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characteristic: sequencing method

characteristic: target gene

text: Kiruna 2007, week 47, target gene 16S

characteristic: title


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: UMEA UNIVERSITY

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: air

characteristic: air environmental package

text: temperate deciduous broadleaf forest

text: agricultural feature

text: air

text: Sweden

text: mimarks-survey

text: air metagenome

text: Airborne biodiversity in Sweden

text: air metagenome

text: Illumina Miseq

text: Ljungbyhed 2007, week 47, target gene 16S


characteristic: ENA-CHECKLIST

characteristic: External Id

text: UMEA UNIVERSITY

text: public

text: air

characteristic: collection date

text: subpolar coniferous forest biome

characteristic: environment (biome)

text: area of mixed forest

characteristic: environment (feature)

text: air

characteristic: environment (material)

characteristic: geographic location (altitude)

text: Sweden

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

text: mimarks-survey

text: air metagenome

text: Airborne biodiversity in Sweden

text: air metagenome

text: Illumina Miseq

text: rbcL

text: Kiruna 2007, week 47, target gene rbcL


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: UMEA UNIVERSITY

text: public

text: air

text: temperate deciduous broadleaf forest

text: agricultural feature

text: air

text: Sweden

characteristic: geographic location (longitude)

text: mimarks-survey

characteristic: investigation type

text: air metagenome

characteristic: organism

text: Airborne biodiversity in Sweden

characteristic: project name

text: air metagenome

text: Illumina Miseq

characteristic: sequencing method

text: rbcL

characteristic: target gene

text: Ljungbyhed 2007, week 47, target gene rbcL

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: External Id

text: UMEA UNIVERSITY

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: air

characteristic: air environmental package

text: subpolar coniferous forest biome

text: area of mixed forest

text: air

text: Sweden

text: mimarks-survey

text: air metagenome

text: Airborne biodiversity in Sweden

text: air metagenome

text: Illumina Miseq

text: ITS

text: Kiruna 2007, week 49, target gene ITS


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: UMEA UNIVERSITY

text: public

text: air

characteristic: collection date

text: temperate deciduous broadleaf forest

characteristic: environment (biome)

text: agricultural feature

characteristic: environment (feature)

text: air

characteristic: environment (material)

characteristic: geographic location (altitude)

text: Sweden

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

text: mimarks-survey

text: air metagenome

text: Airborne biodiversity in Sweden

text: air metagenome

text: Illumina Miseq

text: ITS

text: Ljungbyhed 2007, week 49, target gene ITS


characteristic: ENA-CHECKLIST

characteristic: External Id

text: UMEA UNIVERSITY

text: public

text: air

text: subpolar coniferous forest biome

text: area of mixed forest

text: air

text: Sweden

characteristic: geographic location (longitude)

text: mimarks-survey

characteristic: investigation type

text: air metagenome

characteristic: organism

text: Airborne biodiversity in Sweden

characteristic: project name

text: air metagenome

text: Illumina Miseq

characteristic: sequencing method

characteristic: target gene

text: Kiruna 2007, week 49, target gene 16S

characteristic: title


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: UMEA UNIVERSITY

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: air

characteristic: air environmental package

text: temperate deciduous broadleaf forest

text: agricultural feature

text: air

text: Sweden

text: mimarks-survey

text: air metagenome

text: Airborne biodiversity in Sweden

text: air metagenome

text: Illumina Miseq

text: Ljungbyhed 2007, week 49, target gene 16S


characteristic: ENA-CHECKLIST

characteristic: External Id

text: UMEA UNIVERSITY

text: public

text: air

characteristic: collection date

text: subpolar coniferous forest biome

characteristic: environment (biome)

text: area of mixed forest

characteristic: environment (feature)

text: air

characteristic: environment (material)

characteristic: geographic location (altitude)

text: Sweden

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

text: mimarks-survey

text: air metagenome

text: Airborne biodiversity in Sweden

text: air metagenome

text: Illumina Miseq

text: rbcL

text: Kiruna 2007, week 49, target gene rbcL


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: UMEA UNIVERSITY

text: public

text: air

text: temperate deciduous broadleaf forest

text: agricultural feature

text: air

text: Sweden

characteristic: geographic location (longitude)

text: mimarks-survey

characteristic: investigation type

text: air metagenome

characteristic: organism

text: Airborne biodiversity in Sweden

characteristic: project name

text: air metagenome

text: Illumina Miseq

characteristic: sequencing method

text: rbcL

characteristic: target gene

text: Ljungbyhed 2007, week 49, target gene rbcL

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: External Id

text: UMEA UNIVERSITY

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: air

characteristic: air environmental package

text: subpolar coniferous forest biome

text: area of mixed forest

text: air

text: Sweden

text: mimarks-survey

text: air metagenome

text: Airborne biodiversity in Sweden

text: air metagenome

text: Illumina Miseq

text: ITS

text: Kiruna 2007, week 51, target gene ITS


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: UMEA UNIVERSITY

text: public

text: air

characteristic: collection date

text: temperate deciduous broadleaf forest

characteristic: environment (biome)

text: agricultural feature

characteristic: environment (feature)

text: air

characteristic: environment (material)

characteristic: geographic location (altitude)

text: Sweden

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

text: mimarks-survey

text: air metagenome

text: Airborne biodiversity in Sweden

text: air metagenome

text: Illumina Miseq

text: ITS

text: Ljungbyhed 2007, week 51, target gene ITS


characteristic: ENA-CHECKLIST

characteristic: External Id

text: UMEA UNIVERSITY

text: public

text: air

text: subpolar coniferous forest biome

text: area of mixed forest

text: air

text: Sweden

characteristic: geographic location (longitude)

text: mimarks-survey

characteristic: investigation type

text: air metagenome

characteristic: organism

text: Airborne biodiversity in Sweden

characteristic: project name

text: air metagenome

text: Illumina Miseq

characteristic: sequencing method

characteristic: target gene

text: Kiruna 2007, week 51, target gene 16S

characteristic: title


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: UMEA UNIVERSITY

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: air

characteristic: air environmental package

text: temperate deciduous broadleaf forest

text: agricultural feature

text: air

text: Sweden

text: mimarks-survey

text: air metagenome

text: Airborne biodiversity in Sweden

text: air metagenome

text: Illumina Miseq

text: Ljungbyhed 2007, week 51, target gene 16S


characteristic: ENA-CHECKLIST

characteristic: External Id

text: UMEA UNIVERSITY

text: public

text: air

characteristic: collection date

text: subpolar coniferous forest biome

characteristic: environment (biome)

text: area of mixed forest

characteristic: environment (feature)

text: air

characteristic: environment (material)

characteristic: geographic location (altitude)

text: Sweden

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

text: mimarks-survey

text: air metagenome

text: Airborne biodiversity in Sweden

text: air metagenome

text: Illumina Miseq

text: rbcL

text: Kiruna 2007, week 51, target gene rbcL


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: UMEA UNIVERSITY

text: public

text: air

text: temperate deciduous broadleaf forest

text: agricultural feature

text: air

text: Sweden

characteristic: geographic location (longitude)

text: mimarks-survey

characteristic: investigation type

text: air metagenome

characteristic: organism

text: Airborne biodiversity in Sweden

characteristic: project name

text: air metagenome

text: Illumina Miseq

characteristic: sequencing method

text: rbcL

characteristic: target gene

text: Ljungbyhed 2007, week 51, target gene rbcL

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: External Id

text: UMEA UNIVERSITY

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: air

characteristic: air environmental package

text: air

text: Sweden

text: mimarks-survey

text: air metagenome

text: Airborne biodiversity in Sweden

text: air metagenome

text: Illumina Miseq

text: Blank 16S


blank-ITS

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: UMEA UNIVERSITY

text: public

text: blank-ITS

text: air

characteristic: collection date

text: air

characteristic: environment (material)

