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text: YPG773 YSEQ17

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae


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characteristic: ENA-LAST-UPDATE

characteristic: External Id

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characteristic: INSDC center name

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characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: baker's yeast

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characteristic: description

text: Saccharomyces cerevisiae

characteristic: organism

text: Saccharomyces cerevisiae

characteristic: title

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text: PNRI

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text: Saccharomyces cerevisiae

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text: Saccharomyces cerevisiae

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text: Saccharomyces cerevisiae

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text: Saccharomyces cerevisiae

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text: Saccharomyces cerevisiae

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text: Saccharomyces cerevisiae

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text: Saccharomyces cerevisiae

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text: PNRI

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text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae


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text: Saccharomyces cerevisiae

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text: Saccharomyces cerevisiae

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text: Saccharomyces cerevisiae

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text: Saccharomyces cerevisiae

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text: Saccharomyces cerevisiae

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text: Saccharomyces cerevisiae

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text: Saccharomyces cerevisiae

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text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae


text: PNRI

text: public

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text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae


text: PNRI

text: public

text: baker's yeast

text: YPG796 YSEQ17

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae


text: PNRI

text: public

text: baker's yeast

text: YPG797 YSEQ18

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae


text: PNRI

text: public

text: baker's yeast

text: YPG798 YSEQ18

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae


text: PNRI

text: public

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text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae


text: PNRI

text: public

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text: Saccharomyces cerevisiae

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text: Saccharomyces cerevisiae

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text: Saccharomyces cerevisiae

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text: Saccharomyces cerevisiae

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text: Saccharomyces cerevisiae

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text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae


text: PNRI

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text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae


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text: Saccharomyces cerevisiae

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text: Saccharomyces cerevisiae

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text: Saccharomyces cerevisiae

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text: Saccharomyces cerevisiae

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text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae


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text: Saccharomyces cerevisiae

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text: Saccharomyces cerevisiae

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text: Saccharomyces cerevisiae

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text: Saccharomyces cerevisiae

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text: Saccharomyces cerevisiae

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text: Saccharomyces cerevisiae

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text: Saccharomyces cerevisiae

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text: Saccharomyces cerevisiae

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text: Saccharomyces cerevisiae

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text: Saccharomyces cerevisiae

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text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae


text: PNRI

text: public

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text: Saccharomyces cerevisiae

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text: Saccharomyces cerevisiae

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text: Saccharomyces cerevisiae

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text: Saccharomyces cerevisiae

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text: Saccharomyces cerevisiae

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text: Saccharomyces cerevisiae

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text: Saccharomyces cerevisiae

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text: Saccharomyces cerevisiae

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text: Saccharomyces cerevisiae

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text: Saccharomyces cerevisiae

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text: Saccharomyces cerevisiae

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text: PNRI

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text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae


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text: Saccharomyces cerevisiae

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text: Saccharomyces cerevisiae

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text: Saccharomyces cerevisiae

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text: Saccharomyces cerevisiae

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text: PNRI

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text: Saccharomyces cerevisiae

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text: Saccharomyces cerevisiae

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text: Saccharomyces cerevisiae

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text: PNRI

text: public

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text: Saccharomyces cerevisiae

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text: PNRI

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text: Saccharomyces cerevisiae

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text: PNRI

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text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae


text: PNRI

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text: YPG845 YSEQ19

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae


text: PNRI

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text: YPG846 YSEQ19

text: Saccharomyces cerevisiae

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text: PNRI

text: public

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text: YPG847 YSEQ19

text: Saccharomyces cerevisiae

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text: PNRI

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text: YPG848 YSEQ19

text: Saccharomyces cerevisiae

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text: PNRI

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text: YPG849 YSEQ19

text: Saccharomyces cerevisiae

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text: PNRI

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text: Saccharomyces cerevisiae

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text: PNRI

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text: Saccharomyces cerevisiae

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text: Saccharomyces cerevisiae

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text: Saccharomyces cerevisiae

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text: Saccharomyces cerevisiae

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text: Saccharomyces cerevisiae

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text: PNRI

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text: baker's yeast

text: YPG858 YSEQ19

text: Saccharomyces cerevisiae

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text: PNRI

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text: Saccharomyces cerevisiae

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text: PNRI

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text: baker's yeast

text: YPG860 YSEQ19

text: Saccharomyces cerevisiae

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text: Saccharomyces cerevisiae

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text: Saccharomyces cerevisiae

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text: Saccharomyces cerevisiae

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text: Saccharomyces cerevisiae

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text: Saccharomyces cerevisiae

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text: Saccharomyces cerevisiae

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text: Saccharomyces cerevisiae

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text: Saccharomyces cerevisiae

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text: Saccharomyces cerevisiae

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text: Saccharomyces cerevisiae

