Monreal

characteristic: ENA first public

text: UNICT

characteristic: INSDC center name

text: public

text: Monreal

characteristic: air temperature regimen

text: clementine

characteristic: culture rooting medium

text: Auto compatible mutant of the 'Comune' clementine

characteristic: estimated size

text: Italy

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: field

characteristic: growth facility

text: aa

characteristic: isolation and growth condition

characteristic: light regimen

characteristic: mineral nutrient regimen

characteristic: number of replicons

text: Citrus x clementina

characteristic: organism common name

text: young leaf

characteristic: plant developmental stage

text: soil

characteristic: plant growth medium

text: leaf

characteristic: plant structure

characteristic: plant treatment

text: diploid

characteristic: ploidy

characteristic: propagation

characteristic: rooting conditions

characteristic: rooting medium carbon

characteristic: rooting medium macronutrients

characteristic: rooting medium micronutrients

characteristic: rooting medium organic supplements

characteristic: rooting medium pH

characteristic: rooting medium regulators

characteristic: rooting medium solidifier

characteristic: sample disease status

text: healthy

characteristic: sample health state

text: Citrus x clementina

characteristic: soil pH

characteristic: soil_taxonomic/FAO classification

characteristic: source material identifiers

characteristic: subspecific genetic lineage name

characteristic: subspecific genetic lineage rank

text: Monreal

characteristic: title

characteristic: watering regimen


status: PUBLIC

characteristic: ENA first public

tag: attribute

characteristic: ENA-CHECKLIST

text: TU Braunschweig

characteristic: INSDC center name

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: field

characteristic: broad-scale environmental context

characteristic: collection date

text: common frog

characteristic: common name

text: 18C, intermediate nitrate

characteristic: description

text: gut

characteristic: environmental medium

text: Germany

characteristic: geographic location (country and/or sea)

unit: DD

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: pond

characteristic: local environmental context

text: Rana temporaria

characteristic: organism

characteristic: project name

text: Rana temporaria


characteristic: ENA first public

text: TU Braunschweig

text: public

text: field

text: common frog

text: 18C, high nitrate

text: gut

text: Germany

text: pond

text: Rana temporaria

text: Rana temporaria

characteristic: title


characteristic: ENA-CHECKLIST

text: TU Braunschweig

characteristic: INSDC center name

text: public

text: field

text: common frog

text: 18C, no nitrate

text: gut

text: Germany

text: pond

text: Rana temporaria

text: Rana temporaria


text: TU Braunschweig

text: public

characteristic: INSDC status

characteristic: SRA accession

text: field

text: common frog

text: 22C, intermediate nitrate

text: gut

text: Germany

text: pond

text: Rana temporaria

text: Rana temporaria


text: TU Braunschweig

text: public

characteristic: Submitter Id

text: field

characteristic: broad-scale environmental context

text: common frog

text: 22C, high nitrate

text: gut

text: Germany

text: pond

text: Rana temporaria

text: Rana temporaria


text: TU Braunschweig

text: public

text: field

characteristic: collection date

text: common frog

characteristic: common name

text: 22C, no nitrate

text: gut

text: Germany

text: pond

text: Rana temporaria

text: Rana temporaria


text: TU Braunschweig

text: public

text: field

text: common frog

text: 26C, intermediate nitrate

characteristic: description

text: gut

characteristic: environmental medium

text: Germany

text: pond

text: Rana temporaria

text: Rana temporaria


text: TU Braunschweig

text: public

text: field

text: common frog

text: 26C, high nitrate

text: gut

text: Germany

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

text: pond

text: Rana temporaria

text: Rana temporaria


text: TU Braunschweig

text: public

text: field

text: common frog

text: 26C, no nitrate

text: gut

text: Germany

characteristic: geographic location (longitude)

text: pond

characteristic: local environmental context

text: Rana temporaria

text: Rana temporaria


text: TU Braunschweig

text: public

text: field

text: common frog

text: 28C, intermediate nitrate

text: gut

text: Germany

text: pond

text: Rana temporaria

characteristic: organism

characteristic: project name

text: Rana temporaria


characteristic: ENA first public

text: TU Braunschweig

text: public

text: field

text: common frog

text: 28C, high nitrate

text: gut

text: Germany

text: pond

text: Rana temporaria

text: Rana temporaria

characteristic: title


characteristic: ENA-CHECKLIST

text: TU Braunschweig

characteristic: INSDC center name

text: public

text: field

text: common frog

text: 28C, no nitrate

text: gut

text: Germany

text: pond

text: Rana temporaria

text: Rana temporaria


text: TU Braunschweig

text: public

characteristic: INSDC status

characteristic: SRA accession

text: field

text: common frog

text: extraction control

text: gut

text: Germany

text: pond

text: Rana temporaria

text: Rana temporaria


text: TU Braunschweig

text: public

characteristic: Submitter Id

text: field

characteristic: broad-scale environmental context

text: common frog

text: extraction control

text: gut

text: Germany

text: pond

text: Rana temporaria

text: Rana temporaria

text: Control0711-rep_S264_L001_R2_001.fastq.gz


text: TU Braunschweig

text: public

text: field

characteristic: collection date

text: common frog

characteristic: common name

text: extraction control

text: gut

text: Germany

text: pond

text: Rana temporaria

text: Rana temporaria

text: Control0811-rep_S275_L001_R2_001.fastq.gz


text: TU Braunschweig

text: public

text: field

text: common frog

text: extraction control

characteristic: description

text: gut

characteristic: environmental medium

text: Germany

text: pond

text: Rana temporaria

text: Rana temporaria

text: Control0911-rep_S113_L001_R2_001.fastq.gz


text: TU Braunschweig

text: public

text: field

text: common frog

text: extraction control

text: gut

text: Germany

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

text: pond

text: Rana temporaria

text: Rana temporaria

text: Control1011-rep_S227_L001_R2_001.fastq.gz


text: TU Braunschweig

text: public

text: field

text: common frog

text: extraction control

text: gut

text: Germany

characteristic: geographic location (longitude)

text: pond

characteristic: local environmental context

text: Rana temporaria

text: Rana temporaria

text: Control1111-rep_S249_L001_R2_001.fastq.gz


text: TU Braunschweig

text: public

text: field

text: common frog

text: PCR control

text: gut

text: Germany

text: pond

text: Rana temporaria

characteristic: organism

characteristic: project name

text: Rana temporaria


characteristic: ENA first public

text: TU Braunschweig

text: public

text: field

text: common frog

text: fluctuating temperature, intermediate nitrate

text: gut

text: Germany

text: pond

text: Rana temporaria

text: Rana temporaria

characteristic: title


characteristic: ENA-CHECKLIST

text: TU Braunschweig

characteristic: INSDC center name

text: public

text: field

text: common frog

text: fluctuating temperature, high nitrate

text: gut

text: Germany

text: pond

text: Rana temporaria

text: Rana temporaria


text: TU Braunschweig

text: public

characteristic: INSDC status

characteristic: SRA accession

text: field

text: common frog

text: fluctuating temperature, no nitrate

text: gut

text: Germany

text: pond

text: Rana temporaria

text: Rana temporaria


E-MTAB-13850:Sample 1

text: Instituto de Medicina Molecular João Lobo Antunes

text: public

text: E-MTAB-13850:Sample 1

characteristic: Submitter Id

text: ArrayExpress

characteristic: broker name

text: iPSC derived cell line

text: cardiac muscle cell

text: not collected

text: human

text: Protocols: ll iPSCs were seeded on plates coated with Matrigel™ (Corning) and cultured in mTeSR™1 Medium (Stem Cell Technologies). Medium was changed daily. Cells were split every 3-4 days (when the colonies covered approximately 85% of the surface area of the culture dish) using PBS 0.5mM EDTA dissociation buffer. Before each differentiation process, iPSCs were thawed and maintained in culture for 2-3 passages. Before seeding, cells were incubated with ROCKi (Y-27632, 10μM, Stem Cell Technologies) for 1 h at 37ºC and then treated with Accutase (Sigma) for 7 min at 37ºC for dissociation. Microwell plates (AggreWell™800, Stem Cell Technologies) were used to generate aggregates. Cells were plated at a density of 0.9 x 106cells/well (3,000 cells/microwell) in 1.5 mL/well of mTeSR™1 supplemented with 10μM ROCKi. After 24 hours, the full volume of the medium was replaced and aggregates were maintained in mTeSR™1 without ROCKi for 48h. From this time point on (day 0 of differentiation), RPMI 1640 (Thermo Fisher Scientific) was used as the basal medium. During the first 7 days, cells were cultured in RPMI supplemented with 2%(v/v) B-27 minus insulin (Thermo Fisher Scientific). After day 7, cells were cultured in RPMI supplemented with 2%(v/v) B-27 (Thermo Fisher Scientific) until the end of differentiation. At day 0 of differentiation, the Wnt signaling pathway was activated using the GSK3 inhibitor CHIR99021 (Stemgent) at a final concentration of 11 µM. After 24 hours (day 1), full-volume medium replacement with RPMI + B27 minus insulin was performed. On day 3, half of the medium in each well was replaced and cells were supplemented with Wnt inhibitor IWP-4 (Stemgent) at a final concentration of 5 µM for two days. On day 5, the total volume of medium was changed. On day 7, the aggregates were flushed from the AggreWell™800 plate with RPMI + B27 and transferred to ultra-low attachment 6-well plates (Costar, Corning). On day 10, the full volume of medium was replaced. On day 13, aggregates were dissociated using 0,25% Trypsin-EDTA (Gibco) for 7 min at 37ºC. After dissociation, cells were washed with 2% fetal bovine serum (FBS) and 2mM EDTA in phosphate buffered saline (PBS, 0.1M), and incubated with VCAM1 antibody (BioLegend, 1:50) diluted in PBS/2% FBS for 15 min at 4ºC. Then, cells were washed and suspended in PBS/2% FBS for FACS sorting (BD FACSAria™ III Cell Sorter) using a 100μm nozzle at 4ºC. Purified VCAM1 positive cells were plated on wells coated with Matrigel, at a seeding density between 20,000 – 40,000 cells/cm2. For the remaining time in culture, two-thirds of the total volume of RPMI + B27 was replaced every 2–3 days. At day 30, differentiated cells were dissociated using 0.25% Trypsin-EDTA (Gibco) for 5 min at 37ºC. After stopping the reaction, dissociated cells were resuspended in PBS/0.1% bovine serum albumin (BSA; Life Technologies), filtered through a 100 μm pore filter and stored in ice.  Viable cell suspensions (1x106 cells/mL) were partitioned into Gel Beads-in-emulsion (GEMs), in order to capture approximately 10000 cells in single cell droplets, using the Chromium Single Cell 3ʹ GEM, Library & Gel Bead Kit (version 3, 10X Genomics, PN-1000092) and Chromium Single Cell B Chip Kit (10X Genomics, PN-1000074). Barcoded cDNA was extracted from the GEMs by Post-GEM RT-cleanup, PCR amplified and subjected to quality control and quantification.  Single Cell 3ʹ Gene Expression libraries from single cells was then performed using Chromium i7 Multiplex Kit (PN-120262). All the steps were performed according to the manufacturer’s protocol.

