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text: USA:MN

text: human

text: Homo sapiens

text: 1021 KRJ

text: human gut metagenome

characteristic: organism

text: Mayo Clinic

text: False

text: True

text: completed

text: stool

text: human gut metagenome

text: female

text: 1021 KRJ

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: UCSDMI

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: years

text: 1021 KRJ

text: UBERON:feces

text: UBERON:feces

text: UBERON:feces

text: NCI

text: Day 4

text: EDTA___Day 4

text: True

text: urban biome

text: human-associated habitat

characteristic: env feature

text: feces

characteristic: env matter

text: human-gut

characteristic: env package

text: EDTA

characteristic: extraction method

text: USA:MN

characteristic: geo loc name

text: human

characteristic: host common name

text: Homo sapiens

characteristic: host scientific name

text: 1021 KRJ

characteristic: host subject id

characteristic: host taxid

characteristic: latitude

characteristic: longitude

text: human gut metagenome

text: Mayo Clinic

text: False

text: True

characteristic: public

text: completed

text: stool

characteristic: sample type

text: human gut metagenome

text: female

characteristic: sex

text: 1021 KRJ

characteristic: subject id


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: UCSDMI

characteristic: INSDC center name

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

characteristic: age

text: years

characteristic: age unit

text: 1021 KRJ

characteristic: anonymized name

text: UBERON:feces

characteristic: body habitat

text: UBERON:feces

characteristic: body product

text: UBERON:feces

characteristic: body site

text: NCI

text: Day 4

characteristic: day

text: FOBT_Pre-Treatment__Day 4

characteristic: description

text: True

characteristic: elevation

text: urban biome

characteristic: env biome

text: human-associated habitat

text: feces

text: human-gut

text: FOBT

text: USA:MN

text: human

text: Homo sapiens

text: 1021 KRJ

text: human gut metagenome

characteristic: organism

text: Mayo Clinic

text: False

text: Pre-Treatment

characteristic: preparation

text: True

text: completed

text: stool

text: human gut metagenome

text: female

text: 1021 KRJ

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: UCSDMI

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: years

text: 1021 KRJ

text: UBERON:feces

text: UBERON:feces

text: UBERON:feces

text: NCI

text: Day 4

text: FOBT_Post-Treatment__Day 4

text: True

text: urban biome

text: human-associated habitat

characteristic: env feature

text: feces

characteristic: env matter

text: human-gut

characteristic: env package

text: FOBT

characteristic: extraction method

text: USA:MN

characteristic: geo loc name

text: human

characteristic: host common name

text: Homo sapiens

characteristic: host scientific name

text: 1021 KRJ

characteristic: host subject id

characteristic: host taxid

characteristic: latitude

characteristic: longitude

text: human gut metagenome

text: Mayo Clinic

text: False

text: Post-Treatment

text: True

characteristic: public

text: completed

text: stool

characteristic: sample type

text: human gut metagenome

text: female

characteristic: sex

text: 1021 KRJ

characteristic: subject id


text: Streptococcus pneumoniae

characteristic: ArrayExpress-Species

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: SC

characteristic: INSDC center name

characteristic: INSDC first public

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: Streptococcus pneumoniae

characteristic: common name

text: Streptococcus pneumoniae

characteristic: organism

text: Streptococcus pneumoniae

characteristic: title


text: James Hutton Institute

characteristic: INSDC last update

text: public

tag: Namespace:James Hutton Institute

characteristic: collection date

text: PWN146 assembly

characteristic: description

text: Portugal

characteristic: geographic location (country and/or sea)

text: Avo, Coimbra, Portugal

characteristic: geographic location (region and locality)

text: Bursaphelenchus xylophilus

characteristic: host

text: Cuticle of of the plant parasitic nematode Bursaphelenchus xylophilus extracted from symptomatic Pinus pinaster in Avo (Coimbra, Portugal)

characteristic: isolation source

text: Serratia marcescens

text: Serratia marcescens

text: PWN146 assembly


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: public

tag: Namespace:UMR GQE- Le Moulon, INRA, Univ. Paris-Sud, CNRS, AgroParisTech, Univ. Paris-Saclay

characteristic: cultivar

text: seedling

characteristic: dev stage

text: Zea mays

text: Zea mays

text: Seedling

characteristic: tissue lib

text: FV2 maize line


characteristic: External Id

text: UMR GQE- Le Moulon, INRA, Univ. Paris-Sud, CNRS, AgroParisTech, Univ. Paris-Saclay

characteristic: INSDC center name

characteristic: INSDC first public

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: Self-pollinated ear at 7 DAP (days after pollination)

text: Zea mays

text: Zea mays

text: kernel

text: FV2 maize line


characteristic: INSDC last update

text: public

text: Self-pollinated ear at 15 DAP (days after pollination)

text: Zea mays

characteristic: organism

text: Zea mays

text: Kernel

text: FV2 maize line

characteristic: title


text: public

text: Self-pollinated ear at 33 DAP (days after pollination)

text: Zea mays

text: Zea mays

text: Kernel

text: FV2 maize line


text: public

text: 7 DAS (days after sowing): first leaf expanded (not fully), second leaf rolled

text: Zea mays

text: Zea mays

text: Seedling (aerial parts)

text: FV2 maize line


text: public

text: Zea mays

text: Zea mays

text: Seedling (root)

text: FV2 maize line


text: public

text: Plant at first day of silk appearance, take leaf of primary ear (100% adult with regard to wax and trichomes)

text: Zea mays

text: Zea mays

text: Leaf

text: FV2 maize line


text: public

text: Plant at 50 DAS

text: Zea mays

text: Zea mays

text: Root

text: FV2 maize line


text: public

text: Tassel clearly visible on top, take 10 cm stem next to primary ear, soft at bottom (inside sheath), hard on top (outside sheath)

text: Zea mays

text: Zea mays

text: Stem

text: FV2 maize line


text: public

text: Swelling under leaf, no ear visible, ears 2 to 4 cm

text: Zea mays

text: Zea mays

text: Ear (immature)

text: FV2 maize line


text: public

text: Silks of 2 cm visible (first day), length of ear 6 cm

text: Zea mays

text: Zea mays

text: Ear (mature)

text: FV2 maize line


text: public

text: 40 DAS (days after sowing), tassels between 12 à 15 cm

text: Zea mays

text: Zea mays

text: Tassel (immature)

text: FV2 maize line


text: public

text: Plant producing pollen over half the primary branch

text: Zea mays

text: Zea mays

text: Tassel (mature)

text: FV2 maize line


text: JUSTUS LIEBIG UNIVERSITAT

text: public

text: DEU

tag: Namespace:JUSTUS LIEBIG UNIVERSITAT

text: Escherichia

characteristic: genus

characteristic: isolate

text: Chicken breast

text: Escherichia coli

text: Escherichia coli

text: mcr-1 encoding isolates from retail food

type: AMR curated data - CABBAGE

value: piperacillin

value: broth dilution

value: mg/L

value: Escherichia coli

value: meropenem

value: tigecycline

value: moxifloxacin

value: fosfomycin

value: piperacillin-tazobactam

value: ampicillin-sulbactam

value: ertapenem

value: aztreonam

value: tetracycline

value: trimethoprim-sulfamethoxazole

value: cefuroxime

value: cefotaxime

value: gentamicin

value: amikacin

value: cefpodoxime

value: ceftazidime

value: ampicillin

value: imipenem

value: cefepime


characteristic: ENA-CHECKLIST

text: JUSTUS LIEBIG UNIVERSITAT

text: public

text: DEU

text: Escherichia

text: other (non-clinical isolate)

characteristic: host

text: Minced meat, beef

text: Escherichia coli

text: Escherichia coli

value: broth dilution

value: mg/L

value: Escherichia coli

value: piperacillin

value: colistin

value: ciprofloxacin

value: tobramycin

value: meropenem


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: JUSTUS LIEBIG UNIVERSITAT

text: public

text: DEU

text: Escherichia

text: other (non-clinical isolate)

text: Turkey hen Schnitzel

text: Escherichia coli

text: Escherichia coli

value: cefuroxime

value: piperacillin-tazobactam

value: ertapenem

value: tigecycline

value: ampicillin-sulbactam

value: tetracycline

value: moxifloxacin

value: aztreonam


text: Universita di Bari

text: public

tag: Namespace:Universita di Bari

text: lymphoblastoid cell line

characteristic: cell type

text: Bornean orangutan

characteristic: common name

text: Pongo pygmaeus

text: Pongo pygmaeus

text: PPY chr12 neocen


hyca

characteristic: External Id

text: UNIVERSITY OF EXETER

text: public

text: hyca

tag: Namespace:UNIVERSITY OF EXETER

text: hybrid between Sample SAMN04868781 and SAMN00149432.