characteristic: geographic location (altitude)

text: Sweden

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

text: mimarks-survey

text: air metagenome

text: Airborne biodiversity in Sweden

text: air metagenome

text: Illumina Miseq

text: ITS

text: Blank ITS


blank-rbcL

text: UMEA UNIVERSITY

text: public

text: blank-rbcL

text: air

text: air

text: Sweden

characteristic: geographic location (longitude)

text: mimarks-survey

characteristic: investigation type

text: air metagenome

characteristic: organism

text: Airborne biodiversity in Sweden

characteristic: project name

text: air metagenome

text: Illumina Miseq

characteristic: sequencing method

text: rbcL

characteristic: target gene

text: Blank rbcL

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: External Id

text: EMBL

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: gut metagenome

characteristic: common name

text: stool sample

characteristic: description

text: human-associated habitat [ENVO:00009003]

characteristic: environment (biome)

text: intestine environment [ENVO:2100002]

characteristic: environment (feature)

text: feces [ENVO:00002003]

text: Netherlands

text: human-gut

characteristic: human gut environmental package

text: metagenome

text: gut metagenome

text: Mother-infant transmission

text: gut metagenome

text: Illumina

text: stool sample


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: EMBL

text: public

characteristic: Submitter Id

characteristic: collection date

text: gut metagenome

text: stool sample

text: intestine environment [ENVO:2100002]

text: feces [ENVO:00002003]

characteristic: environment (material)

text: Germany

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: human-gut

text: metagenome

characteristic: investigation type

text: gut metagenome

characteristic: organism

text: Mother-infant transmission

text: gut metagenome

text: Illumina

text: stool sample


characteristic: ENA-CHECKLIST

characteristic: External Id

text: EMBL

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: gut metagenome

text: stool sample

text: intestine environment [ENVO:2100002]

text: feces [ENVO:00002003]

text: Luxembourg

text: human-gut

text: metagenome

text: gut metagenome

text: Mother-infant transmission

characteristic: project name

text: gut metagenome

text: Illumina

characteristic: sequencing method

text: stool sample

characteristic: title


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: public

characteristic: SRA accession

tag: Namespace:Institute of Biotechnology, University of Helsinki

characteristic: Submitter Id

text: food metagenome

text: food metagenome

text: Cheese Metatranscriptomics


text: Institute of Biotechnology, University of Helsinki

text: public

text: food metagenome

text: food metagenome

text: Cheese Metatranscriptomics


text: STATENS SERUM INSTITUT

text: public

tag: Namespace:STATENS SERUM INSTITUT

characteristic: collection date

text: human

characteristic: common name

text: Nasal swabs were collected from short time visitors to pig farms, and professional farm workers

characteristic: description

text: Farm

characteristic: environment (biome)

text: Animals

characteristic: environment (feature)

text: Nasal swabs

characteristic: environment (material)

text: Denmark

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

text: host-associated

characteristic: host-associated environmental package

text: metagenome

text: Homo sapiens

text: Human Nasal Microbiome in pig farm environment

text: Homo sapiens

text: Illumina

text: Human Nasal swab


characteristic: ENA-CHECKLIST

characteristic: External Id

text: STATENS SERUM INSTITUT

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: pig

text: Nasal swabs were collected from pigs

text: Farm

text: Animals

text: Nasal swabs

text: Denmark

characteristic: geographic location (longitude)

text: host-associated

text: metagenome

characteristic: investigation type

text: Sus scrofa

characteristic: organism

text: Sus scrofa

text: Illumina

text: Pig Nasal swab


text: iPSC

text: Homo sapiens

characteristic: ArrayExpress-SPECIES

text: Multiple lines

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: SC

text: public

characteristic: SRA accession

characteristic: Submitter Id

text: human

characteristic: common name

text: Homo sapiens

text: Homo sapiens

characteristic: subject id

characteristic: title


characteristic: ENA-CHECKLIST

text: Wellcome Trust Sanger Institute

text: public

tag: Namespace:Wellcome Trust Sanger Institute

text: ArrayExpress

characteristic: broker name

text: CD4-positive helper T cell

characteristic: cell type

text: house mouse

text: Protocols: 20 million cells from each sample were crosslinked in 1% HCHO (prepared in 1X DPBS) at room temperature for 10 minutes, and HCHO was quenched by the addition of glycine at a final concentration of 0.125 M. Cells were pelleted at 4°C at 2000 x g, washed with ice-cold 1X DPBS twice, and snapped frozen in liquid nitrogen. The cell pellets were stored in -80°C until the experiments were performed. ChIPmentation was performed according to the version 1.0 of the published protocol (Schmidl et al., 2015b) with some modifications at the ChIP stage. Briefly, cell pellets were thawed on ice, and lysed in 300 l ChIP Lysis Buffer I (50 mM HEPES.KOH, pH 7.5, 140 mM NaCl, 1 mM EDTA, pH 8.0, 10% Glycerol, 0.5% NP-40, 0.25% Triton X-100) on ice for 10 minutes. Then cells were pelleted at 4°C at 2000 x g for 5 minutes, and washed by 300 l ChIP Lysis Buffer II (10 mM Tris.Cl, pH 8.0, 200 mM NaCl, 1 mM EDTA, pH 8.0, 0.5 mM EGTA, pH 8.0), and pelleted again at 4°C at 2000 x g for 5 minutes. Nuclei were resuspended in 300 l ChIP Lysis Buffer III (10 mM Tris.Cl, pH 8.0, 100 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 0.1% Sodium Deoxycholate, 0.5% N-Lauryolsarcosine). Chromatin was sonicated using Bioruptor Pico (Diagenode) with 30 seconds ON/30 seconds OFF for 5 cycles. 30 l 10% Triton X-100 were added into each sonicated chromatin, and insoluble chromatin was pelleted at 16,100 x g at 4°C for 10 minutes. 1 l supernatant was taken as input control. The rest of the supernatant was incubated with 10 l Protein A Dynabeads (Invitrogen) pre-bound with 1 g XBP1 antibody (XBP1 (M-186)X - Santa cruz), in a rotating platform in a cold room overnight. Each immunoprecipitation (IP) was washed with 500 l RIPA Buffer (50 mM HEPES.KOH, pH 7.5, 500 mM LiCl, 1 mM EDTA, 1% NP-40, 0.7% Sodium Deoxycholate, check components) for 3 times. Then, each IP was washed with 500 l 10 mM Tris, pH 8.0 twice, and resuspended in 30 l tagmentation reaction mix (10 mM Tris.Cl, pH 8.0, 5 mM Mg2Cl, 1 l TDE1 (Nextera)). Then, the tagmentation reaction was put on a thermomixer at 37°C for 10 minutes at 800 rpm shaking. After the tagmentation reaction, each IP was washed sequentially with 500 l RIPA Buffer twice, and 1X TE NaCl (10 mM Tris.Cl, pH 8.0, 1 mM EDTA, pH 8.0, 50 mM NaCl) once. Elution and reverse-crosslinking was done by resuspending the beads with 100 l ChIP Elution Buffer (50 mM Tris.Cl, pH 8.0, 10 mM EDTA, pH 8.0, 1% SDS) on a thermomixer at 65°C overnight, 1,400 rpm. DNA was purified by MinElute PCR Purification Kit (QIAGEN, cat no. 28004 and eluted in 12.5 l Buffer EB (QIAGEN kit, cat no 28004), which yielded ~10 l ChIPed DNA. ChIPed DNA before amplification was purified using Qiagen MinElute PCR purification kit. After library amplification, DNA was purified using AmpureXP beads with a 0.5X upper cutoff and 1.2X lower cutoff. The library preparation reactions contained the following: 10 l purified DNA (from above), 2.5 l PCR Primer Cocktails (Nextera DNA Library Preparation Kit, Illumina Cat no. FC-121-1030), 2.5 l N5xx (Nextera Index Kit , Illumina cat no.FC-121-1012), 2.5 l N7xx (Nextera index kit , Illumina cat no. FC-121-1012), 7.5 l NPM PCR Master Mix (Nextera DNA Library Preparation Kit, Illumina Cat no. FC-121-1030) PCR was set up as follows: 72°C, 5 mins; 98°C, 2 mins; [98°C, 10 secs, 63°C, 30 secs, 72°C, 20 secs] x 12; 10°C hold

