text: Lausanne University Hospital

text: public

characteristic: SRA accession

tag: Namespace:Lausanne University Hospital

characteristic: Submitter Id

characteristic: collection date

text: France

text: diseased

characteristic: host health state

text: Homo sapiens

characteristic: host scientific name

characteristic: isolate

text: wound, pus

characteristic: isolation source

text: 48.862725, 2.287592000000018

characteristic: lat lon

text: Klebsiella pneumoniae

text: Klebsiella pneumoniae

text: Carbapenemase producing (OXA-48) and colistin-resistant Klebsiella pneumoniae strain


status: PUBLIC

tag: attribute

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

tag: Namespace:Mikocheni Agricultural Research Institute

text: May 2015

text: deep sequencing of small RNA in pooled RNA samples from common bean; southern highlands zone

characteristic: description

text: Tanzania

characteristic: geographic location (country and/or sea)

text: -9.03912; 32.97489

text: Phaseolus vulgaris

characteristic: organism

text: Phaseolus vulgaris

characteristic: title


text: Mikocheni Agricultural Research Institute

text: public

characteristic: SRA accession

characteristic: Submitter Id

text: May 2015

characteristic: collection date

text: deep sequencing of small RNA in pooled RNA samples from common bean; eastern zone

text: Tanzania

text: -6.19722; 37.65000

text: Phaseolus vulgaris

text: Phaseolus vulgaris


text: public

text: May 2015

text: Deep sequencing of small RNA in pooled RNA samples from common bean; northern zone

text: Tanzania

text: -3.36843; 36.95022

text: Phaseolus vulgaris

text: Phaseolus vulgaris


text: public

text: August 2015

text: deep sequencing of small RNA from common bean; RNA from individual plant; isolate TZ:Mor533:2015; Also contains RNA from Manihot esculenta

text: Tanzania

text: -6.99222; 37.85583

text: Phaseolus vulgaris

text: Phaseolus vulgaris


text: public

text: May 2015

text: Deep sequencing of small RNA from individual common bean plant; southern highlands zone

text: Tanzania

text: -7.87972; 31.67194

text: Phaseolus vulgaris

text: Phaseolus vulgaris


text: public

text: May 2015

text: deep sequencing of small RNA in pooled RNA samples; Lake zone

text: Tanzania

text: -1.41944; 31.20500

text: Phaseolus vulgaris

text: Phaseolus vulgaris


text: public

text: May 2017

text: Deep sequencing of small RNA in pooled RNA sample from Western zone

text: Tanzania

text: -4.504666667; 30.27794

text: Phaseolus vulgaris

text: Phaseolus vulgaris


text: public

text: May 2015

text: deep sequencing of small RNA in pooled RNA sample; Lake zone; Also contains Manihot esculenta RNA

text: Tanzania

text: -1.39972; 34.53750

text: Phaseolus vulgaris

text: Phaseolus vulgaris


text: INSTITUTE OF EVOLUTIONARY BIOLOGY

text: public

tag: Namespace:INSTITUTE OF EVOLUTIONARY BIOLOGY

text: Fresh waters

characteristic: environment (biome)

text: Lake

characteristic: environment (feature)

text: water

characteristic: environment (material)

text: Yes

characteristic: environmental sample

text: Spain

unit: DD

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: uncultured eukaryote

text: Reuk454FWD1: CCAGCASCYGCGGTAATTCC; ReukREV3: ACTTTCGTTCTTGATYRA

characteristic: pcr primers

text: uncultured eukaryote

characteristic: target gene

characteristic: target subfragment

text: Sanabria Lake, Spain


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: PUBLIC HEALTH ENGLAND

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

tag: Namespace:PUBLIC HEALTH ENGLAND

characteristic: broker name

text: Neisseria meningitidis

text: Neisseria meningitidis


Baronia brevicornis 167

text: UNIVERSITY OF MONTPELLIER 2

text: public

characteristic: SRA accession

text: Baronia brevicornis 167

tag: Namespace:UNIVERSITY OF MONTPELLIER 2

characteristic: Submitter Id

text: Mexico

characteristic: geographic location (country and/or sea)

text: mitochondrion

characteristic: organelle

text: Baronia brevicornis

characteristic: organism

text: Baronia brevicornis

text: Baronia brevicornis 167

characteristic: title


Battus polydamas 308

text: UNIVERSITY OF MONTPELLIER 2

text: public

text: Battus polydamas 308

characteristic: collection date

text: gold-rim swallowtail

characteristic: common name

text: Panama

text: Canal Zone

characteristic: geographic location (region and locality)

text: mitochondrion

text: Battus polydamas

text: Battus polydamas

text: belus

characteristic: sub species

text: Battus polydamas 308


Luehdorfia japonica 356

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: UNIVERSITY OF MONTPELLIER 2

text: public

text: Luehdorfia japonica 356

text: Japan

text: Kanazawa, Ishikawa

text: mitochondrion

text: Luehdorfia japonica

text: Luehdorfia japonica

text: Luehdorfia japonica 356


Choristoneura fumiferana 399

characteristic: External Id

text: UNIVERSITY OF MONTPELLIER 2

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: Choristoneura fumiferana 399

text: eastern spruce budworm

text: Canada

text: Alberta, Manning, Hawk Hills

text: mitochondrion

text: Choristoneura fumiferana

text: Choristoneura fumiferana

text: Choristoneura fumiferana 399


Teinopalpus imperialis 1566

text: UNIVERSITY OF MONTPELLIER 2

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: Teinopalpus imperialis 1566

text: Myanmar

text: Kachin State, Mitkyina, 2400m

text: mitochondrion

text: Teinopalpus imperialis

text: Teinopalpus imperialis

text: Teinopalpus imperialis 1566


Pharmacophagus antenor 1646

text: UNIVERSITY OF MONTPELLIER 2

text: public

characteristic: SRA accession

text: Pharmacophagus antenor 1646

characteristic: Submitter Id

text: Madagascar

text: mitochondrion

text: Pharmacophagus antenor

text: Pharmacophagus antenor

text: Pharmacophagus antenor 1646


Parnassius smintheus 1706

text: UNIVERSITY OF MONTPELLIER 2

text: public

text: Parnassius smintheus 1706

text: Rocky Mountain parnassian

text: Canada

characteristic: geographic location (country and/or sea)

text: Alberta Mount Allen

text: mitochondrion

characteristic: organelle

text: Parnassius smintheus

text: Parnassius smintheus

text: Parnassius smintheus 1706


Papilio slateri 1796

text: UNIVERSITY OF MONTPELLIER 2

text: public

text: Papilio slateri 1796

text: Malaysia

text: mitochondrion

text: Papilio slateri

characteristic: organism

text: Papilio slateri

text: Papilio slateri 1796

characteristic: title


Cressida cressida 1827

text: UNIVERSITY OF MONTPELLIER 2

text: public

text: Cressida cressida 1827

characteristic: collection date

text: Australia

text: Queensland Wacol Wacol Station Rd

text: mitochondrion

text: Cressida cressida

text: Cressida cressida

text: Cressida cressida 1827


Meandrusa sciron 1896

text: UNIVERSITY OF MONTPELLIER 2

text: public

text: Meandrusa sciron 1896

text: China

text: Sichuan Province Da Ba Mountain

characteristic: geographic location (region and locality)

text: mitochondrion

text: Meandrusa sciron

text: Meandrusa sciron

text: aribbas

text: Meandrusa sciron 1896


Graphium androcles 1904

text: UNIVERSITY OF MONTPELLIER 2

text: public

text: Graphium androcles 1904

text: Indonesia

text: Sulawesi

text: mitochondrion

text: Graphium androcles

text: Graphium androcles

text: Graphium androcles 1904


Lamproptera meges 1955

text: UNIVERSITY OF MONTPELLIER 2

text: public

text: Lamproptera meges 1955

text: Philippines

text: Marinduque

text: mitochondrion

text: Lamproptera meges

text: Lamproptera meges

text: Lamproptera meges 1955


Graphium sarpedon 2021

text: UNIVERSITY OF MONTPELLIER 2

text: public

text: Graphium sarpedon 2021

text: China

text: mitochondrion

text: Graphium sarpedon

text: Graphium sarpedon

text: Graphium sarpedon 2021


Trogonoptera brookiana 2023

text: UNIVERSITY OF MONTPELLIER 2

text: public

text: Trogonoptera brookiana 2023

text: Malaysia

text: mitochondrion

text: Trogonoptera brookiana

text: Trogonoptera brookiana

text: Trogonoptera brookiana 2023


Hypermnestra helios 2069

text: UNIVERSITY OF MONTPELLIER 2

text: public

text: Hypermnestra helios 2069

text: desert apollo

characteristic: common name

text: Uzbekistan

text: Fergana Valley Komsomolabad

text: mitochondrion

text: Hypermnestra helios

text: Hypermnestra helios

text: maxima

characteristic: sub species

text: Hypermnestra helios 2069


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: public

tag: Namespace:Department of Food and Agricultural Sciences, Alma Mater Studiorum - University of Bologna

text: Salmonella enterica

text: Italy

characteristic: isolate

text: Human

characteristic: isolation source

text: Salmonella enterica

text: Salmonella enterica

text: monophasic Salmonella Typhimurium from food and animals


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Department of Food and Agricultural Sciences, Alma Mater Studiorum - University of Bologna

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: Salmonella enterica

text: Italy

text: Human

text: Salmonella enterica

text: Salmonella enterica


characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: Salmonella enterica

text: Italy

text: Swine

text: Salmonella enterica

text: Salmonella enterica


E-MTAB-6258:Sample 1

text: CGRB, Oregon State University

text: public

text: E-MTAB-6258:Sample 1

tag: Namespace:CGRB, Oregon State University

text: ArrayExpress

characteristic: broker name

text: American beaver

text: Protocols: Tissue samples were collected from a trapped wild-caught female beaver. The following tissue samples were pooled: skeletal muscle; kidney; spleen; ovaries; placenta; castor gland; tail; toe webbing; whole blood; brain; lung; liver; heart; stomach; tongue; intestine Zymo Direct-zolâ„¢ RNA MiniPrep Catalog Number R2050 Wafergen PrepX PolyA mRNA Isolation Kit #400047

characteristic: description

text: adult

characteristic: developmental stage

text: normal

characteristic: disease

text: wild type genotype

characteristic: genotype

text: wild caught

characteristic: growth condition

text: Castor canadensis

characteristic: organism

text: Castor canadensis

text: mixed pool

characteristic: organism part

text: Castor canadensis

text: female

characteristic: sex

text: Sample 1

characteristic: title

type: has member


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: OX

text: public

text: Campylobacter jejuni

text: Campylobacter jejuni


text: OX

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: Campylobacter coli

text: Campylobacter coli


text: Technische Universitat Munchen - WZW

text: public

characteristic: SRA accession

tag: Namespace:Technische Universitat Munchen - WZW

characteristic: Submitter Id

text: Smut fungi are biotrophic and compose a large group of plant pathogens where the speciation seems to be closely connected to their specific host range. This project aims to elucidate on the molecular level “host jump” enabling and therefore host range influencing factors in the smut fungus Ustilago bromivora and related smuts by genetics and genome wide comparisons. Therefore the genomes of Ustilago hordeaceus and Ustilago diandrus are sequenced and annotated for subsequent comparative analysis with the available U. bromivora and other genomes.