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text: YPG888 YSEQ19

text: Saccharomyces cerevisiae

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text: male

characteristic: ArrayExpress-SEX

text: Homo Sapiens

characteristic: ArrayExpress-SPECIES

text: SC

text: public

text: human

text: Male

characteristic: gender

text: Homo sapiens

text: Homo sapiens

characteristic: subject id


text: Macrophage

text: male

text: Homo Sapiens

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: SC

text: public

text: human

text: Male

text: Homo sapiens

text: Homo sapiens


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Postdoctoral Fellow

text: public

tag: Namespace:Postdoctoral Fellow

text: ArrayExpress

characteristic: broker name

characteristic: cell line

text: mouse embryonic stem cell

characteristic: cell type

text: house mouse

text: Protocols: 1.We followed the general protocol for in situ Hi-C as described in (Rao et al., 2014) which we adapted for use on low cell numbers. Mainly, differences were related to adjustments on the volume of the reactions, a shortening of the digestion step, a removal of biotin from the un-ligated fragments, and an alternative strategy for size-selection during library preparation. mESC OB2 cells were cultured as described in (Osunkoya et al., 1968)), FACS-sorted, selected for positive GFP expression and collected on PBS. Cells were then pelleted (300 g, 40C for 10 min) and resuspended in 1 ml PBS. 2. mESC OB2 cells were cultured as described in (Osunkoya et al., 1968)), FACS-sorted, selected for positive GFP expression and collected on PBS. Cells were then pelleted (300 g, 40C for 10 min) and resuspended in 1 ml PBS. 3.Cross-linking. In a fume hood, cells were cross-linked on a 1% final concentration (v/v) of 37% Formaldehyde and vigorously shaken prior to 10 min room temperature incubation with gentle rotation (20 rpm). The reaction was quenched for 5 min at room temperature and with gentle rotation (20 rpm) by adding 2.5M Glycine solution to a final concentration of 0.2M. Cells were twice pelleted (300 g, 4C for 5 min) and resuspended on 1 ml of cold 1X PBS. After these washes, cells were finally resuspended in 50 ml, quantified on a Neubauer’s chamber and aliquoted at different cells concentrations (5M, 1M, 100k, 50k, 25k, 10k and 1k). 5. DNA shearing. DNA was precipitated by adding 630 μL Phenol-Chloroform-Isoamyl alcohol (25:24:1) and samples were spun (5 min at 17,000 g). The supernatant was then mixed to 63 μL of 3M sodium acetate pH5.2, 2 μL GlycoBlue (Life Technologies) and 1008 μL pure ethanol, followed by 15 min incubation at -80C. Samples were then spun at 17,000 g at least for 30 min. The supernatant was discarded and the pellet was washed with cold 70% ethanol. All ethanol traces were removed, the pellet was air-dried for no longer than 5 min and then was dissolved in 30 μL (5M to 100k samples) or 15 μL (50k to 1k samples) of Tris pH 8.0 (Applichem) and incubated for 5 min at 370C without rotation. RNA was digested by adding 1 μL RNAse to each sample and the mix was incubated 15 min at 370C. Biotin from unligated fragments was removed by adding 10 μL (5M to 100k samples) or 5 μL (50k to 1k samples) of 10X NEB2 buffer (New England Biolabs), 1mM of a dNTPs mix (2.5 μL for the 5M to 100k samples or 1.25 μL for the 50k to 1k samples), 20mg/ml BSA (0.5 μL for 5M to 100k samples or 0.25 μL for 50k to 1k samples), nuclease-free water (up to 100 μL or 50 μL, respectively) and 3U/μL T4 DNA polymerase (5 μL or 3 μL, respectively; New England Biolabs). Samples were mixed by gentle pipetting up and down and incubated at 200C for 4h with no rotation. Samples were brought to a 120 μL volume with nuclease-free water and DNA was then sheared using a Covaris S220 instrument (2 cycles, each 50 sec long; 10% duty; 4 intensity; 200 cycles/burst). Biotin Pull-down. Dynabeads MyOne Streptavidin C1 beads (Thermo Fisher Scientific) were used to pull down biotinylated fragments according to manufacturers guidelines (https://tools.thermofisher.com/content/sfs/manuals/dynabeads_myone_savC1_man.pdf). Briefly, 120 μL of the sheared Hi-C sample was mixed with an equal amount of the prepared magnetic beads and incubated for 15 min with rotation to allow DNA binding to the beads. The beads were washed twice with 1x B&W buffer + 0.1% Triton X-100 by incubating the samples at 550C with shaking (1000 rpm) for 2 min, followed by a wash with 10 mM Tris-Cl pH 8.0 and finally resuspended in 50 μL of the last wash solution. 4. Lysis. Cells were pelleted and gently resuspended in 500 μL (5M and 1M samples), 250 μL (100k, 50K, 25k and 10k samples), or 125 μL (1k sample) of ice-cold in situ Hi-C lysis buffer (10 mM Tris-Cl pH 8.0, 10 mM NaCl, 0.2% IGEPAL CA-630, cOmplete Ultra protease inhibitors). Following 15 min incubation on ice, cells were spun down (1000 g, 4C for 5 min) and pellet was resuspended in 250 μL (5M and 1M samples), 125 μL (100k, 50K, 25k and 10k samples) or 62.5 μL (1k sample) of ice-cold in situ Hi-C lysis buffer. Lysed cells were then flash-frozen in liquid Nitrogen and stored at -80C.Restriction Enzyme digestion. Frozen aliquots at different cell concentrations were placed on ice to thaw, spun (13,000 g for 5 min at 40C) and resuspended in 500 μL (5M and 1M samples), 250 μL (100k sample), 125 μL (50K, 25k and 10k samples), or 62.5 μL (1k sample) lysis buffer. Following yet another spun (13,000 g for 5 min at 40C), cells were gently resuspended in 500 μL (5M and 1M samples), 250 μL (100k sample), 125 μL (50K, 25k and 10k samples) or 62.5 μL (1k sample) ice-cold 10x NEB2 buffer. Nuclei were permeabilised by resuspending them in 50 μL (5M, 1M and 100k samples), 25 μL (50K, 25k, 10k) or 12.5 μL (1k sample) of 0.4% SDS and incubating for 10 min at 65C without agitation. The SDS was then quenched by adding 25 μL (5M, 1M and 100k samples) or 12.5 μL (50K, 25k, 10k and 1k samples) of 10% Triton X-100 and 145 μL or 72.5 μL of nuclease-free water, respectively, and incubating at 370C for 45 min with rotation (650 rpm). Chromatin was digested by adding either a) 500U of HindIII-HF (5M, 1M and 100k) in 25 μL of 10x NEB2 buffer, or b) 100U (5M, 1M and 100k samples), 50U (50k, 25k and 10k samples) or 25U (1k sample) of MboI in 25 μL (5M, 1M and 100k samples), 35 μL (50k, 25k and 10k samples) or 42.5 μL (1k sample) of 10x NEB2.1 buffer, respectively (New England Biolabs). All the digestions were performed at 370C with gentle rotation for a period of 90 min by adding the restriction enzyme in two instalments. After the digestion, MboI samples were heat-inactivated for 20 min at 62C.Marking of DNA Ends. The overhangs generated by the restriction enzyme cuts were filled-in by adding a mix of 0.4 mM biotin-14-dA/CTP (18.75 μL for the 5M to 100k samples or 10 μL for the 50k to 1k samples; Life Technologies), 10mM dA/CTP, 10mM dGTP and 10mM dTTP (0.75 μL of each dinucleotide for the 5M to 100k samples or 0.5 μL for the 50k to 1k samples), and 5U/μL DNA polymerase I Klenow (5M to 100k samples or 4 μL for the 50k to 1k samples; New England Biolabs), followed by a 90 min incubation at 370C with gentle rotation.Proximity ligation. The DNA fragments were then ligated by adding a master mix containing nuclease-free water (657 μL for the 5M to 100k samples or 328.5 μL for the 50k to 1k samples), 10X T4 DNA ligase buffer (120 μL for the 5M to 100k samples or 60 μL for the 50k to 1k samples), 10% Triton X-100 (100 μL for the 5M to 100k samples or 50 μL for the 50k to 1k samples), 20mg/ml BSA (12 μL for the 5M to 100k samples or 6 μL for the 50k to 1k samples) and 5 Weiss U/μL T4 DNA ligase (5 μL for the 5M to 100k samples or 3.5 μL for the 50k to 1k samples in two instalments; Thermo Fisher Scientific). Samples were mixed by inversion and incubated at 20C with gentle rotation for 4 h.Crosslink reversal. The crosslink was reverted by spinning down the nuclei (2500 g for 5 min at room temperature) and resuspending them in 500 μL (5M to 100k samples) or 250 μL (50k to 1k samples) extraction buffer. To digest the proteins 20 μL (5M to 100k samples) or 10 μL (50k to 1k samples) of 20mg/ml proteinase K (Applichem) was added to the mix, followed by 30 min incubation at 55C with rotation (1000 rpm). 130 μL (5M to 100k samples) or 65 μL (50k to 1k) of 5M sodium chloride was added followed to the mix and was incubated overnight at 65C with shaking (1000rpm).

characteristic: genotype

text: Mus musculus

text: Mus musculus

text: EGFP-positive

characteristic: phenotype

text: Mus musculus


text: Quadram Institute Bioscience

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

tag: Namespace:Quadram Institute Bioscience

characteristic: Submitter Id

characteristic: collection date

text: Clostridium cadaveris isolated from preterm infant faecal sample

text: United Kingdom

characteristic: geographic location (country and/or sea)

text: Homo sapiens

characteristic: host scientific name

text: Clostridium cadaveris

characteristic: isolate

text: Preterm infant faecal sample

characteristic: isolation source

text: Clostridium cadaveris

text: Clostridium cadaveris

characteristic: strain

text: Clostridium cadaveris LH052


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: University Hospital Galway

text: public

tag: Namespace:University Hospital Galway

text: Ireland

text: Homo sapiens

text: Human

text: Salmonella enterica subsp. enterica serovar Stanley

characteristic: organism

text: Stanley

characteristic: serovar

text: Subsp. I

characteristic: sub species

characteristic: title


text: University Hospital Galway

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: Ireland

text: Homo sapiens

text: Human

text: Salmonella enterica subsp. enterica serovar Enteritidis

text: Enteritidis

text: Subsp. I


text: University Hospital Galway

text: public

characteristic: SRA accession

characteristic: Submitter Id

characteristic: collection date

text: Ireland

characteristic: geographic location (country and/or sea)

text: Homo sapiens

text: Human

text: Salmonella enterica subsp. enterica

text: Salmonella enterica subsp. enterica

text: Unnamed

text: Subsp. I


text: University Hospital Galway

text: public

text: Ireland

text: Homo sapiens

characteristic: host scientific name

characteristic: isolate

text: Human

characteristic: isolation source

text: Salmonella enterica subsp. enterica serovar Typhimurium

text: Typhimurium

text: Subsp. I


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: University Hospital Galway

text: public

text: Ireland

text: Homo sapiens

text: Human

text: Salmonella enterica subsp. enterica serovar Typhimurium var. monophasic 4,[5],12:i:-