characteristic: description

text: Mus musculus

text: Mus musculus

text: Mus musculus

text: interleukin-4 (10 nanogram per milliter for 5 days)

characteristic: stimulus


characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

tag: Namespace:Stockholm University, Department of Molecular Biosciences,The Wenner-Gren Institute

text: ArrayExpress

text: Protocols: cells were crosslinked at OD600 0.2, fragmented by sonication. Then the cleared lysate were mixed with Saci_1107 specific antibody, pre-immune serum, respectively. Immunoprecipitated DNA is extracted by IPure kit (Diagenode) according to the manufacturer’s instructions Sequencing libraries were prepared using the ThruPLEX®-FD Prep Kit (Rubicon Genomics) under instructions from the manufacturer.

text: Brock Media, cell cross-link at exponential phase OD600 0.2

characteristic: growth condition

text: Sulfolobus acidocaldarius DSM 639

text: Sulfolobus acidocaldarius DSM 639

text: Sulfolobus acidocaldarius DSM 639

type: has member


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: Stockholm University, Department of Molecular Biosciences,The Wenner-Gren Institute

text: public

text: ArrayExpress

text: Sulfolobus acidocaldarius DSM 639

characteristic: organism

text: Sulfolobus acidocaldarius DSM 639

text: Sulfolobus acidocaldarius DSM 639


text: Vanderbilt University

text: public

characteristic: SRA accession

tag: Namespace:Vanderbilt University

characteristic: Submitter Id

unit: day

characteristic: age

text: ArrayExpress

text: beta cell

text: house mouse

characteristic: common name

text: Protocols: Ins2Apple/+ and MIP-GFP islets were collected from mice at age postnatal day 60. Mice were segregated by sex, and the islets from 2-3 mice of the same sex and genotype were pooled for each sample. Islets were dispersed using Accumax and FACS purified using either Apple or GFP fluorescence and either DAPI or 7AAD viability dye, respectively, to collect only live beta cells. Ins2Apple.LCA/+ mice were generated using homologous recombination into the mouse Ins2 gene locus. The mice used in this experiment (Ins2Apple/+) were generated using RMCE into the Ins2Apple/LCA allele to insert a human growth hormone minigene to improve expression of the fluorescent reporter. Ins2Apple/+ mice were backcrossed into a C57BL/6J background for at least 5 generations prior to use in experiments. MIP-GFP mice (Tg(Ins1-EGFP/GH1)1Hara) were acquired from Jackson Laboratories (stock number 006864) and were maintained in a C57BL/6J background. All mice used for experiments were fed a standard chow diet and were maintained on a 12-hour light/dark cycle. Total RNA was extracted from FACS-purified beta cells using the Maxwell simplyRNA kit (Promega). RNA was amplified using the SMART-Seq v4 Ultra Low Input RNA Kit (Clontech), and cDNA libraries were constructed using the Low Input Library Prep Kit (Clontech).

text: adult

characteristic: developmental stage

text: MIP-GFP

characteristic: genotype

text: Mus musculus

text: Mus musculus

text: endocrine pancreas

characteristic: organism part

text: GFP positive

characteristic: phenotype

text: Mus musculus

text: male

characteristic: sex

characteristic: strain


characteristic: ENA-CHECKLIST

characteristic: External Id

text: Vanderbilt University

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: ArrayExpress

characteristic: broker name

text: beta cell

characteristic: cell type

text: house mouse

characteristic: description

text: adult

text: MIP-GFP

text: Mus musculus

text: Mus musculus

text: endocrine pancreas

text: GFP positive

text: Mus musculus

text: female

characteristic: title


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: Vanderbilt University

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: ArrayExpress

text: beta cell

text: house mouse

text: adult

text: Mus musculus

characteristic: organism

text: Mus musculus

text: endocrine pancreas

text: Apple positive

text: Mus musculus

text: male


text: Vanderbilt University

text: public

characteristic: age

text: ArrayExpress

text: beta cell

text: house mouse

characteristic: common name

text: adult

characteristic: developmental stage

characteristic: genotype

text: Mus musculus

text: Mus musculus

text: endocrine pancreas

characteristic: organism part

text: Apple positive

characteristic: phenotype

text: Mus musculus

text: female

characteristic: sex


characteristic: ENA-CHECKLIST

characteristic: External Id

text: Jiaxing University

characteristic: INSDC center name

characteristic: INSDC first public

text: public

tag: Namespace:Jiaxing University

characteristic: collection date

text: feces

characteristic: environment (biome)

text: feces

characteristic: environment (feature)

text: feces

characteristic: environment (material)

text: China

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: feces metagenome

text: 16S rRNA gene

characteristic: project name

text: feces metagenome

text: MiSeq

characteristic: sequencing method

text: fecal microbiota


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: Postdoctoral Fellow

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

tag: Namespace:Postdoctoral Fellow

characteristic: Submitter Id

text: ArrayExpress

characteristic: broker name

characteristic: cell line

text: embryonic stem cell

characteristic: cell type

text: house mouse

characteristic: common name

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 a lower cell numbers (see a detailed description in Díaz et al., under revision). 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. 2. mESCs were cultured following standard protocols (Ishiuchi et al., 2015). RNAi experiment was performed as described in (Ishiuchi et al., 2015). 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, 4°C for 5 min) and resuspended in 1 ml of cold 1X PBS. 5. DNA precipitation.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 -80°C. 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 of Tris pH 8.0 (Applichem) and incubated for 5 min at 37°C without rotation. RNA was digested by adding 1 μL RNAse to each sample and the mix was incubated 15 min at 37°C. Biotin from unligated fragments was removed by adding 10 μL of 10X NEB2 buffer (New England Biolabs), 1mM of a dNTPs mix (2.5 μL), 20mg/ml BSA (0.5 μL), nuclease-free water (up to 100 μL) and 3U/μL T4 DNA polymerase (5 μL; New England Biolabs). DNA shearing. Samples were mixed by gentle pipetting up and down and incubated at 20°C 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 55°C 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 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, 4°C for 5 min) and pellet was resuspended in 250 μL of ice-cold in situ Hi-C lysis buffer. Lysed cells were then flash-frozen in liquid Nitrogen and stored at -80°C. Restriction Enzyme digestion. Frozen aliquots at different cell concentrations were placed on ice to thaw, spun (13,000 g for 5 min at 4°C) and resuspended in 500 μL lysis buffer. Following yet another spun (13,000 g for 5 min at 4°C), cells were gently resuspended in 500 μL ice-cold 10x NEB2 buffer. Nuclei were permeabilized by resuspending them in 50 μL of 0.4% SDS and incubating for 10 min at 65°C without agitation. The SDS was then quenched by adding 25 μL of 10% Triton X-100 and 145 μL of nuclease-free water, respectively, and incubating at 37°C for 45 min with rotation (650 rpm). Chromatin was digested by adding 100U of MboI in 25 μL of 10x NEB2.1 buffer, respectively (New England Biolabs). All the digestions were performed at 37°C with gentle rotation for a period of 90 min by adding the restriction enzyme in two installments. After the digestion, MboI samples were heat-inactivated for 20 min at 62°C. 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-dATP (18.75 μL; Life Technologies), 10mM dCTP, 10mM dGTP and 10mM dTTP (0.75 μL of each dinucleotide), and 5U/μL DNA polymerase I Klenow (New England Biolabs), followed by a 90 min incubation at 37°C with gentle rotation.Proximity ligation. The DNA fragments were then ligated by adding a master mix containing nuclease-free water (657 μL), 10X T4 DNA ligase buffer (120 μL), 10% Triton X-100 (100 μL), 20mg/ml BSA (12 μL) and 5 Weiss U/μL T4 DNA ligase (5 μL in two installments; Thermo Fisher Scientific). Samples were mixed by inversion and incubated at 20°C 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 extraction buffer. To digest the proteins 20 μL of 20mg/ml proteinase K (Applichem) was added to the mix, followed by 30 min incubation at 55°C with rotation (1000 rpm). 130 μL of 5M sodium chloride was added followed to the mix and was incubated overnight at 65°C with shaking (1000rpm).