characteristic: description

text: Bromus hordeaceus

characteristic: host scientific name

characteristic: mating type

text: Ustilago sp. UG-2017b

text: Ustilago sp. UG-2017b

characteristic: strain

text: Comparative smut fungi project


Ustilago diandrus1

text: Technische Universitat Munchen - WZW

text: public

text: Ustilago diandrus1

text: Ustilago sp. UG-2017a

characteristic: organism

text: Ustilago sp. UG-2017a

text: Comparative smut fungi project


text: public

tag: Namespace:Sanger Institute / Karolinska Institutet

unit: day

characteristic: age

text: ArrayExpress

characteristic: broker name

text: naive T cell

characteristic: cell type

text: human

characteristic: common name

text: Protocols: T-cells from blood (human) and mouse (mouse). CD4+CD62L+ naive T cells were purified from spleens of wild-type C57BL/6JAX adult (6 - 8 weeks) mice using the CD4+CD62L+ T Cell Isolation Kit II (Miltenyii #130-093-227). Cell culture plates were coated with anti-CD3e antibody (1 ug/ml, eBioscences #16-0031-81) in 1X DPBS (Gibco) at 4°C overnight. Purified naive T cells were seeded at a concentration of 1 M cells/ml on the coated plates in IMDM (Gibco) with 10% heat-inactivated FBS (Sigma), supplied with 5 ug/ml anti-CD28 (eBioscience #16-0281-86) with (Th2) or without (Th0) 10 ng/ml mouse recombinant IL-4 (R&D Systems #404-ML-050). Cells were cultured in plates for up to 72 hours. Mononuclear cells were isolated from the cord blood of healthy neonates at Turku University Central Hospital using Ficoll-Paque PLUS (GE Healthcare, #17-1440-02). CD4+ T cells were then isolated using the Dynal bead-based positive isolation kit (Invitrogen). CD4+ cells from three individual donors were activated directly in 24w plates with plate-bound anti-CD3 (500ng/well, Immunotech) and soluble anti-CD28 (500 ng/mL, Immunotech) at a density of 2×106 cells/mL of Yssel’s medium67 containing 1% human AB serum (PAA). Th2 cell polarization was initiated with IL-4 (10 ng/ml, R&D Systems). Cells activated without IL-4 were also cultured (Th0). according to ATAC-seq Experiments were done according to the published protocol with some modification. Briefly, 50,000 cells were washed with ice cold 1X DPBS twice, and resuspended in a sucrose swelling buffer (0.32 M sucrose, 10 mM Tris.Cl, pH 7.5, 3 mM CaCl2, 2 mM MgCl2, 10% glycerol). The cell suspension was left on ice for 10 minutes. Then, a final concentration of 0.5% NP-40 was added, and the cells suspension was vortexed for 10 seconds and left on ice for 10 minutes. Nuclei was pelleted at 500 g at 4°C for 10 minutes. Nuclei were washed once with 1X TD buffer (from Nextera DNA Library Preparation Kit, Illumina, #FC-121-1030), and resuspended in 50 ul tagmentation mix containing: 25 ul 2X TD buffer (Nextera DNA Library Preparation Kit, Illumina #FC-121-1030) 22.5 ul H2O 2.5 ul TDE1 (Nextera DNA Library Preparation Kit, Illumina #FC-121-1030)The tagmentation reaction was carried out on a thermomixer at 37°C, 800 rpm, for 30 minutes. The reaction was stopped by the addition of 250 ul (5 volumes) Buffer PB (from Qiagen MinElute PCR Purification Kit), The tagmented DNA was purified by Qiagen PCR Purification Kit according to manufacturer’s instructions and eluted in 12.5 ul Buffer EB from the kit, which yielded ~10 ul purified DNA.The library amplification was done in a 25 ul reaction include: 10 ul purified DNA (from above) 2.5 ul PCR Primer Cocktail (Nextera DNA Library Preparation Kit, Illumina #FC-121-1030) 2.5 ul N5xx (Nextera index kit , Illumina #FC-121-1012) 2.5 ul N7xx (Nextera index kit , Illumina #FC-121-1012) 7.5 ul NPM PCR master mix (Nextera DNA Library Preparation Kit, Illumina #FC-121-1030)PCR was performed as follows: 72°C 5 minutes 98°C 2 minutes [98°C 10 secs, 63°C 30 secs, 72°C 60 secs] x 12 10°C holdAmplified libraries were purified by double Agencourt AMpureXP beads purifications (Beckman Coulter, #A63882). 0.4X beads:DNA ratio for the first time, flow through was kept (removing large fragments); 1.4X beads:DNA ratio for the second time, beads were kept. Libraries were eluted from the beads by elution in 20 ul Buffer EB (from Qiagen PCR Purification Kit).1 ul library was run on a Agilent Bioanalyzer to check size distribution and quality of the libraries.

characteristic: individual

text: Homo sapiens

text: Homo sapiens

text: umbilical cord blood

characteristic: organism part

text: Homo sapiens


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Sanger Institute / Karolinska Institutet

characteristic: INSDC center name

text: public

text: ArrayExpress

text: naive T cell

text: human

text: Homo sapiens

text: Homo sapiens

text: umbilical cord blood

text: Homo sapiens

characteristic: title


characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: ArrayExpress

text: T-helper 2 cell

text: human

characteristic: description

text: Homo sapiens

text: Homo sapiens

text: umbilical cord blood

text: Homo sapiens


text: public

text: 6 to 8

unit: week

characteristic: age

text: ArrayExpress

characteristic: broker name

text: house mouse

text: wild type genotype

characteristic: genotype

text: Mus musculus

characteristic: organism

text: Mus musculus

text: spleen

text: Mus musculus

characteristic: strain


characteristic: ENA-CHECKLIST

text: public

tag: Namespace:Department of Biosciences and Nutrition, Karolinska Institutet

text: ArrayExpress

characteristic: cell line

text: embryonic stem cell

characteristic: cell type

text: human

characteristic: common name

text: Protocols: Human pluripotent stem cells were grown in E8 and Matrigel conditions. Stem cells were collected at passage 10-17 (CRISPRa iPSCs), passage 38 (SeV iPSCs) and passage 50 (H9 ESCs, WA09). Human foreskin fibroblasts (ATCC, CRL-2429) were grown in DMEM and FBS and collected to Trizol Reagent at passage 9. Sev induced pluripotent stem cells (HEL46.11) were reprogrammed using the Cytotune iPS reprogramming kit, according to manufacturer’s instructions. HEL46.11 were initially cultured on MEF feeders in hES-medium for 10 passages, after which the cells were adapted to grow in E8 medium on Matrigel coated dishes. CRISPR iPSCs (HEL136, HEL139, HEL140, HEL141) were reprogrammed with episomal reprogramming plasmids using dCas9VPH activator containing P53 shRNA and combinations of OCT4, SOX2, KLF4, MYC, LIN28A and EEA-motif targeting guide plasmids (https://www.addgene.org/Timo_Otonkoski/). Plasmids were delivered to the cells with Neon transfection system with 16050V, 10ms and 3x pulse settings. Reprogramming was performed in 1:1 hES-medium/fibroblast medium until colony formation and hES-medium after that, supplemented with 250µM sodium butyrate. Reprogrammed iPS cells were cultured in E8 medium on Matrigel coated dishes. All cell lines were confirmed reprogramming episome negative by PCR (plasmids) or RT-PCR (SeV). hES-medium (KnockOut DMEM (Gibco) supplemented with 20% KO serum replacement (Gibco), 1% GlutaMAX (Gibco), 0.1 mM beta-mercaptoethanol, 1% nonessential amino acids (Gibco), and 6 ng/ml basic fibroblast growth factor (FGF-2; Sigma)). Fibroblast medium (Dulbecco’s modified Eagle’s medium (DMEM; Life Technologies) containing 10% fetal bovine serum (FBS; Life Technologies), 2mM GlutaMAX (Life Technologies), and 100 µg/ml penicillin-streptomycin (Life Technologies)). 100 µl of chloroform per 500 ml of sample was added and mixed with Trizol Reagent. After centrifugation (12 000 g for 15 min) the transparent upper phase was collected and RNA was further purified using NucleoSpin RNA kit (Macherey-Nagel). RIN values were measured by Bioanalyzer (Agilent) and total-RNA concentrations scaled to equal (10 ng/μl) using Qubit assay (Thermo Fisther Scientific). Bulk-RNA transcriptome analysis was performed by the STRT RNA-seq method (PMID: 22481528) with minor modifications (PMID: 26874359). Briefly, ten nanogram of high-quality input RNA was converted to cDNA and amplified to form an Illumina-compatible 46-plex library. ERCC RNA Spike-In Mix 1 (cat. 4456740; ThermoScientific) was used in 1000X dilution. In total, 25 PCR cycles were used, but as six base-pair unique molecular identifiers (UMIs) were applied, only the absolute number of unique reads was calculated per analyzed sample.

text: early embryo

characteristic: developmental stage

text: normal

characteristic: disease

text: wild type genotype

text: Homo sapiens

text: Homo sapiens

text: inner cell mass

characteristic: organism part

text: wild type phenotype

characteristic: phenotype

text: no transfection

characteristic: protocol

text: Homo sapiens


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Department of Biosciences and Nutrition, Karolinska Institutet