text: day 30 of differentiation

characteristic: developmental stage

text: wild type genotype

characteristic: genotype

text: not collected

text: not applicable

characteristic: isolate

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens

text: male

characteristic: sex

text: Sample 1


E-MTAB-13850:Sample 2

text: public

text: E-MTAB-13850:Sample 2

text: ArrayExpress

text: iPSC derived cell line

text: cardiac muscle cell

text: not collected

characteristic: collection date

text: human

characteristic: common name

characteristic: description

text: day 30 of differentiation

text: wild type genotype

text: not collected

characteristic: geographic location (country and/or sea)

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens

text: female

text: Sample 2


text: LIV

text: public

text: not provided

text: negative control

text: not provided

text: water control

text: synthetic metagenome

characteristic: organism

text: synthetic metagenome


characteristic: ENA first public

text: LIV

text: public

text: not provided

text: control

text: not provided

text: control

text: synthetic metagenome

text: synthetic metagenome


text: LIV

text: public

text: not provided

text: positive control

text: not provided

text: zymo control

text: synthetic metagenome

text: synthetic metagenome

characteristic: title


characteristic: ENA-CHECKLIST

text: LIV

text: public

text: not provided

text: Bronchiectasis patient sputum sample

text: not provided

text: sputum

text: lung metagenome

text: lung metagenome


text: Hebrew University, Genetics Department

characteristic: INSDC center name

text: public

text: ArrayExpress

text: Diploid differentiated ESCs

text: not collected

text: human

text: Protocols: Cells were washed with PBS and trypsinized Haploid and diploid neurons were separated into droplet emulsion using Chromium X (10x genomics). scRNAseq libraries were prepared and barcoded with UDIs using Chromium Next GEM Single Cell 3’ Kit v3.1 (10X Genomics), according to the manufacturer protocol.

text: Neuronal differentiation

text: not collected

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: Diploid

characteristic: ploidy

text: Homo sapiens

text: Diploid


text: Hebrew University, Genetics Department

text: public

characteristic: INSDC status

characteristic: SRA accession

text: ArrayExpress

text: Haploid differentiated ESCs

text: not collected

text: human

text: Neuronal differentiation

text: not collected

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: Haploid

text: Homo sapiens

text: Haploid


text: GAUSS

text: public

text: ena-SAMPLE-TAB-16-04-2024-09:49:48:615-20625

characteristic: Submitter Id

text: DNA samples from herbarium voucher B100467880

unit: m

characteristic: elevation

text: Germany

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: Leipzig; Saxony

characteristic: geographic location (region and locality)

text: not applicable

characteristic: isolation and growth condition

text: Xanthium ambrosioides

characteristic: plant developmental stage

text: not applicable

characteristic: plant growth medium

text: leaf

characteristic: plant structure

text: Xanthium ambrosioides


text: GAUSS

text: public

text: ena-SAMPLE-TAB-16-04-2024-09:49:48:616-20626

characteristic: collection date

text: DNA samples from herbarium voucher BA89510

characteristic: description

text: Argentina

characteristic: geographic location (country and/or sea)

text: El Huecú; Neuquén

text: not applicable

text: Xanthium ambrosioides

characteristic: organism

text: not applicable

text: leaf

text: Xanthium ambrosioides


characteristic: ENA first public

characteristic: ENA-CHECKLIST

text: GAUSS

characteristic: INSDC center name

text: public

text: ena-SAMPLE-TAB-16-04-2024-09:49:48:616-20627

text: DNA samples from herbarium voucher BA33212

text: Argentina

text: Loventuel

text: not applicable

text: Xanthium ambrosioides

text: not applicable

text: leaf

text: Xanthium ambrosioides

characteristic: title


text: GAUSS

text: public

characteristic: INSDC status

characteristic: SRA accession

text: ena-SAMPLE-TAB-16-04-2024-09:49:48:616-20628

characteristic: Submitter Id

text: DNA samples from herbarium voucher BA6660

text: Argentina

text: Bahia San Blas

text: not applicable

text: Xanthium ambrosioides

text: not applicable

text: leaf

text: Xanthium ambrosioides


text: GAUSS

text: public

text: ena-SAMPLE-TAB-16-04-2024-09:49:48:616-20629

text: DNA samples from herbarium voucher BA60567

characteristic: elevation

text: Argentina

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: Igarzabal

text: not applicable

text: Xanthium ambrosioides

text: not applicable

text: leaf

text: Xanthium ambrosioides


text: GAUSS

text: public

text: ena-SAMPLE-TAB-16-04-2024-09:49:48:616-20630

text: DNA samples from herbarium voucher BA251015

text: Argentina

text: San Fransisco del Monte de Oro; Mina del Pilón

characteristic: geographic location (region and locality)

text: not applicable

characteristic: isolation and growth condition

text: Xanthium ambrosioides

characteristic: plant developmental stage

text: not applicable

text: leaf

text: Xanthium ambrosioides


text: GAUSS

text: public

text: ena-SAMPLE-TAB-16-04-2024-09:49:48:616-20631

characteristic: collection date

text: DNA samples from herbarium voucher BA46475

text: Argentina

text: Agua de la Chilena; Dep. San Rafael

text: not applicable

text: Xanthium ambrosioides

text: not applicable

characteristic: plant growth medium

text: leaf

characteristic: plant structure

text: Xanthium ambrosioides


text: GAUSS

text: public

text: ena-SAMPLE-TAB-16-04-2024-09:49:48:616-20632

text: DNA samples from herbarium voucher B101067779

characteristic: description

text: Germany

characteristic: geographic location (country and/or sea)

text: Hannover Döhren

text: not applicable

text: Xanthium ambrosioides

characteristic: organism

text: not applicable

text: leaf

text: Xanthium ambrosioides


characteristic: ENA first public

characteristic: ENA-CHECKLIST

text: GAUSS

characteristic: INSDC center name

text: public

text: ena-SAMPLE-TAB-16-04-2024-09:49:48:616-20633

text: not provided

text: DNA samples from herbarium voucher WU0071716

text: Chile

text: Ñuble

text: not applicable

text: Xanthium sp.

text: not applicable

text: leaf

text: Xanthium sp.


text: GAUSS

text: public

characteristic: INSDC status

characteristic: SRA accession

text: ena-SAMPLE-TAB-16-04-2024-09:49:48:616-20634

text: DNA samples from herbarium voucher P04380863

text: France

text: Dunkerque

text: not applicable

text: Xanthium sp.

text: not applicable

text: leaf

text: Xanthium sp.

characteristic: title


text: GAUSS

text: public

text: ena-SAMPLE-TAB-16-04-2024-09:49:48:616-20635

characteristic: Submitter Id

text: DNA samples from herbarium voucher P02537124

text: Chile

characteristic: geographic location (latitude)

text: Chile

text: not applicable

text: Xanthium sp.

text: not applicable

text: leaf

text: Xanthium sp.


text: GAUSS

text: public

text: ena-SAMPLE-TAB-16-04-2024-09:49:48:616-20636

text: DNA samples from herbarium voucher B101067796

characteristic: elevation

text: Ecuador

characteristic: geographic location (longitude)

text: Cuenca; Azuay

characteristic: geographic location (region and locality)

text: not applicable

text: Xanthium sp.

text: not applicable

text: leaf

text: Xanthium sp.


text: GAUSS

text: public

text: ena-SAMPLE-TAB-16-04-2024-09:49:48:616-20637

characteristic: collection date

text: DNA samples from herbarium voucher B100349123

text: Chile

text: San Pedro de Atacama

text: not applicable

characteristic: isolation and growth condition

text: Xanthium sp.

characteristic: plant developmental stage

text: not applicable

text: leaf

text: Xanthium sp.


text: GAUSS

text: public

text: ena-SAMPLE-TAB-16-04-2024-09:49:48:616-20638

text: DNA samples from herbarium voucher BA302808

characteristic: description

text: Bolivia

text: Valle; Cochabamba

text: not applicable

text: Xanthium sp.

text: not applicable

characteristic: plant growth medium

text: leaf

characteristic: plant structure

text: Xanthium sp.


characteristic: ENA first public

text: GAUSS

text: public

text: ena-SAMPLE-TAB-16-04-2024-09:49:48:617-20639

text: DNA samples from herbarium voucher BA12474

text: Argentina

characteristic: geographic location (country and/or sea)

text: Correntoso; Neuquen

text: not applicable

text: Xanthium sp.

characteristic: organism

text: not applicable

text: leaf

text: Xanthium sp.


characteristic: ENA-CHECKLIST

text: GAUSS

characteristic: INSDC center name

text: public

characteristic: INSDC status

text: ena-SAMPLE-TAB-16-04-2024-09:49:48:617-20640

text: not provided

text: DNA samples from herbarium voucher P00320266

text: Ecuador

text: Quito

text: not applicable

text: Xanthium sp.

text: not applicable

text: leaf

text: Xanthium sp.


text: GAUSS

text: public

characteristic: SRA accession

text: ena-SAMPLE-TAB-16-04-2024-09:49:48:617-20641

characteristic: Submitter Id

text: DNA samples from herbarium voucher P02537131

text: Colombia

text: Prov. de Pasto

text: not applicable

text: Xanthium sp.

text: not applicable

text: leaf

text: Xanthium sp.

characteristic: title


text: GAUSS

text: public

text: ena-SAMPLE-TAB-16-04-2024-09:49:48:617-20642

text: not provided

text: DNA samples from herbarium voucher P02537136

characteristic: elevation

text: Ecuador

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: Chillo; Quito

text: not applicable

text: Xanthium sp.

text: not applicable

text: leaf

text: Xanthium sp.


text: GAUSS

text: public

text: ena-SAMPLE-TAB-16-04-2024-09:49:48:617-20643

characteristic: collection date

text: DNA samples from herbarium voucher GOET042660

text: Peru

text: Chuquibamba

characteristic: geographic location (region and locality)

text: not applicable

characteristic: isolation and growth condition

text: Xanthium sp.

text: not applicable

text: leaf

text: Xanthium sp.