characteristic: description

text: 2c::EGFP (MERVL LTR- EGFP-SV40_neo') and CAF-1 siRNA

characteristic: genotype

text: Mus musculus

characteristic: organism

text: Mus musculus

text: GFP negative

characteristic: phenotype

text: MboI

characteristic: restriction digest

text: Mus musculus

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: External Id

text: Postdoctoral Fellow

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: ArrayExpress

text: endogenous 2C-like cell

text: house mouse

text: Mus musculus

text: Mus musculus

text: GFP positive

text: MboI

text: Mus musculus


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: AZ

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: human

text: BRCA2 c.7007+1G>C

text: Homo sapiens

text: Homo sapiens


text: AZ

text: public

characteristic: SRA accession

characteristic: Submitter Id

text: human

text: No pathogenic variant

text: Homo sapiens

text: Homo sapiens


text: AZ

text: public

text: human

characteristic: common name

text: BRCA1 c.4675G>A p.(Glu1559Lys)

text: Homo sapiens

text: Homo sapiens


text: AZ

text: public

text: human

text: BRCA1 c.213-11T>G

characteristic: description

text: Homo sapiens

text: Homo sapiens


text: AZ

text: public

text: human

text: BRCA1 c.1105delG p.(Asp369MetfsTer5)

text: Homo sapiens

text: Homo sapiens


text: AZ

text: public

text: human

text: BRCA1 exon13ins6kb

text: Homo sapiens

text: Homo sapiens


text: AZ

text: public

text: human

text: BRCA2 c.7788delAinsGGGT p.(Gly2596dup)

text: Homo sapiens

text: Homo sapiens


text: AZ

text: public

text: human

text: BRCA2 c.6952C>T p.(Arg2318Ter) - Admix ~5%

text: Homo sapiens

text: Homo sapiens


text: AZ

text: public

text: human

text: BRCA2 c.10024G>A p.(Glu3342Lys) - Admix ~40%

text: Homo sapiens

text: Homo sapiens


text: public

tag: Namespace:J.F. Blumenbach Institute of Zoology and Anthropology University of Goettingen

characteristic: collection date

text: non-filtered data set for protists community in experimental conditions

text: tropical montane rainforest

characteristic: environment (biome)

text: tropical montane rainforest

characteristic: environment (feature)

text: litter

characteristic: environment (material)

text: Yes

characteristic: environmental sample

text: Ecuador

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: uncultured eukaryote

text: 5-CCAGCASCYGCGGTAATTCC-3; 5-ACTTTCGTTCTTGATYRA-3

characteristic: pcr primers

text: uncultured eukaryote

characteristic: target gene

characteristic: target subfragment

text: NGS Ecuador 2000m


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: J.F. Blumenbach Institute of Zoology and Anthropology University of Goettingen

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: tropical montane rainforest

text: tropical montane rainforest

text: litter

text: Yes

text: Ecuador

text: uncultured eukaryote

characteristic: organism

text: uncultured eukaryote

text: NGS Ecuador 2000m

characteristic: title


text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

characteristic: collection date

characteristic: description

text: tropical montane rainforest

characteristic: environment (biome)

text: tropical montane rainforest

characteristic: environment (feature)

text: soil

characteristic: environment (material)

text: Yes

text: Ecuador

text: uncultured eukaryote

text: uncultured eukaryote

text: NGS Ecuador 2000m


characteristic: ENA-CHECKLIST

text: CEBITEC

text: public

text: Complete genome sequence of Acinetobacter baumannii K50

text: Human

text: Human

text: wound material

text: Kuwait

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: human-associated

characteristic: human associated environmental package

text: mimarks-survey

characteristic: investigation type

characteristic: isolate

text: Acinetobacter baumannii

characteristic: project name

text: Acinetobacter baumannii

text: Illumina MiSeq

characteristic: sequencing method


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: James Hutton Institute

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

tag: Namespace:James Hutton Institute

text: potato

characteristic: common name

text: dRenSeq in heritage cultivar

text: Solanum tuberosum

characteristic: organism

text: Solanum tuberosum

characteristic: title


characteristic: ENA-CHECKLIST

text: James Hutton Institute

text: public

characteristic: SRA accession

characteristic: Submitter Id

text: potato

text: dRenSeq in cultivars

characteristic: description

text: Solanum tuberosum

text: Solanum tuberosum


text: CEBITEC

text: public

characteristic: collection date

text: Human

characteristic: environment (biome)

text: Human

characteristic: environment (feature)

text: wound

characteristic: environment (material)

text: Kuwait

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: human-associated

characteristic: human associated environmental package

text: mimarks-survey

characteristic: investigation type

characteristic: isolate

text: Acinetobacter baumannii

text: Acinetobacter baumannii

text: Illumina MiSeq


text: uncultured Ruminococcus sp.

characteristic: ArrayExpress-Species

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: SC

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: uncultured Ruminococcus sp.

characteristic: common name

text: uncultured Ruminococcus sp.

characteristic: sample description

text: uncultured Ruminococcus sp.


Mimoides lysithous 3789

characteristic: ENA-CHECKLIST

text: UNIVERSITY OF MONTPELLIER 2

text: public

characteristic: SRA accession

text: Mimoides lysithous 3789

tag: Namespace:UNIVERSITY OF MONTPELLIER 2

characteristic: Submitter Id

characteristic: collection date

text: Argentina

text: Misiones, Dos de Mayo

characteristic: geographic location (region and locality)

text: mitochondrion

characteristic: organelle

text: Mimoides lysithous

characteristic: organism

text: Mimoides lysithous

text: Mimoides lysithous 3789

characteristic: title


Eurytides dolicaon 11002

characteristic: ENA-FIRST-PUBLIC

text: UNIVERSITY OF MONTPELLIER 2

text: public

text: Eurytides dolicaon 11002

text: Brazil

characteristic: geographic location (country and/or sea)