characteristic: description

text: Hyphochytrium catenoides

text: Hyphochytrium catenoides

text: Hyphochytrium catenoides


text: URMITE

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: Paenibacillus touaregensis was isolated from stool sample in the hospital of Timone (Marseille)

text: Paenibacillus sp. Marseille-P2472

text: Paenibacillus sp. Marseille-P2472

characteristic: strain

text: Paenibacillus touaregensis genome


text: EMBL

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: 10 to 12

unit: hour

characteristic: age

text: ArrayExpress

characteristic: broker name

text: fruit fly

text: Protocols: Genotyped lines were selected from the 205 in the DGRP collection based on three criteria: 1) including lines with the highest quality and depth of genome sequencing, 2) avoiding pairs of highly-related lines and (3) avoiding lines with unusual levels of residual heterozygosity. Freshly enclosed adults were placed in embryo collection vials, with standard apple cap plates. After three/four 1 hr pre-lays, the flies were allowed to lay for 2 hrs, after which the embryos were aged to the appropriate time-point. The embryos were then dochorionated using 50% bleach, snap frozen in liquid Nitrogen and store at -80C. ~100 embryos were homogenized with Cordless Motor for Pellet Mix and pestels (VWR) in ice. RNA was extracted in TRIzol[tm]LS (Life Technologies), digested with RNAse free DNAse I (Roche) and purified with the RNeasy mini kit (QIAGEN) according to the manufacturers' recommendations. Libraries were prepared following instructions of the NEBNext ultra directional RNA library prep kit for Illumina sequencing (NEB).

text: stage 13 to 14

characteristic: developmental stage

text: wild type genotype

characteristic: genotype

text: egg laying

characteristic: initial time point

text: Drosophila melanogaster

text: Drosophila melanogaster

text: Drosophila melanogaster

text: mixed sex

characteristic: sex


text: Escherichia coli

characteristic: ArrayExpress-Species

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: SC

characteristic: INSDC last update

text: public

text: Escherichia coli

text: Escherichia coli

characteristic: organism

text: Escherichia coli

characteristic: title


characteristic: External Id

text: URMITE

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: Blautia phoceensis was isolated from duodenal sample in the hospital of Timone (Marseille)

characteristic: description

text: Ruminococcus sp. Marseille-P328

text: Ruminococcus sp. Marseille-P328

characteristic: strain

text: Blautia phoceensis genome


Ecoli

text: yaser

text: public

characteristic: INSDC status

characteristic: SRA accession

text: Ecoli

characteristic: Submitter Id

text: KACST

characteristic: collected by

characteristic: collection date

text: KACST compassion

text: Yes

characteristic: environmental sample

text: Saudi Arabia

characteristic: geographic location (country and/or sea)

unit: DD

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: diseased

characteristic: host health state

text: human

characteristic: host scientific name

text: Yes

characteristic: is the sequenced pathogen host associated?

text: Bacteria

characteristic: isolate

text: metagenome

text: Ecoli

characteristic: pathotype

text: metagenome

text: KACST


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: ST JUDE CHILDRENS RESEARCH HOSPITAL