text: Subsp. I


characteristic: External Id

text: University Hospital Galway

text: public

text: Ireland

text: Homo sapiens

text: Human

text: Salmonella enterica subsp. enterica serovar Agona

characteristic: organism

text: Agona

characteristic: serovar

text: Subsp. I


text: Quadram Institute Bioscience

characteristic: INSDC center name

text: public

text: Clostridium paraputrificum isolated from preterm infant faecal sample

characteristic: description

text: United Kingdom

text: Home sapiens

text: Clostridium paraputrificum

text: Preterm infant faecal sample

text: Clostridium paraputrificum

text: Clostridium paraputrificum

characteristic: strain

text: Clostridium paraputrificum LH025

characteristic: title


text: Quadram Institute Bioscience

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: United Kingdom

text: Home sapiens

text: Clostridium paraputrificum

text: Preterm infant faecal sample

text: Clostridium paraputrificum

text: Clostridium paraputrificum

text: Clostridium paraputrificum LH058


text: Quadram Institute Bioscience

text: public

characteristic: Submitter Id

characteristic: collection date

text: United Kingdom

characteristic: geographic location (country and/or sea)

text: Home sapiens

characteristic: host scientific name

text: Clostridium paraputrificum

text: Preterm infant faecal sample

text: Clostridium paraputrificum

text: Clostridium paraputrificum

text: Clostridium paraputrificum LH141


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: JUSTUS LIEBIG UNIVERSITAT

text: public

tag: Namespace:JUSTUS LIEBIG UNIVERSITAT

text: Escherichia coli

text: Escherichia coli

text: ESBL isolates from food


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: public

tag: Namespace:Universite Paris-Sud Institute for the integrative biology of the cell (I2BC) Bat 26, CNRS

text: ArrayExpress

characteristic: broker name

text: Protocols: M9 minimal medium supplemented with 0.4% glucose Sigma GenElute bacterial genomic DNA kit Nextera DNA library preparation kit

text: dif hipA

characteristic: genotype

text: 37 degree celsius

characteristic: growth condition

text: Escherichia coli str. K-12 substr. MG1655


text: Universite Paris-Sud Institute for the integrative biology of the cell (I2BC) Bat 26, CNRS