text: Santa Catarina, Sao Bento do Sul

text: mitochondrion

text: Eurytides dolicaon

text: Eurytides dolicaon

text: Eurytides dolicaon 11002


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: PENN STATE

text: public

tag: Namespace:PENN STATE

text: Cassiopea xamachana line asexually propogated from a single polyp

characteristic: description

text: Cassiopea xamachana

text: Cassiopea xamachana

text: Female

characteristic: sex

characteristic: strain

text: Cassiopea xamachana T1-A


text: James Hutton Institute

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: potato

characteristic: common name

text: dRenSeq

text: Solanum tuberosum

text: Solanum tuberosum


Spunta

characteristic: ENA-CHECKLIST

text: James Hutton Institute

text: public

characteristic: SRA accession

text: Spunta

characteristic: Submitter Id

text: potato

text: dRenSeq

text: Solanum tuberosum

text: Solanum tuberosum

text: Spunta


text: UNIVERSITE LAVAL

text: public

tag: Namespace:UNIVERSITE LAVAL

characteristic: collection date

text: uncultured eukaryote

text: marine pelagic biome

characteristic: environment (biome)

text: microbial feature

characteristic: environment (feature)

text: planktonic material

characteristic: environment (material)

text: Yes

characteristic: environmental sample

characteristic: further details

text: Arctic Ocean

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: uncultured eukaryote

characteristic: organism

text: CYGCGGTAATTCCAGCTC AYGGTATCTRATCRTCTTYG

characteristic: pcr primers

text: uncultured eukaryote

characteristic: target gene

characteristic: target subfragment


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: NYU

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: uncultured eukaryote

characteristic: description

text: urban

text: sewage

text: sewage

text: Yes

text: USA

characteristic: geographic location (country and/or sea)

text: New York City, Bronx and Manhattan

characteristic: geographic location (region and locality)

text: uncultured eukaryote

text: CCAGCASCYGCGGTAATTCC,ACTTTCGTTCTTGATYRA

text: uncultured eukaryote

characteristic: title


characteristic: ENA-CHECKLIST

text: NYU

text: public

characteristic: SRA accession

characteristic: Submitter Id

characteristic: collection date

text: uncultured eukaryote

characteristic: common name

text: urban

characteristic: environment (biome)

text: sewage

characteristic: environment (feature)

text: sewage

characteristic: environment (material)

text: Yes

characteristic: environmental sample

characteristic: further details

text: USA

characteristic: geographic location (latitude)

text: New York City, Queens

text: uncultured eukaryote

text: CCAGCASCYGCGGTAATTCC,ACTTTCGTTCTTGATYRA

text: uncultured eukaryote


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: NYU

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: uncultured eukaryote

text: urban

text: sewage

text: sewage

text: Yes

text: USA

characteristic: geographic location (longitude)

text: New York City, Brooklyn

text: uncultured eukaryote

characteristic: organism

text: CCAGCASCYGCGGTAATTCC,ACTTTCGTTCTTGATYRA

characteristic: pcr primers

text: uncultured eukaryote

characteristic: target gene

characteristic: target subfragment


characteristic: ENA-CHECKLIST

text: NYU

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

characteristic: collection date

text: uncultured eukaryote

characteristic: common name

characteristic: description

text: urban

characteristic: environment (biome)

text: sewage

text: sewage

text: Yes

text: USA

characteristic: geographic location (country and/or sea)

text: New York City, Brooklyn and Queens

characteristic: geographic location (region and locality)

text: uncultured eukaryote

text: CCAGCASCYGCGGTAATTCC,ACTTTCGTTCTTGATYRA

text: uncultured eukaryote

characteristic: title


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: NYU

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: uncultured eukaryote

text: urban

text: sewage

characteristic: environment (feature)

text: sewage

characteristic: environment (material)

text: Yes

characteristic: environmental sample

characteristic: further details

text: USA

characteristic: geographic location (latitude)

text: New York City, Bronx

text: uncultured eukaryote

text: CCAGCASCYGCGGTAATTCC,ACTTTCGTTCTTGATYRA

text: uncultured eukaryote


characteristic: ENA-CHECKLIST

text: NYU

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

characteristic: collection date

text: uncultured eukaryote

characteristic: common name

text: urban

text: sewage

text: sewage

text: Yes

text: USA

characteristic: geographic location (longitude)

text: New York City, Manhattan

text: uncultured eukaryote

characteristic: organism

text: CCAGCASCYGCGGTAATTCC,ACTTTCGTTCTTGATYRA

characteristic: pcr primers

text: uncultured eukaryote

characteristic: target gene

characteristic: target subfragment


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: NYU

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: uncultured eukaryote

characteristic: description

text: urban

characteristic: environment (biome)

text: sewage

text: sewage

text: Yes

text: USA

characteristic: geographic location (country and/or sea)

text: New York City, Staten Island

characteristic: geographic location (region and locality)

text: uncultured eukaryote

text: CCAGCASCYGCGGTAATTCC,ACTTTCGTTCTTGATYRA

text: uncultured eukaryote

characteristic: title


characteristic: ENA-CHECKLIST

text: NYU

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

characteristic: collection date

text: uncultured eukaryote

characteristic: common name

text: Mudflat

text: urban

text: mudflat

characteristic: environment (feature)

text: sediment

characteristic: environment (material)

text: Yes

characteristic: environmental sample

characteristic: further details

text: USA

characteristic: geographic location (latitude)

text: New York City, Brooklyn

text: uncultured eukaryote

text: CCAGCASCYGCGGTAATTCC,ACTTTCGTTCTTGATYRA

text: uncultured eukaryote


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: NYU

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: uncultured eukaryote

text: Mudflat

text: urban

text: mudflat

text: sediment

text: Yes

text: USA

characteristic: geographic location (longitude)

text: New York City, Queens

text: uncultured eukaryote

characteristic: organism

text: CCAGCASCYGCGGTAATTCC,ACTTTCGTTCTTGATYRA

characteristic: pcr primers

text: uncultured eukaryote

characteristic: target gene

characteristic: target subfragment


characteristic: ENA-CHECKLIST

text: NYU

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

characteristic: collection date

text: uncultured eukaryote

characteristic: common name

characteristic: description

text: urban

characteristic: environment (biome)

text: building

text: freshwater

text: Yes

text: USA

characteristic: geographic location (country and/or sea)

text: New York City, Manhattan

characteristic: geographic location (region and locality)

text: uncultured eukaryote

text: CCAGCASCYGCGGTAATTCC,ACTTTCGTTCTTGATYRA

text: uncultured eukaryote

characteristic: title


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: NYU

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: uncultured eukaryote

text: urban

characteristic: environment (feature)

text: soil

characteristic: environment (material)

text: Yes

characteristic: environmental sample

characteristic: further details

text: USA

characteristic: geographic location (latitude)

text: New York City, Brooklyn

text: uncultured eukaryote

text: CCAGCASCYGCGGTAATTCC,ACTTTCGTTCTTGATYRA

text: uncultured eukaryote


characteristic: ENA-CHECKLIST

text: NYU

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

characteristic: collection date

text: uncultured eukaryote

characteristic: common name

text: Park

text: urban

text: park

text: soil

text: Yes

text: USA

characteristic: geographic location (longitude)

text: New York City, Brooklyn

text: uncultured eukaryote

characteristic: organism

text: CCAGCASCYGCGGTAATTCC,ACTTTCGTTCTTGATYRA

characteristic: pcr primers

text: uncultured eukaryote

characteristic: target gene

characteristic: target subfragment


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: NYU

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: uncultured eukaryote

characteristic: description

text: urban

characteristic: environment (biome)

text: garden

text: soil

text: Yes

text: USA

characteristic: geographic location (country and/or sea)

text: New York City, Brooklyn

characteristic: geographic location (region and locality)