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

tag: Namespace:ST JUDE CHILDRENS RESEARCH HOSPITAL

text: house mouse

characteristic: common name

text: 1C,Spleen,Foxp3-,CNT1 SPL-

text: Mus musculus

characteristic: organism

text: Mus musculus

characteristic: title


text: ST JUDE CHILDRENS RESEARCH HOSPITAL

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: house mouse

text: 1C,Spleen,Foxp3+,CNT1 SPL+

characteristic: description

text: Mus musculus

text: Mus musculus


text: ST JUDE CHILDRENS RESEARCH HOSPITAL

text: public

text: house mouse

text: 2C,Spleen,Foxp3-,CNT2 SPL-

text: Mus musculus

text: Mus musculus


text: ST JUDE CHILDRENS RESEARCH HOSPITAL

text: public

text: house mouse

text: 2C,Spleen,Foxp3+,CNT2 SPL+

text: Mus musculus

text: Mus musculus


text: ST JUDE CHILDRENS RESEARCH HOSPITAL

text: public

text: house mouse

text: 3C,Spleen,Foxp3-,CNT3 SPL-

text: Mus musculus

text: Mus musculus


text: ST JUDE CHILDRENS RESEARCH HOSPITAL

text: public

text: house mouse

text: 3C,Spleen,Foxp3+,CNT3 SPL+

text: Mus musculus

text: Mus musculus


text: ST JUDE CHILDRENS RESEARCH HOSPITAL

text: public

text: house mouse

text: 3C,Thymus,CD4+CD8+TCRlo,CNT3 Thymus CD4 CD8 DP

text: Mus musculus

text: Mus musculus


text: ST JUDE CHILDRENS RESEARCH HOSPITAL

text: public

text: house mouse

text: 4C,Spleen,Foxp3-,CNT4 SPL-

text: Mus musculus

text: Mus musculus


text: ST JUDE CHILDRENS RESEARCH HOSPITAL

text: public

text: house mouse

text: 4C,Spleen,Foxp3+,CNT4 SPL+

text: Mus musculus

text: Mus musculus


text: ST JUDE CHILDRENS RESEARCH HOSPITAL

text: public

text: house mouse

text: 4C,Thymus,CD4+CD8+TCRlo,CNT4 Thymus CD4 CD8 DP

text: Mus musculus

text: Mus musculus


text: ST JUDE CHILDRENS RESEARCH HOSPITAL

text: public

text: house mouse

text: 5C,Thymus,CD4+CD8+TCRlo,CNT5 Thymus CD4 CD8 DP

text: Mus musculus

text: Mus musculus


text: ST JUDE CHILDRENS RESEARCH HOSPITAL

text: public

text: house mouse

text: 6C,Thymus,CD4+CD8+TCRlo,CNT6 Thymus CD4 CD8 DP

text: Mus musculus

text: Mus musculus


text: ST JUDE CHILDRENS RESEARCH HOSPITAL

text: public

text: house mouse

text: 1E,CNS,Foxp3-,EAE1 CNS-

text: Mus musculus

text: Mus musculus


text: ST JUDE CHILDRENS RESEARCH HOSPITAL

text: public

text: house mouse

text: 1E,CNS,Foxp3+,EAE1 CNS+

text: Mus musculus

text: Mus musculus


text: ST JUDE CHILDRENS RESEARCH HOSPITAL

text: public

text: house mouse

text: 1E,Spleen,Foxp3-,EAE1 SPL-

text: Mus musculus

text: Mus musculus


text: ST JUDE CHILDRENS RESEARCH HOSPITAL

text: public

text: house mouse

text: 1E,Spleen,Foxp3+,EAE1 SPL+

text: Mus musculus

text: Mus musculus


text: ST JUDE CHILDRENS RESEARCH HOSPITAL

text: public

text: house mouse

text: 2E,CNS,Foxp3-,EAE2 CNS-

text: Mus musculus

text: Mus musculus


text: ST JUDE CHILDRENS RESEARCH HOSPITAL

text: public

text: house mouse

text: 2E,CNS,Foxp3+,EAE2 CNS+

text: Mus musculus

text: Mus musculus


text: ST JUDE CHILDRENS RESEARCH HOSPITAL

text: public

text: house mouse

text: 2E,Spleen,Foxp3-,EAE2 SPL-

text: Mus musculus

text: Mus musculus


text: ST JUDE CHILDRENS RESEARCH HOSPITAL

text: public

text: house mouse

text: 2E,Spleen,Foxp3+,EAE2 SPL+

text: Mus musculus

text: Mus musculus


text: ST JUDE CHILDRENS RESEARCH HOSPITAL

text: public

text: house mouse

text: 3E,CNS,Foxp3-,EAE3 CNS-

text: Mus musculus

text: Mus musculus


text: ST JUDE CHILDRENS RESEARCH HOSPITAL

text: public

text: house mouse

text: 3E,CNS,Foxp3+,EAE3 CNS+

text: Mus musculus

text: Mus musculus


text: ST JUDE CHILDRENS RESEARCH HOSPITAL

text: public

text: house mouse

text: 3E,Spleen,Foxp3-,EAE3 SPL-

text: Mus musculus

text: Mus musculus


text: ST JUDE CHILDRENS RESEARCH HOSPITAL

text: public

text: house mouse

text: 3E,Spleen,Foxp3+,EAE3 SPL+

text: Mus musculus

text: Mus musculus


text: ST JUDE CHILDRENS RESEARCH HOSPITAL

text: public

text: house mouse

text: 4E,CNS,Foxp3-,EAE4 CNS-

text: Mus musculus

text: Mus musculus


text: ST JUDE CHILDRENS RESEARCH HOSPITAL

text: public

text: house mouse

text: 4E,CNS,Foxp3+,EAE4 CNS+

text: Mus musculus

text: Mus musculus


text: ST JUDE CHILDRENS RESEARCH HOSPITAL

text: public

text: house mouse

text: 4E,Spleen,Foxp3-,EAE4 SPL-

text: Mus musculus

text: Mus musculus


text: ST JUDE CHILDRENS RESEARCH HOSPITAL

text: public

text: house mouse

text: 4E,Spleen,Foxp3+,EAE4 SPL+

text: Mus musculus

text: Mus musculus


text: ST JUDE CHILDRENS RESEARCH HOSPITAL

text: public

text: house mouse

text: Mus musculus

text: Mus musculus


text: ST JUDE CHILDRENS RESEARCH HOSPITAL

text: public

text: house mouse

text: 9E,Spleen,Foxp3-,EAE9 SPL-

text: Mus musculus

text: Mus musculus


text: ST JUDE CHILDRENS RESEARCH HOSPITAL

text: public

text: house mouse

text: 9E,Spleen,Foxp3+,EAE9 SPL+

text: Mus musculus

text: Mus musculus


text: ST JUDE CHILDRENS RESEARCH HOSPITAL

text: public

text: house mouse

text: 10E,CNS,Foxp3-,EAE10 CNS-

text: Mus musculus

text: Mus musculus


text: ST JUDE CHILDRENS RESEARCH HOSPITAL

text: public

text: house mouse

text: 10E,CNS,Foxp3+,EAE10 CNS+

text: Mus musculus

text: Mus musculus


text: ST JUDE CHILDRENS RESEARCH HOSPITAL

text: public

text: house mouse

text: 10E,Spleen,CD45RbhiCD44loFoxp3-,EAE10 Spleen Na?ve Foxp3-

text: Mus musculus

text: Mus musculus


text: ST JUDE CHILDRENS RESEARCH HOSPITAL

text: public

text: house mouse

text: 10E,Spleen,CD45RbloCD44hiFoxp3-,EAE10 Spleen Mem Foxp3-

text: Mus musculus

text: Mus musculus


text: ST JUDE CHILDRENS RESEARCH HOSPITAL

text: public

text: house mouse

text: 10E,Spleen,Foxp3+,EAE10 Spleen Foxp3+

text: Mus musculus

text: Mus musculus


text: ST JUDE CHILDRENS RESEARCH HOSPITAL

text: public

text: house mouse

text: 11E,CNS,Foxp3-,EAE11 CNS-

text: Mus musculus

text: Mus musculus


text: ST JUDE CHILDRENS RESEARCH HOSPITAL

text: public

text: house mouse

text: 11E,CNS,Foxp3+,EAE11 CNS+

text: Mus musculus

text: Mus musculus


text: ST JUDE CHILDRENS RESEARCH HOSPITAL

text: public

text: house mouse

text: 11E,Spleen,CD45RbhiCD44loFoxp3-,EAE11 Spleen Na?ve Foxp3-

text: Mus musculus

text: Mus musculus


text: ST JUDE CHILDRENS RESEARCH HOSPITAL

text: public

text: house mouse

text: 11E,Spleen,CD45RbloCD44hiFoxp3-,EAE11 Spleen Mem Foxp3-

text: Mus musculus

text: Mus musculus


text: ST JUDE CHILDRENS RESEARCH HOSPITAL

text: public

text: house mouse

text: 11E,Spleen,Foxp3+,EAE11 Spleen Foxp3+

text: Mus musculus

text: Mus musculus


text: ST JUDE CHILDRENS RESEARCH HOSPITAL

text: public

text: house mouse

text: 12E,CNS,Foxp3-,EAE12 CNS-

text: Mus musculus

text: Mus musculus


text: ST JUDE CHILDRENS RESEARCH HOSPITAL

text: public

text: house mouse

text: 12E,CNS,Foxp3+,EAE12 CNS+

text: Mus musculus

text: Mus musculus


text: ST JUDE CHILDRENS RESEARCH HOSPITAL

text: public

text: house mouse

text: 12E,Spleen,CD45RbhiCD44loFoxp3-,EAE12 Spleen Na?ve Foxp3-

text: Mus musculus

text: Mus musculus


text: ST JUDE CHILDRENS RESEARCH HOSPITAL

text: public

text: house mouse

text: 12E,Spleen,CD45RbloCD44hiFoxp3-,EAE12 Spleen Mem Foxp3-

text: Mus musculus

text: Mus musculus


text: ST JUDE CHILDRENS RESEARCH HOSPITAL

text: public

text: house mouse

text: 12E,Spleen,Foxp3+,EAE12 Spleen Foxp3+

text: Mus musculus

text: Mus musculus


text: ST JUDE CHILDRENS RESEARCH HOSPITAL

text: public

text: house mouse

text: 13E,CNS,Foxp3-,EAE13 CNS-

text: Mus musculus

text: Mus musculus


text: ST JUDE CHILDRENS RESEARCH HOSPITAL

text: public

text: house mouse

text: 13E,CNS,Foxp3+,EAE13 CNS+

text: Mus musculus

text: Mus musculus


text: ST JUDE CHILDRENS RESEARCH HOSPITAL

text: public

text: house mouse

text: 13E,Spleen,CD45RbhiCD44loFoxp3-,EAE13 Spleen Na?ve Foxp3-

text: Mus musculus

text: Mus musculus


text: ST JUDE CHILDRENS RESEARCH HOSPITAL

text: public

text: house mouse

text: 13E,Spleen,CD45RbloCD44hiFoxp3-,EAE13 Spleen Mem Foxp3-

text: Mus musculus

text: Mus musculus


text: ST JUDE CHILDRENS RESEARCH HOSPITAL

text: public

text: house mouse

text: 13E,Spleen,Foxp3+,EAE13 Spleen Foxp3+

text: Mus musculus

text: Mus musculus


text: ST JUDE CHILDRENS RESEARCH HOSPITAL

text: public

text: house mouse

text: 14E,CNS,Foxp3-,EAE14 CNS-

text: Mus musculus

text: Mus musculus


text: ST JUDE CHILDRENS RESEARCH HOSPITAL

text: public

text: house mouse

text: 14E,CNS,Foxp3+,EAE14 CNS+

text: Mus musculus

text: Mus musculus


text: ST JUDE CHILDRENS RESEARCH HOSPITAL

text: public

text: house mouse

text: 14E,Spleen,CD45RbhiCD44loFoxp3-,EAE14 Spleen Na?ve Foxp3-

text: Mus musculus

text: Mus musculus


text: ST JUDE CHILDRENS RESEARCH HOSPITAL

text: public

text: house mouse

text: 14E,Spleen,CD45RbloCD44hiFoxp3-,EAE14 Spleen Mem Foxp3-

text: Mus musculus

text: Mus musculus


text: ST JUDE CHILDRENS RESEARCH HOSPITAL

text: public

text: house mouse

text: 14E,Spleen,Foxp3+,EAE14 Spleen Foxp3+

text: Mus musculus

text: Mus musculus


text: ST JUDE CHILDRENS RESEARCH HOSPITAL

text: public

text: house mouse

text: 5L,CNS,Foxp3-,EAE5 CNS-

text: Mus musculus

text: Mus musculus


text: ST JUDE CHILDRENS RESEARCH HOSPITAL

text: public

text: house mouse

text: 5L,CNS,Foxp3+,EAE5 CNS+

text: Mus musculus

text: Mus musculus


text: ST JUDE CHILDRENS RESEARCH HOSPITAL

text: public

text: house mouse

text: 5L,Spleen,Foxp3-,EAE5 SPL-

text: Mus musculus

text: Mus musculus


text: ST JUDE CHILDRENS RESEARCH HOSPITAL

text: public

text: house mouse

text: 5L,Spleen,Foxp3+,EAE5 SPL+

text: Mus musculus

text: Mus musculus


text: ST JUDE CHILDRENS RESEARCH HOSPITAL

text: public

text: house mouse

text: 6L,CNS,Foxp3-,EAE6 CNS-

text: Mus musculus

text: Mus musculus


text: ST JUDE CHILDRENS RESEARCH HOSPITAL

text: public

text: house mouse

text: 6L,CNS,Foxp3+,EAE6 CNS+

text: Mus musculus

text: Mus musculus


text: ST JUDE CHILDRENS RESEARCH HOSPITAL

text: public

text: house mouse

text: 6L,Spleen,Foxp3-,EAE6 SPL-

text: Mus musculus

text: Mus musculus


text: ST JUDE CHILDRENS RESEARCH HOSPITAL

text: public

text: house mouse

text: 6L,Spleen,Foxp3+,EAE6 SPL+

text: Mus musculus

text: Mus musculus


text: ST JUDE CHILDRENS RESEARCH HOSPITAL

text: public

text: house mouse

text: 7L,CNS,Foxp3-,EAE7 CNS-

text: Mus musculus

text: Mus musculus


text: ST JUDE CHILDRENS RESEARCH HOSPITAL

text: public

text: house mouse

text: 7L,CNS,Foxp3+,EAE7 CNS+

text: Mus musculus

text: Mus musculus


text: ST JUDE CHILDRENS RESEARCH HOSPITAL

text: public

text: house mouse

text: 7L,Spleen,Foxp3-,EAE7 SPL-

text: Mus musculus

text: Mus musculus


text: ST JUDE CHILDRENS RESEARCH HOSPITAL

text: public

text: house mouse

text: 7L,Spleen,Foxp3+,EAE7 SPL+

text: Mus musculus

text: Mus musculus


text: URMITE

text: public

text: Africanella massiliensis was isolated from stool sample in the hospital of Timone (Marseille)

text: Clostridium sp. Marseille-P2538

text: Clostridium sp. Marseille-P2538

characteristic: strain

text: Africanella massiliensis genome


CH Reads

text: yaser

text: public

text: CH Reads

text: KACST

characteristic: collected by

characteristic: collection date

text: metagenomics study

text: Yes

characteristic: environmental sample

text: Saudi Arabia

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: diseased

characteristic: host health state

text: human

characteristic: host scientific name

text: Yes

characteristic: is the sequenced pathogen host associated?