characteristic: INSDC center name

text: public

text: ArrayExpress

characteristic: description

text: dif hipA recB

text: 37 degree celsius

characteristic: organism


characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: ArrayExpress

text: recB

text: 37 degree celsius

characteristic: title


text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: ArrayExpress

text: terB

text: 37 degree celsius


text: public

text: ArrayExpress

text: terB recB

text: 37 degree celsius


text: public

text: ArrayExpress

text: terB tus

text: 37 degree celsius


text: public

text: ArrayExpress

text: terB tus recB

text: 37 degree celsius


text: public

text: ArrayExpress

text: tus

text: 37 degree celsius


text: public

text: ArrayExpress

text: tus recB

text: 37 degree celsius


text: public

text: ArrayExpress

text: xerC

text: 37 degree celsius


text: public

text: ArrayExpress

text: xerCrecB

text: 37 degree celsius


text: public

text: ArrayExpress

text: FtsAts

text: 42 degree celsius


text: public

text: ArrayExpress

text: FtsAts recB

text: 30 degree celsius


text: public

text: ArrayExpress

text: FtsAts recB

text: 42 degree celsius


text: public

text: ArrayExpress

text: FtsAts recB tus

text: 42 degree celsius


text: public

text: ArrayExpress

text: FtsAts tus

text: 42 degree celsius


text: public

text: ArrayExpress

text: FtsI-ts

text: 42 degree celsius


text: public

text: ArrayExpress

text: FtsI-ts recB

text: 30 degree celsius


text: public

text: ArrayExpress

text: FtsI-ts recB

text: 42 degree celsius


text: public

text: ArrayExpress

text: FtsI-ts tus recB

text: 42 degree celsius


text: public

text: ArrayExpress

text: FtsKATPase-

text: 37 degree celsius


text: public

text: ArrayExpress

text: FtsKATPase- recB

text: 37 degree celsius


text: public

text: ArrayExpress

text: FtsKATPase- tus

text: 37 degree celsius


text: public

text: ArrayExpress

text: FtsKATPase- tus recB

text: 37 degree celsius


text: public

text: ArrayExpress

text: 37 degree celsius


text: public

text: ArrayExpress

text: invT2 recB

text: 37 degree celsius


text: public

text: ArrayExpress

text: invT2 tus

text: 37 degree celsius


text: public

text: ArrayExpress

text: invT2 tus recB

text: 37 degree celsius


text: public

text: ArrayExpress

text: invT3 recB

text: 37 degree celsius


text: public

text: ArrayExpress

text: invT3 FtsKATPase-

text: 37 degree celsius


text: public

text: ArrayExpress

text: invT3 FtsKATPase- recB

text: 37 degree celsius


text: public

text: ArrayExpress

text: LC3-R111 recB

text: 37 degree celsius


text: public

text: ArrayExpress

text: LC3-R111 FtsKC

text: 37 degree celsius


text: public

text: E-MTAB-6030:LC3_R111_FtsK_Cter_recB_7509

text: ArrayExpress

text: LC3-R111 FtsKC recB

text: 37 degree celsius


text: public

text: ArrayExpress

text: wild type genotype

text: 37 degree celsius


Clone 1

text: LSHTM

text: public

text: Clone 1

text: Trypanosoma cruzi

text: Trypanosoma cruzi

text: Drug resistant T.cruzi isolates


Clone 2

text: LSHTM

text: public

text: Clone 2

text: Trypanosoma cruzi

text: Trypanosoma cruzi

text: Drug resistant T.cruzi isolates


Clone 3

text: LSHTM

text: public

text: Clone 3

text: Trypanosoma cruzi

text: Trypanosoma cruzi

text: Drug resistant T.cruzi isolates


Parental

text: LSHTM

text: public

text: Parental

text: Trypanosoma cruzi

text: Trypanosoma cruzi

text: Parental strain T.cruzi


E-MTAB-6048:14028s WT rep1

text: public

text: E-MTAB-6048:14028s WT rep1

tag: Namespace:Wadsworth Center, NYS Department of Health

text: ArrayExpress

text: Protocols: Subcultures were grown to an OD600 of 0.5-0.7. Transfer 1mL of subculture to new microcentrifuge tube. Overnight cultures were started from single colonies in 2 mL LB at 37 degrees Celsius shaking at 225 rpm and grown for ~18 hours. Subcultures were grown in LB at 37 degrees Celsius to an OD600 of 0.5-0.7. Hot phenol RNA prep: transfer 1mL of subculture to a microcentrifuge tube. Spin at max speed for 1 min and remove supernatant. Resuspend in 0.4mL ethanol+5% acid phenol/chloroform, spin 1 min at max speed and remove supernatant. Resuspend in 1mL 1x TBS, spin 1 min at max speed and remove supernatant. Resuspend in 0.5mL RNA Lysis Buffer (2% SDS, 4mM EDTA) and boil samples for 3 min. Add 0.5mL acid phenol/chloroform to tube and incubate for 6 min at 65 °C. Incubate 5 min on ice then spin tubes at max speed for 6 min. Transfer upper phase to phase lock tube, add equal volume (0.4mL) chloroform:isoamyl alcohol 24:1 and spin 6 min at max speed. Transfer upper phase to new phase lock tube, add equal volume (0.4mL) chloroform:isoamyl alcohol 24:1 and spin 6 min at max speed. Transfer upper phase to new tube containing 40uL 3M Na Acetate+2uL glycogen (20mg/mL stock). Add 1mL ice cold EtOH and precipitate at -20 °C overnight or at -80 °C for at least 30 min. Spin samples for 30 min at 4 °C at max speed. Pipet off supernatant. Wash with 0.7mL of 70% EtOH (in DEPC H2O), spin 5 min at max speed at 4 °C and remove supernatant. Wash again with 0.7mL of 70% EtOH (in DEPC H2O), spin for 5 min at max speed at 4 °C and pipet off supernatant. Dry pellet at room temperature and resuspend in 15uL nuclease free water. DNase treat RNA - set up 50uL reaction including 8-10ug RNA, 5uL of 10X buffer and 1uL DNase enzyme (Ambion). Incubate 30 min at 37 °C. Stop reaction by adding 352uL DEPC H2O + 134uL acid phenol:chloroform + 268uL chloroform:isoamyl alcohol 24:1. Transfer all to phase lock tube and spin at max speed for 6 min. Transfer upper phase to new microcentrifuge tube containing 40uL 3M Na Acetate + 2uL glycogen (20mg/mL stock). Add 1mL ice cold EtOH and precipitate at -20 °C overnight at -80 °C for at least 30 min. Spin samples for 30 min at 4 °C at max speed. Pipet off supernatant. Wash with 0.7mL of 70% EtOH (in DEPC H2O), spin 5 min at max speed at 4 °C and remove supernatant. Wash again with 0.7mL of 70% EtOH (in DEPC H2O), spin for 5 min at max speed at 4 °C and pipet off supernatant. Dry pellet at room temperature and resuspend in 15uL nuclease free water. Remove ribosomal RNA using the RiboZero kit from EpiCentre - wash magnetic beads 2x in RNase free water, then resuspend in Resuspension Solution. Add 32.5uL beads to each tube then add 0.5uL RNase inhibitor. Mix together in final volume of 20uL: 2.5ug DNase treated RNA + 2uL Ribozero reaction buffer + 4uL Ribozero rRNA removal solution. Incubate at 68 °C for 10 min followed by RT for 5 min. Add RNA to beads, mix by pipetting and vortexing for 10 s. Incubate at RT for 5 min. Vortex for 5 s then incubate at 50 °C for 5 min. Place tubes on magnetic stand for 1 min and transfer RNA to new tube. Bring volume to 180uL with DEPC H2O, then add 18uL 3M Na Acetate + 2uL glycogen (20mg/mL stock). Add 0.6mL ice cold EtOH and precipitate at -20 °C overnight. Spin samples for 30 min at 4 °C at max speed. Pipet off supernatant. Wash with 0.7mL of 70% EtOH (in DEPC H2O), spin 5 min at max speed at 4 °C and remove supernatant. Wash again with 0.7mL of 70% EtOH (in DEPC H2O), spin for 5 min at max speed at 4 °C and pipet off supernatant. Dry pellet at room temperature and resuspend in 8uL nuclease free water. Prepare libraries using EpiCentre ScriptSeq v2 kit following kit protocol. Fragment RNA and anneal cDNA synthesis primer in 12uL reaction containing nuclease free water + 40ng rRNA depleted RNA + 1uL RNA Fragmentation solution + 2uL cDNA Synthesis primer. Incubate at 85 °C for 5 min then place tubes on ice. Synthesize cDNA by adding 3uL cDNA Synthesis Premix + 0.5uL 100mM DTT + 0.5uL StarScript Reverse Transcriptase. Incubate at 25 °C for 5 min then 42 °C for 20 min. Cool tubes to 37 °C. Add 1uL Finishing solution and incubate at 37 °C for 10 min then 95 °C for 3 min. Cool tubes to 25 °C then add 7.5uL Terminal Tagging Premix + 0.5uL DNA Polymerase to terminally tag the cDNA. Incubate at 25 °C for 15 min, 95 °C for 3 min, then cool to 4 °C. Purify the cDNA using the Qiagen MinElute PCR Purification Kit - Add 5V Buffer PB to sample and transfer all to MinElute column. Spin 1 min at max speed. Discard flow through. Add 0.75mL Buffer PE to column and spin 1 min at max speed. Discard flow through. Spin column for 1 min at max speed then transfer column to new tube. Add 23.4uL Buffer EB to column, incubate 1 min at room temp, then spin 1 min at max speed. Amplify library by setting up 50uL PCR using 22.5uL purified DNA. Add 25uL FailSafe PCR Premix E + 1uL Forward PCR primer + 1uL ScriptSeq Index PCR Primer + 0.5uL FailSafe PCR Enzyme (1.25U). Heat at 95 °C for 1 min, then 12 cycles of 95 °C for 30 sec, 55 °C for 30 sec and 68 °C for 3 min. Incubate at 68 °C for 7 minutes. Purify sample using AMPure XP Purification protocol. Add 50uL beads to each PCR sample. Mix by pipetting 10x. Transfer beads+sample to new tube and incubate at room temp for 15 min. Put tubes on magnetic stand for 5 min then remove supernatant. Wash beads 2x, each time with 0.2mL of 80% EtOH, let stand 1 min then remove supernatant. Air dry beads at room temp for 15 min. Add 12uL nuclease free water, remove tubes from magnetic stand and resuspend beads in water. Incubate at room temp for 2 min. Place tubes on magnetic stand for 5 min. Library is in supernatant. Transfer to new tube. Quantify using Qubit.

text: wild type genotype

text: wild type phenotype

characteristic: phenotype

text: 14028s WT rep1


E-MTAB-6048:14028s WT rep2

characteristic: ENA-CHECKLIST

text: Wadsworth Center, NYS Department of Health

text: public

text: E-MTAB-6048:14028s WT rep2

text: ArrayExpress

text: wild type genotype

text: wild type phenotype

text: 14028s WT rep2


E-MTAB-6048:del-rpoF rep1

characteristic: ENA-FIRST-PUBLIC

text: public

text: E-MTAB-6048:del-rpoF rep1

text: ArrayExpress

text: rpoF deletion

text: fliA deletion

text: del-rpoF rep1


E-MTAB-6048:del-rpoF rep2

characteristic: ENA-LAST-UPDATE

text: public

text: E-MTAB-6048:del-rpoF rep2

text: ArrayExpress

text: rpoF deletion

text: fliA deletion

text: del-rpoF rep2


characteristic: External Id

text: INRA

text: public

text: French dry-type sausage

text: Lactobacillus sakei

text: Lactobacillus sakei

characteristic: strain

text: food sample


text: University Hospital Galway

text: public

characteristic: collection date

text: Ireland

characteristic: geographic location (country and/or sea)

text: Homo sapiens

characteristic: host scientific name

characteristic: isolate

text: Human

characteristic: isolation source

text: Salmonella enterica subsp. enterica serovar Hessarek

text: Hessarek

characteristic: serovar

text: Subsp. I

characteristic: sub species


text: University Hospital Galway

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: Ireland

text: Homo sapiens

text: Human

text: Salmonella enterica subsp. enterica serovar Virginia

characteristic: organism

text: Virginia

text: Subsp. I

characteristic: title


characteristic: ENA-CHECKLIST

text: University Hospital Galway

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: Ireland

text: Homo sapiens

text: Human

text: Salmonella enterica subsp. enterica

text: Salmonella enterica subsp. enterica

text: Unnamed

text: Subsp. I


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: University Hospital Galway