text: uncultured eukaryote

text: CCAGCASCYGCGGTAATTCC,ACTTTCGTTCTTGATYRA

text: uncultured eukaryote

characteristic: title


characteristic: ENA-CHECKLIST

text: NYU

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

characteristic: collection date

text: uncultured eukaryote

characteristic: common name

text: Park

text: urban

text: park

characteristic: environment (feature)

text: soil

characteristic: environment (material)

text: Yes

characteristic: environmental sample

characteristic: further details

text: USA

characteristic: geographic location (latitude)

text: New York City, Bronx

text: uncultured eukaryote

text: CCAGCASCYGCGGTAATTCC,ACTTTCGTTCTTGATYRA

text: uncultured eukaryote


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Ausgem

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: Clinical ExPEC sourced from Sydney

text: Australia

text: Greater Sydney, NSW; Wahroonga

text: diseased

characteristic: host health state

text: Homo sapiens

characteristic: host scientific name

characteristic: isolate

text: Midstream urine

characteristic: isolation source

characteristic: lat lon

text: Escherichia coli

characteristic: organism

text: Escherichia coli

characteristic: serovar

characteristic: strain

text: Human ExPEC


characteristic: ENA-CHECKLIST

text: Ausgem

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

characteristic: collection date

text: Clinical ExPEC sourced from Sydney

characteristic: description

text: Australia

characteristic: geographic location (country and/or sea)

text: Greater Sydney, NSW; Wahroonga

characteristic: geographic location (region and locality)

text: diseased

text: Homo sapiens

text: Midstream urine

text: Escherichia coli

text: Escherichia coli

text: n.d.

text: Human ExPEC

characteristic: title


E-MTAB-6342:Sample 1

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: UC Irvine

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: E-MTAB-6342:Sample 1

tag: Namespace:UC Irvine

text: ArrayExpress

characteristic: broker name

text: postman butterfly

characteristic: common name

text: Protocols: Pupa were sent from Costa Rica and upon eclosure, adult butterflies were frozen at -80 degrees celsius until RNA extraction. TriZol was used for RNA extraction Illumina Tru-Seq kit v. 2 was used to make libraries

text: adult

characteristic: developmental stage

text: Heliconius melpomene

text: Heliconius melpomene

text: head

characteristic: organism part

text: Heliconius melpomene

text: female

characteristic: sex

text: Sample 1


E-MTAB-6342:Sample 2

characteristic: ENA-CHECKLIST

text: UC Irvine

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-6342:Sample 2

characteristic: Submitter Id

text: ArrayExpress

text: postman butterfly

text: adult

text: Heliconius melpomene

characteristic: organism

text: Heliconius melpomene

text: head

text: Heliconius melpomene

text: female

text: Sample 2


E-MTAB-6342:Sample 5

text: UC Irvine

text: public

text: E-MTAB-6342:Sample 5

text: ArrayExpress

text: postman butterfly

characteristic: description

text: adult

text: Heliconius melpomene

text: Heliconius melpomene

text: head

text: Heliconius melpomene

text: male

text: Sample 5

characteristic: title


E-MTAB-6342:Sample 6

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: UC Irvine

text: public

text: E-MTAB-6342:Sample 6

text: ArrayExpress

text: postman butterfly

text: adult

text: Heliconius melpomene

text: Heliconius melpomene

text: head

text: Heliconius melpomene

text: male

text: Sample 6


characteristic: External Id

text: Chengdu instute of biology

characteristic: INSDC center name

text: public

tag: Namespace:Chengdu instute of biology

characteristic: collection date

text: Additives effect the local microbial communities in the simulated Cd-contaminated paddy soil

text: pot experiment

characteristic: environment (biome)

text: soil

characteristic: environment (feature)

text: soil

characteristic: environment (material)

text: China

characteristic: geographic location (country and/or sea)

characteristic: geographic location (depth)

characteristic: geographic location (elevation)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: metagenome

characteristic: investigation type

text: metagenomes

text: Cadmium contamination

characteristic: project name

text: metagenomes

text: Hiseq

characteristic: sequencing method

text: soil

characteristic: soil environmental package

text: Cadmium contamination


text: uncultured Lachnospiraceae bacterium

characteristic: ArrayExpress-Species

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: SC

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: uncultured Lachnospiraceae bacterium

characteristic: common name

text: uncultured Lachnospiraceae bacterium

characteristic: organism

characteristic: sample description

text: uncultured Lachnospiraceae bacterium

characteristic: title


E-MTAB-6333:RAC1 ColxLer F1 ~300 CO

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: University of Cambridge

characteristic: INSDC center name

text: public

text: E-MTAB-6333:RAC1 ColxLer F1 ~300 CO

tag: Namespace:University of Cambridge

unit: week

characteristic: age

text: ArrayExpress

characteristic: broker name

text: thale cress

text: Columbia/Landsberg F1 hybrid

characteristic: cultivar

text: Protocols: Whole Arabidopsis thaliana inflorescences were collected and immerged in ice-cold 10 % sucrose and then frozen at −20 °C. Arabidopsis thaliana were grown under long day conditions (16 hr light) and 20 degrees Celcius. Pollen genomic DNA was extracted and purified following the protocol described in Choi et al, 2017. Choi K., Yelina N.E., Serra H., Henderson I.R. (2017) Quantification and Sequencing of Crossover Recombinant Molecules from Arabidopsis Pollen DNA. In: Tiemann-Boege I., Betancourt A. (eds) Haplotyping. Methods in Molecular Biology, vol 1551. Humana Press, New York, NY ~300 or ~1000 PCR amplified crossover molecules were pooled, concentrated by isopropanol precipitation and gel purified. ~2 μg of DNA in 100 μl of TE (10 mM Tris, 1mM EDTA, pH 8.0) buffer was then sonicated to a size range of 300-400 bp using a Bioruptor (Diagenode). Sonicated DNA was gel purified, end-repaired and used to generate libraries (Tru-seq DNA sample prep kit, Illumina).

characteristic: description

text: whole plant flowering stage

characteristic: developmental stage

text: wild type genotype

characteristic: genotype

text: Arabidopsis thaliana

text: Arabidopsis thaliana

text: pollen

characteristic: organism part

text: Arabidopsis thaliana

text: RAC1 ColxLer F1 ~300 CO


E-MTAB-6333:RAC1 ColxMh F1 ~300 CO

tag: attribute

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: University of Cambridge

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: E-MTAB-6333:RAC1 ColxMh F1 ~300 CO