text: blood

characteristic: isolate

text: human

characteristic: isolation source non-host-associated

text: metagenome

text: metagenome

text: PM


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: yaser

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: KACST

text: comparing the data with ours

text: Yes

text: Saudi Arabia

text: diseased

text: Human

text: No

text: blood

text: metagenome

characteristic: organism

text: metagenome

characteristic: title


text: IPK-Gatersleben

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: domesticated barley

characteristic: common name

text: untreated

characteristic: description

text: Hordeum vulgare subsp. vulgare

text: Hordeum vulgare subsp. vulgare

text: barley aDNA


text: IPK-Gatersleben

text: public

text: domesticated barley

text: treated with uracil-DNA-glycosylase (UDG)

text: Hordeum vulgare subsp. vulgare

text: Hordeum vulgare subsp. vulgare

text: barley aDNA


text: FISABIO - Public Health

text: public

tag: Namespace:FISABIO - Public Health

characteristic: collection date

text: human

text: human-associated biome

characteristic: environment (biome)

text: human saliva

characteristic: environment (feature)

text: saliva

characteristic: environment (material)

text: Slovakia

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: human-oral

characteristic: humam oral environmental package

text: metagenome

characteristic: investigation type

text: Homo sapiens

text: Saliva

characteristic: project name

text: Homo sapiens

text: Illumina MiSeq

characteristic: sequencing method


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

tag: Namespace:Institute of Medical Microbiology and Hospital Epidemiology

text: Quadruple restriction endonuclease mutant of 26695

text: Helicobacter pylori

characteristic: organism

text: Helicobacter pylori

text: Contig assembly of Helicobacter pylori str. BAC555-2

characteristic: title


text: Institute of Medical Microbiology and Hospital Epidemiology

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

characteristic: description

text: Helicobacter pylori

text: Helicobacter pylori

text: Contig assembly of Helicobacter pylori str. BAC555-8


text: FISABIO - Public Health

text: public

characteristic: collection date

text: human

characteristic: common name

text: human-associated habitat

characteristic: environment (biome)

text: human saliva

characteristic: environment (feature)

text: saliva

characteristic: environment (material)

text: Slovakia

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: human-oral

characteristic: humam oral environmental package

text: metagenome

text: Homo sapiens

text: Saliva

text: Homo sapiens

text: Illumina MiSeq


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: AZ

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: house mouse

text: Mus musculus

text: Mus musculus


text: AZ

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: house mouse

text: sourced from ATCC then passaged 3 times by intravenous injection in mice at AZ

text: Mus musculus

characteristic: organism

text: Mus musculus

characteristic: title


text: AZ

text: public

text: house mouse

characteristic: common name

text: sourced from ATCC

characteristic: description

text: Mus musculus

text: Mus musculus


BALBc

text: AZ

text: public

text: BALBc

text: house mouse

text: tail tip

text: Mus musculus

text: Mus musculus

text: BALBc


text: AZ

text: public

text: house mouse

text: tail tip

text: Mus musculus

text: Mus musculus


text: AZ

text: public

text: house mouse

text: cell sample

text: Mus musculus

text: Mus musculus


text: AZ

text: public

text: house mouse

text: tumor (from subcutaneous injection of cells in Balb/c mouse)

text: Mus musculus

text: Mus musculus


DBA

text: AZ

text: public

text: DBA

text: house mouse

text: tail tip

text: Mus musculus

text: Mus musculus

text: DBA


RENCA

text: AZ

text: public

text: RENCA

text: house mouse

text: Mus musculus

text: Mus musculus

text: RENCA


text: public

tag: Namespace:State Key Laboratory of Lake Science and Environment

characteristic: collection date

unit: m

characteristic: depth

text: lake sediment

characteristic: environment (biome)

text: anaerobic

characteristic: environment (feature)

text: sediment slurry

characteristic: environment (material)

text: China

characteristic: geographic location (country and/or sea)

characteristic: geographic location (elevation)

characteristic: geographic location (latitude)

text: metagenome

characteristic: investigation type

text: Clostridium algifaecis

text: Genome sequencing of Clostridium undefined species THMB8

characteristic: project name

text: Clostridium algifaecis

text: sediment

characteristic: sediment environmental package

text: Illumina Miseq plus pacbio RS

characteristic: sequencing method


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: State Key Laboratory of Lake Science and Environment

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: lake sediment

text: anaerobic

text: sediment slurry

text: China

characteristic: geographic location (longitude)

text: metagenome

text: Tumebacillus algifaecis

text: Genome sequencing of Tumebacillus algifaecis THMBR28

text: Tumebacillus algifaecis

text: sediment

text: Illumina Miseq


text: public

tag: Namespace:ALBERTA AGRICULTURE AND RURAL DEVELOPMEN

text: metagenome

characteristic: organism

text: metagenome

text: Microbiome

characteristic: title


text: ALBERTA AGRICULTURE AND RURAL DEVELOPMEN

text: public

text: metagenome

text: metagenome

text: Microbiome


text: UNIVERSITY OF MELBOURNE

text: public

tag: Namespace:UNIVERSITY OF MELBOURNE

text: Staphylococcus epidermidis

text: Staphylococcus epidermidis

text: Se_BPH0662 PacBio sequences


text: UNIVERSITY OF MELBOURNE

text: public

text: Escherichia coli

text: Escherichia coli

text: DC10B-MS1 PacBio sequences


text: UNIVERSITY OF MELBOURNE

text: public

text: Escherichia coli

text: Escherichia coli

text: DC10B-MS2 PacBio sequences


text: UNIVERSITY OF MELBOURNE

text: public

text: BPH0662 chromosome and three plasmids

characteristic: description

text: Staphylococcus epidermidis

text: Staphylococcus epidermidis

text: BPH0662 complete genome


text: URMITE

text: public

text: Culturomics study

text: Clostridium sp. Marseille-P2414

text: Clostridium sp. Marseille-P2414

characteristic: strain

text: Study of nigerian microbiota


text: UMR CNRS 6290

text: public

tag: Namespace:UMR CNRS 6290

text: hepatocyte

characteristic: cell type

text: human

characteristic: common name

text: Homo sapiens

characteristic: patient number

text: Homo sapiens

text: liver

characteristic: tissue type

text: NT

characteristic: treatment


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: UMR CNRS 6290

text: public

text: hepatocyte

text: human

text: Homo sapiens

text: Homo sapiens

text: liver


text: UMR CNRS 6290

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: myotube

text: human

text: Homo sapiens

text: Homo sapiens

text: NT


text: UMR CNRS 6290

text: public

characteristic: SRA accession

characteristic: Submitter Id

text: myotube

text: human

text: Homo sapiens

characteristic: organism

text: Homo sapiens


text: Mus musculus

characteristic: ArrayExpress-Species

text: SC

text: public

text: house mouse

text: Mus musculus

text: Mus musculus

characteristic: title


OSR microbiome

text: Institute of Technology Carlow

text: public

text: OSR microbiome

tag: Namespace:Institute of Technology Carlow

characteristic: collection date

text: Plant

characteristic: environment (biome)

text: Soil

characteristic: environment (feature)

text: Plant

characteristic: environment (material)

text: Ireland

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: host-associated

characteristic: host-associated environmental package

text: metagenome

characteristic: investigation type

text: phyllosphere metagenome

text: Oilseed rape microbiome

characteristic: project name

text: phyllosphere metagenome

text: 16S rDNA amplicon Illumina MiSeq sequencing

characteristic: sequencing method

text: 16S rDNA amplicon based metagenomic study of oilseed rape microbiome


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: JLU

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: Lactobacillus delbrueckii Strain #22 Isolated from a Patient with Short Bowel Syndrome, D-lactic Acidosis, and Encephalopathy

characteristic: description

text: Human

characteristic: host

text: Lactobacillus delbrueckii

text: Lactobacillus delbrueckii

text: Lactobacillus delbrueckii 22L


text: public

characteristic: SRA accession

tag: Namespace:INSERM U1170, Equipe Labellisee Ligue Contre le Cancer, Villejuif, France Institut Gustave Roussy, Villejuif, France  Universite Paris Diderot, Paris, France

characteristic: Submitter Id

text: ArrayExpress

characteristic: broker name

text: human

characteristic: common name

text: Protocols: Human AMKL patient blood or bone marrow samples were subjected to Ficoll gradient, immunophenotyped, and amplified by xenotransplantation in immunodeficient animals. AMKL cells were used after purification by flow cytometry. RNeasy kit (QIAGEN) according to manufacturer's protocol FASTERIS services

text: acute megakaryoblastic leukaemia

characteristic: disease

characteristic: individual

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: Homo sapiens

characteristic: title

text: human acute megakaryoblastic leukaemia cells

characteristic: xenograft

text: immunodeficient mouse

characteristic: xenograft host organism


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: INSERM U1170, Equipe Labellisee Ligue Contre le Cancer, Villejuif, France Institut Gustave Roussy, Villejuif, France Universite Paris Diderot, Paris, France

text: public

text: ArrayExpress

text: human

text: acute megakaryoblastic leukaemia

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens

text: immunodeficient mouse


text: WUR

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: A plasmid degradation assay with CRISPR Cas3 was performed on different plasmids to investigate the respective degradation patterns. This sample contains sequence data of the degraded plasmid fragments of plasmid pWUR836 (wild type plasmid).