text: GAUSS

text: public

text: ena-SAMPLE-TAB-16-04-2024-09:49:48:617-20644

text: DNA samples from herbarium voucher GOET042990

characteristic: description

text: Germany

text: Cult. Bot. Gard. Münster (orig Bot. Gard. Lyon)

text: not applicable

text: Xanthium spinosum

characteristic: plant developmental stage

text: not applicable

characteristic: plant growth medium

text: leaf

text: Xanthium spinosum


characteristic: ENA first public

text: GAUSS

text: public

text: ena-SAMPLE-TAB-16-04-2024-09:49:48:617-20645

text: DNA samples from herbarium voucher P04114960

text: France

characteristic: geographic location (country and/or sea)

text: Saint-Sulpice la Pointe; Toulouse

text: not applicable

text: Xanthium spinosum

text: not applicable

text: leaf

characteristic: plant structure

text: Xanthium spinosum


characteristic: ENA-CHECKLIST

text: GAUSS

characteristic: INSDC center name

text: public

text: ena-SAMPLE-TAB-16-04-2024-09:49:48:617-20646

text: DNA samples from herbarium voucher P04108168

text: France

text: Bédarieux; Hérault

text: not applicable

text: Xanthium spinosum

characteristic: organism

text: not applicable

text: leaf

text: Xanthium spinosum


text: GAUSS

text: public

characteristic: INSDC status

characteristic: SRA accession

text: ena-SAMPLE-TAB-16-04-2024-09:49:48:617-20647

characteristic: Submitter Id

text: DNA samples from herbarium voucher GOET042994

text: Uruguay

text: Miguelete; Dep. Montevideo

text: not applicable

text: Xanthium spinosum

text: not applicable

text: leaf

text: Xanthium spinosum


text: GAUSS

text: public

text: ena-SAMPLE-TAB-16-04-2024-09:49:48:617-20648

text: not provided

text: DNA samples from herbarium voucher GOET043082

characteristic: elevation

text: Germany

characteristic: geographic location (latitude)

text: Hannover Döhren

text: not applicable

text: Xanthium spinosum

text: not applicable

text: leaf

text: Xanthium spinosum

characteristic: title


text: GAUSS

text: public

text: ena-SAMPLE-TAB-16-04-2024-09:49:48:617-20649

characteristic: collection date

text: DNA samples from herbarium voucher GOET043085

text: Germany

characteristic: geographic location (longitude)

text: Hannover Döhren

characteristic: geographic location (region and locality)

text: not applicable

text: Xanthium spinosum

text: not applicable

text: leaf

text: Xanthium spinosum


text: GAUSS

text: public

text: ena-SAMPLE-TAB-16-04-2024-09:49:48:617-20650

text: DNA samples from herbarium voucher B101095040

characteristic: description

text: Germany

text: Dresden; Saxony

text: not applicable

characteristic: isolation and growth condition

text: Xanthium spinosum

characteristic: plant developmental stage

text: not applicable

text: leaf

text: Xanthium spinosum


characteristic: ENA first public

text: GAUSS

text: public

text: ena-SAMPLE-TAB-16-04-2024-09:49:48:617-20651

text: DNA samples from herbarium voucher PR240794

text: Spain

characteristic: geographic location (country and/or sea)

text: Madrid

text: not applicable

text: Xanthium spinosum

text: not applicable

characteristic: plant growth medium

text: leaf

text: Xanthium spinosum


characteristic: ENA-CHECKLIST

text: GAUSS

characteristic: INSDC center name

text: public

text: ena-SAMPLE-TAB-16-04-2024-09:49:48:617-20652

text: DNA samples from herbarium voucher P04115576

text: Spain

text: Gràcia; Barcelona

text: not applicable

text: Xanthium spinosum

text: not applicable

text: leaf

characteristic: plant structure

text: Xanthium spinosum


text: GAUSS

text: public

characteristic: INSDC status

characteristic: SRA accession

text: ena-SAMPLE-TAB-16-04-2024-09:49:48:617-20653

text: DNA samples from herbarium voucher BC39008

text: Spain

text: Lit du Besòs; Barcelona

text: not applicable

text: Xanthium spinosum

characteristic: organism

text: not applicable

text: leaf

text: Xanthium spinosum


text: GAUSS

text: public

text: ena-SAMPLE-TAB-16-04-2024-09:49:48:618-20654

characteristic: Submitter Id

text: DNA samples from herbarium voucher GOET061876

characteristic: elevation

text: Italy

characteristic: geographic location (latitude)

text: Ventimiglia; Sicily

text: not applicable

text: Xanthium spinosum

text: not applicable

text: leaf

text: Xanthium spinosum


text: GAUSS

text: public

text: ena-SAMPLE-TAB-16-04-2024-09:49:48:618-20655

characteristic: collection date

text: DNA samples from herbarium voucher GOET061879

text: Germany

characteristic: geographic location (longitude)

text: Cult. Bot. Gard. Göttingen

text: not applicable

text: Xanthium spinosum

text: not applicable

text: leaf

text: Xanthium spinosum

characteristic: title


text: GAUSS

text: public

text: ena-SAMPLE-TAB-16-04-2024-09:49:48:618-20656

text: DNA samples from herbarium voucher GOET061880

characteristic: description

text: Italy

text: Salerno; Campania

characteristic: geographic location (region and locality)

text: not applicable

characteristic: isolation and growth condition

text: Xanthium spinosum

text: not applicable

text: leaf

text: Xanthium spinosum


characteristic: ENA first public

text: GAUSS

text: public

text: ena-SAMPLE-TAB-16-04-2024-09:49:48:618-20658

text: DNA samples from herbarium voucher GOET043090

text: Portugal

characteristic: geographic location (country and/or sea)

text: Lisbon

text: not applicable

text: Xanthium spinosum

characteristic: plant developmental stage

text: not applicable

text: leaf

text: Xanthium spinosum


characteristic: ENA-CHECKLIST

text: GAUSS

characteristic: INSDC center name

text: public

text: ena-SAMPLE-TAB-16-04-2024-09:49:48:618-20659

text: DNA samples from herbarium voucher BA62708

text: Argentina

text: Avellaneda; Buenos Aires

text: not applicable

text: Xanthium spinosum

text: not applicable

characteristic: plant growth medium

text: leaf

text: Xanthium spinosum


text: GAUSS

text: public

characteristic: INSDC status

characteristic: SRA accession

text: ena-SAMPLE-TAB-16-04-2024-09:49:48:618-20660

text: not provided

text: DNA samples from herbarium voucher PR86412

text: Germany

text: Rheinland

text: not applicable

text: Xanthium spinosum

text: not applicable

text: leaf

characteristic: plant structure

text: Xanthium spinosum


text: GAUSS

text: public

text: ena-SAMPLE-TAB-16-04-2024-09:49:48:618-20662

characteristic: Submitter Id

text: DNA samples from herbarium voucher BC135959

characteristic: elevation

text: Spain

text: La Bordeta; Barcelona

text: not applicable

text: Xanthium spinosum

characteristic: organism

text: not applicable

text: leaf

text: Xanthium spinosum


text: GAUSS

text: public

text: ena-SAMPLE-TAB-16-04-2024-09:49:48:618-20663

characteristic: collection date

text: DNA samples from herbarium voucher B100261444

text: Argentina

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: San Agustin; Dep. Salta

text: not applicable

text: Xanthium spinosum

text: not applicable

text: leaf

text: Xanthium spinosum


text: GAUSS

text: public

text: ena-SAMPLE-TAB-16-04-2024-09:49:48:618-20664

text: DNA samples from herbarium voucher M-0158771

characteristic: description

text: Namibia

text: Avis Dam; Windhuk

characteristic: geographic location (region and locality)

text: not applicable

text: Xanthium spinosum

text: not applicable

text: leaf

text: Xanthium spinosum

characteristic: title


characteristic: ENA first public

text: GAUSS

text: public

text: ena-SAMPLE-TAB-16-04-2024-09:49:48:618-20665

text: DNA samples from herbarium voucher BA89509

text: Argentina

characteristic: geographic location (country and/or sea)

text: El Maiten

text: not applicable

characteristic: isolation and growth condition

text: Xanthium sp.

text: not applicable

text: leaf

text: Xanthium sp.


characteristic: ENA-CHECKLIST

text: GAUSS

characteristic: INSDC center name

text: public

text: ena-SAMPLE-TAB-16-04-2024-09:49:48:618-20666

text: DNA samples from herbarium voucher TEX00561301

text: Chile

text: San Carlos; Cartagena

text: not applicable

text: Xanthium sp.

characteristic: plant developmental stage

text: not applicable

text: leaf

text: Xanthium sp.


text: GAUSS

text: public

characteristic: INSDC status

characteristic: SRA accession

text: ena-SAMPLE-TAB-16-04-2024-09:49:48:618-20667

text: cocklebur

characteristic: common name

text: DNA samples from herbarium voucher B100618346

text: France

text: Strasbourg

text: not applicable

text: Xanthium strumarium

text: not applicable

characteristic: plant growth medium

text: leaf

text: Xanthium strumarium


text: UNIVERSITY COLLEGE CORK

text: public

characteristic: Submitter Id

text: PCR blank

text: Ireland

characteristic: host scientific name

text: feces metagenome

characteristic: organism

text: feces metagenome

text: PCR blank


text: UNIVERSITY COLLEGE CORK

text: public

characteristic: collection date

text: extraction blank

text: Ireland

text: feces metagenome

text: feces metagenome

text: extraction blank


text: UNIVERSITY COLLEGE CORK

text: public

text: great tit feces sample

characteristic: description

text: Ireland

text: Parus major

text: feces metagenome

text: feces metagenome

text: great tit feces sample


text: UNIVERSITY COLLEGE CORK

text: public

text: control sample

text: Ireland

text: feces metagenome

text: feces metagenome

text: control sample


text: UNIVERSITY COLLEGE CORK

text: public

text: mealworm sample stored in ethanol

text: Ireland

text: Tenebrio molitor

text: feces metagenome

text: feces metagenome

text: mealworm sample


text: UNIVERSITY COLLEGE CORK

text: public

text: mealworm sample stored without ethanol

text: Ireland

text: Tenebrio molitor

text: feces metagenome

text: feces metagenome

text: mealworm sample


text: National Bioinformatics Infrastructure Sweden

text: public

characteristic: broker name

text: Anna-Lisa Wrange

text: Cyprid larvae subjected to high salinity (33 PSU) and normal CO2 concentration (380 ppm)

text: cyprid larvae

text: Sweden

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: Bohuslän, Tjärnö

characteristic: geographic location (region and locality)

text: Amphibalanus improvisus

text: Amphibalanus improvisus


characteristic: ENA first public

text: public

text: Anna-Lisa Wrange

text: Cyprid larvae subjected to low salinity (6 PSU) and normal CO2 concentration (380 ppm)

text: cyprid larvae

text: Sweden

characteristic: geographic location (country and/or sea)

text: Bohuslän, Tjärnö

text: Amphibalanus improvisus

text: Amphibalanus improvisus

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: INSDC center name

text: public

text: Anna-Lisa Wrange

text: Cyprid larvae subjected to high salinity (33 PSU) and high CO2 concentration (970 ppm)

text: cyprid larvae

text: Sweden

text: Bohuslän, Tjärnö

text: Amphibalanus improvisus

text: Amphibalanus improvisus


text: public

characteristic: INSDC status

characteristic: SRA accession

text: Anna-Lisa Wrange

text: Cyprid larvae subjected to low salinity (6 PSU) and high CO2 concentration (970 ppm)

text: cyprid larvae

text: Sweden

text: Bohuslän, Tjärnö

text: Amphibalanus improvisus

text: Amphibalanus improvisus


text: IMCB

text: public

text: Immediate ancestor of the surface exposure evolution experiment in high-organic humid conditions.

text: Estonia

text: Escherichia coli ATCC 8739

text: Escherichia coli ATCC 8739

text: ATCC 8739

characteristic: strain


text: IMCB

text: public

characteristic: Submitter Id

text: Population exposed to copper surface in high-organic humid conditions after 30 exposure cycles.

text: Estonia

text: Escherichia coli ATCC 8739

text: Escherichia coli ATCC 8739

text: ATCC 8739


text: IMCB

text: public

text: Population exposed to silver surface in high-organic humid conditions after 30 exposure cycles.

text: Estonia

text: Escherichia coli ATCC 8739

text: Escherichia coli ATCC 8739

text: ATCC 8739


text: IMCB

text: public

text: Population exposed to stainless steel surface in high-organic humid conditions after 30 exposure cycles.