text: ArrayExpress

text: thale cress

text: Columbia/Muhlen F1 hybrid

text: whole plant flowering stage

text: wild type genotype

text: Arabidopsis thaliana

text: Arabidopsis thaliana

text: pollen

text: Arabidopsis thaliana

text: RAC1 ColxMh F1 ~300 CO


E-MTAB-6333:fancm ~1000 CO

text: University of Cambridge

text: public

characteristic: SRA accession

text: E-MTAB-6333:fancm ~1000 CO

characteristic: Submitter Id

text: ArrayExpress

text: thale cress

characteristic: common name

text: Columbia/Landsberg F1 hybrid

text: whole plant flowering stage

text: fancm mutant

text: Arabidopsis thaliana

characteristic: organism

text: Arabidopsis thaliana

text: pollen

text: Arabidopsis thaliana

text: fancm ~1000 CO


E-MTAB-6333:fancm ~300 CO

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: University of Cambridge

characteristic: INSDC center name

text: public

text: E-MTAB-6333:fancm ~300 CO

text: ArrayExpress

text: thale cress

text: Columbia/Landsberg F1 hybrid

text: whole plant flowering stage

text: fancm mutant

text: Arabidopsis thaliana

text: Arabidopsis thaliana

text: pollen

text: Arabidopsis thaliana

text: fancm ~300 CO

characteristic: title


name: E-MTAB-6333:recq4a recq4b fancm ~1000 CO

text: University of Cambridge

text: public

characteristic: age

text: ArrayExpress

characteristic: broker name

text: thale cress

text: Columbia/Landsberg F1 hybrid

characteristic: cultivar

characteristic: description

text: whole plant flowering stage

text: recq4a, recq4b, fancm mutant

text: Arabidopsis thaliana

text: Arabidopsis thaliana

text: pollen

text: Arabidopsis thaliana

text: recq4a recq4b fancm ~1000 CO


E-MTAB-6333:recq4a recq4b fancm ~300 CO

characteristic: ENA-CHECKLIST

text: University of Cambridge

text: public

text: E-MTAB-6333:recq4a recq4b fancm ~300 CO

text: ArrayExpress

text: thale cress

text: Columbia/Landsberg F1 hybrid

text: whole plant flowering stage

characteristic: developmental stage

text: recq4a, recq4b, fancm mutant

characteristic: genotype

text: Arabidopsis thaliana

text: Arabidopsis thaliana

text: pollen

characteristic: organism part

text: Arabidopsis thaliana

text: recq4a recq4b fancm ~300 CO


E-MTAB-6333:recq4a recq4b ~1000 CO

characteristic: ENA-FIRST-PUBLIC

text: University of Cambridge

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: E-MTAB-6333:recq4a recq4b ~1000 CO

text: ArrayExpress

text: thale cress

text: Columbia/Landsberg F1 hybrid

text: whole plant flowering stage

text: recq4a, recq4b mutant

text: Arabidopsis thaliana

text: Arabidopsis thaliana

text: pollen

text: Arabidopsis thaliana

text: recq4a recq4b ~1000 CO


E-MTAB-6333:recq4a recq4b ~300 CO

text: University of Cambridge

text: public

characteristic: SRA accession

text: E-MTAB-6333:recq4a recq4b ~300 CO

characteristic: Submitter Id

text: ArrayExpress

text: thale cress

characteristic: common name

text: Columbia/Landsberg F1 hybrid

text: whole plant flowering stage

text: recq4a, recq4b mutant

text: Arabidopsis thaliana

characteristic: organism

text: Arabidopsis thaliana

text: pollen

text: Arabidopsis thaliana

text: recq4a recq4b ~300 CO


E-MTAB-6333:WT ~1000 CO

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: University of Cambridge

characteristic: INSDC center name

text: public

text: E-MTAB-6333:WT ~1000 CO

text: ArrayExpress

text: thale cress

text: Columbia/Landsberg F1 hybrid

text: whole plant flowering stage

text: wild type genotype

text: Arabidopsis thaliana

text: Arabidopsis thaliana

text: pollen

text: Arabidopsis thaliana

text: WT ~1000 CO

characteristic: title


E-MTAB-6333:WT ~300 CO

text: University of Cambridge

text: public

text: E-MTAB-6333:WT ~300 CO

characteristic: age

text: ArrayExpress

characteristic: broker name

text: thale cress

text: Columbia/Landsberg F1 hybrid

characteristic: cultivar

characteristic: description

text: whole plant flowering stage

text: wild type genotype

text: Arabidopsis thaliana

text: Arabidopsis thaliana

text: pollen

text: Arabidopsis thaliana

text: WT ~300 CO


text: uncultured Ruminococcaceae bacterium

characteristic: ArrayExpress-Species

characteristic: ENA-CHECKLIST

text: SC

text: public

text: uncultured Ruminococcaceae bacterium

text: uncultured Ruminococcaceae bacterium

characteristic: sample description

text: uncultured Ruminococcaceae bacterium


text: [Eubacterium] rectale

characteristic: ENA-FIRST-PUBLIC

text: SC

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: [Eubacterium] rectale

text: [Eubacterium] rectale

text: [Eubacterium] rectale


text: uncultured Blautia sp.

text: SC

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: uncultured Blautia sp.

text: uncultured Blautia sp.

text: uncultured Blautia sp.


text: Bacteroides stercoris

characteristic: ENA-LAST-UPDATE

text: SC

text: public

text: Bacteroides stercoris

characteristic: common name

text: Bacteroides stercoris

characteristic: organism

text: Bacteroides stercoris


text: Bacteroides ovatus

characteristic: ArrayExpress-SPECIES

characteristic: External Id

text: SC

characteristic: INSDC center name

text: public

text: Bacteroides ovatus

text: Bacteroides ovatus

text: Bacteroides ovatus

characteristic: subject id

characteristic: title


text: Bacteroides ovatus

characteristic: ArrayExpress-Species

text: SC

text: public

text: Bacteroides ovatus

text: Bacteroides ovatus

text: Bacteroides ovatus


text: uncultured Lachnoclostridium sp.

characteristic: ENA-CHECKLIST

text: SC

text: public

text: uncultured Lachnoclostridium sp.

text: uncultured Lachnoclostridium sp.

text: uncultured Lachnoclostridium sp.


text: uncultured Blautia sp.

text: SC

text: public

text: uncultured Blautia sp.

text: uncultured Blautia sp.

text: uncultured Blautia sp.


text: Dorea longicatena

text: SC

text: public

text: Dorea longicatena

text: Dorea longicatena

characteristic: sample description

text: Dorea longicatena


text: Roseburia intestinalis

characteristic: ENA-FIRST-PUBLIC

text: SC

text: public

text: Roseburia intestinalis

text: Roseburia intestinalis

text: Roseburia intestinalis


text: Parabacteroides distasonis

text: SC

characteristic: INSDC first public

text: public

text: Parabacteroides distasonis

text: Parabacteroides distasonis

text: Parabacteroides distasonis


text: Bacteroides clarus

text: SC

characteristic: INSDC last update

text: public

text: Bacteroides clarus

text: Bacteroides clarus

text: Bacteroides clarus


text: Bifidobacterium adolescentis

text: SC

text: public

characteristic: INSDC status

text: Bifidobacterium adolescentis

text: Bifidobacterium adolescentis

text: Bifidobacterium adolescentis


text: Collinsella aerofaciens

text: SC

text: public

characteristic: SRA accession

text: Collinsella aerofaciens

text: Collinsella aerofaciens

text: Collinsella aerofaciens


text: Bacteroides vulgatus

text: SC

text: public

characteristic: Submitter Id

text: Bacteroides vulgatus

text: Bacteroides vulgatus

text: Bacteroides vulgatus


E-MTAB-6214:Sample 10

characteristic: ENA-LAST-UPDATE

text: UZH

text: public

text: E-MTAB-6214:Sample 10

text: ArrayExpress

characteristic: broker name

text: mononuclear cell

characteristic: cell type

text: human

text: Protocols: CD14+CD16-HLA-DRhiLin- (CD3, CD4, CD19, CD45RO) monocytes were sorted from frozen PBMC form blood samples from HD (healthy donor), R (responder) and NR (non-responder) at baseline. Representative samples (n=4, each) of responders/non responders/ and healthy donors were selected from archival samples stored in the dermatology biobank according to the same clinical criteria used in the discovery and validation cohorts for CyTOF and FACS analysis. RNA was isolated using the RNA plus micro kit (Qiagen). We used the SMARTer Stranded total rna-seq pico kit (Clontech) for RNA preparations. Libraries for sequencing were generated with the TruSeq RNA Sample Preparation kit (Illumina).