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: ArrayExpress

text: embryonic stem cell

text: human

text: early embryo

text: normal

text: wild type genotype

text: Homo sapiens

text: Homo sapiens

text: inner cell mass

text: wild type phenotype

text: no transfection

text: Homo sapiens

characteristic: title


characteristic: ENA-CHECKLIST

text: public

characteristic: Submitter Id

text: ArrayExpress

characteristic: broker name

characteristic: cell line

text: induced pluripotent stem cell

text: human

characteristic: description

text: neonate

text: normal

text: pCXLE-dCas9VP192-T2A-EGFP-shP53; GG-EBNA-OMKSL-PP; GG-EBNA-EEA-5guides-PGK-Puro

characteristic: genotype

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: dermis

text: expression of p53 shRNA and OCT4, SOX2, KLF4, MYC, LIN28A and EEA-motif targeting guide plasmids

characteristic: progenitor cell type

text: non-integrative CRISPRa plasmids

text: Homo sapiens


characteristic: ENA-FIRST-PUBLIC

text: public

text: ArrayExpress

text: induced pluripotent stem cell

characteristic: cell type

text: human

characteristic: common name

text: adult

characteristic: developmental stage

text: normal

characteristic: disease

text: pCXLE-dCas9VP192-T2A-EGFP-shP53; GG-EBNA-OMKSL-PP; GG-EBNA-EEA-5guides-PGK-Puro; GG-EBNA-KM-PP

text: Homo sapiens

text: Homo sapiens

text: dermis

characteristic: organism part

characteristic: phenotype

text: skin fibroblast

text: non-integrative CRISPRa plasmids

characteristic: protocol

text: Homo sapiens


characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: ArrayExpress

text: induced pluripotent stem cell

text: human

text: neonate

text: normal

text: pCXLE-dCas9VP192-T2A-EGFP-shP53; GG-EBNA-OMKSL-PP, EBNA-EEA-5guides-PGK-Puro; GG-EBNA-KM-PP

text: Homo sapiens

text: Homo sapiens

text: dermis

text: non-integrative CRISPRa plasmids

text: Homo sapiens

characteristic: title


characteristic: ENA-CHECKLIST

text: public

characteristic: Submitter Id

text: ArrayExpress

characteristic: broker name

characteristic: cell line

text: induced pluripotent stem cell

text: human

characteristic: description

text: neonate

text: normal

text: pCXLE-dCas9VP192-T2A-EGFP-shP53; GG-EBNA-EEA-5guides-PGKPuro, GG-EBNA-KM-PP; GG-EBNA-OS-PP

characteristic: genotype

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: dermis

characteristic: progenitor cell type

text: non-integrative CRISPRa plasmids

text: Homo sapiens


characteristic: ENA-FIRST-PUBLIC

text: public

text: ArrayExpress

text: induced pluripotent stem cell

characteristic: cell type

text: human

characteristic: common name

text: neonate

characteristic: developmental stage

text: normal

characteristic: disease

text: OCT3/4; KLF4; SOX2 and c-Myc plasmids

text: Homo sapiens

text: Homo sapiens

text: dermis

characteristic: organism part

text: expression of OCT3/4; KLF4; SOX2 and L-Myc plasmids

characteristic: phenotype

text: non-integrative Sendai virus via Cytotune iPS reprogramming kit

characteristic: protocol

text: Homo sapiens


characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: ArrayExpress

text: CCD-1112Sk (CRL-2429)

text: fibroblast

text: human

text: neonate

text: normal

text: wild type genotype

text: Homo sapiens

text: Homo sapiens

text: foreskin

text: wild type phenotype

text: no transfection

text: Homo sapiens

characteristic: title


characteristic: ENA-CHECKLIST

text: UNIVERSITY LYON 1

text: public

tag: Namespace:UNIVERSITY LYON 1

characteristic: Submitter Id

text: female mosquito from Binh Duong Vietnam

characteristic: description

text: metagenome

characteristic: organism

text: metagenome


characteristic: ENA-FIRST-PUBLIC

text: UNIVERSITY LYON 1

text: public

text: female mosquito from Ho Chi Minh City Vietnam

text: metagenome

text: metagenome


text: UNIVERSITY LYON 1

text: public

text: female mosquito from Mananjary Madagascar

text: metagenome

text: metagenome


text: UNIVERSITY LYON 1

text: public

text: female mosquito from Nice France

text: metagenome

text: metagenome


Neg

text: UNIVERSITY LYON 1

text: public

text: Neg

text: negative control

text: metagenome

text: metagenome

text: Neg


text: UNIVERSITY LYON 1

text: public

text: female mosquito from Portes les Valence France

text: metagenome

text: metagenome


text: UNIVERSITY LYON 1

text: public

text: female mosquito from Saint Priest France

text: metagenome

text: metagenome


text: UNIVERSITY LYON 1

text: public

text: female mosquito from Toamasina Madagascar

text: metagenome

text: metagenome


text: UNIVERSITY LYON 1

text: public

text: female mosquito from Tsimbazaza Park Madagascar

text: metagenome

text: metagenome


text: UNIVERSITY LYON 1

text: public

text: female mosquito from Vung Tau City Vietnam

text: metagenome

text: metagenome


text: public

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

characteristic: collection date

text: soil samples

text: tropical lowland

characteristic: environment (biome)

text: rainforest

characteristic: environment (feature)

text: soil

characteristic: environment (material)

text: Yes

characteristic: environmental sample

text: Indonesia

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: uncultured eukaryote

text: TA-Reuk454FWD1 (5�-CCAGCASCYGCGGTAATTCC-3�) and TA-ReukREV3 (5�-ACTTTCGTTCTTGATYRA-3�)

characteristic: pcr primers

text: uncultured eukaryote

text: yes

characteristic: soil samples

characteristic: target gene

characteristic: target subfragment

text: Indonesia


characteristic: ENA-CHECKLIST

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

characteristic: INSDC status

characteristic: SRA accession

text: soil samples

text: tropical lowland

text: rainforest

text: soil

text: Yes

text: Indonesia

text: uncultured eukaryote

text: uncultured eukaryote

text: yes

text: Indonesia

characteristic: title


characteristic: ENA-FIRST-PUBLIC

text: public

characteristic: Submitter Id

characteristic: collection date

text: soil samples

characteristic: description

text: tropical lowland

characteristic: environment (biome)

text: jungle rubber

characteristic: environment (feature)

text: soil

characteristic: environment (material)

text: Yes

characteristic: environmental sample

text: Indonesia

text: uncultured eukaryote

characteristic: organism

text: uncultured eukaryote

text: yes

text: Indonesia


characteristic: ENA-CHECKLIST

characteristic: ENA-LAST-UPDATE

text: public

text: soil samples

text: tropical lowland

text: oil palm

text: soil

text: Yes

text: Indonesia

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: uncultured eukaryote

characteristic: pcr primers

text: uncultured eukaryote

text: yes

characteristic: soil samples

characteristic: target gene

characteristic: target subfragment

text: Indonesia


characteristic: ENA-FIRST-PUBLIC

characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: soil samples

text: tropical lowland

text: rubber

text: soil

text: Yes

text: Indonesia

text: uncultured eukaryote

text: uncultured eukaryote

text: yes

text: Indonesia

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-LAST-UPDATE

text: Functional Genomics Genter Zurich

text: public

tag: Namespace:Functional Genomics Genter Zurich

characteristic: collection date

text: Switzerland

text: diseased

characteristic: host health state

text: Homo sapiens

characteristic: host scientific name

characteristic: isolate

text: Clinical

characteristic: isolation source

text: Shigella sonnei

characteristic: organism

text: Shigella sonnei

text: Shigella sonnei Switzerland


text: Plasmodium falciparum

characteristic: ArrayExpress-SPECIES

characteristic: ENA-FIRST-PUBLIC

text: SC

text: public

text: malaria parasite P. falciparum

characteristic: common name

text: Plasmodium falciparum

text: Plasmodium falciparum

characteristic: subject id


characteristic: External Id

text: INSTITUT DE CIENCIES DEL MAR

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

tag: Namespace:INSTITUT DE CIENCIES DEL MAR

text: uncultured eukaryote

text: sample from the Amundsen Sea

characteristic: description

text: marine biome

characteristic: environment (biome)

text: open water

characteristic: environment (feature)

text: coastal sea water

characteristic: environment (material)

text: Yes

characteristic: environmental sample

characteristic: fluorescence

characteristic: further details

text: Southern Ocean

characteristic: geographic location (country and/or sea)

unit: m

characteristic: geographic location (depth)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: 454 GS FLX

text: uncultured eukaryote

characteristic: oxygen

characteristic: par

text: F 5'-CCAGCASCYGCGGTAATTCC-3' R 5'-ACTTTCGTTCTTGATYRA-3'

characteristic: pcr primers

unit: practical salinity unit

characteristic: salinity

text: uncultured eukaryote

characteristic: size fraction lower threshold

characteristic: size fraction upper threshold

characteristic: target gene

characteristic: target subfragment

characteristic: temperature

text: ASPIRE expedition


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: OX

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

characteristic: broker name

characteristic: description

text: Shigella flexneri

characteristic: organism

text: Shigella flexneri

characteristic: title


text: OX

text: public

text: Shigella sonnei

text: Shigella sonnei


text: public

tag: Namespace:Zentrum fur Molekulare Biologie der Universitat Heidelberg (ZMBH)

text: ArrayExpress

text: Protocols: The EC50 value around the time of the experiment was roughly 45 nM, 1.5xEC50 was roughly 70 nM and 2xEC50 was roughly 90 nM (with some differences among the cell lines), depending on the stock and whether this is freshly made or it has been at -20°C for some time. T. brucei 427 grown in culture; cells were then centrifuged and collected gDNA extraction protocol for T. brucei NEBNext DNA library preparation Kit with NEBNext multiplex oligos for Illumina; Fragmentation with Covaris S2 System

text: bloodstream form

characteristic: developmental stage

text: wild type genotype

characteristic: genotype

text: Trypanosoma brucei brucei

text: Trypanosoma brucei brucei

text: intermediate resistant to AN7973

characteristic: phenotype

text: Trypanosoma brucei brucei

text: Lister 427

characteristic: strain


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: Zentrum fur Molekulare Biologie der Universitat Heidelberg (ZMBH)

text: public

text: ArrayExpress

text: bloodstream form

text: wild type genotype

text: Trypanosoma brucei brucei

text: Trypanosoma brucei brucei

text: intermediate resistant to AN7973

text: Trypanosoma brucei brucei

text: Lister 427


E-MTAB-6307:Wild type

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: public

text: E-MTAB-6307:Wild type

text: ArrayExpress

text: bloodstream form

text: wild type genotype

text: Trypanosoma brucei brucei

text: Trypanosoma brucei brucei

text: wild type

text: Trypanosoma brucei brucei

text: Lister 427

text: Wild type


characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: ArrayExpress

text: bloodstream form

text: wild type genotype

text: Trypanosoma brucei brucei

text: Trypanosoma brucei brucei

text: resistant to AN7973

text: Trypanosoma brucei brucei

text: Lister 427


text: European robin

characteristic: ArrayExpress-SPECIES

text: SC

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: European robin

characteristic: common name

text: Erithacus rubecula

text: Erithacus rubecula

characteristic: subject id

text: bEriRub


text: Carlsberg Research Laboratory

text: public

characteristic: SRA accession

tag: Namespace:Carlsberg Research Laboratory

characteristic: Submitter Id

text: CBS 7425

characteristic: culture collection

text: S. schoenii genome wide gene expression alone or in co-culture with S. cerevisiae, under four different media conditions (YPD, CSM, CSM-Met and SD)

characteristic: description

text: Saccharomycopsis schoenii

characteristic: organism

text: Saccharomycopsis schoenii

text: Genomewide gene expression of Saccharomycopsis schoenii (CBS 7425) during predatory conditions


text: Department of Biosciences and Nutrition, Karolinska Institutet

text: public

text: ArrayExpress

characteristic: broker name

characteristic: cell line

text: epithelial cell

characteristic: cell type

text: human

text: Protocols: HEK293 cells were transfected using FuGENE HD with PiggyBac plasmid encoding trimethoprim stabilizable catalytically inactivated DDdCas9GFP under a doxycycline inducible promoter, PiggyBac rtTA-IRES-Neo, PiggyBac plasmid encoding EEA-motif targeting guide 1 (CCCAGCACTTTGGG) with Puro selection and PiggyBac transposase plasmid. CRISPR plasmids will be available on Addgene (https://www.addgene.org/Timo_Otonkoski/). Transfected cells were selected with puromycin and G418 and subcloned. Clones were selected for further experiments based on absence of GFP in non-induced state and homogenous GFP expression upon doxycycline and trimethoprim addition. Inducible HEK293 cell subclones containing DDdCas9GFP and EEA-g1 were treated for three days with doxycycline (1µg/ml) and trimethoprim (1mM) to express the dCas9 construct. Treated cells and non-treated control cells were dissociated as single cell suspension from four clones (C3, C5, D2 and E2). 50 000 cells from each sample were collected for further processing. Cells were cultured in DMEM + 10% FBS. Nuclei were isolated from 50,000 cells using mild lysis buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl2, 3 mM MgCl2 and 0.1% IGEPAL) Library amplification required 12 cycles and was performed using Phusion HotStart Mastermix. Purified by AMPureXP beads.