text: Estonia

text: Escherichia coli ATCC 8739

text: Escherichia coli ATCC 8739

text: ATCC 8739


text: IMCB

text: public

text: Population exposed to  glass surface in high-organic humid conditions after 30 exposure cycles.

text: Estonia

text: Escherichia coli ATCC 8739

text: Escherichia coli ATCC 8739

text: ATCC 8739


text: IMCB

text: public

text: Immediate ancestor of the surface exposure evolution experiment in low-organic dry conditions.

text: Estonia

text: Escherichia coli ATCC 8739

text: Escherichia coli ATCC 8739

text: ATCC 8739


text: IMCB

text: public

text: Population exposed to  copper surface in low-organic dry conditions after 30 exposure cycles.

text: Estonia

text: Escherichia coli ATCC 8739

text: Escherichia coli ATCC 8739

text: ATCC 8739


text: IMCB

text: public

text: Population exposed to  silver surface in low-organic dry conditions after 30 exposure cycles.

text: Estonia

text: Escherichia coli ATCC 8739

text: Escherichia coli ATCC 8739

text: ATCC 8739


text: IMCB

text: public

text: Population exposed to  stainless steel surface in low-organic dry conditions after 30 exposure cycles.

text: Estonia

text: Escherichia coli ATCC 8739

text: Escherichia coli ATCC 8739

text: ATCC 8739


text: IMCB

text: public

text: Population exposed to glass surface in low-organic dry conditions after 30 exposure cycles.

text: Estonia

text: Escherichia coli ATCC 8739

text: Escherichia coli ATCC 8739

text: ATCC 8739


text: IMCB

text: public

text: Silver and copper tolerant isolate isolated post evolution experiment from an MBC assay.

text: Estonia

text: Escherichia coli ATCC 8739

text: Escherichia coli ATCC 8739

text: ATCC 8739


text: IMCB

text: public

text: TnaA M266I mutation carrying isolate isolated post evolution experiment from population evolvedon silver surface.

text: Estonia

text: Escherichia coli ATCC 8739

text: Escherichia coli ATCC 8739

text: ATCC 8739


text: IMCB

text: public

text: IS-disrupted ydjN mutation carrying isolate isolated post evolution experiment from population evolvedon silver surface.

text: Estonia

text: Escherichia coli ATCC 8739

text: Escherichia coli ATCC 8739

text: ATCC 8739


text: FUNCTIONAL GENOMICS CENTER ZURICH

text: public

text: human

characteristic: common name

text: Switzerland

text: Homo sapiens

text: Homo sapiens


E-MTAB-13967:Sample 1

text: Quadram Institute Biosciences

text: public

text: E-MTAB-13967:Sample 1

text: ArrayExpress

text: not collected

text: Protocols: Each preservative stress condition was made up of eight lineages: two preservative-exposed planktonic lineages (P1 and P2), two unexposed biofilm lineages (C1 and C2), and four exposed biofilm lineages (A, B, C, D) (Trampari et al., 2021). Biofilm lineages were comprised of three 5 mm stainless steel beads (from Simply Bearings) in 5 mL LB broth without salt. Planktonic lineages were set up the same but did not contain beads. Approximately 10^5 CFU/mL of Salmonella enterica subsp. enterica serovar Typhimurium strain 14028S was inoculated into each condition and cultures were incubated at 30°C for 72 hrs horizontally with mild agitation at 40 rpm. Cultures were exposed to preservatives at subinhibitory concentrations, corresponding to 5% Sodium chloride, 7 % Potassium chloride, 5 % Sodium lactate or 0.06 % Sodium nitrite. Subinhibitory concentrations were selected as those that inhibited the growth of S. Typhimurium by 25-35 %.   Cultures were passaged into new media every 72 hours. For biofilm lineages, one steel bead was washed in sterile PBS and transferred to fresh media to seed the next passage. For planktonic conditions, 5 µL of culture was added to fresh media. A sample of each condition was stored at each passage: this consisted of 1 mL of planktonic culture or one bead from the biofilm lineages. Beads were washed with sterile PBS to remove planktonic cells and vortexed in fresh sterile PBS to resuspend the biofilm. Both planktonic cultures and resuspended biofilms were mixed with 7.5 % DMSO and stored at -20 °C. To prepare cultures for DNA extraction, frozen stocks were inoculated in 5 mL LB broth and grown for 18 hours at 37 °C with shaking. To extract genomic DNA for sequencing, selected strains were grown O/N in a 96-deep-well plate in LB, at a final volume of 1.5 mL. Cells were recovered by centrifugation at 3500 × g and were resuspended in 100 μL of lysis buffer (5 μg/mL lysozyme, 0.1 mg/mL RNAse in Tris-EDTA, pH 8) per well. The resuspended cells were then transferred in a new semi-skirted, low-bind polymerase chain reaction (PCR) plate, secured with an adhesive seal and incubated at 37 °C, 550 × g for 25 min. Ten microliters of a lysis additive buffer (5% sodium dodecyl sulfate, 1 mg/mL proteinase K, 1 mg/mL RNAse in Tris-EDTA, pH 8) was added to each well and the plate was sealed with PCR strip lids before being incubated at 65 °C, 550 × g for 25 min. The plate was briefly centrifuged and 100 μL were moved to a new PCR plate. For the DNA isolation, 50 μL of DNA-binding magnetic beads (KAPA Pure Beads, Roche Diagnostics) were added to each well and were incubated at room temperature for 5 min. The plate was then placed on a magnetic base and the supernatant was removed by pipetting. The beads were washed three times with 80% freshly prepared ethanol. After removing the last wash, the beads were left to dry for 2 min before eluting the DNA. For the DNA elution, the plate was removed from the magnetic apparatus and 50 μL of 10 mM Tris-Cl, pH 8.5, were added to each well. The beads were pulled using the magnetic apparatus and the isolated DNA was transferred to a new PCR plate. DNA concentration was determined using the Qubit ds DNA HS Assay Kit (Q32851) following the manufacturer’s instructions. Genomic DNA was normalised to 0.5 ng/µL with 10 mM Tris-HCl. A measure of 0.9 µL of TD Tagment DNA Buffer (Illumina, Catalogue No. 15027866) was mixed with 0.09 µL TDE1, Tagment DNA Enzyme (Illumina, Catalogue No. 15027865) and 2.01 µL PCR grade water in a master mix and 3 µl added to a chilled 96-well plate. Two microlitres of normalised DNA (1 ng total) was mixed with the 3 µL of the Tagmentation mix and heated to 55 °C for 10 min in a PCR block. A PCR master mix was made up using 4 µl KAPA2G buffer, 0.4 µL dNTPs, 0.08 µL polymerase and 4.52 µL PCR grade water, contained in the KAPA2G Robust PCR Kit (Sigma, Catalogue No. KK5005) per sample and 11 µL added to each well need to be used in a 96-well plate. Two microlitres of each P7 and P5 of Nextera XT Index Kit v2 index primers (Illumina, Catalogue No. FC-131-2001 to 2004) were added to each well. Finally, the 5 µL Tagmentation mix was added and mixed. The PCR was run with 72 °C for 3 min, 95 °C for 1 min, 14 cycles of 95 °C for 10 s, 55 °C for 20 s and 72 °C for 3 min. Following the PCR reaction, the libraries were quantified using the Quant-iT dsDNA Assay Kit, High-Sensitivity Kit (Catalogue No. 10164582) and run on a FLUOstar Optima plate reader. Libraries were pooled following quantification in equal quantities. The final pool was double-SPRI size selected between 0.5 and 0.7× bead volumes using KAPA Pure Beads (Roche, Catalogue No. 07983298001). The final pool was quantified on a Qubit 3.0 instrument and run on a High Sensitivity D1000 ScreenTape (Agilent, Catalogue No. 5067-5579) using the Agilent Tapestation 4200 to calculate the final library pool molarity.

text: not collected

text: Sodium chloride

characteristic: growth condition

text: not applicable

characteristic: isolate

text: Salmonella enterica

characteristic: organism

text: Salmonella enterica

text: whole organism

characteristic: organism part

text: Biofilm

characteristic: phenotype

text: A

characteristic: replicate

text: Salmonella enterica

text: Sample 1


E-MTAB-13967:Sample 10

text: Quadram Institute Biosciences

text: public

text: E-MTAB-13967:Sample 10

text: ArrayExpress

characteristic: broker name

text: not collected

characteristic: collection date

characteristic: description

text: not collected

text: Untreated

text: not applicable

text: Salmonella enterica

text: Salmonella enterica

text: whole organism

text: Biofilm

text: Salmonella enterica

text: Salmonella enterica subsp. enterica serovar Typhimurium

text: Sample 10


E-MTAB-13967:Sample 11

characteristic: ENA first public

text: Quadram Institute Biosciences

text: public

text: E-MTAB-13967:Sample 11

text: ArrayExpress

text: not collected

text: not collected

characteristic: geographic location (country and/or sea)

text: Untreated

text: not applicable

text: Salmonella enterica

text: Salmonella enterica

text: whole organism

text: Biofilm

text: Salmonella enterica

text: Sample 11

characteristic: title


E-MTAB-13967:Sample 12

characteristic: ENA-CHECKLIST

text: Quadram Institute Biosciences

characteristic: INSDC center name

text: public

characteristic: INSDC status

text: E-MTAB-13967:Sample 12

text: ArrayExpress

text: not collected

text: not collected

text: Untreated

text: not applicable

text: Salmonella enterica

text: Salmonella enterica

text: whole organism

text: Biofilm

text: Salmonella enterica

text: Sample 12


E-MTAB-13967:Sample 13

text: Quadram Institute Biosciences

text: public

characteristic: SRA accession

text: E-MTAB-13967:Sample 13

characteristic: Submitter Id

text: ArrayExpress

text: not collected

text: not collected

text: Sodium chloride

text: not applicable

text: Salmonella enterica

text: Salmonella enterica

text: whole organism

text: Planktonic

text: Salmonella enterica

characteristic: strain

text: Sample 13


E-MTAB-13967:Sample 14

text: Quadram Institute Biosciences

text: public

text: E-MTAB-13967:Sample 14

text: ArrayExpress

text: not collected

text: not collected

text: Sodium chloride

characteristic: growth condition

text: not applicable

characteristic: isolate

text: Salmonella enterica

text: Salmonella enterica

text: whole organism

text: Planktonic

text: Salmonella enterica

text: Sample 14


E-MTAB-13967:Sample 15

text: Quadram Institute Biosciences

text: public

text: E-MTAB-13967:Sample 15

text: ArrayExpress

text: not collected

text: not collected

text: Sodium chloride

text: not applicable

text: Salmonella enterica

characteristic: organism

text: Salmonella enterica

text: whole organism

characteristic: organism part

text: Planktonic

text: Salmonella enterica

text: Sample 15


E-MTAB-13967:Sample 16

text: Quadram Institute Biosciences

text: public

text: E-MTAB-13967:Sample 16

text: ArrayExpress

text: not collected

text: not collected

text: Sodium chloride

text: not applicable

text: Salmonella enterica

text: Salmonella enterica

text: whole organism

text: Planktonic

characteristic: phenotype

characteristic: replicate

text: Salmonella enterica

text: Sample 16


E-MTAB-13967:Sample 17

text: Quadram Institute Biosciences

text: public

text: E-MTAB-13967:Sample 17

text: ArrayExpress

characteristic: broker name

text: not collected

characteristic: collection date

text: not collected

text: Potassium chloride

text: not applicable

text: Salmonella enterica

text: Salmonella enterica

text: whole organism

text: Biofilm

text: A

text: Salmonella enterica

text: Sample 17


E-MTAB-13967:Sample 18

characteristic: ENA first public

text: Quadram Institute Biosciences

text: public

text: E-MTAB-13967:Sample 18

text: ArrayExpress

text: not collected

characteristic: description

text: not collected

text: Potassium chloride

text: not applicable

text: Salmonella enterica

text: Salmonella enterica

text: whole organism

text: Biofilm

text: A

text: Salmonella enterica

text: Sample 18


E-MTAB-13967:Sample 19

text: Quadram Institute Biosciences

text: public

text: E-MTAB-13967:Sample 19

text: ArrayExpress

text: not collected

text: not collected

characteristic: geographic location (country and/or sea)