text: synthetic construct

text: synthetic construct

text: CRISPR Cas3 Plasmid degradation assay


text: WUR

text: public

characteristic: SRA accession

characteristic: Submitter Id

text: A plasmid degradation assay with CRISPR Cas3 was performed on different plasmids to investigate the respective degradation patterns. This sample contains sequence data of the degraded plasmid fragments of plasmid pWUR853 (mutant target plasmid).

characteristic: description

text: synthetic construct

text: synthetic construct

text: CRISPR Cas3 Plasmid degradation assay


text: WUR

text: public

text: A plasmid degradation assay with CRISPR Cas3 was performed on different plasmids to investigate the respective degradation patterns. This sample contains sequence data of the degraded plasmid fragments of plasmid m13mp8.

text: synthetic construct

text: synthetic construct

text: CRISPR Cas3 Plasmid degradation assay


text: public

tag: Namespace:CENTRE FOR GEOGENETICS, NATURAL HISTORY MUSEUM OF DENMARK

text: horse

characteristic: common name

text: Equus caballus

text: Equus caballus

text: NewBotai35 (1.8%)


text: CENTRE FOR GEOGENETICS, NATURAL HISTORY MUSEUM OF DENMARK

text: public

text: horse

text: Equus caballus

text: Equus caballus

text: NewBotai10 (2.5%)


text: public

text: horse

text: Equus caballus

text: Equus caballus

text: NewBotai4 (12.4%)


text: public

text: horse

text: Equus caballus

text: Equus caballus

text: NewBotai46 (28.3%)


text: public

text: horse

text: Equus caballus

text: Equus caballus

text: Arz2 (32.2%)


text: public

text: horse

text: Equus caballus

text: Equus caballus

text: Arz1 (57.5%)


text: public

characteristic: collection date

characteristic: depth

text: lake sediment

characteristic: environment (biome)

text: anaerobic

characteristic: environment (feature)

text: sediment slurry

characteristic: environment (material)

text: China

characteristic: geographic location (country and/or sea)

characteristic: geographic location (elevation)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: metagenome

characteristic: investigation type

text: Chryseobacterium taihuense

text: Genome sequencing of Chryseobacterium taihuense THMBM1

characteristic: project name

text: Chryseobacterium taihuense

text: sediment

characteristic: sediment environmental package

text: Illumina Miseq plus pacbio RS

characteristic: sequencing method


Wild Type1

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: DUNDEE

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: Wild Type1

text: Mitat1.2 (VSG-2 expressing) RNA-seq of wild type T. brucei

text: Trypanosoma brucei brucei

characteristic: organism

text: Trypanosoma brucei brucei

text: Wild Type

characteristic: title


Wild Type2

text: DUNDEE

text: public

text: Wild Type2

characteristic: Submitter Id

characteristic: description

text: Trypanosoma brucei brucei

text: Trypanosoma brucei brucei

text: Wild Type


text: public

characteristic: collection date

characteristic: depth

text: lake sediment

characteristic: environment (biome)

text: anaerobic

characteristic: environment (feature)

text: sediment slurry

characteristic: environment (material)

text: China

characteristic: geographic location (country and/or sea)

characteristic: geographic location (elevation)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: metagenome

characteristic: investigation type

text: Paenibacillus taihuensis

text: Genome sequencing of Paenibacillus taihuensis THMBG22

text: Paenibacillus taihuensis

text: sediment

text: Illumina Miseq plus pacbio RS


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: UNIVERSITY OF WESTERN ONTARIO

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

tag: Namespace:UNIVERSITY OF WESTERN ONTARIO

text: Peatland forest

text: Boreal

text: soil

text: Canada

text: metagenome

text: fungus metagenome

text: Climate change

characteristic: project name

text: fungus metagenome

text: Illumina

characteristic: sequencing method

text: soil

characteristic: soil environmental package

text: Asco-BG 8 and 12 months


tag: attribute

text: FZB

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: Mycobacterium abscessus

characteristic: common name

text: Mycobacterium abscessus

characteristic: organism

text: Mycobacterium abscessus

text: WGS of Mycobacterium abscessus isolates

characteristic: title


BOT

text: FZB

text: public

text: BOT

text: Mycobacterium abscessus

text: Mycobacterium abscessus

text: Mycobacterium abscessus

text: WGS of Mycobacterium abscessus isolates


text: public

tag: Namespace:Institute of Molecular Life Sciences, University of Zurich

text: ArrayExpress

characteristic: broker name

text: Protocols: C. elegans CPEB homolog mutants and wild-type N2 were metabolically labelled at lysine and arginine amino acids by feeding light (Lys0 and Arg0) labelled bacteria using SILAC protocol, as previously described [Subasic et al. 2015]. Samples were harvested after two generations at different developmental stages (fog-1 at L3; cpb-2 at L4; cpb-3 at YA; and N2 at L3, L4 and YA) in biological triplicates. RNA extraction was done using TRIzol reagent (15596-026; Life Technologies) in accordance with the manufacturer’s protocol and further purified by using DNA-free kit (AM1906; Ambion). Random primed cDNA library was generated from each sample by GATC Biotech as per their InView Transcriptome Explore package.

characteristic: description

text: L3 larva

characteristic: developmental stage

text: fog-1(q253ts) I

characteristic: genotype

text: 25.6 C

characteristic: growth condition

text: Caenorhabditis elegans

text: Caenorhabditis elegans

text: Caenorhabditis elegans

characteristic: strain


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Institute of Molecular Life Sciences, University of Zurich

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: ArrayExpress

text: L3 larva

text: fog-1(q253ts) I

text: 25.6 C

text: Caenorhabditis elegans

text: Caenorhabditis elegans

text: Caenorhabditis elegans


characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: ArrayExpress

text: L3 larva

text: wild type genotype

text: 25.6 C

text: Caenorhabditis elegans

text: Caenorhabditis elegans

text: Caenorhabditis elegans


text: public

characteristic: Submitter Id

text: ArrayExpress

text: L4 larva

text: wild type genotype

text: 20 C

text: Caenorhabditis elegans

characteristic: organism

text: Caenorhabditis elegans

text: Caenorhabditis elegans


text: public

text: ArrayExpress

characteristic: broker name

text: Young Adult

text: cpb-3(op234) I

text: 20 C

text: Caenorhabditis elegans

text: Caenorhabditis elegans

text: Caenorhabditis elegans

characteristic: title


E-MTAB-2758:Sample 1

text: Warwick University

text: public

text: E-MTAB-2758:Sample 1

tag: Namespace:Warwick University

text: ArrayExpress

characteristic: cell line

text: ovarian cancer cell lines

characteristic: cell type

text: human

characteristic: common name

text: Protocols: A2780 ovarian cancer cells were obtained from ECACC (European Collection of Animal Cell Culture) and grown in RPMI-1640 medium supplemented with 10% (v/v) fetal calf serum, 1% (v/v) 2mL L-glutamine and 1% (v/v) penicillin (10 k units/mL)/streptomycin (10 mg/mL), at 310 K in a humidified atmosphere containing 5% CO2. Maintenance passages were done at ca. 80% confluency. Cells were seeded at 3 × 10^6 in P100 petri dishes and left to incubate for 24 h at 310 K in a humidified atmosphere containing 5% CO2. Stock solutions of the negative control and compound 1 were prepared in 5% DMSO, 10% saline, and 85% RPMI-1640 medium. Cells were exposed to compound 1 at a final concentration of 0.15 μM. After 4, 12, 24 and 48 h exposure, medium was removed from triplicate compound-exposed and control-exposed dishes, and cells were washed twice with PBS and collected using trypsin. Between 5 × 10^6 and 1 × 10^7 cells in each sample were taken forward for RNA extraction. Using QIAshredder spin columns (Qiagen) the cells were lysed, as per manufacturers instructions. DNA was eliminated from each sample using gDNA spin columns, and the RNA was purified using RNeasy spin columns and buffer solutions (RNeasy plus mini kit, QIagen) as per the manufacturers instructions. RNA was collected in 70 μL RNase-free water and stored at -70 C. Libraries were prepped using Truseq by the Oxford Genomics Centre, UK