text: public

text: Ireland

text: Homo sapiens

text: Human

text: Salmonella enterica subsp. enterica serovar Sandiego

text: Sandiego

text: Subsp. I


E-MTAB-6049:14028s RpoF rep1

text: public

text: E-MTAB-6049:14028s RpoF rep1

text: ArrayExpress

characteristic: broker name

text: Protocols: Subcultures were grown in LB at 37 degrees Celsius to an OD600 of 0.5-0.7. Salmonella FliA was N-terminally epitope tagged with a 3x-FLAG tag at the native chromosomal locus. Anti-FLAG antibody is from Sigma-Aldrich, catalog number F3165-1MG. The product name is Monoclonal ANTI-FLAG® M2 antibody produced in mouse. Overnight cultures were started from single colonies in 2 mL LB at 37 degrees Celsius shaking at 225 rpm and grown for ~18 hours. 40 ml subcultures were grown in LB at 37 degrees Celsius to an OD600 of 0.5-0.7. Cells were crosslinked for 20 minutes with formaldehyde (1% final concentration), pelleted by centrifugation and washed once with Tris-buffered saline (TBS). Cell pellets were resuspended in 1 ml FA lysis buffer (50 mM Hepes-KOH, pH 7, 150 mM NaCl, 1 mM EDTA, 1% Triton X-100, 0.1% sodium deoxycholate, 0.1% SDS) with 4 mg/ml lysozyme and incubated at 37 degrees Celsius for 30 minutes. Samples were then chilled and sonicated for 30 minutes in a Bioruptor sonicator (Diagenode) with 30 s on/30 s off pulsing at maximum amplitude. Samples were pelleted in a microcentrifuge to remove debris and supernatants (chromatin) were saved, 2.5 ml FA lysis buffer was added, and samples were stored indefinitely at -20 degrees Celsius. For the immunoprecipitation (IP), 800 ul chromatin was incubated with 25 ul Protein A Sepharose slurry (50%) in TBS and 2 ul anti-FLAG (Sigma) for 90 minutes at room temperature with gentle mixing on a rotisserie rotator. Following the 90 min incubation, beads were washed twice with FA lysis buffer and twice with 10 mM Tris-HCl, pH 7.5 (please note: all wash steps involved incubation of samples with the wash solution for 3 min with gentle mixing on a rotisserie rotator before pelleting beads at 1,500 x g in a microcentrifuge for 1 min). Beads were resuspended in 100 uL 1X Quick Blunting Buffer (NEB) containing dNTPs (concentration specified by NEB Quick Blunting kit) and 1 uL Quick Blunting enzyme mix (NEB), and incubated at room temperature for 30 min with gentle mixing. Beads were washed twice with FA lysis buffer and twice with 10 mM Tris-HCl, pH 8.0. Beads were resuspended in 100 uL Buffer 2 (NEB) containing 2 mM dATP and 2 uL Klenow DNA polymerase (NEB), and incubated for 30 min at 37 degrees Celsius with gentle mixing. Beads were washed twice with FA lysis buffer and twice with 10 mM Tris-HCl, pH 7.5. Beads were resuspended in 1X DNA Quick Ligase buffer (NEB), 1 uL NEXTflex ChIP-seq Barcoded adapter (BioO) and 2 uL Quick DNA Ligase (NEB), and incubated at room temperature for 15 min with gentle mixing. Beads were washed twice with FA lysis buffer, and once each with high salt FA lysis buffer (50 mM Hepes-KOH, pH 7, 500 mM NaCl, 1 mM EDTA, 1% Triton X-100, 0.1% sodium deoxycholate, 0.1% SDS), ChIP wash buffer (10 mM Tris-HCl, pH 8.0, 250 mM LiCl, 1 mM EDTA, 0.5% Nonidet-P40, 0.5% sodium deoxycholate) and TE (10 mM Tris-HCl, pH 7.5, 1 mM EDTA). After the TE wash, beads were transferred to a fresh Spin-X column and eluted with 100 ul ChIP elution buffer (50 mM Tris-HCl, pH 7.5, 10 mM EDTA, 1% SDS) for 10 minutes at 65 degrees Celsius with occasional agitation. Samples were decrosslinked by boiling for 10 minutes. DNA was extracted with phenol/chlorofom/isoamyl alcohol, ethanol precipitated, and resuspended in 11 uL H2O. 1 uL DNA was diluted 1:8 and 2 ul were used for real time PCR amplification (three technical replicates)with NEXTflex ChIP-seq Primer Mix (JW3764-AATGATACGGCGACCACCGAGATCTACAC and JW3765-CAAGCAGAAGACGGCATACGAGAT) using an ABI 7500 Fast real time PCR machine. The number of cycles required to reach a Delta Rn score of 0.1 was recorded (ÒXÓ). 8 uL of the remaining DNA was amplified using conventional PCR with oligonucleotides JW3764 and JW3765 (100 uM) for X+3 cycles with an annealing temperature of 60 degrees Celsius. PCR products were purified using Ampure XP magnetic beads (Ampure) and resuspended in 20 uL H2O. Purified PCR products between 200 bp and 600 bp were gel purified from an 8% non-denaturing polyacrylamide gel, eluted overnight in DNA extraction buffer (0.3 M NaCl, 10 mM Tris-HCl pH 8.0, 1 mM EDTA) and ethanol precipitated to generate the final ChIP-seq library. The library was resuspended in 11 uL H2O and quantified using a Qubit fluorimeter (Invitrogen). The library was sequenced using a HiSeq 2000 sequencer (Illumina; University at Buffalo Next Generation Sequencing Core Facility).

characteristic: description

characteristic: genotype

text: 14028s RpoF rep1


E-MTAB-6049:14028s RpoF rep2

text: public

text: E-MTAB-6049:14028s RpoF rep2

text: ArrayExpress

text: 14028s RpoF rep2


E-MTAB-6049:14028s WT rep1

text: public

text: E-MTAB-6049:14028s WT rep1

text: ArrayExpress

text: wild type genotype

text: 14028s WT rep1


E-MTAB-6049:14028s WT rep2

text: public

text: E-MTAB-6049:14028s WT rep2

text: ArrayExpress

text: wild type genotype

text: 14028s WT rep2


text: ROBERT KOCH-INSTITUTE

text: public

tag: Namespace:ROBERT KOCH-INSTITUTE

characteristic: collection date

text: Enterobacter cloacae isolate from a German clinic

text: Germany

characteristic: geographic location (country and/or sea)

text: not provided

characteristic: host health state

text: Homo sapiens

characteristic: host scientific name

characteristic: isolate

text: brain abscess

characteristic: isolation source

text: Enterobacter cloacae subsp. cloacae

text: Enterobacter cloacae subsp. cloacae

text: multilocus sequence type (ST) 815

characteristic: serovar

text: clinial isolate

characteristic: strain

text: clinical isolate of E. cloacae


characteristic: ENA-CHECKLIST

text: ROBERT KOCH-INSTITUTE

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: Germany

text: not provided

text: Homo sapiens

text: perianal swab

text: Enterobacter cloacae subsp. cloacae

characteristic: organism

text: Enterobacter cloacae subsp. cloacae

text: multilocus sequence type (ST) 815

text: clinial isolate

text: clinical isolate of E. cloacae

characteristic: title


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: ROBERT KOCH-INSTITUTE

text: public

characteristic: SRA accession

characteristic: Submitter Id

characteristic: description

text: Germany

text: not provided

text: Homo sapiens

text: blood culture

text: Enterobacter cloacae subsp. cloacae

text: Enterobacter cloacae subsp. cloacae

text: multilocus sequence type (ST) 815

text: clinial isolate

text: clinical isolate of E. cloacae


text: ROBERT KOCH-INSTITUTE

text: public

characteristic: collection date

text: Germany

characteristic: geographic location (country and/or sea)

text: not provided

characteristic: host health state

text: Homo sapiens

characteristic: host scientific name

characteristic: isolate

text: nasopharyngeal swab

text: Enterobacter cloacae subsp. cloacae

text: Enterobacter cloacae subsp. cloacae

text: multilocus sequence type (ST) 815

text: clinial isolate

text: clinical isolate of E. cloacae


characteristic: ENA-CHECKLIST

text: ROBERT KOCH-INSTITUTE

characteristic: INSDC center name

text: public

text: Germany

text: not provided

text: Homo sapiens

text: perianal swab

characteristic: isolation source

text: Enterobacter cloacae subsp. cloacae

text: Enterobacter cloacae subsp. cloacae

text: multilocus sequence type (ST) 104

characteristic: serovar

text: clinial isolate

characteristic: strain

text: clinical isolate of E. cloacae


text: ROBERT KOCH-INSTITUTE

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: Germany

text: not provided

text: siphon NICU

text: Enterobacter cloacae subsp. cloacae

characteristic: organism

text: Enterobacter cloacae subsp. cloacae

text: multilocus sequence type (ST) 815

text: clinial isolate

text: environmental isolate of E. cloacae

characteristic: title


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: ROBERT KOCH-INSTITUTE

text: public

characteristic: SRA accession

characteristic: Submitter Id

text: Germany

text: not provided

text: Homo sapiens

text: perianal swab

text: Enterobacter cloacae subsp. cloacae

text: Enterobacter cloacae subsp. cloacae

text: multilocus sequence type (ST) 118

text: clinial isolate

text: clinical isolate of E. cloacae


text: ROBERT KOCH-INSTITUTE

text: public

characteristic: collection date

characteristic: description

text: Germany

characteristic: geographic location (country and/or sea)