text: Potassium chloride

text: not applicable

text: Salmonella enterica

text: Salmonella enterica

text: whole organism

text: Biofilm

text: B

text: Salmonella enterica

text: Sample 19

characteristic: title


E-MTAB-13967:Sample 2

characteristic: ENA-CHECKLIST

text: Quadram Institute Biosciences

characteristic: INSDC center name

text: public

text: E-MTAB-13967:Sample 2

text: ArrayExpress

text: not collected

text: not collected

text: Sodium chloride

text: not applicable

text: Salmonella enterica

text: Salmonella enterica

text: whole organism

text: Biofilm

text: A

text: Salmonella enterica

text: Sample 2


E-MTAB-13967:Sample 20

text: Quadram Institute Biosciences

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-13967:Sample 20

text: ArrayExpress

text: not collected

text: not collected

text: Potassium chloride

text: not applicable

text: Salmonella enterica

text: Salmonella enterica

text: whole organism

text: Biofilm

text: B

text: Salmonella enterica

text: Sample 20


E-MTAB-13967:Sample 21

text: Quadram Institute Biosciences

text: public

text: E-MTAB-13967:Sample 21

characteristic: Submitter Id

text: ArrayExpress

text: not collected

text: not collected

text: Potassium chloride

text: not applicable

text: Salmonella enterica

text: Salmonella enterica

text: whole organism

text: Biofilm

text: C

text: Salmonella enterica

characteristic: strain

text: Sample 21


E-MTAB-13967:Sample 22

text: Quadram Institute Biosciences

text: public

text: E-MTAB-13967:Sample 22

text: ArrayExpress

text: not collected

text: not collected

text: Potassium chloride

characteristic: growth condition

text: not applicable

characteristic: isolate

text: Salmonella enterica

text: Salmonella enterica

text: whole organism

text: Biofilm

text: C

text: Salmonella enterica

text: Sample 22


E-MTAB-13967:Sample 23

text: Quadram Institute Biosciences

text: public

text: E-MTAB-13967:Sample 23

text: ArrayExpress

text: not collected

text: not collected

text: Potassium chloride

text: not applicable

text: Salmonella enterica

characteristic: organism

text: Salmonella enterica

text: whole organism

characteristic: organism part

text: Biofilm

text: D

text: Salmonella enterica

text: Sample 23


E-MTAB-13967:Sample 24

text: Quadram Institute Biosciences

text: public

text: E-MTAB-13967:Sample 24

text: ArrayExpress

text: not collected

text: not collected

text: Potassium chloride

text: not applicable

text: Salmonella enterica

text: Salmonella enterica

text: whole organism

text: Biofilm

characteristic: phenotype

text: D

characteristic: replicate

text: Salmonella enterica

text: Sample 24


E-MTAB-13967:Sample 25

text: Quadram Institute Biosciences

text: public

text: E-MTAB-13967:Sample 25

text: ArrayExpress

characteristic: broker name

text: not collected

characteristic: collection date

text: not collected

text: Untreated

text: not applicable

text: Salmonella enterica

text: Salmonella enterica

text: whole organism

text: Biofilm

text: Salmonella enterica

text: Sample 25


E-MTAB-13967:Sample 26

characteristic: ENA first public

text: Quadram Institute Biosciences

text: public

text: E-MTAB-13967:Sample 26

text: ArrayExpress

text: not collected

characteristic: description

text: not collected

text: Untreated

text: not applicable

text: Salmonella enterica

text: Salmonella enterica

text: whole organism

text: Biofilm

text: Salmonella enterica

text: Sample 26


E-MTAB-13967:Sample 27

text: Quadram Institute Biosciences

text: public

text: E-MTAB-13967:Sample 27

text: ArrayExpress

text: not collected

text: not collected

characteristic: geographic location (country and/or sea)

text: Untreated

text: not applicable

text: Salmonella enterica

text: Salmonella enterica

text: whole organism

text: Biofilm

text: Salmonella enterica

text: Sample 27

characteristic: title


E-MTAB-13967:Sample 28

characteristic: ENA-CHECKLIST

text: Quadram Institute Biosciences

characteristic: INSDC center name

text: public

text: E-MTAB-13967:Sample 28

text: ArrayExpress

text: not collected

text: not collected

text: Untreated

text: not applicable

text: Salmonella enterica

text: Salmonella enterica

text: whole organism

text: Biofilm

text: Salmonella enterica

text: Sample 28


E-MTAB-13967:Sample 29

text: Quadram Institute Biosciences

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-13967:Sample 29

text: ArrayExpress

text: not collected

text: not collected

text: Potassium chloride

text: not applicable

text: Salmonella enterica

text: Salmonella enterica

text: whole organism

text: Planktonic

text: Salmonella enterica

text: Sample 29


E-MTAB-13967:Sample 3

text: Quadram Institute Biosciences

text: public

text: E-MTAB-13967:Sample 3

characteristic: Submitter Id

text: ArrayExpress

text: not collected

text: not collected

text: Sodium chloride

text: not applicable

text: Salmonella enterica

text: Salmonella enterica

text: whole organism

text: Biofilm

text: B

text: Salmonella enterica

characteristic: strain

text: Sample 3


E-MTAB-13967:Sample 30

text: Quadram Institute Biosciences

text: public

text: E-MTAB-13967:Sample 30

text: ArrayExpress

text: not collected

text: not collected

text: Potassium chloride

characteristic: growth condition

text: not applicable

characteristic: isolate

text: Salmonella enterica

text: Salmonella enterica

text: whole organism

text: Planktonic

text: Salmonella enterica

text: Sample 30


E-MTAB-13967:Sample 31

text: Quadram Institute Biosciences

text: public

text: E-MTAB-13967:Sample 31

text: ArrayExpress

text: not collected

text: not collected

text: Potassium chloride

text: not applicable

text: Salmonella enterica

characteristic: organism

text: Salmonella enterica

text: whole organism

characteristic: organism part

text: Planktonic

text: Salmonella enterica

text: Sample 31


E-MTAB-13967:Sample 32

text: Quadram Institute Biosciences

text: public

text: E-MTAB-13967:Sample 32

text: ArrayExpress

text: not collected

text: not collected

text: Potassium chloride

text: not applicable

text: Salmonella enterica

text: Salmonella enterica

text: whole organism

text: Planktonic

characteristic: phenotype

characteristic: replicate

text: Salmonella enterica

text: Sample 32


E-MTAB-13967:Sample 33

text: Quadram Institute Biosciences

text: public

text: E-MTAB-13967:Sample 33

text: ArrayExpress

characteristic: broker name

text: not collected

characteristic: collection date

text: not collected

text: Sodium nitrite

text: not applicable

text: Salmonella enterica

text: Salmonella enterica

text: whole organism

text: Biofilm

text: A

text: Salmonella enterica

text: Sample 33


E-MTAB-13967:Sample 34

characteristic: ENA first public

text: Quadram Institute Biosciences

text: public

text: E-MTAB-13967:Sample 34

text: ArrayExpress

text: not collected

characteristic: description

text: not collected

text: Sodium nitrite

text: not applicable

text: Salmonella enterica

text: Salmonella enterica

text: whole organism

text: Biofilm

text: A

text: Salmonella enterica

text: Sample 34


E-MTAB-13967:Sample 35

text: Quadram Institute Biosciences

text: public

text: E-MTAB-13967:Sample 35

text: ArrayExpress

text: not collected

text: not collected

characteristic: geographic location (country and/or sea)

text: Sodium nitrite

text: not applicable

text: Salmonella enterica

text: Salmonella enterica

text: whole organism

text: Biofilm

text: B

text: Salmonella enterica

text: Sample 35

characteristic: title


E-MTAB-13967:Sample 36

characteristic: ENA-CHECKLIST

text: Quadram Institute Biosciences

characteristic: INSDC center name

text: public

text: E-MTAB-13967:Sample 36

text: ArrayExpress

text: not collected

text: not collected

text: Sodium nitrite

text: not applicable

text: Salmonella enterica

text: Salmonella enterica

text: whole organism

text: Biofilm

text: B

text: Salmonella enterica

text: Sample 36


E-MTAB-13967:Sample 37

text: Quadram Institute Biosciences

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-13967:Sample 37

text: ArrayExpress

text: not collected

text: not collected

text: Sodium nitrite

text: not applicable

text: Salmonella enterica

text: Salmonella enterica

text: whole organism

text: Biofilm

text: C

text: Salmonella enterica

text: Sample 37


E-MTAB-13967:Sample 38

text: Quadram Institute Biosciences

text: public

text: E-MTAB-13967:Sample 38

characteristic: Submitter Id

text: ArrayExpress

text: not collected

text: not collected

text: Sodium nitrite

text: not applicable

text: Salmonella enterica

text: Salmonella enterica

text: whole organism

text: Biofilm

text: C

text: Salmonella enterica

characteristic: strain

text: Sample 38


E-MTAB-13967:Sample 39

text: Quadram Institute Biosciences

text: public

text: E-MTAB-13967:Sample 39

text: ArrayExpress

text: not collected

text: not collected

text: Sodium nitrite

characteristic: growth condition

text: not applicable

characteristic: isolate

text: Salmonella enterica

text: Salmonella enterica

text: whole organism

text: Biofilm

text: D

text: Salmonella enterica

text: Sample 39


E-MTAB-13967:Sample 4

text: Quadram Institute Biosciences

text: public

text: E-MTAB-13967:Sample 4

text: ArrayExpress

text: not collected

text: not collected

text: Sodium chloride

text: not applicable

text: Salmonella enterica

characteristic: organism

text: Salmonella enterica

text: whole organism

characteristic: organism part

text: Biofilm

text: B

text: Salmonella enterica

text: Sample 4


E-MTAB-13967:Sample 40

text: Quadram Institute Biosciences

text: public

text: E-MTAB-13967:Sample 40

text: ArrayExpress

text: not collected

text: not collected

text: Sodium nitrite

text: not applicable

text: Salmonella enterica

text: Salmonella enterica

text: whole organism

text: Biofilm

characteristic: phenotype

text: D

characteristic: replicate

text: Salmonella enterica

text: Sample 40


E-MTAB-13967:Sample 41

text: Quadram Institute Biosciences

text: public

text: E-MTAB-13967:Sample 41

text: ArrayExpress

characteristic: broker name

text: not collected

characteristic: collection date

text: not collected

text: Untreated

text: not applicable

text: Salmonella enterica

text: Salmonella enterica

text: whole organism

text: Biofilm

text: Salmonella enterica

text: Sample 41


E-MTAB-13967:Sample 42

characteristic: ENA first public

text: Quadram Institute Biosciences

text: public

text: E-MTAB-13967:Sample 42

text: ArrayExpress

text: not collected

characteristic: description

text: not collected

text: Untreated

text: not applicable

text: Salmonella enterica

text: Salmonella enterica

text: whole organism

text: Biofilm

text: Salmonella enterica

text: Sample 42


E-MTAB-13967:Sample 43

text: Quadram Institute Biosciences

text: public

text: E-MTAB-13967:Sample 43

text: ArrayExpress

text: not collected

text: not collected

characteristic: geographic location (country and/or sea)