text: late embryo

characteristic: developmental stage

text: normal

characteristic: disease

text: PB-tight-DDdCas9GFP-IRES-Neo; PB-CAG-rtTA-IRES-Neo; PB-EEA-g1-PGK-Puro

characteristic: genotype

text: Homo sapiens

text: Homo sapiens

text: kidney

characteristic: organism part

text: wild type phenotype

characteristic: phenotype

text: Homo sapiens

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: ArrayExpress

text: epithelial cell

text: human

text: late embryo

text: normal

text: Homo sapiens

text: Homo sapiens

text: kidney

text: DDdCas9GFP-mediated targeting of EEA-motif

text: Homo sapiens

text: trimethoprim 1 micromolar and doxycycline 1 microgram per milliliter

characteristic: stimulus


text: UNIVERSITY OF SZEGED

text: public

characteristic: SRA accession

tag: Namespace:UNIVERSITY OF SZEGED

characteristic: Submitter Id

text: Veterinary Diagnostic Directorate of the National Food Chain Safety Office, Budapest, Hungary

characteristic: collecting institution

characteristic: collection date

text: Béla Dénes

characteristic: collector name

text: Chlorocebus sabaeus kidney epithelial lines were infected with vaccinia virus (VACV) strain WR. Polyadenylated RNA was isolated and reverse transcribed into cDNA.

characteristic: description

text: Hungary

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: Budapest

characteristic: geographic location (region and locality)

characteristic: host age

text: African green monkey

characteristic: host common name

text: Chlorocebus sabaeus

characteristic: host scientific name

characteristic: host subject id

text: WR - ATCC VR-2035

characteristic: isolate

text: Vaccinia virus WR

characteristic: organism

characteristic: receipt date

text: other

characteristic: sample capture status

text: Vaccinia virus WR

text: Vaccinia virus infection of African green monkey kidney epithelial cells


Ornithoptera priamus 1919

tag: attribute

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: UNIVERSITY OF MONTPELLIER 2

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: Ornithoptera priamus 1919

characteristic: Submitter Id

text: Papua New Guinea

text: mitochondrion

characteristic: organelle

text: Ornithoptera priamus

text: Ornithoptera priamus

text: Ornithoptera priamus 1919

characteristic: title


text: Virginia Commonwealth University

text: public

characteristic: collection date

text: Human metagenome

characteristic: common name

characteristic: description

text: City

characteristic: environment (biome)

text: Indoors

characteristic: environment (feature)

text: Biological Samples

characteristic: environment (material)

text: USA

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: human-associated

characteristic: human associated environmental package

text: metagenome

characteristic: investigation type

characteristic: nucleic acid amplification

text: human metagenome

text: Microbial Quantification of Body Fluid Samples

characteristic: project name

text: human metagenome

text: MiSeq

characteristic: sequencing method

text: 16S rDNA

characteristic: target gene


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Virginia Commonwealth 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: Human metagenome

text: Fecal

text: City

text: Indoors

text: Biological Samples

text: USA

text: human-associated

text: metagenome

text: human metagenome

characteristic: organism

text: human metagenome

text: MiSeq

text: 16S rDNA

text: Fecal


text: Virginia Commonwealth University

text: public

characteristic: collection date

text: Human metagenome

characteristic: common name

text: Saliva

characteristic: description

text: City

characteristic: environment (biome)

text: Indoors

characteristic: environment (feature)

text: Biological Samples

characteristic: environment (material)

text: USA

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: human-associated

characteristic: human associated environmental package

text: metagenome

text: human metagenome

text: human metagenome

text: MiSeq

text: 16S rDNA

text: Saliva

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Virginia Commonwealth University

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: Human metagenome

text: Urine

text: City

text: Indoors

text: Biological Samples

text: USA

text: human-associated

text: metagenome

characteristic: investigation type

characteristic: nucleic acid amplification

text: human metagenome

characteristic: project name

text: human metagenome

text: MiSeq

characteristic: sequencing method

text: 16S rDNA

characteristic: target gene

text: Urine


text: Carlsberg Research Laboratory

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: CBS 7425

characteristic: culture collection

text: Yeast in the genus Saccharomycopsis share a feature; they have the ability to attack and kill other yeast and filamentous fungi. Descriptive cell culture based studies on the Saccharomycopsis clade have been performed by Lachance et al., but with recent advances in bioinformatics and next generation sequencing, significant additional insights into the life, predatory behaviour and the potential usefulness of Saccharomycopsis yeasts can be made. Our group therefore de novo sequenced, assembled and annotated the genome of Saccharomycopsis schoenii, using a combination of Illumina MiSeq paired-end reads and PacBio sequencing reads.

characteristic: description

text: Saccharomycopsis schoenii

characteristic: organism

text: Saccharomycopsis schoenii

text: Draft genome of the predatory yeast Saccharomycopsis schoenii (CBS 7425) [PacBio]


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: KYUNG HEE UNIV.

text: public

tag: Namespace:KYUNG HEE UNIV.

characteristic: collection date

text: Korean kimchi

text: food

characteristic: environment (biome)

text: Korea

characteristic: environment (feature)

text: plant

characteristic: environment (material)

text: South Korea

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: metagenome

text: miscellaneous natural or artificial environment

characteristic: miscellaneous environmental package

text: food production metagenome

text: Bacterial and viral communities within fermented foods

text: food production metagenome

text: Illumina Hiseq 4000

text: fermented food

characteristic: title


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: KYUNG HEE UNIV.

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: Chinese kimchi

text: food

text: China

text: plant

text: South Korea

text: metagenome

characteristic: investigation type

text: food production metagenome

characteristic: project name

text: food production metagenome

text: Illumina Hiseq 4000

characteristic: sequencing method

text: fermented food


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: public

characteristic: SRA accession

tag: Namespace:NATIONAL CANCER CENTER, REPUBLIC OF KOREA

characteristic: Submitter Id

characteristic: age

text: human

characteristic: common name

characteristic: fnclcc

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: F

characteristic: sex

text: Undifferentiated pleomorphic sarcoma

characteristic: type


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: NATIONAL CANCER CENTER, REPUBLIC OF KOREA

characteristic: INSDC center name

text: public

text: human

text: Homo sapiens

text: Homo sapiens

text: M

characteristic: title

text: Undifferentiated pleomorphic sarcoma


characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: human

text: Homo sapiens

text: Homo sapiens

text: F

text: Leiomyosarcoma


characteristic: ENA-CHECKLIST

text: public

text: human

text: Homo sapiens

text: Homo sapiens

text: M

text: Leiomyosarcoma


characteristic: ENA-FIRST-PUBLIC

text: public

text: human

text: Homo sapiens

text: Homo sapiens

text: F

text: Undifferentiated pleomorphic sarcoma


text: public

characteristic: SRA accession

text: human

text: Homo sapiens

text: Homo sapiens

text: M

text: Ewing sarcoma


text: public

characteristic: Submitter Id

text: human

text: Homo sapiens

text: Homo sapiens

text: M

text: Myxofibrosarcoma


text: public

characteristic: age

text: human

text: Homo sapiens

text: Homo sapiens

text: F


text: public

text: human

characteristic: common name

text: Homo sapiens

text: Homo sapiens

text: M


text: URMITE

text: public

text: stool

characteristic: isolation source

text: Eisenbergiella massiliensis

text: Eisenbergiella massiliensis

characteristic: strain

text: Eisenbergiella massiliensis genome


text: IRD

text: public

characteristic: collection date

text: coffee

text: Coffea arabica embryo at 150 days after flowering (stage 5)

characteristic: description

text: Reunion

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: Field conditions

characteristic: isolation and growth condition

text: Coffea arabica

characteristic: organism

text: Developing seeds

characteristic: plant developmental stage

text: Mature trees planted in 2002

characteristic: plant structure

text: Coffea arabica


characteristic: ENA-CHECKLIST

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: IRD

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: coffee

text: Coffea arabica endosperm at 150 days after flowering (stage 5)

text: Reunion

text: Field conditions

text: Coffea arabica

text: Developing seeds

text: Mature trees planted in 2002

text: Coffea arabica

characteristic: title


characteristic: ENA-FIRST-PUBLIC

text: IRD

text: public

characteristic: SRA accession

characteristic: Submitter Id

characteristic: collection date

text: coffee

characteristic: common name

text: Coffea arabica embryo at 200 days after flowering (stage 6)

text: Reunion

text: Field conditions

text: Coffea arabica

text: Developing seeds

text: Mature trees planted in 2002

text: Coffea arabica


text: IRD

text: public

text: coffee

text: Coffea arabica endosperm at 200 days after flowering (stage 6)