characteristic: description

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens

text: Sample 1


E-MTAB-2758:Sample 2

characteristic: ENA-CHECKLIST

text: Warwick University

text: public

text: E-MTAB-2758:Sample 2

text: ArrayExpress

text: ovarian cancer cell lines

text: human

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens

text: Sample 2


E-MTAB-2758:Sample 3

characteristic: ENA-FIRST-PUBLIC

text: Warwick University

text: public

text: E-MTAB-2758:Sample 3

text: ArrayExpress

text: ovarian cancer cell lines

text: human

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens

text: Sample 3


E-MTAB-2758:Sample 4

characteristic: ENA-LAST-UPDATE

text: Warwick University

text: public

text: E-MTAB-2758:Sample 4

text: ArrayExpress

text: ovarian cancer cell lines

text: human

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens

text: Sample 4


E-MTAB-2758:Sample 5

characteristic: External Id

text: Warwick University

text: public

text: E-MTAB-2758:Sample 5

text: ArrayExpress

text: ovarian cancer cell lines

text: human

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens

text: Sample 5


E-MTAB-2758:Sample 6

text: Warwick University

characteristic: INSDC center name

text: public

text: E-MTAB-2758:Sample 6

text: ArrayExpress

text: ovarian cancer cell lines

text: human

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens

text: Sample 6


E-MTAB-2758:Sample 7

text: Warwick University

characteristic: INSDC first public

text: public

text: E-MTAB-2758:Sample 7

text: ArrayExpress

text: ovarian cancer cell lines

text: human

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens

text: Sample 7


E-MTAB-2758:Sample 8

text: Warwick University

characteristic: INSDC last update

text: public

text: E-MTAB-2758:Sample 8

text: ArrayExpress

text: ovarian cancer cell lines

text: human

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens

text: Sample 8


E-MTAB-2758:Sample 9

text: Warwick University

text: public

characteristic: INSDC status

text: E-MTAB-2758:Sample 9

text: ArrayExpress

text: ovarian cancer cell lines

text: human

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens

text: Sample 9


E-MTAB-2758:Sample 10

text: Warwick University

text: public

characteristic: SRA accession

text: E-MTAB-2758:Sample 10

text: ArrayExpress

text: ovarian cancer cell lines

text: human

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens

text: Sample 10


E-MTAB-2758:Sample 11

text: Warwick University

text: public

text: E-MTAB-2758:Sample 11

characteristic: Submitter Id

text: ArrayExpress

text: ovarian cancer cell lines

text: human

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens

text: Sample 11


E-MTAB-2758:Sample 12

text: Warwick University

text: public

text: E-MTAB-2758:Sample 12

text: ArrayExpress

text: ovarian cancer cell lines

text: human

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: Homo sapiens

text: Sample 12


E-MTAB-2758:Sample 13

text: Warwick University

text: public

text: E-MTAB-2758:Sample 13

text: ArrayExpress

characteristic: broker name

text: ovarian cancer cell lines

text: human

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens

text: Sample 13


E-MTAB-2758:Sample 14

text: Warwick University

text: public

text: E-MTAB-2758:Sample 14

text: ArrayExpress

text: ovarian cancer cell lines

text: human

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens

text: Sample 14

characteristic: title


E-MTAB-2758:Sample 15

text: Warwick University

text: public

text: E-MTAB-2758:Sample 15

text: ArrayExpress

characteristic: cell line

text: ovarian cancer cell lines

text: human

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens

text: Sample 15


E-MTAB-2758:Sample 16

text: Warwick University

text: public

text: E-MTAB-2758:Sample 16

text: ArrayExpress

text: ovarian cancer cell lines

characteristic: cell type

text: human

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens

text: Sample 16


E-MTAB-2758:Sample 17

text: Warwick University

text: public

text: E-MTAB-2758:Sample 17

text: ArrayExpress

text: ovarian cancer cell lines

text: human

characteristic: common name

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens

text: Sample 17


E-MTAB-2758:Sample 18

text: Warwick University

text: public

text: E-MTAB-2758:Sample 18

text: ArrayExpress

text: ovarian cancer cell lines

text: human

characteristic: description

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens

text: Sample 18


E-MTAB-2758:Sample 19

characteristic: ENA-CHECKLIST

text: Warwick University

text: public

text: E-MTAB-2758:Sample 19

text: ArrayExpress

text: ovarian cancer cell lines

text: human

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens

text: Sample 19


E-MTAB-2758:Sample 20

characteristic: ENA-FIRST-PUBLIC

text: Warwick University

text: public

text: E-MTAB-2758:Sample 20

text: ArrayExpress

text: ovarian cancer cell lines

text: human

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens

text: Sample 20


E-MTAB-2758:Sample 21

characteristic: ENA-LAST-UPDATE

text: Warwick University

text: public

text: E-MTAB-2758:Sample 21

text: ArrayExpress

text: ovarian cancer cell lines

text: human

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens

text: Sample 21


E-MTAB-2758:Sample 22

characteristic: External Id

text: Warwick University

text: public

text: E-MTAB-2758:Sample 22

text: ArrayExpress

text: ovarian cancer cell lines

text: human

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens

text: Sample 22


E-MTAB-2758:Sample 23

text: Warwick University

characteristic: INSDC center name

text: public

text: E-MTAB-2758:Sample 23

text: ArrayExpress

text: ovarian cancer cell lines

text: human

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens

text: Sample 23


E-MTAB-2758:Sample 24

text: Warwick University

characteristic: INSDC first public

text: public

text: E-MTAB-2758:Sample 24

text: ArrayExpress

text: ovarian cancer cell lines

text: human

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens

text: Sample 24


E-MTAB-2758:Sample 25

text: Warwick University

characteristic: INSDC last update

text: public

text: E-MTAB-2758:Sample 25

text: ArrayExpress

text: ovarian cancer cell lines

text: human

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens

text: Sample 25


E-MTAB-2758:Sample 26

text: Warwick University

text: public

characteristic: INSDC status

text: E-MTAB-2758:Sample 26

text: ArrayExpress

text: ovarian cancer cell lines

text: human

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens

text: Sample 26


E-MTAB-2758:Sample 27

text: Warwick University

text: public

characteristic: SRA accession

text: E-MTAB-2758:Sample 27

text: ArrayExpress

text: ovarian cancer cell lines

text: human

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens

text: Sample 27


E-MTAB-2758:Sample 28

text: Warwick University

text: public

text: E-MTAB-2758:Sample 28

characteristic: Submitter Id

text: ArrayExpress

text: ovarian cancer cell lines

text: human

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens

text: Sample 28


E-MTAB-2758:Sample 29

text: Warwick University

text: public

text: E-MTAB-2758:Sample 29

text: ArrayExpress

text: ovarian cancer cell lines

text: human

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: Homo sapiens

text: Sample 29


E-MTAB-2758:Sample 30

text: Warwick University

text: public

text: E-MTAB-2758:Sample 30

text: ArrayExpress

characteristic: broker name

text: ovarian cancer cell lines

text: human

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens

text: Sample 30


text: BUGS

text: public

text: GBR

characteristic: collection date

text: Mycobacterium

characteristic: genus

text: United Kingdom

characteristic: geographic location (country and/or sea)

text: Homo sapiens

characteristic: host

text: diseased

characteristic: host health state

text: Human

characteristic: host scientific name

characteristic: isolate

text: sputum

characteristic: isolation source

text: respiratory tract

text: Mycobacterium tuberculosis

text: Mycobacterium tuberculosis

characteristic: title

value: ethambutol

value: susceptible

value: Mycobacterium tuberculosis

value: streptomycin

value: ethionamide

value: intermediate

value: pyrazinamide


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: BUGS

characteristic: INSDC center name

text: public

text: GBR

text: Mycobacterium

text: United Kingdom

text: Homo sapiens

text: diseased

text: Human

text: sputum

text: respiratory tract

text: Mycobacterium tuberculosis

text: Mycobacterium tuberculosis

value: resistant


text: BUGS

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: GBR

characteristic: SRA accession

characteristic: Submitter Id

text: Mycobacterium

text: United Kingdom

text: Homo sapiens

text: diseased

text: Human

text: sputum

text: respiratory tract

text: Mycobacterium tuberculosis

text: Mycobacterium tuberculosis


text: BUGS

text: public

text: GBR

characteristic: collection date

text: Mycobacterium

characteristic: genus

text: United Kingdom

characteristic: geographic location (country and/or sea)

text: Homo sapiens

text: diseased

text: Human

text: sputum

text: respiratory tract

text: Mycobacterium tuberculosis

characteristic: organism

text: Mycobacterium tuberculosis


text: BUGS

text: public

text: GBR

text: Mycobacterium

text: United Kingdom

text: Homo sapiens

characteristic: host

text: diseased

characteristic: host health state

text: Human

characteristic: host scientific name

characteristic: isolate

text: sputum

text: respiratory tract

text: Mycobacterium tuberculosis

text: Mycobacterium tuberculosis


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: BUGS

text: public

text: GBR

text: Mycobacterium

text: United Kingdom

text: Homo sapiens

text: diseased

text: Human

text: sputum

characteristic: isolation source

text: respiratory tract

text: Mycobacterium tuberculosis

text: Mycobacterium tuberculosis

characteristic: title

value: isoniazid

value: rifampin


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: BUGS

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: GBR

text: Mycobacterium

text: United Kingdom

text: Homo sapiens

text: diseased

text: Human

text: sputum

text: respiratory tract

text: Mycobacterium tuberculosis

text: Mycobacterium tuberculosis


text: BUGS

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: GBR

characteristic: SRA accession

characteristic: Submitter Id

text: Mycobacterium

text: United Kingdom

text: other (non-clinical isolate)