text: Untreated

text: not applicable

text: Salmonella enterica

text: Salmonella enterica

text: whole organism

text: Biofilm

text: Salmonella enterica

text: Sample 43

characteristic: title


E-MTAB-13967:Sample 44

characteristic: ENA-CHECKLIST

text: Quadram Institute Biosciences

characteristic: INSDC center name

text: public

text: E-MTAB-13967:Sample 44

text: ArrayExpress

text: not collected

text: not collected

text: Untreated

text: not applicable

text: Salmonella enterica

text: Salmonella enterica

text: whole organism

text: Biofilm

text: Salmonella enterica

text: Sample 44


E-MTAB-13967:Sample 45

text: Quadram Institute Biosciences

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-13967:Sample 45

text: ArrayExpress

text: not collected

text: not collected

text: Sodium nitrite

text: not applicable

text: Salmonella enterica

text: Salmonella enterica

text: whole organism

text: Planktonic

text: Salmonella enterica

text: Sample 45


E-MTAB-13967:Sample 46

text: Quadram Institute Biosciences

text: public

text: E-MTAB-13967:Sample 46

characteristic: Submitter Id

text: ArrayExpress

text: not collected

text: not collected

text: Sodium nitrite

text: not applicable

text: Salmonella enterica

text: Salmonella enterica

text: whole organism

text: Planktonic

text: Salmonella enterica

characteristic: strain

text: Sample 46


E-MTAB-13967:Sample 47

text: Quadram Institute Biosciences

text: public

text: E-MTAB-13967:Sample 47

text: ArrayExpress

text: not collected

text: not collected

text: Sodium nitrite

characteristic: growth condition

text: not applicable

characteristic: isolate

text: Salmonella enterica

text: Salmonella enterica

text: whole organism

text: Planktonic

text: Salmonella enterica

text: Sample 47


E-MTAB-13967:Sample 48

text: Quadram Institute Biosciences

text: public

text: E-MTAB-13967:Sample 48

text: ArrayExpress

text: not collected

text: not collected

text: Sodium nitrite

text: not applicable

text: Salmonella enterica

characteristic: organism

text: Salmonella enterica

text: whole organism

characteristic: organism part

text: Planktonic

text: Salmonella enterica

text: Sample 48


E-MTAB-13967:Sample 49

text: Quadram Institute Biosciences

text: public

text: E-MTAB-13967:Sample 49

text: ArrayExpress

text: not collected

text: not collected

text: Sodium lactate

text: not applicable

text: Salmonella enterica

text: Salmonella enterica

text: whole organism

text: Biofilm

characteristic: phenotype

text: A

characteristic: replicate

text: Salmonella enterica

text: Sample 49


E-MTAB-13967:Sample 5

text: Quadram Institute Biosciences

text: public

text: E-MTAB-13967:Sample 5

text: ArrayExpress

characteristic: broker name

text: not collected

characteristic: collection date

text: not collected

text: Sodium chloride

text: not applicable

text: Salmonella enterica

text: Salmonella enterica

text: whole organism

text: Biofilm

text: C

text: Salmonella enterica

text: Sample 5


E-MTAB-13967:Sample 50

characteristic: ENA first public

text: Quadram Institute Biosciences

text: public

text: E-MTAB-13967:Sample 50

text: ArrayExpress

text: not collected

characteristic: description

text: not collected

text: Sodium lactate

text: not applicable

text: Salmonella enterica

text: Salmonella enterica

text: whole organism

text: Biofilm

text: A

text: Salmonella enterica

text: Sample 50


E-MTAB-13967:Sample 51

text: Quadram Institute Biosciences

text: public

text: E-MTAB-13967:Sample 51

text: ArrayExpress

text: not collected

text: not collected

characteristic: geographic location (country and/or sea)

text: Sodium lactate

text: not applicable

text: Salmonella enterica

text: Salmonella enterica

text: whole organism

text: Biofilm

text: B

text: Salmonella enterica

text: Sample 51

characteristic: title


E-MTAB-13967:Sample 52

characteristic: ENA-CHECKLIST

text: Quadram Institute Biosciences

characteristic: INSDC center name

text: public

text: E-MTAB-13967:Sample 52

text: ArrayExpress

text: not collected

text: not collected

text: Sodium lactate

text: not applicable

text: Salmonella enterica

text: Salmonella enterica

text: whole organism

text: Biofilm

text: B

text: Salmonella enterica

text: Sample 52


E-MTAB-13967:Sample 53

text: Quadram Institute Biosciences

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-13967:Sample 53

text: ArrayExpress

text: not collected

text: not collected

text: Sodium lactate

text: not applicable

text: Salmonella enterica

text: Salmonella enterica

text: whole organism

text: Biofilm

text: C

text: Salmonella enterica

text: Sample 53


E-MTAB-13967:Sample 54

text: Quadram Institute Biosciences

text: public

text: E-MTAB-13967:Sample 54

characteristic: Submitter Id

text: ArrayExpress

text: not collected

text: not collected

text: Sodium lactate

text: not applicable

text: Salmonella enterica

text: Salmonella enterica

text: whole organism

text: Biofilm

text: C

text: Salmonella enterica

characteristic: strain

text: Sample 54


E-MTAB-13967:Sample 55

text: Quadram Institute Biosciences

text: public

text: E-MTAB-13967:Sample 55

text: ArrayExpress

text: not collected

text: not collected

text: Sodium lactate

characteristic: growth condition

text: not applicable

characteristic: isolate

text: Salmonella enterica

text: Salmonella enterica

text: whole organism

text: Biofilm

text: D

text: Salmonella enterica

text: Sample 55


E-MTAB-13967:Sample 56

text: Quadram Institute Biosciences

text: public

text: E-MTAB-13967:Sample 56

text: ArrayExpress

text: not collected

text: not collected

text: Sodium lactate

text: not applicable

text: Salmonella enterica

characteristic: organism

text: Salmonella enterica

text: whole organism

characteristic: organism part

text: Biofilm

text: D

text: Salmonella enterica

text: Sample 56


E-MTAB-13967:Sample 57

text: Quadram Institute Biosciences

text: public

text: E-MTAB-13967:Sample 57

text: ArrayExpress

text: not collected

text: not collected

text: Untreated

text: not applicable

text: Salmonella enterica

text: Salmonella enterica

text: whole organism

text: Biofilm

characteristic: phenotype

characteristic: replicate

text: Salmonella enterica

text: Sample 57


E-MTAB-13967:Sample 58

text: Quadram Institute Biosciences

text: public

text: E-MTAB-13967:Sample 58

text: ArrayExpress

characteristic: broker name

text: not collected

characteristic: collection date

text: not collected

text: Untreated

text: not applicable

text: Salmonella enterica

text: Salmonella enterica

text: whole organism

text: Biofilm

text: Salmonella enterica

text: Sample 58


E-MTAB-13967:Sample 59

characteristic: ENA first public

text: Quadram Institute Biosciences

text: public

text: E-MTAB-13967:Sample 59

text: ArrayExpress

text: not collected

characteristic: description

text: not collected

text: Untreated

text: not applicable

text: Salmonella enterica

text: Salmonella enterica

text: whole organism

text: Biofilm

text: Salmonella enterica

text: Sample 59


E-MTAB-13967:Sample 6

text: Quadram Institute Biosciences

text: public

text: E-MTAB-13967:Sample 6

text: ArrayExpress

text: not collected

text: not collected

characteristic: geographic location (country and/or sea)

text: Sodium chloride

text: not applicable

text: Salmonella enterica

text: Salmonella enterica

text: whole organism

text: Biofilm

text: C

text: Salmonella enterica

text: Sample 6

characteristic: title


E-MTAB-13967:Sample 60

characteristic: ENA-CHECKLIST

text: Quadram Institute Biosciences

characteristic: INSDC center name

text: public

text: E-MTAB-13967:Sample 60

text: ArrayExpress

text: not collected

text: not collected

text: Untreated

text: not applicable

text: Salmonella enterica

text: Salmonella enterica

text: whole organism

text: Biofilm

text: Salmonella enterica

text: Sample 60


E-MTAB-13967:Sample 61

text: Quadram Institute Biosciences

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-13967:Sample 61

text: ArrayExpress

text: not collected

text: not collected

text: Sodium lactate

text: not applicable

text: Salmonella enterica

text: Salmonella enterica

text: whole organism

text: Planktonic

text: Salmonella enterica

text: Sample 61


E-MTAB-13967:Sample 62

text: Quadram Institute Biosciences

text: public

text: E-MTAB-13967:Sample 62

characteristic: Submitter Id

text: ArrayExpress

text: not collected

text: not collected

text: Sodium lactate

text: not applicable

text: Salmonella enterica

text: Salmonella enterica

text: whole organism

text: Planktonic

text: Salmonella enterica

characteristic: strain

text: Sample 62


E-MTAB-13967:Sample 63

text: Quadram Institute Biosciences

text: public

text: E-MTAB-13967:Sample 63

text: ArrayExpress

text: not collected

text: not collected

text: Sodium lactate

characteristic: growth condition

text: not applicable

characteristic: isolate

text: Salmonella enterica

text: Salmonella enterica

text: whole organism

text: Planktonic

text: Salmonella enterica

text: Sample 63


E-MTAB-13967:Sample 64

text: Quadram Institute Biosciences

text: public

text: E-MTAB-13967:Sample 64

text: ArrayExpress

text: not collected

text: not collected

text: Sodium lactate

text: not applicable

text: Salmonella enterica

characteristic: organism

text: Salmonella enterica

text: whole organism

characteristic: organism part

text: Planktonic

text: Salmonella enterica

text: Sample 64


E-MTAB-13967:Sample 7

text: Quadram Institute Biosciences

text: public

text: E-MTAB-13967:Sample 7

text: ArrayExpress

text: not collected

text: not collected

text: Sodium chloride

text: not applicable

text: Salmonella enterica

text: Salmonella enterica

text: whole organism

text: Biofilm

characteristic: phenotype

text: D

characteristic: replicate

text: Salmonella enterica

text: Sample 7


E-MTAB-13967:Sample 8

text: Quadram Institute Biosciences

text: public

text: E-MTAB-13967:Sample 8

text: ArrayExpress

characteristic: broker name

text: not collected

characteristic: collection date

text: not collected

text: Sodium chloride

text: not applicable

text: Salmonella enterica

text: Salmonella enterica

text: whole organism

text: Biofilm

text: D

text: Salmonella enterica

text: Sample 8


E-MTAB-13967:Sample 9

characteristic: ENA first public

text: Quadram Institute Biosciences

text: public

text: E-MTAB-13967:Sample 9

text: ArrayExpress

text: not collected

characteristic: description

text: not collected

text: Untreated

text: not applicable

text: Salmonella enterica

text: Salmonella enterica

text: whole organism

text: Biofilm

text: Salmonella enterica

text: Sample 9


text: School of Medicine, Cardiff University, UK UK Dementia Research Institute, Cardiff University, Cardiff

text: public

unit: day

characteristic: age

text: ArrayExpress

text: not collected

text: fruit fly

characteristic: common name

text: Protocols: 10 heads from 14 day old Drosophila melanogaster were dissected and pooled per replicate, per genotype. Tissue was snap frozen prior to extraction. Pooled heads were manually homogenised and RNA was subsequently extracted using the RNAqueous-Micro kit (AM1931) as per the manufacturer's instructions. The Cardiff University Genome Hub performed Qubit and Tapestation quality/quantity controls prior to library preparation. Samples were then normalised and library prep was performed. The latter was achieved following the Illumina TruSeq stranded mRNA kit. Here mRNA was enriched by poly-A selection and Truseq3 adapters added.

