: TGAC

text: public

text: rape

text: Brassica napus 2 replicate 2, doubled haploid progeny from B. oleracea A12DH x B. rapa Ro18 cross (B. oleracea maternal)

text: Brassica napus

text: Brassica napus


text: TGAC

text: public

text: rape

text: Cultivar 'Ceska'

text: Brassica napus

text: Brassica napus


text: TGAC

text: public

text: field mustard

text: B. rapa Ro18 replicate 2

text: Brassica rapa

text: Brassica rapa


text: TGAC

text: public

text: rape

text: Brassica napus 1 replicate 4, doubled haploid progeny from B. rapa Ro18 X B.oleracea A12DH cross (B. rapa maternal)

text: Brassica napus

text: Brassica napus


text: TGAC

text: public

text: rape

text: Brassica napus 2 replicate 1, doubled haploid progeny from B. oleracea A12DH x B. rapa Ro18 cross (B. oleracea maternal)

text: Brassica napus

text: Brassica napus


text: TGAC

text: public

text: rape

text: Brassica napus 1 replicate 3, doubled haploid progeny from B. rapa Ro18 X B.oleracea A12DH cross (B. rapa maternal)

text: Brassica napus

text: Brassica napus


text: TGAC

text: public

text: rape

text: Brassica napus 2 replicate 4, doubled haploid progeny from B. oleracea A12DH x B. rapa Ro18 cross (B. oleracea maternal)

text: Brassica napus

text: Brassica napus


text: TGAC

text: public

text: rape

text: Brassica napus 1 replicate 2, doubled haploid progeny from B. rapa Ro18 X B.oleracea A12DH cross (B. rapa maternal)

text: Brassica napus

text: Brassica napus


text: SC

text: public

text: Med__WGA_started_with_1ng_DNA-sc-2010-05-07-10738

text: Caenorhabditis elegans

text: Caenorhabditis elegans


text: Caenorhabditis elegans

characteristic: ArrayExpress-Species

characteristic: ENA-LAST-UPDATE

text: SC

text: public

text: Caenorhabditis_elegans-sc-2011-10-21T11:39:07Z-1290447

text: Caenorhabditis elegans

text: Caenorhabditis elegans


text: Caenorhabditis elegans

text: SC

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: Caenorhabditis_elegans-sc-2011-10-21T11:39:36Z-1290449