text: not provided

characteristic: host health state

text: Homo sapiens

characteristic: host scientific name

text: nasopharyngeal swab

text: Enterobacter cloacae subsp. cloacae

text: Enterobacter cloacae subsp. cloacae

text: multilocus sequence type (ST) 190

text: clinial isolate

text: environmental isolate of E. cloacae


characteristic: ENA-CHECKLIST

text: ROBERT KOCH-INSTITUTE

characteristic: INSDC center name

text: public

text: Germany

text: not provided

characteristic: isolate

text: siphon

characteristic: isolation source

text: Enterobacter cloacae subsp. cloacae

text: Enterobacter cloacae subsp. cloacae

text: multilocus sequence type (ST) 907

characteristic: serovar

text: clinial isolate

text: clinical isolate of E. cloacae


text: ROBERT KOCH-INSTITUTE

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: Germany

text: not provided

text: Homo sapiens

text: stool sample

text: Enterobacter cloacae subsp. cloacae

characteristic: organism

text: Enterobacter cloacae subsp. cloacae

text: multilocus sequence type (ST) 128

text: clinial isolate

characteristic: strain

text: clinical isolate of E. cloacae


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: ROBERT KOCH-INSTITUTE

text: public

characteristic: SRA accession

text: Germany

text: not provided

text: Homo sapiens

text: stool sample

text: Enterobacter cloacae subsp. cloacae

text: Enterobacter cloacae subsp. cloacae

text: multilocus sequence type (ST) 816

text: clinial isolate

text: clinical isolate of E. cloacae

characteristic: title


text: ROBERT KOCH-INSTITUTE

text: public

characteristic: Submitter Id

characteristic: collection date

characteristic: description

text: Germany

characteristic: geographic location (country and/or sea)

text: not provided

characteristic: host health state

text: Homo sapiens

text: perianal swab

text: Enterobacter cloacae subsp. cloacae

text: Enterobacter cloacae subsp. cloacae

text: multilocus sequence type (ST) 97

text: clinial isolate

text: clinical isolate of E. cloacae


characteristic: ENA-CHECKLIST

text: ROBERT KOCH-INSTITUTE

characteristic: INSDC center name

text: public

text: Germany

text: not provided

text: Homo sapiens

characteristic: host scientific name

characteristic: isolate

text: nasopharyngeal swab

characteristic: isolation source

text: Enterobacter cloacae subsp. cloacae

text: Enterobacter cloacae subsp. cloacae

text: multilocus sequence type (ST) 145

text: clinial isolate

text: clinical isolate of E. cloacae


text: ROBERT KOCH-INSTITUTE

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: Germany

text: not provided

text: Homo sapiens

text: perianal swab

text: Enterobacter cloacae subsp. cloacae

characteristic: organism

text: Enterobacter cloacae subsp. cloacae

text: multilocus sequence type (ST) 278

characteristic: serovar

text: clinial isolate

text: clinical isolate of E. cloacae


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: ROBERT KOCH-INSTITUTE

text: public

characteristic: SRA accession

text: Germany

text: not provided

text: Homo sapiens

text: nasopharyngeal swab

text: Enterobacter cloacae subsp. cloacae

text: Enterobacter cloacae subsp. cloacae

text: multilocus sequence type (ST) 254

text: clinial isolate

characteristic: strain

text: clinical isolate of E. cloacae


text: ROBERT KOCH-INSTITUTE

text: public

characteristic: Submitter Id

characteristic: collection date

characteristic: description

text: Germany

characteristic: geographic location (country and/or sea)

text: not provided

text: Homo sapiens

text: perianal swab

text: Enterobacter cloacae subsp. cloacae

text: Enterobacter cloacae subsp. cloacae

text: multilocus sequence type (ST) 114

text: clinial isolate

text: clinical isolate of E. cloacae

characteristic: title


characteristic: ENA-CHECKLIST

text: LUDWIG-MAXIMILIANS-UNIVERSITAET MUENCHEN

characteristic: INSDC center name

text: public

characteristic: cell type

text: fruit fly

characteristic: common name

text: r2d2 mutant clone #1, beta-eliminated

text: Drosophila melanogaster

text: Drosophila melanogaster

text: LoqsPD/Dcr-2 form an alternative RLC in Drosophila


1-19-3 nb

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: 1-19-3 nb

text: fruit fly

text: r2d2 mutant clone #1, untreated

text: Drosophila melanogaster

text: Drosophila melanogaster


2-7-13 beta

characteristic: ENA-FIRST-PUBLIC

text: public

text: 2-7-13 beta

text: fruit fly

text: r2d2 mutant clone #2, beta-eliminated

text: Drosophila melanogaster

characteristic: organism

text: Drosophila melanogaster


2-7-13 nb

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: public

text: 2-7-13 nb

text: fruit fly

text: r2d2 mutant clone #2, untreated

text: Drosophila melanogaster

text: Drosophila melanogaster


3-19-35 beta

text: public

characteristic: SRA accession

text: 3-19-35 beta

text: fruit fly

text: loqs mutant clone #1, beta-eliminated

text: Drosophila melanogaster

text: Drosophila melanogaster


3-19-35 nb

text: public

text: 3-19-35 nb

characteristic: Submitter Id

text: fruit fly

text: loqs mutant clone #1, untreated

text: Drosophila melanogaster

text: Drosophila melanogaster


3-7-25 beta

text: public

text: 3-7-25 beta

text: fruit fly

text: loqs mutant clone #2, beta-eliminated

text: Drosophila melanogaster

text: Drosophila melanogaster


3-7-25 nb

text: public

text: 3-7-25 nb

text: fruit fly

text: loqs mutant clone #2, untreated

text: Drosophila melanogaster

text: Drosophila melanogaster


text: UNIVERSITY OF GLASGOW

text: public

tag: Namespace:UNIVERSITY OF GLASGOW

text: fruit fly

text: Larva

characteristic: dev stage

text: Drosophila melanogaster

text: Drosophila melanogaster

text: Larval Carcass (Mir)

characteristic: tissue lib

text: Carcass

characteristic: tissue type

text: FlyAtlas2 (Mir)


text: Escherichia coli

characteristic: ArrayExpress-SPECIES

text: SC

text: public

text: Escherichia coli

text: Escherichia coli

text: Escherichia coli

characteristic: subject id

characteristic: title


text: Salmonella enterica

characteristic: ENA-CHECKLIST

text: SC

characteristic: INSDC center name

text: public

text: Salmonella enterica

text: Salmonella enterica

text: Salmonella enterica


text: UNIVERSITY OF GLASGOW

characteristic: INSDC first public

text: public

text: fruit fly

characteristic: common name

text: Larva

text: Drosophila melanogaster

text: Drosophila melanogaster

text: Larval CNS (Mir)

text: Central Nervous System

text: FlyAtlas2 Mir


text: UNIVERSITY OF GLASGOW

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: fruit fly

text: Larva

text: Drosophila melanogaster

text: Drosophila melanogaster

text: Larval FatBody (Mir)

text: Fat Body

text: FlyAtlas 2 (Mir)


characteristic: ENA-FIRST-PUBLIC

text: UNIVERSITY OF GLASGOW

text: public

text: fruit fly

text: Larva

text: Drosophila melanogaster

characteristic: organism

text: Drosophila melanogaster

text: Larval Hindgut (Mir)

text: Hindgut

text: FlyAtlas2 Mir


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: THE ROSLIN INSTITUTE

text: public

tag: Namespace:THE ROSLIN INSTITUTE

characteristic: age

text: year

characteristic: age unit

text: transcription profiling by high throughput sequencing

characteristic: assay type

text: Thoroughbred

characteristic: breed

characteristic: cell or tissue type

text: horse

text: bone marrow derived macrophages (+ lipopolysaccharide, 0 hr.) from 10 year old gelding Thoroughbred

characteristic: description

text: total RNA

characteristic: experiment target

characteristic: extraction protocol

text: Edinburgh Genomics, The University of Edinburgh, EH9 3FL, Edinburgh, Scotland

text: decimal degrees

text: decimal degrees

text: Equus caballus

text: Trizol, frozen

characteristic: sample storage

text: cryopreservation,other

characteristic: sample storage processing

text: Equus caballus

text: decimal degrees

text: decimal degrees

text: male (gelding)

characteristic: sex


characteristic: ENA-CHECKLIST

text: THE ROSLIN INSTITUTE

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: SRA accession

characteristic: Submitter Id

text: year

text: Thoroughbred

text: horse

characteristic: common name

text: bone marrow derived macrophages (+ lipopolysaccharide, 0 hr.) from 6 year old gelding Thoroughbred

text: total RNA

text: decimal degrees

text: decimal degrees

text: Equus caballus

text: Trizol, frozen

text: cryopreservation,other

text: Equus caballus

text: decimal degrees

text: decimal degrees

text: male (gelding)

characteristic: title


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: THE ROSLIN INSTITUTE

text: public

characteristic: INSDC status

characteristic: age

text: year

characteristic: age unit

characteristic: assay type

text: Thoroughbred

text: horse

text: bone marrow derived macrophages (+ lipopolysaccharide, 0 hr.) from 19 year old gelding Thoroughbred

text: total RNA

text: decimal degrees

text: decimal degrees

text: Equus caballus

characteristic: organism

text: Trizol, frozen

text: cryopreservation,other

text: Equus caballus

text: decimal degrees

text: decimal degrees

text: male (gelding)


text: THE ROSLIN INSTITUTE

text: public

text: year

text: Thoroughbred

characteristic: breed

text: bone marrow derived macrophages (+ lipopolysaccharide, 0 hr.)