characteristic: description

text: Reunion

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: Field conditions

characteristic: isolation and growth condition

text: Coffea arabica

text: Developing seeds

text: Mature trees planted in 2002

text: Coffea arabica


E-MTAB-6310:Barcode 1

characteristic: ENA-CHECKLIST

characteristic: ENA-LAST-UPDATE

text: University of Bergen

text: public

text: E-MTAB-6310:Barcode 1

tag: Namespace:University of Bergen

text: 24 to 30

unit: hour

characteristic: age

text: ArrayExpress

characteristic: broker name

text: zebrafish

text: Protocols: For detailed protocols refer to Gagnon et al., 2014, Methods section with details in Supplementary Protocols. Here we listed shortened version as we can't upload images. There may be a more up-to-date version of this protocol on this website - http://labs.mcb.harvard.edu/schier/index.html Target site selection for the initial screen: Briefly, target sites were selected in exons across the genome that matched the sequence GG-N19-GG, GA-N19-GG, or AG-N19-GG. These sites were checked for uniqueness in RefSeq protein coding regions using Bowtie and the initially defined specificity rules, which suggested an intolerance for mismatches in the 3′ twelve bases of the target site. Cas9 cloning and protein expression: For in vivo expression of Cas9, the Cas9 open reading frame was amplified from hCas9 and cloned into the pCS2 vector to generate pCS2-Cas9. For in vitro expression of Cas9, the hCas9 open reading frame cloned into pET-28b to generate pET-28b-Cas9-His. Cas9 protein was expressed in E. coli Rosetta cells (Novagen) using the auto-induction method, growing for 12 hours at 37°C, followed by 24 hour expression at 18°C. Purification was performed using his-tag resin (G-Biosciences). Buffers were 20 mM Tris pH 8, 30 mM Imidazole, 500 mM NaCl for washes and 20 mM Tris pH 8, 500 mM Imidazole, 500 mM NaCl for elutions. Fractions were dialyzed into 20 mM Tris, 200 mM KCl, 10 mM MgCl2 and single-use aliquots were frozen in liquid nitrogen and stored at −80°C. Plasmids are available from Addgene at http://www.addgene.org/Alex_Schier/. sgRNA template generation and transcription: To generate templates for sgRNA transcription, gene-specific oligonucleotides containing the T7 (5′-TAATACGACTCACTATA-3′) or SP6 (5′- ATTTAGGTGACACTATA-3′) promoter sequence, the 20 base target site without the PAM, and a complementary region were annealed to a constant oligonucleotide encoding the reverse-complement of the tracrRNA tail (Supplementary Figure S1 and Table S1). The ssDNA overhangs were filled in with T4 DNA polymerase (NEB), and the resulting sgRNA template were purified using Qiaquick columns (Qiagen). sgRNAs were transcribed using Megascript kits (Ambion). All sgRNAs were then DNase treated and precipitated with ammonium actetate/ethanol. Cas9 mRNA was transcribed from linearized template DNA using mMachine SP6 kit (Ambion), DNase treated, and precipitated with lithium chloride. RNA concentration was quantified using Nanodrop spectrophotometer and diluted and aliquoted as a 500 ng/ul 20× stock (sgRNAs) or 600 ng/ul 2× stock (Cas9 mRNA). Fish husbandry and microinjection: For the initial screen, zebrafish TLAB strain zygotes were collected and injected through the chorion with a mix of 25 pg sgRNA, 300 pg Cas9 mRNA, and phenol red dye in a single mix. Embryos were grown to 24-30hpf and genomic DNA extracted from pools of 8-10 embryos using the HotSHOT method. For comparison between Cas9 mRNA and protein, higher levels of sgRNA were co-injected (200-300 pg). Cas9/sgRNA complex was formed by incubating protein with sgRNA at room temperature for 5 minutes before injection. Determination of somatic mutagenesis rates: To determine indel percentage using sequencing, a fusion PCR method was used to attach Illumina P5 sequencing adapters and barcodes to amplicons designed to surround the target site. Amplicons were quantified by visualization on agarose gel before being pooled at roughly equal molar ratios. Pools of amplicons were gel extracted and sequenced with MiSeq Personal Sequencer (Illumina), 150 bp paired-end sequencing.

text: embryo

characteristic: developmental stage

text: targeted mutation

characteristic: genetic modification

characteristic: loci sets

text: Danio rerio

characteristic: organism

text: Danio rerio

text: Danio rerio

text: TLAB

characteristic: strain

text: Barcode 1


E-MTAB-6310:Barcode 10

characteristic: ENA-FIRST-PUBLIC

characteristic: External Id

text: University of Bergen

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-6310:Barcode 10

characteristic: Submitter Id

text: 24 to 30

text: ArrayExpress

text: zebrafish

text: embryo

text: targeted mutation

text: Danio rerio

text: Danio rerio

text: Danio rerio

text: TLAB

text: Barcode 10

characteristic: title


E-MTAB-6310:Barcode 11

characteristic: ENA-CHECKLIST

characteristic: ENA-LAST-UPDATE

text: University of Bergen

text: public

text: E-MTAB-6310:Barcode 11

text: 24 to 30

text: ArrayExpress

text: zebrafish

characteristic: common name

characteristic: description

text: embryo

text: targeted mutation

text: Danio rerio

text: Danio rerio

text: Danio rerio

text: TLAB

text: Barcode 11


E-MTAB-6310:Barcode 12

text: University of Bergen

text: public

text: E-MTAB-6310:Barcode 12

text: 24 to 30

characteristic: age

text: ArrayExpress

characteristic: broker name

text: zebrafish

text: embryo

characteristic: developmental stage

text: targeted mutation

characteristic: genetic modification

text: Danio rerio

text: Danio rerio

text: Danio rerio

text: TLAB

text: Barcode 12


E-MTAB-6310:Barcode 13

characteristic: ENA-FIRST-PUBLIC

text: University of Bergen

text: public

text: E-MTAB-6310:Barcode 13

text: 24 to 30

text: ArrayExpress

text: zebrafish

text: embryo

text: targeted mutation

characteristic: loci sets

text: Danio rerio

characteristic: organism

text: Danio rerio

text: Danio rerio

text: TLAB

characteristic: strain

text: Barcode 13


E-MTAB-6310:Barcode 14

characteristic: External Id

text: University of Bergen

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: E-MTAB-6310:Barcode 14

text: 24 to 30

text: ArrayExpress

text: zebrafish

text: embryo

text: targeted mutation

text: Danio rerio

text: Danio rerio

text: Danio rerio

text: TLAB

text: Barcode 14


E-MTAB-6310:Barcode 15

text: University of Bergen

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-6310:Barcode 15

characteristic: Submitter Id

text: 24 to 30

text: ArrayExpress

text: zebrafish

text: embryo

text: targeted mutation

text: Danio rerio

text: Danio rerio

text: Danio rerio

text: TLAB

text: Barcode 15

characteristic: title


E-MTAB-6310:Barcode 16

characteristic: ENA-CHECKLIST

characteristic: ENA-LAST-UPDATE

text: University of Bergen

text: public

text: E-MTAB-6310:Barcode 16

text: 24 to 30

text: ArrayExpress

text: zebrafish

characteristic: common name

characteristic: description

text: embryo

text: targeted mutation

text: Danio rerio

text: Danio rerio

text: Danio rerio

text: TLAB

text: Barcode 16


E-MTAB-6310:Barcode 19

text: University of Bergen

text: public

text: E-MTAB-6310:Barcode 19

text: 24 to 30

characteristic: age

text: ArrayExpress

characteristic: broker name

text: zebrafish

text: embryo

characteristic: developmental stage

text: targeted mutation

characteristic: genetic modification

text: Danio rerio

text: Danio rerio

text: Danio rerio

text: TLAB

text: Barcode 19


E-MTAB-6310:Barcode 2

characteristic: ENA-FIRST-PUBLIC

text: University of Bergen

text: public

text: E-MTAB-6310:Barcode 2

text: 24 to 30

text: ArrayExpress

text: zebrafish

text: embryo

text: targeted mutation

characteristic: loci sets

text: Danio rerio

characteristic: organism

text: Danio rerio

text: Danio rerio

text: TLAB

characteristic: strain

text: Barcode 2


E-MTAB-6310:Barcode 3

characteristic: External Id

text: University of Bergen

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: E-MTAB-6310:Barcode 3

text: 24 to 30

text: ArrayExpress

text: zebrafish

text: embryo

text: targeted mutation

text: Danio rerio

text: Danio rerio

text: Danio rerio

text: TLAB

text: Barcode 3


E-MTAB-6310:Barcode 4

text: University of Bergen

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-6310:Barcode 4

characteristic: Submitter Id

text: 24 to 30

text: ArrayExpress

text: zebrafish

text: embryo

text: targeted mutation

text: Danio rerio

text: Danio rerio

text: Danio rerio

text: TLAB

text: Barcode 4

characteristic: title


E-MTAB-6310:Barcode 5

characteristic: ENA-CHECKLIST

characteristic: ENA-LAST-UPDATE

text: University of Bergen

text: public

text: E-MTAB-6310:Barcode 5

text: 24 to 30

text: ArrayExpress

text: zebrafish

characteristic: common name

characteristic: description

text: embryo

text: targeted mutation

text: Danio rerio

text: Danio rerio

text: Danio rerio

text: TLAB

text: Barcode 5


E-MTAB-6310:Barcode 6

text: University of Bergen

text: public

text: E-MTAB-6310:Barcode 6

text: 24 to 30

characteristic: age

text: ArrayExpress

characteristic: broker name

text: zebrafish

text: embryo

characteristic: developmental stage

text: targeted mutation

characteristic: genetic modification

text: Danio rerio

text: Danio rerio

text: Danio rerio

text: TLAB

text: Barcode 6


E-MTAB-6310:Barcode 7

characteristic: ENA-FIRST-PUBLIC

text: University of Bergen

text: public

text: E-MTAB-6310:Barcode 7

text: 24 to 30

text: ArrayExpress

text: zebrafish

text: embryo

text: targeted mutation

characteristic: loci sets

text: Danio rerio

characteristic: organism

text: Danio rerio

text: Danio rerio

text: TLAB

characteristic: strain

text: Barcode 7


E-MTAB-6310:Barcode 8

characteristic: External Id

text: University of Bergen

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: E-MTAB-6310:Barcode 8

text: 24 to 30

text: ArrayExpress

text: zebrafish

text: embryo

text: targeted mutation

text: Danio rerio

text: Danio rerio

text: Danio rerio

text: TLAB

text: Barcode 8


E-MTAB-6310:Barcode 9

text: University of Bergen

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-6310:Barcode 9

characteristic: Submitter Id

text: 24 to 30

text: ArrayExpress

text: zebrafish

text: embryo

text: targeted mutation

text: Danio rerio

text: Danio rerio

text: Danio rerio

text: TLAB

text: Barcode 9

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-LAST-UPDATE

text: URMITE

text: public

text: Argas lagenoplastis ticks

characteristic: isolation source

text: Rickettsia sp. AUS118

text: Rickettsia sp. AUS118

text: Rickettsia fournieri genome


text: UNIVERSITY OF HELSINKI

text: public

tag: Namespace:UNIVERSITY OF HELSINKI

characteristic: collection date

text: marine

characteristic: environment (biome)

text: pancake ice

characteristic: environment (feature)

text: sea ice

characteristic: environment (material)

text: Yes

characteristic: environmental sample

text: Antarctica

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: uncultured eukaryote

text: fwd_seq: CYGCGGTAATTCCAGCTC, rev_seq: AGAGGTGRAATTCTHRGA

characteristic: pcr primers

text: uncultured eukaryote

characteristic: target gene

characteristic: target subfragment


characteristic: ENA-FIRST-PUBLIC

characteristic: External Id

text: UNIVERSITY OF HELSINKI

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: marine

text: sea ice

text: sea ice

text: Yes

text: Antarctica

text: uncultured eukaryote

characteristic: organism

text: uncultured eukaryote


characteristic: ENA-CHECKLIST

characteristic: ENA-LAST-UPDATE

text: UNIVERSITY OF HELSINKI

text: public

characteristic: Submitter Id

characteristic: collection date

text: marine

characteristic: environment (biome)

text: sea ice

characteristic: environment (feature)

text: slush ice

text: Yes

text: Antarctica

text: uncultured eukaryote

text: uncultured eukaryote

characteristic: title


text: UNIVERSITY OF HELSINKI

text: public

text: marine

text: sea ice

text: brine

characteristic: environment (material)