text: Caenorhabditis elegans

text: Caenorhabditis elegans


text: Caenorhabditis elegans

text: SC

text: public

characteristic: INSDC status

text: Caenorhabditis_elegans-sc-2011-10-21T11:39:18Z-1290448

text: Caenorhabditis elegans

text: Caenorhabditis elegans


text: Caenorhabditis elegans

text: SC

text: public

characteristic: SRA accession

text: Caenorhabditis_elegans-sc-2011-10-21T11:39:52Z-1290450

text: Caenorhabditis elegans

text: Caenorhabditis elegans


text: SC

text: public

text: Low__WGA_started_with_0_1ng_DNA-sc-2010-05-07-10740

characteristic: Submitter Id

text: Caenorhabditis elegans

text: Caenorhabditis elegans


text: Streptococcus pneumoniae

text: SC

text: public

text: Streptococcus pneumoniae

characteristic: organism

text: Streptococcus pneumoniae


text: Streptococcus pneumoniae

text: SC

text: public

text: W00927KA-sc-2011-10-25T11:06:29Z-1290960

text: Streptococcus pneumoniae

text: Streptococcus pneumoniae


text: Streptococcus pneumoniae

text: SC

text: public

text: W01150KA-sc-2011-10-25T11:06:30Z-1290962

text: Streptococcus pneumoniae

text: Streptococcus pneumoniae


text: Streptococcus pneumoniae

text: SC

text: public

text: W01356KB-sc-2011-10-25T11:06:32Z-1290965

text: Streptococcus pneumoniae

text: Streptococcus pneumoniae


text: Streptococcus pneumoniae

text: SC

text: public

text: W00857KA-sc-2011-10-25T11:06:36Z-1290971

text: Streptococcus pneumoniae

text: Streptococcus pneumoniae


text: Streptococcus pneumoniae

text: SC

text: public

text: W00927KB-sc-2011-10-25T11:06:30Z-1290961

text: Streptococcus pneumoniae

text: Streptococcus pneumoniae


text: Streptococcus pneumoniae

text: SC

text: public

text: W00857KB-sc-2011-10-25T11:06:37Z-1290972

text: Streptococcus pneumoniae

text: Streptococcus pneumoniae


text: Streptococcus pneumoniae

text: SC

text: public

text: W00748KA-sc-2011-10-25T11:06:38Z-1290976

text: Streptococcus pneumoniae

text: Streptococcus pneumoniae


text: Streptococcus pneumoniae

text: SC

text: public

text: W01356KA-sc-2011-10-25T11:06:32Z-1290964

text: Streptococcus pneumoniae

text: Streptococcus pneumoniae


text: Streptococcus pneumoniae

text: SC

text: public

text: W01150KB-sc-2011-10-25T11:06:31Z-1290963

text: Streptococcus pneumoniae

text: Streptococcus pneumoniae


text: Streptococcus pneumoniae

text: SC

text: public

text: W00748KB-sc-2011-10-25T11:06:39Z-1290977

text: Streptococcus pneumoniae

text: Streptococcus pneumoniae


text: MPI-EVA

text: public

text: western lowland gorilla

text: Individual Gorilla, liver

text: Gorilla gorilla gorilla

text: Gorilla gorilla gorilla


text: MPI-EVA

text: public

text: Sumatran orangutan

text: Individual Orangutan, brain

text: Pongo abelii

text: Pongo abelii


text: MPI-EVA

text: public

text: Sumatran orangutan

text: Individual Orangutan, liver

text: Pongo abelii

text: Pongo abelii


text: MPI-EVA

text: public

text: western lowland gorilla

text: Individual Gorilla, brain

text: Gorilla gorilla gorilla

text: Gorilla gorilla gorilla


text: Caenorhabditis elegans

text: SC

text: public

text: Caenorhabditis elegans

text: Caenorhabditis elegans

characteristic: title


text: Staphylococcus aureus

characteristic: ENA-FIRST-PUBLIC

text: SC

text: public

text: Staphylococcus aureus

text: Staphylococcus aureus


text: Staphylococcus aureus

text: SC

text: public

text: GBR

text: SASCBU10-sc-2011-11-04T13:36:38Z-1296939

text: Staphylococcus

characteristic: genus

text: Homo sapiens

characteristic: host

text: Staphylococcus aureus

text: Staphylococcus aureus

type: AMR curated data - CABBAGE

value: gentamicin

value: BSAC

value: disk diffusion

value: resistant

value: Staphylococcus aureus

value: fusidic acid

value: susceptible

value: tetracycline

value: rifampin

value: erythromycin

value: neomycin

value: cefoxitin

value: ciprofloxacin

value: mupirocin

value: vancomycin


text: Staphylococcus aureus

text: SC

text: public

text: GBR

text: SASCBU17-sc-2011-11-04T13:36:43Z-1296946

text: Staphylococcus

text: Homo sapiens

text: Staphylococcus aureus

text: Staphylococcus aureus


text: Staphylococcus aureus

text: SC

text: public

text: GBR

text: Staphylococcus

text: Homo sapiens

text: Staphylococcus aureus

text: Staphylococcus aureus


text: Staphylococcus aureus

text: SC

text: public

text: GBR

text: Staphylococcus