text: diseased

text: Human

text: sputum

text: respiratory tract

text: Mycobacterium tuberculosis

text: Mycobacterium tuberculosis

value: clarithromycin


text: BUGS

text: public

text: GBR

characteristic: collection date

text: Mycobacterium

characteristic: genus

text: United Kingdom

characteristic: geographic location (country and/or sea)

text: Homo sapiens

text: diseased

text: Human

text: sputum

text: respiratory tract

text: Mycobacterium tuberculosis

characteristic: organism

text: Mycobacterium tuberculosis


text: BUGS

text: public

text: GBR

text: Mycobacterium

text: United Kingdom

text: Homo sapiens

characteristic: host

text: diseased

characteristic: host health state

text: Human

characteristic: host scientific name

characteristic: isolate

text: sputum

text: respiratory tract

text: Mycobacterium tuberculosis

text: Mycobacterium tuberculosis


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: BUGS

text: public

text: GBR

text: Mycobacterium

text: United Kingdom

text: Homo sapiens

text: diseased

text: Human

text: sputum

characteristic: isolation source

text: respiratory tract

text: Mycobacterium tuberculosis

text: Mycobacterium tuberculosis

characteristic: title


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: BUGS

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: GBR

text: Mycobacterium

text: United Kingdom

text: Homo sapiens

text: diseased

text: Human

text: sputum

text: respiratory tract

text: Mycobacterium tuberculosis

text: Mycobacterium tuberculosis


text: BUGS

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: GBR

characteristic: SRA accession

characteristic: Submitter Id

text: Mycobacterium

text: United Kingdom

text: Homo sapiens

text: diseased

text: Human

text: sputum

text: respiratory tract

text: Mycobacterium tuberculosis

text: Mycobacterium tuberculosis


text: BUGS

text: public

characteristic: collection date

text: United Kingdom

characteristic: geographic location (country and/or sea)

text: diseased

text: Human

text: sputum

text: Mycobacterium tuberculosis

characteristic: organism

text: Mycobacterium tuberculosis


text: BUGS

text: public

text: GBR

text: Mycobacterium

characteristic: genus

text: United Kingdom

text: Homo sapiens

characteristic: host

text: diseased

characteristic: host health state

text: Human

characteristic: host scientific name

text: sputum

text: respiratory tract

text: Mycobacterium tuberculosis

text: Mycobacterium tuberculosis


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: BUGS

text: public

text: GBR

text: Mycobacterium

text: United Kingdom

text: Homo sapiens

text: diseased

text: Human

characteristic: isolate

text: sputum

characteristic: isolation source

text: respiratory tract

text: Mycobacterium tuberculosis

text: Mycobacterium tuberculosis


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: BUGS

characteristic: INSDC center name

text: public

text: United Kingdom

text: Culture

text: culture

text: Mycobacterium tuberculosis

text: Mycobacterium tuberculosis

characteristic: title


text: IBERS

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: depth

text: arable

characteristic: environment (biome)

text: Arable

characteristic: environment (feature)

text: soil

characteristic: environment (material)

text: United Kingdom

characteristic: geographic location (elevation)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: metagenome

characteristic: investigation type

text: soil metagenome

text: Prosoil

characteristic: project name

text: soil metagenome

text: Ion-Torrent

characteristic: sequencing method

text: soil

characteristic: soil environmental package

text: The legacy effect of cover crops on soil fungal populations in a cereal rotation


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Friedrich-Loeffler-Institute

characteristic: INSDC center name

text: public

characteristic: Submitter Id

text: State Office for agriculture, food safety and fishery, Mecklenburg-Western Pomerania

characteristic: collecting institution

characteristic: collection date

text: Bergermann, Christian

characteristic: collector name

text: High prevalence of highly variable Atypical Porcine Pestiviruses found in Germany

characteristic: description

text: Germany

characteristic: geographic location (country and/or sea)

text: domestic pig

characteristic: host common name

text: Sus scrofa

characteristic: host scientific name

text: not collected

characteristic: host sex

characteristic: host subject id

characteristic: isolate

text: Porcine pestivirus 1

characteristic: organism

text: Porcine pestivirus 1

characteristic: virus identifier


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

tag: Namespace:EMBL/CRG Systems Biology Research Unit. Centre for Genomic Regulation (CRG), Barcelona. Spain. -Universitat Pompeu Fabra (UPF), Barcelona. Spain.

text: ArrayExpress

characteristic: broker name

text: Protocols: M129 cells were grown in 150 cm2 dishes for 6 (exponential phase) or 96 hours (stationary phase) Non-ligated adapters were removed by reclaiming the Hi-C DNA bound beads and washing the beads twice with 400 μl TB, once with 200 μl NTB, once with 200 μl and then 50 μl NEBuffer 2. After the last wash, the beads were resuspended in 25 μl NEBuffer 2. The library was PCR amplified with Phusion (Next kit, NEB), 2 μl of the suspension in a 50 μl reaction, and 1.0 and 2.1 Illumina primers (1 μl 10 uM), for 16 cycles and sequenced in the HiSeq Illumina platform. Chromatin was prepared as above. When indicated, 100 μg/ml Novobiocin (Sigma) was added directly to the medium 30 min prior to fixation. Cells were lysed with 4 ml Hi-C Lysis buffer (10 mM Tris·HCl pH 8.0, 10 mM NaCl, 0.2% NP-40, 5 mM EGTA and protease inhibitors) at 4oC, passed 5x through a syringe/needle /G25) and chromatin was collected by centrifugation (5,000 rpm for 5 min, 4oC, table -top centrifuge). Only one pellet was further used (the rest were frozen at -80oC), and was washed twice in 1 ml of NEBuffer 1 plus 5 mM EGTA at 4oC. Before digestion chromatin was solubilized by adding 300 μl NEBuffer 1, 5 mM EGTA and 0.1% SDS and incubated 1h at 37oC, and stopped with Tx-100 (2% final). Afterwards, 100 U HpaII was added and incubated O/N at 37oC. The reaction was stopped adding SDS to 1.3% final, and incubating 1h at 50oC. Half of the sample was ligated by adding 5 ml 10x NEB T4 Ligase buffer, 2.5 ml 20% Tx-100, 0.5 ml 0.5M EGTA, in a final volume of 50 ml; and ligated with 20U (50 μl) T4 DNA ligase, O/N at 16oC. The sample was decrosslinked with 375 μl proteinase K, 2h at 65oC and purified with phenol extraction and Maxtract resin and ethanol precipitated as above. Further fragmentation was performed with Covaris to reduce the size of DNA to ~200-500 bases (Duty cycle: 10%, int.: 2, 200 cycles, 20 sec at 4oC). DNA was submitted to the CRG Ultrasequencing facility for standard Illumina library prep and paired-end sequencing.

text: Mycoplasma pneumoniae M129

text: Mycoplasma pneumoniae M129

text: Mycoplasma pneumoniae M129

characteristic: title


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: EMBL/CRG Systems Biology Research Unit. Centre for Genomic Regulation (CRG), Barcelona. Spain. -Universitat Pompeu Fabra (UPF), Barcelona. Spain.