text: Yes

characteristic: environmental sample

text: Antarctica

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: uncultured eukaryote

characteristic: pcr primers

text: uncultured eukaryote

characteristic: target gene


characteristic: ENA-FIRST-PUBLIC

characteristic: External Id

text: UNIVERSITY OF HELSINKI

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: marine

text: water

text: water

text: Yes

text: Antarctica

text: uncultured eukaryote

text: uncultured eukaryote

characteristic: target subfragment


characteristic: ENA-CHECKLIST

characteristic: ENA-LAST-UPDATE

text: URMITE

text: public

characteristic: SRA accession

characteristic: Submitter Id

text: Yogurt

characteristic: isolation source

text: Lactobacillus reuteri

characteristic: organism

text: Lactobacillus reuteri

characteristic: strain

text: Lactobacillus reuteri from yogurt and urine


E-MTAB-6314:Sample 15

text: public

text: E-MTAB-6314:Sample 15

tag: Namespace:Laboratory of Microbial Genetics and Gene Expression, Institute of Microbiology, v.v.i. AS CR

text: ArrayExpress

characteristic: broker name

text: Protocols: Bacillus subtilis wt, ∆sigI-rsgI and ∆rsgI strains were inoculated from single colony to 10 ml of LB medium. Cultures were grown overnight at 37°C. Next day, the cultures were inoculated into 20 ml of LB medium (RT) to OD600∼0.01 and grown at 37°C and 52°C, respectively. Cells were harvested in exponential phase (OD600∼0.5). Three ml of culture were immediately treated with a double volume of RNAprotect Bacteria reagent (QIAGEN) for 5 min at RT to prevent degradation of RNA. Cells were pelleted and frozen immediately. In all steps of cultivation (with the exception of the last step of cultivation for total RNA isolation) medium for ∆sigI-rsgI strain was supplemented with spectinomycin 100 μg/ml; medium for ∆rsgI strain was supplemented with linkomycin 12.5 μg/ml and erythromycin 0.5 μg/ml. The experiment was repeated three times. RNA was extracted using RNeasy Mini Kit 50 (QIAGEN) according to the manufacturer’s protocol. Finally, RNA was treated twice with DNase (TURBO DNA-free Kit, Ambion). Two micrograms of total RNA were rRNA-depleted with RiboMinus Transcriptome Isolation Kit, bacteria (Invitrogen). A strand-specific library was prepared for each sample with Illumina compatible NEXTflex Rapid Directional RNA-Seq Kit (Bioo Scientific) according to manufacturer’s protocol.

characteristic: description

text: gene disruption

characteristic: genetic modification

text: rsgI mutant

characteristic: genotype

text: 37C LB broth

characteristic: growth condition

text: Bacillus subtilis subsp. subtilis str. 168

characteristic: replicate

text: Sample 15

characteristic: title


E-MTAB-6314:Sample 3

characteristic: ENA-FIRST-PUBLIC

characteristic: External Id

text: Laboratory of Microbial Genetics and Gene Expression, Institute of Microbiology, v.v.i. AS CR

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: E-MTAB-6314:Sample 3

text: ArrayExpress

text: gene disruption

text: rsgI mutant

text: 37C LB broth

text: Sample 3


E-MTAB-6314:Sample 9

characteristic: ENA-CHECKLIST

characteristic: ENA-LAST-UPDATE

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-6314:Sample 9

text: ArrayExpress

text: gene disruption

text: rsgI mutant

text: 37C LB broth

text: Sample 9


E-MTAB-6314:Sample 12

text: public

text: E-MTAB-6314:Sample 12

characteristic: Submitter Id

text: ArrayExpress

text: gene disruption

text: rsgI mutant

text: 52C LB broth

characteristic: organism

text: Sample 12


E-MTAB-6314:Sample 6

text: public

text: E-MTAB-6314:Sample 6

text: ArrayExpress

characteristic: broker name

characteristic: description

text: gene disruption

text: rsgI mutant

text: 52C LB broth

text: Sample 6


E-MTAB-6314:Sample 18

text: public

text: E-MTAB-6314:Sample 18

text: ArrayExpress

text: gene disruption

characteristic: genetic modification

text: rsgI mutant

characteristic: genotype

text: 52C LB broth

text: Sample 18


E-MTAB-6314:Sample 14

text: public

text: E-MTAB-6314:Sample 14

text: ArrayExpress

text: deletion of the whole operon

text: sigI-rsgI knockout

text: 37C LB broth

characteristic: growth condition

characteristic: replicate

text: Sample 14


E-MTAB-6314:Sample 2

characteristic: ENA-FIRST-PUBLIC

text: public

text: E-MTAB-6314:Sample 2

text: ArrayExpress

text: deletion of the whole operon

text: sigI-rsgI knockout

text: 37C LB broth

text: Sample 2

characteristic: title


E-MTAB-6314:Sample 8

characteristic: External Id

characteristic: INSDC center name

text: public

text: E-MTAB-6314:Sample 8

text: ArrayExpress

text: deletion of the whole operon

text: sigI-rsgI knockout

text: 37C LB broth

text: Sample 8


E-MTAB-6314:Sample 11

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: E-MTAB-6314:Sample 11

text: ArrayExpress

text: deletion of the whole operon

text: sigI-rsgI knockout

text: 52C LB broth

text: Sample 11


E-MTAB-6314:Sample 17

characteristic: ENA-CHECKLIST

characteristic: ENA-LAST-UPDATE

text: public

text: E-MTAB-6314:Sample 17

text: ArrayExpress

text: deletion of the whole operon

text: sigI-rsgI knockout

text: 52C LB broth

text: Sample 17


E-MTAB-6314:Sample 5

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-6314:Sample 5

text: ArrayExpress

text: deletion of the whole operon

text: sigI-rsgI knockout

text: 52C LB broth

text: Sample 5


E-MTAB-6314:Sample 13

text: public

text: E-MTAB-6314:Sample 13

characteristic: Submitter Id

text: ArrayExpress

text: wild type genotype

text: 37C LB broth

characteristic: organism

text: Sample 13


E-MTAB-6314:Sample 7

text: public

text: E-MTAB-6314:Sample 7

text: ArrayExpress

characteristic: broker name

characteristic: description

text: wild type genotype

text: 37C LB broth

text: Sample 7


E-MTAB-6314:Sample 1

text: public

text: E-MTAB-6314:Sample 1

text: ArrayExpress

text: wild type genotype

characteristic: genotype

text: 37C LB broth

text: Sample 1


E-MTAB-6314:Sample 10

text: public

text: E-MTAB-6314:Sample 10

text: ArrayExpress

text: wild type genotype

text: 52C LB broth

characteristic: growth condition

text: Sample 10


E-MTAB-6314:Sample 16

text: public

text: E-MTAB-6314:Sample 16

text: ArrayExpress

text: wild type genotype

text: 52C LB broth

characteristic: replicate

text: Sample 16


E-MTAB-6314:Sample 4

characteristic: ENA-FIRST-PUBLIC

text: public

text: E-MTAB-6314:Sample 4

text: ArrayExpress

text: wild type genotype

text: 52C LB broth

text: Sample 4


text: Postdoctoral Fellow

text: public

tag: Namespace:Postdoctoral Fellow

text: ArrayExpress

text: zebrafish

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. 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. Embryos were reared following Westerfield et al., (2009) recommendations. Briefly, once collected on a Petri dish filled with E3 medium (5 mM NaCl, 0.17 mM KCl, 0.33 mM CaCl2, 0.33 mM MgSO4 and 0.00001% (w/v) of Methylene blue) at 28°C, 10 embryos per replicate were manually dechorionated using a pair of Dumont’s #5 forceps. Dechorionated embryos were rinsed thrice with 400 μL of warmed Ringer’s solution (116 mM NaCl, 2.9 mM KCl, 5.0 mM HEPES at pH7.2) and collected into a 1.5 mL eppendorf tube using a plastic Pasteur pipette. Then the tube was placed on ice to sedate the embryos. The tube containing the embryos was then removed from the ice, the liquid was fully removed and the embryos were resuspended in 200 μL of Deyolking buffer (Ringer’s solution, 0.3 mM PMSF, 1 mM EDTA). Energetic up and down movements with a 200 μL pipette were done in order to separate yolks from embryos. Once the clean embryos sunk down the liquid was fully removed and the embryos were rinsed twice with Ringer’s solution and embryos were finally resuspended in 400 μL PBS and homogenized using a syringe (size 24G). 2. Zebrafish embryos were reared as described in (Westerfield et al., 2009). Briefly, once collected on a Petri dish filled with E3 medium (5 mM NaCl, 0.17 mM KCl, 0.33 mM CaCl2, 0.33 mM MgSO4 and 0.00001% (w/v) of Methylene blue) at 28°C, 10 embryos per replicate were manually dechorionated using a pair of Dumont’s #5 forceps. Dechorionated embryos were rinsed thrice with 400 μL of warmed Ringer’s solution (116 mM NaCl, 2.9 mM KCl, 5.0 mM HEPES at pH7.2) and collected into a 1.5 mL eppendorf tube using a plastic Pasteur pipette. Then the tube was placed on ice to sedate the embryos. The tube containing the embryos was then removed from the ice, the liquid was fully removed and the embryos were resuspended in 200 μL of Deyolking buffer (Ringer’s solution, 0.3 mM PMSF, 1 mM EDTA). Energetic up and down movements with a 200 μL pipette were done in order to separate yolks from embryos. Once the clean embryos sunk down the liquid was fully removed and the embryos were rinsed twice with Ringer’s solution and embryos were finally resuspended in 400 μL PBS and homogenized using a syringe (size 24G). 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 on 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).