text: Homo sapiens

text: Staphylococcus aureus

text: Staphylococcus aureus


text: Staphylococcus aureus

text: SC

text: public

text: SASCBU11-sc-2011-11-04T13:36:39Z-1296940

text: Staphylococcus aureus

text: Staphylococcus aureus


text: Staphylococcus aureus

text: SC

text: public

text: GBR

text: Staphylococcus

text: Homo sapiens

text: Staphylococcus aureus

text: Staphylococcus aureus


text: Staphylococcus aureus

text: SC

text: public

text: SASCBU20-sc-2011-11-04T13:36:46Z-1296949

text: Staphylococcus aureus

text: Staphylococcus aureus


text: Staphylococcus aureus

text: SC

text: public

text: GBR

text: Staphylococcus

text: Homo sapiens

text: Staphylococcus aureus

text: Staphylococcus aureus


text: Staphylococcus aureus

text: SC

text: public

text: GBR

text: Staphylococcus

text: Homo sapiens

text: Staphylococcus aureus

text: Staphylococcus aureus


text: Staphylococcus aureus

text: SC

text: public

text: SASCBU21-sc-2011-11-04T13:36:46Z-1296950

text: Staphylococcus aureus

text: Staphylococcus aureus


text: Staphylococcus aureus

text: SC

text: public

text: SASCBU22-sc-2011-11-04T13:36:47Z-1296951

text: Staphylococcus aureus

text: Staphylococcus aureus


text: Staphylococcus aureus

text: SC

text: public

text: GBR

text: SASCBU12-sc-2011-11-04T13:36:40Z-1296941

text: Staphylococcus

text: Homo sapiens

text: Staphylococcus aureus

text: Staphylococcus aureus


text: Staphylococcus aureus

text: SC

text: public

text: SASCBU13-sc-2011-11-04T13:36:40Z-1296942

text: Staphylococcus aureus

text: Staphylococcus aureus


text: Staphylococcus aureus

text: SC

text: public

text: GBR

text: Staphylococcus

text: Homo sapiens

text: Staphylococcus aureus

text: Staphylococcus aureus


text: Staphylococcus aureus

text: SC

text: public

text: GBR

text: SASCBU18-sc-2011-11-04T13:36:44Z-1296947

text: Staphylococcus

text: Homo sapiens

text: Staphylococcus aureus

text: Staphylococcus aureus


text: Staphylococcus aureus

text: SC

text: public

text: SASCBU24-sc-2011-11-04T13:36:48Z-1296953

text: Staphylococcus aureus

text: Staphylococcus aureus


text: Staphylococcus aureus

text: SC

text: public

text: GBR

text: Staphylococcus

text: Homo sapiens

text: Staphylococcus aureus

text: Staphylococcus aureus


text: Staphylococcus aureus

text: SC

text: public

text: GBR

text: SASCBU14-sc-2011-11-04T13:36:41Z-1296943

text: Staphylococcus

text: Homo sapiens

text: Staphylococcus aureus

text: Staphylococcus aureus


text: Staphylococcus aureus

text: SC

text: public

text: SASCBU23-sc-2011-11-04T13:36:48Z-1296952

text: Staphylococcus aureus

text: Staphylococcus aureus


text: Staphylococcus aureus

text: SC

text: public

text: SASCBU19-sc-2011-11-04T13:36:45Z-1296948

text: Staphylococcus aureus

text: Staphylococcus aureus


E-MTAB-825:TGFbeta treated input

text: IBMB-CSIC

text: public

text: E-MTAB-825:TGFbeta treated input

text: ArrayExpress

characteristic: broker name

text: neural stem cell

characteristic: cell type

text: house mouse

characteristic: common name

text: Protocols: Neural stem cells grown with a media composed by equal parts of DMEM F12 (without Phenol Red, Gibco) and Neural Basal Media (Gibco) containing Penicillin/Streptomycin and Glutamax (1%), N2 and B27 supplements (Gibco), non essential aminoacids (0.1mM), sodium pyruvat (1mM), Hepes (5 mM), Heparin (2 mg/l), bovine serum albumin (25 mg/l) and ?mercaptoethanol (0.01 mM). We add fresh recombinant human EGF (R&D systems) and FGF (Invitrogen) to 20 ng/ml and 10 ng/ml final concentrations respectively e> we added TGFbeta1 30 minutes to the growth mediaChIPs from NSCs were carried out using previously described procedures {Frank, 2001 #110} with modifications: 3x106 NSCs untreated or treated with TGF? (5 ng/ml, for the indicated times) were fixed with di (N-succinimidyl) glutarate (DSG, Sigma) 0.2 mM, 45 min at room temperature followed of FA 1% 20 min. Fixation was stopped by addition of 0.125 mM glycine. The sonication step was performed in a Bioruptor sonicator (12 min, 30 sec ON, 30 sec OFF) and 1 mg of protein was used for each immunoprecipitation. Antibody-protein complex was captured with pre-blocked protein A (Amersham) and DNA purification was carried out using Nucleospin Extract II (Macherey-Nagel) columns. ChIP DNA was analyzed by qPCR with SYBR Green (Roche) in a LightCycler 480 PCR system (Roche)