characteristic: INSDC center name

text: public

characteristic: Submitter Id

text: ArrayExpress

characteristic: description

text: Mycoplasma pneumoniae M129

text: Mycoplasma pneumoniae M129

text: Mycoplasma pneumoniae M129


text: public

text: ArrayExpress

text: Protocols: M129 cells were grown in 150 cm2 dishes for 6 (exponential phase) or 96 hours (stationary phase) Non-ligated adapters were removed by reclaiming the Hi-C DNA bound beads and washing the beads twice with 400 μl TB, once with 200 μl NTB, once with 200 μl and then 50 μl NEBuffer 2. After the last wash, the beads were resuspended in 25 μl NEBuffer 2. The library was PCR amplified with Phusion (Next kit, NEB), 2 μl of the suspension in a 50 μl reaction, and 1.0 and 2.1 Illumina primers (1 μl 10 uM), for 16 cycles and sequenced in the HiSeq Illumina platform. Mycoplasma pneumoniae M129 cells were grown in 150 cm2 dishes for 6 (exponential phase) or 96 hours (stationary phase) and cross-linked with 1% Formaldehyde (methanol free, Pierce) for 10 min at room temperature (RT). The reaction was stopped with 0.125 M glycine and cells were washed prior to lysis. Four ml lysis buffer (10 mM Tris·HCl pH 8.0, 10 mM NaCl, 0.2% NP-40, protease inhibitors from Roche, 1 mM EGTA) was added and cells were broken with the help of a syringe/G25 needle (5x). The lysate was distributed into four tubes and spun in a tabletop centrifuge at 5,000 rpm for 5 min. The supernatant was removed and three pellets frozen for later use. One chromatin pellet was washed twice with 1.4 ml NEBuffer 2/3 (HindIII). After resuspension in 1 ml NEBuffer 2/3, 10 μl 10% SDS was added, mixed carefully and incubated at 65oC for 10 minutes to allow accessibility of restriction enzymes. Tubes were placed back on ice immediately after incubation. SDS was quenched by adding 110 μl 20% Triton X-100 and mixed carefully. Chromatin was digested by adding 100 μl 20,000 U/ml HindIII + 5 mM EGTA and incubated at 37oC overnight (O/N) while shaking. The next steps include marking the DNA ends with biotin and performing blunt-end ligation of cross-linked fragments. This step will allow ligation junctions to be purified later. To fill in the restriction fragment overhangs and mark the DNA ends with biotin, 5 μL of a mixture containing 10 mM dATP, dGTP and dTTP, 62.5 μl 0.4 mM biotin-14-dCTP, and 41 μl 2 U/μl Klenow was added to the Hi-C tubes, mixed carefully and incubated for 45 minutes at 37oC. To inactivate the enzymes, 250 μl 10% SDS was added to the Hi-C tubes, before incubation at 65oC for exactly 30 minutes and placed on ice immediately. The ligation is performed under extremely dilute conditions in order to favor ligation events between cross-linked fragments. Working on ice, 9 ml ligation mix (0.5 ml 20% Triton X-100, 1 ml 10x T4 ligation buffer, and 7.5 ml water) was added to a 50 ml falcon tube and the digested chromatin was incorporated into the mixture to the corresponding tube. After mixing by flipping the tubes, the ligation was performed for 4 hours at 17oC. Cross-links were reversed and proteins degraded by adding 50 μl 20 mg/ml proteinase K per Hi-C tube and incubating the tubes O/N at 65oC. An additional 50 μl 20 mg/ml proteinase K was added per tube the next day and incubated at 65oC for another 2 hours. The reaction mixture was cooled to RT and DNA was purified by performing an extraction in Maxtract tubes (Qiagen) with one volume phenol pH 8.0 and then with phenol/chloroform/IAA (25:25:1) (at each step the tube was vortexed for 2 minutes, spun for 5 min, 1500g m, RT and carefully as much of the aqueous phase as possible transferred to a new 50 ml tube). Then DNA was precipitated by adding 2 μl glycogen, 0.1x volume of 3 M sodium acetate, pH 5.5 and 2x volumes ethanol, left 30 min at -20°C and spun 25 minutes at 12,000 rpm (Beckman-Coulter 25,50 rotor) at 4oC. The pellet was washed with ~5 ml 75% ethanol and air-dried before dissolving it in 400 μl TE (10 mM Tris·HCl pH 8.0, 1 mM EDTA). The DNA mixture was transferred to a clean 1.5 ml centrifuge tube and a gel was run to see if everything went fine. Another round of purification was performed by doing once a phenol/chloroform/IAA extraction and DNA precipitation by adding 0.1x volume of 3 M sodium acetate, 2x volume of ethanol and incubating 30 minutes at -80oC. After spinning down the precipitated DNA, the DNA pellet was washed with 70% ethanol and resuspended in 25 μl TE. To degrade any RNA that might be present, 1 μl 1 mg/ml RNAse A was added per tube and incubated for 30 minutes at 37oC. Some fragments will not have been ligated: to avoid pulling them down later, biotin was removed from these unligated ends using the exonuclease activity of T4 DNA polymerase, as follows. Ca. 5 μg (~25 μl) of Hi-C DNA was mixed with 1 μl 10 mg/ml BSA, 10 μl 10x NEBuffer 2, 1 μl 10 mM dATP, 1 μl 10 mM dGTP and 5 U T4 DNA polymerase in a total volume of 100 μl and incubated at 12oC for 2 hours. The reaction was stopped by adding 2 μl 0.5 M EDTA pH 8.0. To purify the DNA, a phenol/chloroform/IAA extraction is done followed by ethanol precipitation as above. The supernatant is discarded and the DNA pellets are resuspended in 50 μl water. Then the DNA was sheared and size selected, to get a uniform size, suitable for high-throughput sequencing. The DNA must be sheared to a size of 300-500 bp with a Covaris nebulizer (10% duty cycle, intensity: 2, 200 cycles, 45 sec at 4oC) in a minimum of 55 μl TE. Size was checked on a 2% agarose gel and concentration was measured with Qubit (DNA, High sensitivity, Invitrogen). To repair the sheared DNA ends, the Next (NEB) protocol was followed (blunting and A tailing). Then the junctions were enriched by biotin pull-down allowing for identification of interacting chromatin fragments by paired-end sequencing, as follows. Ligation junctions were purified from the DNA pool, first, 150 μl resuspended streptavidin Dynabeads (Invitrogen) beads were washed twice with 400 μl Tween Buffer (TB: 5 mM Tris·HCl pH 8.0, 0.5 mM EDTA, 1 M NaCl, 0.05% Tween). All washes were done in the same manner: 1. Add buffer to the beads, 2. Rotate the sample for 3 minutes at RT, 3. Spin briefly to collect all the suspension, 4. Reclaim the beads using a magnetic particle concentrator, 5. Remove the supernatant. Beads were resuspended in 600 μl No Tween Buffer (5 mM Tris-HCl pH 8.0, 0.5 mM EDTA, 1 M NaCl) plus Hi-C DNA (~500 ng). Binding was allowed by incubating the mixture at RT for 15 minutes with rotation, and reclaiming the DNA bound streptavidin beads as above, before washing in 400 μl NTB followed by 100 μl T4 ligase buffer (NEB). Finally the beads were resuspended in 50 μl ligation buffer and Illumina paired end adapters were ligated (ratio: 1 μl 2 μM primers per 10 ng DNA) with 1200 Units T4 DNA Ligase (NEB) for 2 hours at RT. Non-ligated adapters were removed by reclaiming the Hi-C DNA bound beads and washing the beads twice with 400 μl TB, once with 200 μl NTB, once with 200 μl and then 50 μl NEBuffer 2. After the last wash, the beads were resuspended in 25 μl NEBuffer 2. The library was PCR amplified with Phusion (Next kit, NEB), 2 μl of the suspension in a 50 μl reaction, and 1.0 and 2.1 Illumina primers (1 μl 10 uM), for 16 cycles and sequenced in the HiSeq Illumina platform.

text: Mycoplasma pneumoniae M129

text: Mycoplasma pneumoniae M129

text: Mycoplasma pneumoniae M129


text: public

text: ArrayExpress

text: Mycoplasma pneumoniae M129

text: Mycoplasma pneumoniae M129

text: Mycoplasma pneumoniae M129

text: HPAII


text: CRUK CAMBRIDGE RESEARCH INSTITUTE

text: public

tag: Namespace:CRUK CAMBRIDGE RESEARCH INSTITUTE

text: Adenocarcinoma

characteristic: cell type

text: human

characteristic: common name

text: Public Health England Culture Collection

characteristic: culture collection

text: GEJ Adenocarcinoma

text: Homo sapiens

text: Homo sapiens

text: Esophagus

characteristic: tissue type


characteristic: ENA-CHECKLIST

text: CRUK CAMBRIDGE RESEARCH INSTITUTE

text: public

text: Adenocarcinoma

text: human

text: Dista Esophageal Adenocarcinoma

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: Esophagus


characteristic: ENA-FIRST-PUBLIC

text: CRUK CAMBRIDGE RESEARCH INSTITUTE

characteristic: INSDC first public

text: public

text: Adenocarcinoma

text: human

text: Distal esophageal Adenocarcinoma

text: Homo sapiens

text: Homo sapiens

text: Esophagus


text: CRUK CAMBRIDGE RESEARCH INSTITUTE

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: Adenocarcinoma

text: human

text: Esophageal Adenocarcinoma

text: Homo sapiens

text: Homo sapiens

text: Esophagus


text: CRUK CAMBRIDGE RESEARCH INSTITUTE

text: public

characteristic: SRA accession

text: Adenocarcinoma

text: human

text: Lymph node metastases of oesophageal adenocarcinoma

text: Homo sapiens

text: Homo sapiens

text: Esophagus


OACP4 C

text: CRUK CAMBRIDGE RESEARCH INSTITUTE

text: public

text: OACP4 C

text: Adenocarcinoma

text: human

text: Gastric cardia adenocarcinom

text: Homo sapiens

text: Homo sapiens

text: Esophagus

text: OACP4 C

characteristic: title


characteristic: ENA-LAST-UPDATE

text: CRUK CAMBRIDGE RESEARCH INSTITUTE

text: public

text: Adenocarcinoma

text: human

text: Distal esophageal adenocarcinoma

text: Homo sapiens

text: Homo sapiens

text: Esophagus