text: pharyngula prim-5

characteristic: developmental stage

text: AB strain

text: Danio rerio

text: Danio rerio

text: MboI

characteristic: restriction digest

text: Danio rerio

characteristic: title


characteristic: External Id

text: Postdoctoral Fellow

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: ArrayExpress

text: zebrafish

text: hatching long-pec

text: AB strain

text: Danio rerio

text: Danio rerio

text: MboI

text: Danio rerio


Salat v21

characteristic: ENA-CHECKLIST

characteristic: ENA-LAST-UPDATE

text: CEBITEC

text: public

characteristic: INSDC status

characteristic: SRA accession

text: Salat v21

characteristic: collection date

text: Draft genome sequence of Lactuca sativa cv. Tizican

text: Salad

characteristic: environment (biome)

text: Salad

characteristic: environment (feature)

text: Salad

characteristic: environment (material)

text: Germany

characteristic: geographic location (country and/or sea)

characteristic: geographic location (depth)

characteristic: geographic location (elevation)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: mimarks-survey

characteristic: investigation type

text: Lactuca sativa

text: Salat v2

characteristic: project name

text: Lactuca sativa

text: HiSeq 1500

characteristic: sequencing method

text: soil

characteristic: soil environmental package


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: External Id

text: URMITE

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: Submitter Id

text: urine

characteristic: isolation source

text: Lactobacillus reuteri

characteristic: organism

text: Lactobacillus reuteri

characteristic: strain

characteristic: title


characteristic: ENA-LAST-UPDATE

text: University of Goettingen

text: public

characteristic: INSDC status

characteristic: SRA accession

tag: Namespace:University of Goettingen

text: chicken

characteristic: common name

text: WL_A individual sequence

characteristic: description

text: Gallus gallus

text: Gallus gallus


text: University of Goettingen

text: public

text: chicken

text: ABwa pooled sequence

text: Gallus gallus

text: Gallus gallus


text: University of Goettingen

text: public

text: chicken

text: ARsch pooled sequence

text: Gallus gallus

text: Gallus gallus


text: University of Goettingen

text: public

text: chicken

text: ASrb pooled sequence

text: Gallus gallus

text: Gallus gallus


text: University of Goettingen

text: public

text: chicken

text: BAsch pooled sequence

text: Gallus gallus

text: Gallus gallus


text: University of Goettingen

text: public

text: chicken

text: BHrg pooled sequence

text: Gallus gallus

text: Gallus gallus


text: University of Goettingen

text: public

text: chicken

text: BKschg pooled sequence

text: Gallus gallus

text: Gallus gallus


text: University of Goettingen

text: public

text: chicken

text: CHgesch pooled sequence

text: Gallus gallus

text: Gallus gallus


text: University of Goettingen

text: public

text: chicken

text: COsch pooled sequence

text: Gallus gallus

text: Gallus gallus


text: University of Goettingen

text: public

text: chicken

text: CHschw pooled sequence

text: Gallus gallus

text: Gallus gallus


text: University of Goettingen

text: public

text: chicken

text: DZgh pooled sequence

text: Gallus gallus

text: Gallus gallus


text: University of Goettingen

text: public

text: chicken

text: DLla pooled sequence

text: Gallus gallus

text: Gallus gallus


text: University of Goettingen

text: public

text: chicken

text: FZgpo pooled sequence

text: Gallus gallus

text: Gallus gallus


text: University of Goettingen

text: public

text: chicken

text: GGg pooled sequence

text: Gallus gallus

text: Gallus gallus


text: University of Goettingen

text: public

text: chicken

text: GGsc pooled sequence

text: Gallus gallus

text: Gallus gallus


text: University of Goettingen

text: public

text: chicken

text: HOxx pooled sequence

text: Gallus gallus

text: Gallus gallus


text: University of Goettingen

text: public

text: chicken

text: ITrh pooled sequence

text: Gallus gallus

text: Gallus gallus


text: University of Goettingen

text: public

text: chicken

text: KAsch pooled sequence

text: Gallus gallus

text: Gallus gallus


text: University of Goettingen

text: public

text: chicken

text: KSgw pooled sequence

text: Gallus gallus

text: Gallus gallus


text: University of Goettingen

text: public

text: chicken

text: KRsch pooled sequence

text: Gallus gallus

text: Gallus gallus


text: University of Goettingen

text: public

text: chicken

text: KRw pooled sequence

text: Gallus gallus

text: Gallus gallus


text: University of Goettingen

text: public

text: chicken

text: LER11 pooled sequence

text: Gallus gallus

text: Gallus gallus


text: University of Goettingen

text: public

text: chicken

text: MAxx pooled sequence

text: Gallus gallus

text: Gallus gallus


text: University of Goettingen

text: public

text: chicken

text: MRschk pooled sequence

text: Gallus gallus

text: Gallus gallus


text: University of Goettingen

text: public

text: chicken

text: NHL68 pooled sequence

text: Gallus gallus

text: Gallus gallus


text: University of Goettingen

text: public

text: chicken

text: OFrbx pooled sequence

text: Gallus gallus

text: Gallus gallus


text: University of Goettingen

text: public

text: chicken

text: OHsh pooled sequence

text: Gallus gallus

text: Gallus gallus


text: University of Goettingen

text: public

text: chicken

text: OMsschg pooled sequence

text: Gallus gallus

text: Gallus gallus


text: University of Goettingen

text: public

text: chicken

text: ORge pooled sequence

text: Gallus gallus

text: Gallus gallus


text: University of Goettingen

text: public

text: chicken

text: PAxx pooled sequence

text: Gallus gallus

text: Gallus gallus


text: University of Goettingen

text: public

text: chicken

text: BL_A pooled sequence

text: Gallus gallus

text: Gallus gallus


text: University of Goettingen

text: public

text: chicken

text: SAsch pooled sequence

text: Gallus gallus

text: Gallus gallus


text: University of Goettingen

text: public

text: chicken

text: SBsschs pooled sequence

text: Gallus gallus

text: Gallus gallus


text: University of Goettingen

text: public

text: chicken

text: SEw pooled sequence

text: Gallus gallus

text: Gallus gallus


text: University of Goettingen

text: public

text: chicken

text: SHsch pooled sequence

text: Gallus gallus

text: Gallus gallus


text: University of Goettingen

text: public

text: chicken

text: SNwsch pooled sequence

text: Gallus gallus

text: Gallus gallus


text: University of Goettingen

text: public

text: chicken

text: TOgh pooled sequence

text: Gallus gallus

text: Gallus gallus


text: University of Goettingen

text: public

text: chicken

text: BL_D pooled sequence

text: Gallus gallus

text: Gallus gallus


text: University of Goettingen

text: public

text: chicken

text: WTs pooled sequence

text: Gallus gallus

text: Gallus gallus


text: University of Goettingen

text: public

text: chicken

text: WYw pooled sequence

text: Gallus gallus

text: Gallus gallus


text: University of Goettingen

text: public

text: chicken

text: YOwr pooled sequence

text: Gallus gallus

text: Gallus gallus


text: University of Goettingen

text: public

text: chicken

text: ZCw pooled sequence

text: Gallus gallus

text: Gallus gallus


text: URMITE

text: public

text: urine

text: Lactobacillus reuteri

text: Lactobacillus reuteri


text: public

characteristic: collection date

text: Belgium

characteristic: geographic location (country and/or sea)

text: not provided

characteristic: host health state

characteristic: isolate

text: Clostridioides difficile

text: Clostridioides difficile

text: C. difficile reference strain for establishment of cgMLST scheme


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: External Id

characteristic: INSDC center name

text: public

text: Spain

text: not provided

text: Clostridioides difficile

text: Clostridioides difficile


characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: Submitter Id

text: Slovenia

text: not provided

text: Clostridioides difficile

text: Clostridioides difficile


text: public

text: USA

text: not provided

text: Clostridioides difficile

characteristic: organism

text: Clostridioides difficile

characteristic: strain

characteristic: title


characteristic: ENA-LAST-UPDATE

text: public

characteristic: INSDC status

characteristic: SRA accession

text: United Kingdom

text: not provided

text: Clostridioides difficile

text: Clostridioides difficile


text: public

characteristic: collection date

text: France

text: not provided

text: Clostridioides difficile

text: Clostridioides difficile


text: public

text: Australia

characteristic: geographic location (country and/or sea)