text: adult

characteristic: developmental stage

text: Repo-GAL4/UAS-Sl RNAi BDSC 32906

characteristic: genotype

text: not collected

characteristic: geographic location (country and/or sea)

text: not applicable

text: Drosophila melanogaster

text: Drosophila melanogaster

text: head

text: Drosophila melanogaster

text: female

characteristic: sex

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: INSDC center name

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: ArrayExpress

text: not collected

text: fruit fly

text: adult

text: Repo-GAL4/UAS-TRiP RNAi Control BDSC 8622

text: not collected

text: not applicable

text: Drosophila melanogaster

text: Drosophila melanogaster

text: head

text: Drosophila melanogaster

text: female


text: Swedish University of Agricultural Science, Uppsala

text: public

text: ArrayExpress

text: mixed

text: not collected

characteristic: collection latitude

characteristic: collection longitude

text: Protocols: L. sclopetarius adult female spiders were collected in the wild in a small habitat in Uppsala, Sweden. Taxonomic identity of the spider was verified by the Museum of Natural History, Stockholm, Sweden. The spiders were kept in big containers that allowed them to spin webs. They were fed with meal worms or Drosophila flies weekly and watered daily. Whole opisthosomas of spiders were flash-frozen in OCT medium on an isopentane-dry ice bath and samples were stored at –80°C until use. The samples were sectioned in a cryotome (10 μm) with knife temperature set at –23°C and sample holder temperature at –10°C. Eight sections from five individual spiders were carefully mounted on the capture areas (6.5 x 6.5 mm) of the Visium spatial slide (10X genomics) and permeabilized for 30 minutes following the 10X Visium spatial tissue optimization protocol.  The libraries were constructed according to Visium spatial gene expression protocol (10X genomics). For cDNA amplification 13-16 PCR cycles were performed and for the indexing 13 PCR cycles were used.

text: adult

text: Sweden

characteristic: environmental history

text: Skarholmen, Uppsala

text: wild type genotype

text: not collected

text: not applicable

characteristic: individual

text: not applicable

characteristic: isolate

text: Larinioides sclopetarius

characteristic: organism

text: Larinioides sclopetarius

text: Whole abdome (opsthosoma) sections

characteristic: organism part

characteristic: replicate

text: caught in the wild

characteristic: sampling site

text: Larinioides sclopetarius

text: female


characteristic: ENA first public

text: public

text: E-MTAB-14082:P22555_1001_P18163_V10A21-050_B1

text: ArrayExpress

characteristic: broker name

text: mixed

text: not collected

characteristic: collection date

characteristic: description

text: adult

characteristic: developmental stage

text: Sweden

text: Skarholmen, Uppsala

text: wild type genotype

characteristic: genotype

text: not collected

characteristic: geographic location (country and/or sea)

text: not applicable

text: not applicable

text: Larinioides sclopetarius

text: Larinioides sclopetarius

text: Whole abdome (opsthosoma) sections

text: caught in the wild

text: Larinioides sclopetarius

text: female


characteristic: ENA-CHECKLIST

characteristic: INSDC center name

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-14082:P22555_1002_P18163_V10A21-050_C1

characteristic: Submitter Id

text: ArrayExpress

text: mixed

text: not collected

text: adult

text: Sweden

text: Skarholmen, Uppsala

text: wild type genotype

text: not collected

text: not applicable

text: not applicable

text: Larinioides sclopetarius

text: Larinioides sclopetarius

text: Whole abdome (opsthosoma) sections

text: caught in the wild

text: Larinioides sclopetarius

text: female

characteristic: sex

characteristic: title


text: public

text: E-MTAB-14082:P22555_1003_P18163_V10A21-050_D1

text: ArrayExpress

text: mixed

text: not collected

characteristic: collection latitude

characteristic: collection longitude

text: adult

text: Sweden

characteristic: environmental history

text: Skarholmen, Uppsala

text: wild type genotype

text: not collected

text: not applicable

characteristic: individual

text: not applicable

characteristic: isolate

text: Larinioides sclopetarius

characteristic: organism

text: Larinioides sclopetarius

text: Whole abdome (opsthosoma) sections

characteristic: organism part

text: caught in the wild

text: Larinioides sclopetarius

text: female


characteristic: ENA first public

text: College of Horticulture, Northwest Agriculture and Forestry University, Yangling, China

text: public

text: ArrayExpress

characteristic: broker name

text: not collected

characteristic: collection date

text: tomato

characteristic: common name

text: Protocols: 3-week-old seedling roots of tomato, which were grown in 1/2 Hoagland’s nutrient solution, were collected. 3-week-old seedling roots, which were grown in 1/2 Hoagland’s nutrient solution. RNA extraction using RNA Isolater Total RNA Extraction Reagent Kit (Vazyme#R401) following the manufacturer’s instructions. The generation of the cDNA library was accomplished by utilizing the TruSeq RNA Sample Prep Kit (Illumina, San Diego, CA).

characteristic: description

text: fer

text: not collected

text: not applicable

text: Solanum lycopersicum

text: Solanum lycopersicum

text: root

text: Solanum lycopersicum


characteristic: ENA-CHECKLIST

characteristic: INSDC center name

text: public

characteristic: INSDC status

text: ArrayExpress

text: not collected

text: tomato

text: wild type genotype

characteristic: genotype

text: not collected

characteristic: geographic location (country and/or sea)

text: not applicable

text: Solanum lycopersicum

text: Solanum lycopersicum

text: root

text: Solanum lycopersicum


text: UniFR

text: public

characteristic: SRA accession

characteristic: Submitter Id

text: blood

text: not provided

text: Switzerland

text: yes

characteristic: germline

text: Homo sp.

text: patient

text: affected

characteristic: sample_descriptionot affected

text: Homo sp.

text: XX

characteristic: sex


text: CNRS

text: public

text: microcosm sediment from Avenheimerbach riverbed and deionised water

characteristic: broad-scale environmental context

text: metolachlor  microcosm from the sediment phase,  replicata at day 0

text: sediment phase

characteristic: environmental medium

text: France

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

characteristic: local environmental context

text: freshwater metagenome

characteristic: organism

text: SYN

characteristic: project name

text: freshwater metagenome

text: SiSa

characteristic: title


characteristic: ENA first public

characteristic: ENA-CHECKLIST

text: CNRS

characteristic: INSDC center name

text: public

characteristic: collection date

text: metolachlor microcosm from the sediment phase,  replicatb at day 0

characteristic: description

text: sediment phase

text: France

text: freshwater metagenome

text: SYN

text: freshwater metagenome

text: SiSb


text: CNRS

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: metolachlor microcosm from the sediment phase,  replicatc at day 0

text: sediment phase

text: France

characteristic: geographic location (country and/or sea)

text: freshwater metagenome

text: SYN

text: freshwater metagenome

text: SiSc


text: CNRS

text: public

characteristic: broad-scale environmental context

text: metolachlor microcosm from the water phase,  replicata at day 0

text: water phase

text: France

text: freshwater metagenome

text: SYN

text: freshwater metagenome

text: SiWa


text: CNRS

text: public

text: metolachlor microcosm from the water phase,  replicatb at day 0

text: water phase

characteristic: environmental medium

text: France

text: freshwater metagenome

text: SYN

text: freshwater metagenome

text: SiWb


text: CNRS

text: public

text: metolachlor microcosm from the water phase,  replicatc at day 0

text: water phase

text: France

characteristic: geographic location (latitude)

text: freshwater metagenome

text: SYN

text: freshwater metagenome

text: SiWc


text: CNRS

text: public

text: terbutryn microcosm from the sediment phase,  replicata at day 0

text: sediment phase

text: France

characteristic: geographic location (longitude)

text: freshwater metagenome

text: SYN

text: freshwater metagenome

text: TiSa


text: CNRS

text: public

text: terbutryn microcosm from the sediment phase,  replicatb at day 0

text: sediment phase

text: France

characteristic: local environmental context

text: freshwater metagenome

text: SYN

text: freshwater metagenome

text: TiSb


text: CNRS

text: public

text: terbutryn microcosm from the sediment phase,  replicatc at day 0

text: sediment phase

text: France

text: freshwater metagenome

characteristic: organism

text: SYN

text: freshwater metagenome

text: TiSc


text: CNRS

text: public

text: terbutryn microcosm from the water phase,  replicata at day 0

text: water phase

text: France

text: freshwater metagenome

text: SYN

characteristic: project name

text: freshwater metagenome

text: TiWa


text: CNRS

text: public

text: terbutryn microcosm from the water phase,  replicatb at day 0

text: water phase

text: France

text: freshwater metagenome

text: SYN

text: freshwater metagenome

text: TiWb

characteristic: title


characteristic: ENA first public

text: CNRS

text: public

text: terbutryn microcosm from the water phase,  replicatc at day 0

text: water phase

text: France

text: freshwater metagenome

text: SYN

text: freshwater metagenome

text: TiWc


characteristic: ENA-CHECKLIST

text: CNRS

text: public

text: metformin microcosm from the sediment phase,  replicata at day 0

text: sediment phase

text: France

text: freshwater metagenome

text: SYN

text: freshwater metagenome

text: MiSa


text: CNRS

characteristic: INSDC center name

text: public

text: metformin microcosm from the sediment phase,  replicatb at day 0

text: sediment phase

text: France

text: freshwater metagenome

text: SYN

text: freshwater metagenome

text: MiSb


text: CNRS

text: public

characteristic: collection date

text: metformin microcosm from the water phase,  replicata at day 0

text: water phase

text: France

text: freshwater metagenome

text: SYN

text: freshwater metagenome

text: MiWa


text: CNRS

text: public

text: metformin microcosm from the water phase,  replicatb at day 0

characteristic: description

text: water phase

text: France

text: freshwater metagenome

text: SYN

text: freshwater metagenome

text: MiWb


text: CNRS

text: public

characteristic: INSDC status

text: microcosm sediment from Avenheimerbach riverbed and deionised water

text: metformin microcosm from the water phase,  replicatc at day 0

text: water phase

text: France

text: freshwater metagenome

text: SYN

text: freshwater metagenome

text: MiWc


text: CNRS

text: public

characteristic: SRA accession

text: mixture microcosm from the sediment phase,  replicata at day 0

text: sediment phase

text: France

text: freshwater metagenome

text: SYN

text: freshwater metagenome

text: CiSa


text: CNRS

text: public

characteristic: Submitter Id

text: mixture microcosm from the sediment phase,  replicatb at day 0

text: sediment phase

text: France

text: freshwater metagenome

text: SYN

text: freshwater metagenome

text: CiSb


text: CNRS

text: public

text: mixture microcosm from the sediment phase,  replicatc at day 0

text: sediment phase

text: France

characteristic: geographic location (country and/or sea)