text: embryo

characteristic: developmental stage

text: Mus musculus

text: Mus musculus

text: Mus musculus

text: TGFbeta treated input


E-MTAB-825:TGFbeta treated JMJD3

characteristic: External Id

text: IBMB-CSIC

characteristic: INSDC center name

text: public

text: E-MTAB-825:TGFbeta treated JMJD3

text: ArrayExpress

text: neural stem cell

text: house mouse

characteristic: description

text: embryo

text: Mus musculus

text: Mus musculus

text: Mus musculus

text: TGFbeta treated JMJD3


E-MTAB-825:TGFbeta treated Smad3

characteristic: ENA-LAST-UPDATE

text: IBMB-CSIC

characteristic: INSDC first public

text: public

text: E-MTAB-825:TGFbeta treated Smad3

text: ArrayExpress

text: neural stem cell

text: house mouse

text: embryo

text: Mus musculus

text: Mus musculus

text: Mus musculus

text: TGFbeta treated Smad3


name: Monitoring Endangered Freshwater Biodiversity by Environmental DNA

text: SRA-Webin

characteristic: ENA-SUBMISSION-TOOL

text: CGG-UCop

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: vertebrates

text: Vertebrata

text: Vertebrata


text: Tallin University of Technology

text: public

characteristic: SRA accession

tag: Namespace:Tallin University of Technology

characteristic: Submitter Id

text: ArrayExpress

characteristic: cell line

text: breast cancer cell

text: human

text: Protocols: Ishikawa and MCF7 ells were grown in DMEM medium, supplemented with 10% FBS and 1% penicillin/streptomycin; T47D cells were grown in RPMI 1640 medium, supplemented with 10% FBS and 1% penicillin/streptomycin. Total RNA was extracted in addition to untreated cells at four different time points - 3h, 6h, 12h and 24h using an RNeasy Mini Kit (Qiagen).

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: Homo sapiens


characteristic: ENA-FIRST-PUBLIC

text: Tallin University of Technology

text: public

text: ArrayExpress

text: breast cancer cell

text: human

text: Protocols: Ishikawa and MCF7 ells were grown in DMEM medium, supplemented with 10% FBS and 1% penicillin/streptomycin; T47D cells were grown in RPMI 1640 medium, supplemented with 10% FBS and 1% penicillin/streptomycin. 10 -8M estrogen and progesterone; 10 -6M Tam, ICI, RU Total RNA was extracted in addition to untreated cells at four different time points - 3h, 6h, 12h and 24h using an RNeasy Mini Kit (Qiagen).

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens

characteristic: title


E-MTAB-822:Ish_Tam. 12h

text: Tallin University of Technology

text: public

text: E-MTAB-822:Ish_Tam. 12h

text: ArrayExpress

characteristic: broker name

text: Ishikawa

text: endometrial epithelial cell

characteristic: cell type

text: human

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens

text: Ish_Tam. 12h


text: Tallin University of Technology

text: public

text: ArrayExpress

text: Ishikawa

text: endometrial epithelial cell

text: human

characteristic: common name

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens


characteristic: External Id

text: Tallin University of Technology

text: public

text: ArrayExpress

text: Ishikawa

text: endometrial epithelial cell

text: human

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens


text: ICT

characteristic: INSDC center name

text: public

text: Soil sample obtained after 4-day stable isotope probing incubation with 13C-labeled biphenyl.

text: PowerMax Soil DNA Isolation Kit (MoBio Laboratories Inc., USA)

characteristic: nucleic acid extraction

text: soil metagenome

text: f: AYTGGGYDTAAAGNG; r: CCGTCAATTCMTTTRAGT

characteristic: pcr primers

text: Three times 2.5 g

characteristic: sample size

text: Contaminated soil

characteristic: sample type

text: soil metagenome

text: GS FLX Titanium (454 Life Sciences)

characteristic: sequencing method


Ctrl

characteristic: ENA-LAST-UPDATE

text: ICT

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: Ctrl

characteristic: description

text: soil metagenome

text: Three times 2.5 g

text: Contaminated soil

text: soil metagenome

text: GS FLX Titanium (454 Life Sciences)


text: GSC:MIxS v2.1

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: GSC, MIxS, MIMARKS

characteristic: ENA-KEYWORD

text: McMurdo Dry Valleys of Antarctica

text: ICTAR

text: public

characteristic: SRA accession

characteristic: Submitter Id

unit: grams

characteristic: amount or size of sample collected

characteristic: collection date

unit: m

characteristic: depth

text: Soil sample was collected aseptically from the top 5 cm of soil at the new site and underneath the abdomen of the mummified seal carcass. Sample collection was carried out during the 2008-2009 austral summer (i.e., after seal transplantation). Intermediate Sample ID: T3_NS2

characteristic: elevation

text: soil

characteristic: enviornmental package

text: Antarctic Cold Desert

characteristic: environment (biome)

text: cold temperature habitat

characteristic: environment (featurel)

text: glacial ground moraine

characteristic: environment (material)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: Not recorded

characteristic: humidity

text: MIxS

characteristic: investigation type

text: Not recorded

characteristic: light intensity

text: DOI: 10.1111/j.1462-2920.2008.01593.x

text: soil metagenome

characteristic: organism

text: Not recorded

characteristic: oxygen

text: Forward Primer: (5’-GGATTAGAWACCCBGGTAGTC-3’). Reverse Primer: (5'-GACGGGCRGTGWGTRCA-3’)

characteristic: ph

text: Seal Movement

characteristic: project name

unit: conductivity (µS/cm)