characteristic: cell or tissue type

text: horse

characteristic: description

text: total RNA

characteristic: experiment target

characteristic: extraction protocol

text: decimal degrees

text: decimal degrees

text: Equus caballus

text: Trizol, frozen

characteristic: sample storage

text: cryopreservation,other

characteristic: sample storage processing

text: Equus caballus

text: decimal degrees

text: decimal degrees

text: male (gelding)

characteristic: sex


characteristic: ENA-CHECKLIST

text: THE ROSLIN INSTITUTE

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: SRA accession

characteristic: Submitter Id

text: year

text: Thoroughbred

text: horse

characteristic: common name

text: bone marrow derived macrophages (+ lipopolysaccharide, 7 hr.) from 6 year old gelding Thoroughbred

text: total RNA

text: decimal degrees

text: decimal degrees

text: Equus caballus

text: Trizol, frozen

text: cryopreservation,other

text: Equus caballus

text: decimal degrees

text: decimal degrees

text: male (gelding)

characteristic: title


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: THE ROSLIN INSTITUTE

text: public

characteristic: INSDC status

characteristic: age

text: year

characteristic: age unit

characteristic: assay type

text: Thoroughbred

text: horse

text: bone marrow derived macrophages (+ lipopolysaccharide, 7 hr.) from 19 year old gelding Thoroughbred

text: total RNA

text: decimal degrees

text: decimal degrees

text: Equus caballus

characteristic: organism

text: Trizol, frozen

text: cryopreservation,other

text: Equus caballus

text: decimal degrees

text: decimal degrees

text: male (gelding)


text: INRA

text: public

text: French dry-type sausage

characteristic: description

text: Lactobacillus sakei

text: Lactobacillus sakei

characteristic: strain

text: food sample


characteristic: ENA-CHECKLIST

text: UNIVERSITY OF GLASGOW

characteristic: INSDC center name

text: public

text: fruit fly

text: Larval

characteristic: dev stage

text: Drosophila melanogaster

text: Drosophila melanogaster

text: Larval Midgut (Mir)

characteristic: tissue lib

text: Midgut

characteristic: tissue type

text: FlyAtlas2 Mir


text: UNIVERSITY OF GLASGOW

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: SRA accession

characteristic: Submitter Id

text: fruit fly

characteristic: common name

text: Larval

text: Drosophila melanogaster

text: Drosophila melanogaster

text: Larval Salivary Gland (Mir)

text: Salivary Gland

text: FlyAtlas2 Mir


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Genoscope CEA

text: public

characteristic: INSDC status

tag: Namespace:Genoscope CEA

text: Desulfovibrio profundus

text: Desulfovibrio profundus

text: Prokaryotic genome sequencing

characteristic: title


text: UNIVERSITY OF GLASGOW

text: public

text: fruit fly

text: Larva

text: Drosophila melanogaster

characteristic: organism

text: Drosophila melanogaster

text: Larval Trachea (Mir)

text: Trachea

text: FlyAtlas2 Mir


text: UNIVERSITY OF GLASGOW

text: public

text: fruit fly

text: Larva

text: Drosophila melanogaster

text: Drosophila melanogaster

text: Larval Tubule (Mir)

text: Malpighian Tubules

text: FlyAtlas2 Mir


text: UNIVERSITY OF GLASGOW

text: public

text: fruit fly

text: Larva

text: Drosophila melanogaster

text: Drosophila melanogaster

text: Larval Whole (Mir)

text: Whole flies

text: FlyAtlas2 Mir


text: UNIVERSITY OF OXFORD

text: public

tag: Namespace:UNIVERSITY OF OXFORD

text: red-bellied lemur

text: Eulemur rubriventer

text: Eulemur rubriventer

text: Eulemur gut microbiome sample


text: UNIVERSITY OF OXFORD

text: public

text: red-bellied lemur

text: Eulemur rubriventer

text: Eulemur rubriventer

text: Eulemur gut microbiome sample


text: BAYLOR COLLEGE OF ME

text: public

tag: Namespace:BAYLOR COLLEGE OF ME

text: Escherichia coli K-12

text: Escherichia coli K-12


text: DRI

text: public

text: uncultured bacterium

text: uncultured bacterium

text: Prokaryotic microbial community from full-scale drinking water treatment plant with parallel GAC filters.


text: DRI

text: public

text: uncultured bacterium

text: uncultured bacterium

text: Prokaryotic microbial community from pilot-scale skid containing parallel GAC and anthracite filters located at full-scale drinking water treatment plant.


text: DRI

text: public

text: uncultured bacterium

text: uncultured bacterium

text: Prokaryotic microbial community from pilot-scale ozone-biofiltration system containing parallel BAC and anthracite filters located at full-scale wastewater treatment plant.


CH

text: DRI

text: public

text: CH

text: uncultured bacterium

text: uncultured bacterium

text: Prokaryotic microbial community from a pilot-scale ozone-biofiltration system containing either BAC or anthracite located at a full-scale water reclamation facility.


CL

text: DRI

text: public

text: CL

text: uncultured bacterium

text: uncultured bacterium


OAH

text: DRI

text: public

text: OAH

text: uncultured bacterium

text: uncultured bacterium


OAL

text: DRI

text: public

text: OAL

text: uncultured bacterium

text: uncultured bacterium


text: DRI

text: public

text: uncultured bacterium

text: uncultured bacterium


text: NEIKER TECNALIA

text: public

tag: Namespace:NEIKER TECNALIA

characteristic: collection date

text: metagenome

characteristic: description

text: marine hydrothermal vent biome

characteristic: environment (biome)

text: microbial mat

characteristic: environment (feature)

text: hydroxide

characteristic: environment (material)

text: Pacific Ocean

characteristic: geographic location (country and/or sea)

unit: m

characteristic: geographic location (depth)

characteristic: geographic location (elevation)

unit: DD

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: mimarks-survey

characteristic: investigation type

text: microbial mat/biofilm

characteristic: microbial mat/biofilm environmental package

text: metagenome

text: LauBasin

characteristic: project name

text: metagenome

text: pyrosequencing

characteristic: sequencing method

text: metagenome


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: NEIKER TECNALIA

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: metagenome

characteristic: common name

text: Vai Lili_439-2-B1

text: marine hydrothermal vent biome

text: microbial mat

text: hydroxide

text: Pacific Ocean

text: mimarks-survey

text: microbial mat/biofilm

text: metagenome

text: LauBasin

text: metagenome

text: pyrosequencing

text: metagenome


text: NEIKER TECNALIA

text: public

characteristic: collection date

text: metagenome

text: Vai Lili_439-2-B2

characteristic: description

text: marine hydrothermal vent biome

characteristic: environment (biome)

text: microbial mat

characteristic: environment (feature)

text: hydroxide

characteristic: environment (material)

text: Pacific Ocean

characteristic: geographic location (country and/or sea)

characteristic: geographic location (depth)

characteristic: geographic location (elevation)

characteristic: geographic location (latitude)

text: mimarks-survey

text: microbial mat/biofilm

text: metagenome

characteristic: organism

text: LauBasin

text: metagenome

text: pyrosequencing

text: metagenome

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: UTRECHT UNIVERSITY

characteristic: INSDC center name

characteristic: INSDC first public

text: public

tag: Namespace:UTRECHT UNIVERSITY

text: Azolla filiculoides kept in culture

text: Urban

text: water surface

text: ditch water

text: Netherlands

characteristic: geographic location (longitude)

text: metagenome

characteristic: investigation type

text: Azolla filiculoides

text: plant-associated

characteristic: plant-associated environmental package

text: The metagenome of the floating fern symbiosis Azolla/Nostoc reveals persistent Rhizobiales endophytes