characteristic: description

text: metastatic melanoma

characteristic: disease

text: Homo sapiens

text: Homo sapiens

text: blood

characteristic: organism part

characteristic: phenotype

text: non-responder

characteristic: response to treatment

text: Homo sapiens

text: Sample 10

text: anti-PD-1 immunotherapy

characteristic: treatment


E-MTAB-6214:Sample 11

characteristic: ENA-CHECKLIST

characteristic: External Id

text: UZH

characteristic: INSDC center name

text: public

text: E-MTAB-6214:Sample 11

text: ArrayExpress

text: mononuclear cell

text: human

characteristic: common name

text: metastatic melanoma

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: blood

text: non-responder

text: Homo sapiens

text: Sample 11

characteristic: title

text: anti-PD-1 immunotherapy


E-MTAB-6214:Sample 12

characteristic: ENA-FIRST-PUBLIC

text: UZH

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-6214:Sample 12

text: ArrayExpress

text: mononuclear cell

text: human

text: metastatic melanoma

text: Homo sapiens

text: Homo sapiens

text: blood

text: non-responder

text: Homo sapiens

text: Sample 12

text: anti-PD-1 immunotherapy


E-MTAB-6214:Sample 5

characteristic: ENA-LAST-UPDATE

text: UZH

text: public

text: E-MTAB-6214:Sample 5

characteristic: Submitter Id

text: ArrayExpress

characteristic: broker name

text: mononuclear cell

characteristic: cell type

text: human

characteristic: description

text: metastatic melanoma

text: Homo sapiens

text: Homo sapiens

text: blood

text: responder

text: Homo sapiens

text: Sample 5

text: anti-PD-1 immunotherapy


E-MTAB-6214:Sample 6

text: UZH

text: public

text: E-MTAB-6214:Sample 6

text: ArrayExpress

text: mononuclear cell

text: human

text: metastatic melanoma

characteristic: disease

text: Homo sapiens

text: Homo sapiens

text: blood

characteristic: organism part

characteristic: phenotype

text: responder

characteristic: response to treatment

text: Homo sapiens

text: Sample 6

text: anti-PD-1 immunotherapy

characteristic: treatment


E-MTAB-6214:Sample 7

characteristic: ENA-CHECKLIST

characteristic: External Id

text: UZH

characteristic: INSDC center name

text: public

text: E-MTAB-6214:Sample 7

text: ArrayExpress

text: mononuclear cell

text: human

characteristic: common name

text: metastatic melanoma

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: blood

text: responder

text: Homo sapiens

text: Sample 7

text: anti-PD-1 immunotherapy


E-MTAB-6214:Sample 8

characteristic: ENA-FIRST-PUBLIC

text: UZH

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: E-MTAB-6214:Sample 8

text: ArrayExpress

text: mononuclear cell

text: human

text: metastatic melanoma

text: Homo sapiens

text: Homo sapiens

text: blood

text: responder

text: Homo sapiens

text: Sample 8

characteristic: title

text: anti-PD-1 immunotherapy


E-MTAB-6214:Sample 9

characteristic: ENA-LAST-UPDATE

text: UZH

text: public

characteristic: SRA accession

text: E-MTAB-6214:Sample 9

characteristic: Submitter Id

text: ArrayExpress

characteristic: broker name

text: mononuclear cell

characteristic: cell type

text: human

text: metastatic melanoma

text: Homo sapiens

text: Homo sapiens

text: blood

text: non-responder

text: Homo sapiens

text: Sample 9

text: anti-PD-1 immunotherapy


E-MTAB-6214:Sample 1

text: UZH

text: public

text: E-MTAB-6214:Sample 1

text: ArrayExpress

text: mononuclear cell

text: human

characteristic: description

text: normal

characteristic: disease

text: Homo sapiens

text: Homo sapiens

text: blood

characteristic: organism part

characteristic: phenotype

text: Homo sapiens

text: Sample 1


E-MTAB-6214:Sample 2

characteristic: ENA-CHECKLIST

characteristic: External Id

text: UZH

characteristic: INSDC center name

text: public

text: E-MTAB-6214:Sample 2

text: ArrayExpress

text: mononuclear cell

text: human

text: normal

text: Homo sapiens

text: Homo sapiens

text: blood

text: Homo sapiens

text: Sample 2


E-MTAB-6214:Sample 3

characteristic: ENA-FIRST-PUBLIC

text: UZH

text: public

text: E-MTAB-6214:Sample 3

text: ArrayExpress

text: mononuclear cell

text: human

characteristic: common name

text: normal

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: blood

text: Homo sapiens

text: Sample 3


E-MTAB-6214:Sample 4

text: UZH

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: E-MTAB-6214:Sample 4

text: ArrayExpress

text: mononuclear cell

text: human

text: normal

text: Homo sapiens

text: Homo sapiens

text: blood

text: Homo sapiens

text: Sample 4


characteristic: ENA-LAST-UPDATE

text: NIOO-KNAW

text: public

characteristic: SRA accession

text: Metagenomic Shotgun of Microorganisms grown in culture medium with acidobacterial EPS as sole carbon source.

text: Yes

characteristic: environmental sample

text: soil metagenome

text: soil metagenome

text: Metagenomic Shotgun of microorganisms cultivated with EPS

characteristic: title


text: public

characteristic: Latitude End

characteristic: Longitude End

tag: Namespace:State Key Laboratory of Marine Environmental Science and Marine Biodiversity and Global Change Research

characteristic: Submitter Id

text: uncultured eukaryote

characteristic: depth

text: sample extraction

characteristic: description

text: sea

characteristic: environment (biome)

text: summer

characteristic: environment (feature)

text: lysis buffer

characteristic: environment (material)

text: water

characteristic: environmental package

characteristic: event date/time

characteristic: latitude start

characteristic: longitude start

text: Taiwan street

characteristic: marine region

text: uncultured eukaryote

text: F: GGCAAGTCTGGTGCCAG

characteristic: pcr primers

text: Diversity investigation

characteristic: project name

text: CTAB

characteristic: protocol label

unit: practical salinity unit

characteristic: salinity

text: filtration

characteristic: sampling campaign

text: CTD

characteristic: sampling platform

text: deck

characteristic: sampling site

text: uncultured eukaryote

characteristic: size fraction

characteristic: target gene

characteristic: target region

unit: ºC

characteristic: temperature

text: EukBank Test


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: State Key Laboratory of Marine Environmental Science and Marine Biodiversity and Global Change Research

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: Latitude End

characteristic: Longitude End

characteristic: SRA accession

characteristic: Submitter Id

text: uncultured eukaryote

characteristic: common name

characteristic: depth

text: sample extraction

characteristic: description

text: sea

characteristic: environment (biome)

text: summer

characteristic: environment (feature)

text: lysis buffer

characteristic: environment (material)

text: water

text: Taiwan street

text: uncultured eukaryote

characteristic: organism

text: R: GACTACGACGGTATCTRATCRTCTTCG

text: Diversity investigation

text: CTAB

text: filtration

text: CTD

text: deck

text: uncultured eukaryote

text: EukBank Test

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: public

text: uncultured eukaryote

text: sample extraction

text: sea

text: summer

text: lysis buffer

text: water

characteristic: environmental package

characteristic: event date/time

characteristic: latitude start

characteristic: longitude start

text: Taiwan street

characteristic: marine region

text: uncultured eukaryote

text: F: GGCAAGTCTGGTGCCAG

characteristic: pcr primers

text: Diversity investigation

characteristic: project name

text: CTAB

characteristic: protocol label

characteristic: salinity

text: filtration

characteristic: sampling campaign

text: CTD

characteristic: sampling platform

text: deck

characteristic: sampling site

text: uncultured eukaryote

characteristic: size fraction

characteristic: target gene

characteristic: target region

characteristic: temperature

text: EukBank Test