text: not provided

text: Clostridioides difficile

text: Clostridioides difficile


text: public

text: USA

text: not provided

characteristic: host health state

text: IS 25

text: Clostridioides difficile

text: Clostridioides difficile

text: IS 25


text: public

text: Australia

text: not provided

text: IS 58

characteristic: isolate

text: Clostridioides difficile

text: Clostridioides difficile

text: IS 58


characteristic: ENA-CHECKLIST

text: public

text: Japan

text: not provided

text: Clostridioides difficile

text: Clostridioides difficile


characteristic: ENA-FIRST-PUBLIC

text: public

text: United Kingdom

text: not provided

text: R 10870

text: Clostridioides difficile

text: Clostridioides difficile

text: R 10870


characteristic: External Id

text: public

text: United Kingdom

text: not provided

text: R 11402

text: Clostridioides difficile

text: Clostridioides difficile

text: R 11402


characteristic: INSDC center name

text: public

text: USA

text: not provided

text: R 9385

text: Clostridioides difficile

text: Clostridioides difficile

text: R 9385


characteristic: INSDC first public

text: public

text: France

text: not provided

text: SE 881

text: Clostridioides difficile

text: Clostridioides difficile

text: SE 881


characteristic: INSDC last update

text: public

text: Indonesia

text: not provided

text: Clostridioides difficile

text: Clostridioides difficile


text: ETHZ

text: public

characteristic: Submitter Id

text: Adipocytes

characteristic: cell type

text: house mouse

characteristic: common name

text: Female_Brite_cell Rep1

characteristic: description

text: Mus musculus

text: Mus musculus


characteristic: ENA-LAST-UPDATE

text: ETHZ

text: public

text: Adipocytes

text: house mouse

text: Female_Brite_cell Rep2

text: Mus musculus

characteristic: organism

text: Mus musculus

characteristic: title


text: ETHZ

text: public

characteristic: INSDC status

characteristic: SRA accession

text: Adipocytes

text: house mouse

text: Female_Brite_cell Rep3

text: Mus musculus

text: Mus musculus


text: ETHZ

text: public

text: Adipocytes

text: house mouse

text: Female_Brite_cell Rep4

text: Mus musculus

text: Mus musculus


text: ETHZ

text: public

text: Adipocytes

text: house mouse

text: Female_Brite_cell Rep5

text: Mus musculus

text: Mus musculus


text: ETHZ

text: public

text: Adipocytes

text: house mouse

text: Female_Brown_cell Rep1

text: Mus musculus

text: Mus musculus


text: ETHZ

text: public

text: Adipocytes

text: house mouse

text: Female_Brown_cell Rep2

text: Mus musculus

text: Mus musculus


text: ETHZ

text: public

text: Adipocytes

text: house mouse

text: Female_Brown_cell Rep3

text: Mus musculus

text: Mus musculus


text: ETHZ

text: public

text: Adipocytes

text: house mouse

text: Female_Brown_cell Rep4

text: Mus musculus

text: Mus musculus


text: ETHZ

text: public

text: Adipocytes

text: house mouse

text: Female_Brown_cell Rep5

text: Mus musculus

text: Mus musculus


text: ETHZ

text: public

text: Adipocytes

text: house mouse

text: Female_White_cell Rep1

text: Mus musculus

text: Mus musculus


text: ETHZ

text: public

text: Adipocytes

text: house mouse

text: Female_White_cell Rep2

text: Mus musculus

text: Mus musculus


text: ETHZ

text: public

text: Adipocytes

text: house mouse

text: Female_White_cell Rep3

text: Mus musculus

text: Mus musculus


text: ETHZ

text: public

text: Adipocytes

text: house mouse

text: Female_White_cell Rep4

text: Mus musculus

text: Mus musculus


text: ETHZ

text: public

text: Adipocytes

text: house mouse

text: Female_White_cell Rep5

text: Mus musculus

text: Mus musculus


text: ETHZ

text: public

text: Adipocytes

text: house mouse

text: Male_Brite_cell Rep1

text: Mus musculus

text: Mus musculus


text: ETHZ

text: public

text: Adipocytes

text: house mouse

text: Male_Brite_cell Rep2

text: Mus musculus

text: Mus musculus


text: ETHZ

text: public

text: Adipocytes

text: house mouse

text: Male_Brite_cell Rep3

text: Mus musculus

text: Mus musculus


text: ETHZ

text: public

text: Adipocytes

text: house mouse

text: Male_Brite_cell Rep4

text: Mus musculus

text: Mus musculus


text: ETHZ

text: public

text: Adipocytes

text: house mouse

text: Male_Brite_cell Rep5

text: Mus musculus

text: Mus musculus


text: ETHZ

text: public

text: Adipocytes

text: house mouse

text: Male_Brown_cell Rep1

text: Mus musculus

text: Mus musculus


text: ETHZ

text: public

text: Adipocytes

text: house mouse

text: Male_Brown_cell Rep2

text: Mus musculus

text: Mus musculus


text: ETHZ

text: public

text: Adipocytes

text: house mouse

text: Male_Brown_cell Rep3

text: Mus musculus

text: Mus musculus


text: ETHZ

text: public

text: Adipocytes

text: house mouse

text: Male_Brown_cell Rep4

text: Mus musculus

text: Mus musculus


text: ETHZ

text: public

text: Adipocytes

text: house mouse

text: Male_Brown_cell Rep5

text: Mus musculus

text: Mus musculus


text: ETHZ

text: public

text: Adipocytes

text: house mouse

text: Male_White_cell Rep1

text: Mus musculus

text: Mus musculus


text: ETHZ

text: public

text: Adipocytes

text: house mouse

text: Male_White_cell Rep2

text: Mus musculus

text: Mus musculus


text: ETHZ

text: public

text: Adipocytes

text: house mouse

text: Male_White_cell Rep3

text: Mus musculus

text: Mus musculus


text: ETHZ

text: public

text: Adipocytes

text: house mouse

text: Male_White_cell Rep4

text: Mus musculus

text: Mus musculus


text: ETHZ

text: public

text: Adipocytes

text: house mouse

text: Male_White_cell Rep5

text: Mus musculus

text: Mus musculus


Fish mixture A

text: WUR

text: public

text: Fish mixture A

text: Fish mixture containing Pleuronectes platessa (74.91% w/w), Limanda limanda (4.92% w/w), Microstomus kitt (4.97% w/w), Limanda aspera (5.13% w/w), Platichthys flesus (5.12% w/w), Scophthalmus rhombus (4.95% w/w)

text: mixed sample

text: mixed sample

text: Experimental fish mixture A


Fish mixture B

text: WUR

text: public

text: Fish mixture B

text: Fish mixture containing Pleuronectes platessa (8.39% w/w), Limanda limanda (8.36% w/w), Limanda aspera (8.25% w/w), Platichthys flesus (8.19% w/w), Agonus cataphractus (8.15% w/w), Microstomus kitt (16.7% w/w), Myoxocephalus scorpius (8.27% w/w), Hippoglossoides platessoides (8.39% w/w), Zoarces viviparus (8.45% w/w), Osmerus eperlanus (8.43% w/w), Scophthalmus maximus (8.41% w/w)

text: mixed sample

text: mixed sample

text: Experimental fish mixture B


text: public

text: human

text: Homo sapiens

text: Homo sapiens


text: JHI

text: public

text: Ver54 mapping study resistant parent

text: Solanum verrucosum

text: Solanum verrucosum


text: JHI

text: public

text: Ver54 mapping study susceptible parent

text: Solanum verrucosum

text: Solanum verrucosum


text: JHI

text: public

text: Ver54 mapping study resistant bulk

text: Solanum verrucosum

text: Solanum verrucosum


text: JHI

text: public

text: Ver54 mapping study susceptible bulk

text: Solanum verrucosum

text: Solanum verrucosum


text: JHI

text: public

text: Resistance Pool of Verrucosum population

text: Solanum verrucosum

text: Solanum verrucosum


text: JHI

text: public

text: Susceptibility Pool of verrucosum population

text: Solanum verrucosum

text: Solanum verrucosum


text: JHI

text: public

text: Resistant line of Verrucosum population

text: Solanum verrucosum

text: Solanum verrucosum


text: JHI

text: public

text: Susceptible line of Verrucosum population

text: Solanum verrucosum

text: Solanum verrucosum


text: LSA-DISTAL-UNIBO

text: public

characteristic: collection date

text: GOS normal

text: chicken

characteristic: environment (biome)

text: caeca content

characteristic: environment (feature)

text: caeca content

characteristic: environment (material)

text: Italy

characteristic: geographic location (country and/or sea)

text: 44°26'4272 N

characteristic: geographic location (latitude)

text: 11°28'3540 E

characteristic: geographic location (longitude)

text: host-associated

characteristic: host-associated environmental package

text: metagenome

characteristic: investigation type

text: metagenome

text: SIR

characteristic: project name

text: metagenome

text: targeted

characteristic: sequencing method


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: External Id

text: LSA-DISTAL-UNIBO

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: Submitter Id

text: GOS shock

characteristic: description

text: chicken

text: caeca content

text: caeca content

text: Italy

text: 44°26'4272 N

text: 11°28'3540 E

text: host-associated

text: metagenome

text: metagenome

text: SIR

text: metagenome

text: targeted


Allancastria cerisyi 2081

characteristic: ENA-LAST-UPDATE

text: UNIVERSITY OF MONTPELLIER 2

text: public

characteristic: INSDC status

characteristic: SRA accession

text: Allancastria cerisyi 2081

tag: Namespace:UNIVERSITY OF MONTPELLIER 2

characteristic: collection date

text: Kosovo

text: Kachanik, 750m

characteristic: geographic location (region and locality)

text: mitochondrion

characteristic: organelle

text: Allancastria cerisyi

characteristic: organism

text: Allancastria cerisyi

text: ferdinandi

characteristic: sub species

text: Allancastria cerisyi 2081

characteristic: title


Bhutanitis mansfieldi 2097

characteristic: ENA-CHECKLIST

text: UNIVERSITY OF MONTPELLIER 2

text: public

text: Bhutanitis mansfieldi 2097

text: China

characteristic: geographic location (country and/or sea)

text: Yunnan, 1200m

text: mitochondrion

text: Bhutanitis mansfieldi

text: Bhutanitis mansfieldi

text: Bhutanitis mansfieldi 2097


characteristic: ENA-FIRST-PUBLIC

characteristic: External Id

text: CARDIFF SCHOOL OF BIOSCIENCES

text: public

tag: Namespace:CARDIFF SCHOOL OF BIOSCIENCES

text: This strain was obtained from the Unilever culture collection

text: Pseudomonas aeruginosa

text: Pseudomonas aeruginosa

text: A Pseudomonas aeruginosa industrial strain


text: WTCMP

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: Uninduced sample, 24 hour timepoint, replicate 1, clone 19047

text: Trypanosoma brucei brucei TREU927

text: Trypanosoma brucei brucei TREU927

text: 24 hour timepoint, uninduced, replicate 1, clone 19047


text: WTCMP

characteristic: INSDC last update

text: public

characteristic: Submitter Id

text: Tet-induced sample, 24 hour timepoint, replicate 1, clone 19047

text: Trypanosoma brucei brucei TREU927

text: Trypanosoma brucei brucei TREU927

text: 24 hour timepoint, tet-induced, replicate 1, clone 19047


characteristic: ENA-LAST-UPDATE

text: WTCMP

text: public

text: Uninduced sample, 36 hour timepoint, replicate 1, clone 19047

characteristic: description

text: Trypanosoma brucei brucei TREU927

text: Trypanosoma brucei brucei TREU927

text: 36 hour timepoint, uninduced, replicate 1, clone 19047


text: WTCMP

text: public

characteristic: INSDC status

characteristic: SRA accession

text: Tet-induced sample, 36 hour timepoint, replicate 1, clone 19047

text: Trypanosoma brucei brucei TREU927

text: Trypanosoma brucei brucei TREU927

text: 36 hour timepoint, tet-induced, replicate 1, clone 19047


text: WTCMP

text: public

text: Uninduced sample, 24 hour timepoint, replicate 2, clone 17970

text: Trypanosoma brucei brucei TREU927

text: Trypanosoma brucei brucei TREU927

text: 24 hour timepoint, uninduced, replicate 2, clone 17970


text: WTCMP

text: public

text: Tet-induced sample, 24 hour timepoint, replicate 2, clone 17970

text: Trypanosoma brucei brucei TREU927

text: Trypanosoma brucei brucei TREU927

text: 24 hour timepoint, tet-induced, replicate 2, clone 17970


text: WTCMP

text: public

text: Uninduced sample, 36 hour timepoint, replicate 2, clone 17970

text: Trypanosoma brucei brucei TREU927

text: Trypanosoma brucei brucei TREU927

text: 36 hour timepoint, uninduced, replicate 2, clone 17970


text: WTCMP

text: public

text: Tet-induced sample, 36 hour timepoint, replicate 2, clone 17970

text: Trypanosoma brucei brucei TREU927

text: Trypanosoma brucei brucei TREU927

text: 36 hour timepoint, tet-induced, replicate 2, clone 17970


text: WTCMP

text: public

text: Uninduced sample, 24 hour timepoint, replicate 3, clone 17970

text: Trypanosoma brucei brucei TREU927

text: Trypanosoma brucei brucei TREU927

text: 24 hour timepoint, uninduced, replicate 3, clone 17970


text: WTCMP

text: public

text: Tet-induced sample, 24 hour timepoint, replicate 3, clone 17970

text: Trypanosoma brucei brucei TREU927

text: Trypanosoma brucei brucei TREU927

text: 24 hour timepoint, tet-induced, replicate 3, clone 17970


text: WTCMP

text: public

text: Uninduced sample, 36 hour timepoint, replicate 3, clone 17970

text: Trypanosoma brucei brucei TREU927

text: Trypanosoma brucei brucei TREU927

text: 36 hour timepoint, uninduced, replicate 3, clone 17970


text: WTCMP

text: public

text: Tet-induced sample, 36 hour timepoint, replicate 3, clone 17970

text: Trypanosoma brucei brucei TREU927

text: Trypanosoma brucei brucei TREU927

text: 36 hour timepoint, tet-induced, replicate 3, clone 17970


text: INSTITUTE OF MICROBIOLOGY ASCR

text: public

tag: Namespace:INSTITUTE OF MICROBIOLOGY ASCR

text: Kasia Piwosz

characteristic: collected by

characteristic: collection date

text: uncultured eukaryote

characteristic: common name

text: nanoplankton

characteristic: environment (biome)

characteristic: environment (feature)

characteristic: environment (material)

text: Yes

characteristic: environmental sample

characteristic: further details

text: Baltic Sea

characteristic: geographic location (depth)

text: 54.517540 N

characteristic: geographic location (latitude)

text: 018.556630 E

characteristic: geographic location (longitude)

text: surface water

characteristic: isolation source

text: uncultured eukaryote

text: TAReuk454FWD1: CCAGCASCYGCGGTAATTCC; TAReukREV3:ACTTTCGTTCTTGATYRA

characteristic: pcr primers

characteristic: salinity

text: uncultured eukaryote

text: 20 micrometers

characteristic: size fraction upper threshold

characteristic: target gene

characteristic: target subfragment

text: Diversity and ecology of nanophytoplankton in the Gulf of Gdansk (Baltic Sea)