characteristic: project name

text: Azolla filiculoides

text: Illumina

characteristic: sequencing method


text: UTRECHT UNIVERSITY

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

characteristic: collection date

text: Azolla filiculoides rid of cyanobacteria

characteristic: description

text: Urban

characteristic: environment (biome)

text: water surface

characteristic: environment (feature)

text: ditch water

characteristic: environment (material)

text: Netherlands

characteristic: geographic location (country and/or sea)

text: metagenome

text: Azolla filiculoides

text: plant-associated

text: Azolla filiculoides

text: Illumina


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: UTRECHT UNIVERSITY

characteristic: INSDC center name

text: public

text: Azolla mexicana kept in culture irri.org ME2001

text: not collected

text: not collected

text: not collected

text: USA

characteristic: geographic location (latitude)

text: metagenome

text: Azolla mexicana

characteristic: organism

text: plant-associated

text: Azolla mexicana

text: Illumina

characteristic: title


text: UTRECHT UNIVERSITY

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: Azolla microphylla kept in culture irri.org MI4021

text: not collected

text: not collected

text: not collected

text: Ecuador

characteristic: geographic location (longitude)

text: metagenome

characteristic: investigation type

text: Azolla microphylla

text: plant-associated

characteristic: plant-associated environmental package

characteristic: project name

text: Azolla microphylla

text: Illumina

characteristic: sequencing method


text: UTRECHT UNIVERSITY

text: public

characteristic: SRA accession

characteristic: Submitter Id

characteristic: collection date

text: Azolla nilotica kept in culture irri.org NI5001

characteristic: description

text: not collected

characteristic: environment (biome)

text: not collected

characteristic: environment (feature)

text: not collected

characteristic: environment (material)

text: Sudan

characteristic: geographic location (country and/or sea)

text: metagenome

text: Azolla nilotica

text: plant-associated

text: Azolla nilotica

text: Illumina


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: UTRECHT UNIVERSITY

characteristic: INSDC center name

text: public

text: Azolla rubra kept in culture irri.org RU6502

text: not collected

text: not collected

text: not collected

text: Australia

characteristic: geographic location (latitude)

text: metagenome

text: Azolla rubra

characteristic: organism

text: plant-associated

text: Azolla rubra

text: Illumina

characteristic: title


text: UTRECHT UNIVERSITY

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: mosquito fern

characteristic: common name

text: Azolla caroliniana kept in culture irri.org CA3017

text: not collected

text: not collected

text: not collected

text: Brazil

characteristic: geographic location (longitude)

text: metagenome

characteristic: investigation type

text: Azolla caroliniana

text: plant-associated

characteristic: plant-associated environmental package

characteristic: project name

text: Azolla caroliniana

text: Illumina

characteristic: sequencing method


characteristic: ENA-CHECKLIST

text: UTRECHT UNIVERSITY

text: public

characteristic: SRA accession

characteristic: Submitter Id

characteristic: collection date

text: mosquito fern

text: Azolla caroliniana kept in culture irri.og CA3004

characteristic: description

text: not collected

characteristic: environment (biome)

text: not collected

characteristic: environment (feature)

text: not collected

characteristic: environment (material)

text: Uruguay

characteristic: geographic location (country and/or sea)

text: metagenome

text: Azolla caroliniana

text: plant-associated

text: Azolla caroliniana

text: Illumina


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: UNIVERSITY OF GLASGOW

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: fruit fly

text: Drosophila melanogaster

characteristic: organism

text: Drosophila melanogaster

text: Male

characteristic: sex

text: Male AccesoryGland (Mir)

characteristic: tissue lib

text: Accessory Gland

characteristic: tissue type

text: FlyAtlas2 Mir

characteristic: title


characteristic: ENA-CHECKLIST

text: UNIVERSITY OF GLASGOW

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: fruit fly

characteristic: common name

text: Drosophila melanogaster

text: Drosophila melanogaster

text: Male

text: Male Carcass (Mir)

text: Carcass

text: FlyAtlas2 Mir


text: UNIVERSITY OF GLASGOW

text: public

text: fruit fly

text: Drosophila melanogaster

text: Drosophila melanogaster

text: Male

text: Male Head Mir

text: Head

text: FlyAtlas2 (Mir)


text: UNIVERSITY OF GLASGOW

text: public

text: fruit fly

text: Drosophila melanogaster

text: Drosophila melanogaster

text: Male

text: Male Hindgut (Mir)

text: Hindgut

text: FlyAtlas2 Mir


text: UNIVERSITY OF GLASGOW

text: public

text: fruit fly

text: Drosophila melanogaster

text: Drosophila melanogaster

text: Male

text: Male Midgut (Mir)

text: Midgut

text: FlyAtlas2 Mir


text: UNIVERSITY OF GLASGOW

text: public

text: fruit fly

text: Drosophila melanogaster

text: Drosophila melanogaster

text: Male

text: Male Testis (Mir)

text: Testis

text: FlyAtlas2 Mir


text: UNIVERSITY OF GLASGOW

text: public

text: fruit fly

text: Drosophila melanogaster

text: Drosophila melanogaster

text: Male

text: Male Tubule (Mir)

text: Malpighian Tubules

text: FlyAtlas2 Mir


text: UNIVERSITY OF GLASGOW

text: public

text: fruit fly

text: Drosophila melanogaster

text: Drosophila melanogaster

text: Male

text: Male Whole (Mir)

text: Whole Flies

text: FlyAtlas2 Mir


text: ETH ZURICH

text: public

tag: Namespace:ETH ZURICH

text: Pool exposed/gut (colony N1)

characteristic: description

text: Switzerland

characteristic: geographic location (country and/or sea)

text: Neunforn

characteristic: geographic location (region and locality)

text: metagenomes

text: metagenomes

text: Microbiota V3/V4 region 16S rRNA by universal primers


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: ETH ZURICH

text: public

text: Pool exposed/gut (colony N2)

text: Switzerland

text: Neunforn

text: metagenomes

text: metagenomes


text: ETH ZURICH

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: Pool exposed/gut (colony N3)

text: Switzerland

text: Neunforn

text: metagenomes

text: metagenomes


text: ETH ZURICH

text: public

text: Pool exposed/gut (colony N4)

text: Switzerland

text: Neunforn

text: metagenomes

characteristic: organism

text: metagenomes


text: ETH ZURICH

text: public

text: Pool exposed/gut (colony N5)

text: Switzerland

text: Neunforn

text: metagenomes

text: metagenomes


text: ETH ZURICH

text: public

text: Pool exposed/gut (colony N6)

text: Switzerland

text: Neunforn

text: metagenomes

text: metagenomes


text: ETH ZURICH

text: public

text: Pool exposed/gut (colony A1)

text: Switzerland

text: Aesch

text: metagenomes

text: metagenomes


text: ETH ZURICH

text: public

text: Pool exposed/gut (colony A2)

text: Switzerland

text: Aesch

text: metagenomes

text: metagenomes


text: ETH ZURICH

text: public

text: Pool exposed/gut (colony A3)

text: Switzerland

text: Aesch

text: metagenomes

text: metagenomes


text: ETH ZURICH

text: public

text: Pool exposed/gut (colony A4)

text: Switzerland

text: Aesch

text: metagenomes

text: metagenomes


text: ETH ZURICH

text: public

text: Naturals age-controlled/gut (colony N1)

text: Switzerland

text: Neunforn

text: metagenomes

text: metagenomes


text: ETH ZURICH

text: public

text: Naturals age-controlled/gut (colony N2)

text: Switzerland

text: Neunforn

text: metagenomes

text: metagenomes


text: ETH ZURICH

text: public

text: Naturals age-controlled/gut (colony N3)

text: Switzerland

text: Neunforn

text: metagenomes

text: metagenomes


text: ETH ZURICH

text: public

text: Naturals age-controlled/gut (colony N4)

text: Switzerland

text: Neunforn

text: metagenomes

text: metagenomes


text: ETH ZURICH

text: public

text: Naturals non age-controlled/gut (colony N5)

text: Switzerland

text: Neunforn

text: metagenomes

text: metagenomes


text: ETH ZURICH

text: public

text: Naturals age-controlled/gut (colony N6)

text: Switzerland

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