characteristic: salinity

characteristic: sample weight for DNA extraction

text: soil metagenome

text: Pyrosequencing

text: 16S rRNA

characteristic: target gene

text: Not recorded

characteristic: temperature

text: New Site

characteristic: total carbon

characteristic: total nitrogen

characteristic: total organic carbon

characteristic: total organic nitrogen


MVS2-49 S2

text: GSC:MIxS v2.1

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: GSC, MIxS, MIMARKS

characteristic: ENA-KEYWORD

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: McMurdo Dry Valleys of Antarctica

text: ICTAR

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: MVS2-49 S2

characteristic: Submitter Id

characteristic: amount or size of sample collected

characteristic: collection date

characteristic: depth

text: Soil sample was collected aseptically from the top 5 cm of soil at the original site and underneath the mummified seal carcass. Sample collection was carried out during the 2004-2005 austral summer (i.e., prior to seal transplantation). Intermediate Sample ID: -T1_S2

characteristic: description

characteristic: elevation

text: soil

characteristic: enviornmental package

text: Antarctic Cold Desert

characteristic: environment (biome)

text: cold temperature habitat

characteristic: environment (featurel)

text: glacial ground moraine

characteristic: environment (material)

characteristic: geographic location (latitude)

text: Not recorded

text: MIxS

text: Not recorded

text: DOI: 10.1111/j.1462-2920.2008.01593.x

characteristic: nucleic acid extraction

text: soil metagenome

text: Not recorded

characteristic: pcr primers

text: Seal Movement

text: soil metagenome

text: Pyrosequencing

characteristic: sequencing method

text: 16S rRNA

text: Not recorded

text: Original Site

characteristic: title


text: GSC:MIxS v2.1

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: GSC, MIxS, MIMARKS

characteristic: ENA-KEYWORD

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: McMurdo Dry Valleys of Antarctica

text: ICTAR

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: Soil sample was collected aseptically from the top 5 cm of soil at a control site >10 m away from the mummified seal carcass. Sample collection was carried out during the 2006-2007 austral summer (i.e., after seal transplantation). Intermediate Sample ID: T1_NSCtrl

text: soil

text: Antarctic Cold Desert

text: cold temperature habitat

text: glacial ground moraine

characteristic: geographic location (longitude)

text: Not recorded

characteristic: humidity

text: MIxS

characteristic: investigation type

text: Not recorded

characteristic: light intensity

text: DOI: 10.1111/j.1462-2920.2008.01593.x

text: soil metagenome

characteristic: organism

text: Not recorded

characteristic: oxygen

characteristic: ph

text: Seal Movement

characteristic: project name

characteristic: salinity

characteristic: sample weight for DNA extraction

text: soil metagenome

text: Pyrosequencing

text: 16S rRNA

characteristic: target gene

text: Not recorded

characteristic: temperature

text: Control Site

characteristic: total carbon

characteristic: total nitrogen

characteristic: total organic carbon

characteristic: total organic nitrogen


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: CRI

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: StrainOrLine

characteristic: Submitter Id

text: ArrayExpress

characteristic: broker name

text: house mouse

characteristic: common name

text: Protocols: Samples were prepared by direct perfusion of the tissue with buffered salt solution, followed by % formaldehyde. After 10 minutes, the tissue was removed and diced in 500 mM glycine buffer to neutralize the formaldehyde. After homogenization, the cells were rinsed with PBS. The animal tissues were crosslinked with formaldehyde treatment and chromatin fragmented to an average of 300 bp by sonication. Chromatin from an mass equivalent of 1/4 mouse liver was used for each ChIP experiment. Solexa libraries were prepared following the instructions of Illumina (Sample preparation for genomic DNA - version 2.2) with the following modifications. The ChIP-enriched DNA was not further fragmented. After end-repair and addition of an A base to the 3prime ends, the adapters were ligated to the ends of the DNA Fragments using 2 ul of fortyfold diluted 'Adapter oligo mix' in a total reaction volume of 25 ul. Between these steps, the DNA was purified using the DNA Clean-and-Concentrator-5 kit (Zymo Research). Subsequently, the DNA was amplified by 18 cycles of PCR, purified with QIAquick PCR purification Kit, and eluted with 33.5 ul of 10 mM tris buffer at pH7.0. The PCR-product was sized fractionated on 2% agarose gel and a gel slice containing the 200-300 bp fragments was excised. The flowcells were prepared and processed according to the manufacturer's protocols, with single-end sequencing for 36 to 45 cycles.

characteristic: description

text: adult

characteristic: developmental stage

text: Mus musculus

text: Mus musculus

text: liver

characteristic: organism part

text: Mus musculus

text: male

characteristic: sex

characteristic: title