text: freshwater metagenome

text: SYN

text: freshwater metagenome

text: CiSc


text: CNRS

text: public

characteristic: broad-scale environmental context

text: mixture microcosm from the water phase,  replicata at day 0

text: water phase

text: France

text: freshwater metagenome

text: SYN

text: freshwater metagenome

text: CiWa


text: CNRS

text: public

text: mixture microcosm from the water phase,  replicatb at day 0

text: water phase

characteristic: environmental medium

text: France

text: freshwater metagenome

text: SYN

text: freshwater metagenome

text: CiWb


text: CNRS

text: public

text: mixture microcosm from the water phase,  replicatc at day 0

text: water phase

text: France

characteristic: geographic location (latitude)

text: freshwater metagenome

text: SYN

text: freshwater metagenome

text: CiWc


text: CNRS

text: public

text: control microcosm from the sediment phase,  replicata at day 0

text: sediment phase

text: France

characteristic: geographic location (longitude)

text: freshwater metagenome

text: SYN

text: freshwater metagenome

text: BiSa


text: CNRS

text: public

text: control microcosm from the sediment phase,  replicatb at day 0

text: sediment phase

text: France

characteristic: local environmental context

text: freshwater metagenome

text: SYN

text: freshwater metagenome

text: BiSb


text: CNRS

text: public

text: control microcosm from the sediment phase,  replicatc at day 0

text: sediment phase

text: France

text: freshwater metagenome

characteristic: organism

text: SYN

text: freshwater metagenome

text: BiSc


text: CNRS

text: public

text: control microcosm from the water phase,  replicata at day 0

text: water phase

text: France

text: freshwater metagenome

text: SYN

characteristic: project name

text: freshwater metagenome

text: BiWa


text: CNRS

text: public

text: control microcosm from the water phase,  replicatb at day 0

text: water phase

text: France

text: freshwater metagenome

text: SYN

text: freshwater metagenome

text: BiWb

characteristic: title


characteristic: ENA first public

text: CNRS

text: public

text: control microcosm from the water phase,  replicatc at day 0

text: water phase

text: France

text: freshwater metagenome

text: SYN

text: freshwater metagenome

text: BiWc


characteristic: ENA-CHECKLIST

text: CNRS

text: public

text: metolachlor microcosm from the sediment phase,  replicata at day 70

text: sediment phase

text: France

text: freshwater metagenome

text: SYN

text: freshwater metagenome

text: SfSa


text: CNRS

characteristic: INSDC center name

text: public

text: metolachlor microcosm from the sediment phase,  replicatb at day 70

text: sediment phase

text: France

text: freshwater metagenome

text: SYN

text: freshwater metagenome

text: SfSb


text: CNRS

text: public

characteristic: collection date

text: metolachlor microcosm from the sediment phase,  replicatc at day 70

text: sediment phase

text: France

text: freshwater metagenome

text: SYN

text: freshwater metagenome

text: SfSc


text: CNRS

text: public

text: microcosm sediment from Avenheimerbach riverbed and deionised water

text: metolachlor microcosm from the water phase,  replicata at day 70

characteristic: description

text: water phase

text: France

text: freshwater metagenome

text: SYN

text: freshwater metagenome

text: SfWa


text: CNRS

text: public

characteristic: INSDC status

text: metolachlor microcosm from the water phase,  replicatb at day 70

text: water phase

text: France

text: freshwater metagenome

text: SYN

text: freshwater metagenome

text: SfWb


text: CNRS

text: public

characteristic: SRA accession

text: metolachlor microcosm from the water phase,  replicatc at day 70

text: water phase

text: France

text: freshwater metagenome

text: SYN

text: freshwater metagenome

text: SfWc


text: CNRS

text: public

characteristic: Submitter Id

text: terbutryn microcosm from the sediment phase,  replicata at day 70

text: sediment phase

text: France

text: freshwater metagenome

text: SYN

text: freshwater metagenome

text: TfSa


text: CNRS

text: public

text: terbutryn microcosm from the sediment phase,  replicatb at day 70

text: sediment phase

text: France

characteristic: geographic location (country and/or sea)

text: freshwater metagenome

text: SYN

text: freshwater metagenome

text: TfSb


text: CNRS

text: public

characteristic: broad-scale environmental context

text: terbutryn microcosm from the sediment phase,  replicatc at day 70

text: sediment phase

text: France

text: freshwater metagenome

text: SYN

text: freshwater metagenome

text: TfSc


text: CNRS

text: public

text: terbutryn microcosm from the water phase,  replicata at day 70

text: water phase

characteristic: environmental medium

text: France

text: freshwater metagenome

text: SYN

text: freshwater metagenome

text: TfWa


text: CNRS

text: public

text: terbutryn microcosm from the water phase,  replicatb at day 70

text: water phase

text: France

characteristic: geographic location (latitude)

text: freshwater metagenome

text: SYN

text: freshwater metagenome

text: TfWb


text: CNRS

text: public

text: terbutryn microcosm from the water phase,  replicatc at day 70

text: water phase

text: France

characteristic: geographic location (longitude)

text: freshwater metagenome

text: SYN

text: freshwater metagenome

text: TfWc


text: CNRS

text: public

text: metformin microcosm from the sediment phase,  replicata at day 70

text: sediment phase

text: France

characteristic: local environmental context

text: freshwater metagenome

text: SYN

text: freshwater metagenome

text: MfSa


text: CNRS

text: public

text: metformin microcosm from the sediment phase,  replicatb at day 70

text: sediment phase

text: France

text: freshwater metagenome

characteristic: organism

text: SYN

text: freshwater metagenome

text: MfSb


text: CNRS

text: public

text: metformin microcosm from the sediment phase,  replicatc at day 70

text: sediment phase

text: France

text: freshwater metagenome

text: SYN

characteristic: project name

text: freshwater metagenome

text: MfSc


text: CNRS

text: public

text: metformin microcosm from the water phase,  replicata at day 70

text: water phase

text: France

text: freshwater metagenome

text: SYN

text: freshwater metagenome

text: MfWa

characteristic: title


characteristic: ENA first public

text: CNRS

text: public

text: metformin microcosm from the water phase,  replicatb at day 70

text: water phase

text: France

text: freshwater metagenome

text: SYN

text: freshwater metagenome

text: MfWb


characteristic: ENA-CHECKLIST

text: CNRS

text: public

text: metformin microcosm from the water phase,  replicatc at day 70

text: water phase

text: France

text: freshwater metagenome

text: SYN

text: freshwater metagenome

text: MfWc


text: CNRS

characteristic: INSDC center name

text: public

text: mixture microcosm from the sediment phase,  replicata at day 70

text: sediment phase

text: France

text: freshwater metagenome

text: SYN

text: freshwater metagenome

text: CfSa


text: CNRS

text: public

text: microcosm sediment from Avenheimerbach riverbed and deionised water

characteristic: collection date

text: mixture microcosm from the sediment phase,  replicatb at day 70

text: sediment phase

text: France

text: freshwater metagenome

text: SYN

text: freshwater metagenome

text: CfSb


text: CNRS

text: public

text: mixture microcosm from the sediment phase,  replicatc at day 70

characteristic: description

text: sediment phase

text: France

text: freshwater metagenome

text: SYN

text: freshwater metagenome

text: CfSc


text: CNRS

text: public

characteristic: INSDC status

text: mixture microcosm from the water phase,  replicata at day 70

text: water phase

text: France

text: freshwater metagenome

text: SYN

text: freshwater metagenome

text: CfWa


text: CNRS

text: public

characteristic: SRA accession

text: mixture microcosm from the water phase,  replicatb at day 70

text: water phase

text: France

text: freshwater metagenome

text: SYN

text: freshwater metagenome

text: CfWb


text: CNRS

text: public

characteristic: Submitter Id

text: mixture microcosm from the water phase,  replicatc at day 70

text: water phase

text: France

text: freshwater metagenome

text: SYN

text: freshwater metagenome

text: CfWc


text: CNRS

text: public

text: control microcosm from the sediment phase,  replicata at day 70

text: sediment phase

text: France

characteristic: geographic location (country and/or sea)

text: freshwater metagenome

text: SYN

text: freshwater metagenome

text: BfSa


text: CNRS

text: public

characteristic: broad-scale environmental context

text: control microcosm from the sediment phase,  replicatb at day 70

text: sediment phase

text: France

text: freshwater metagenome

text: SYN

text: freshwater metagenome

text: BfSb


text: CNRS

text: public

text: control microcosm from the sediment phase,  replicatc at day 70

text: sediment phase

characteristic: environmental medium

text: France

text: freshwater metagenome

text: SYN

text: freshwater metagenome

text: BfSc


text: CNRS

text: public

text: control microcosm from the water phase,  replicata at day 70

text: water phase

text: France

characteristic: geographic location (latitude)

text: freshwater metagenome

text: SYN

text: freshwater metagenome

text: BfWa


text: CNRS

text: public

text: control microcosm from the water phase,  replicatb at day 70

text: water phase

text: France

characteristic: geographic location (longitude)

text: freshwater metagenome

text: SYN

text: freshwater metagenome

text: BfWb


text: CNRS

text: public

text: control microcosm from the water phase,  replicatc at day 70

text: water phase

text: France

characteristic: local environmental context

text: freshwater metagenome

text: SYN

text: freshwater metagenome

text: BfWc


text: UCL

text: public

text: 12 pcw

unit: week

characteristic: age

text: ArrayExpress

characteristic: broker name

text: not collected

text: human

characteristic: common name

text: Protocols: Lung tissue for this project was obtained from the MRC-Wellcome Trust Human Developmental Biology Resource (https://www.hdbr.org). The HDBR obtain human embryonic and fetal samples from medical or surgical terminations of pregnancy. We requested lung tissue samples from fetuses aged between 8 and 20 post-conception weeks (pcw). We received whole lungs or lung fragments in refrigerated Hibernate E medium. Any trachea or non-lung tissue was removed by dissection. To enrich lung samples for CD45+ immune cells, we utilised fluorescence activated cell sorting (FACS). Cells were first blocked, to prevent non-specific antibody binding, using Human TruStain FcX (Biolegend, 422301) and then stained for 30 minutes on ice, using flurochrome-conjugated antibodies, CD45-PE, CD31-BV421, EpCAM-APC and CD235a-FITC. After staining, cells were resuspended in buffer containing DAPI, to enable the determination of live versus dead cells. FACS was performed on a BD FACS Aria. Appropriate ‘fluorescence minus one’ controls were used to determine FACS gating. Samples were gated to allow the collection of live single cells that were negative for CD235a (red blood cells), CD31 (endothelial cells) and EpCAM (epithelial cells), and positive for CD45 (immune cells). CD45+ immune cells were frozen prior to CITE-Seq or scRNAseq. Nucleic acid was extracted according to the standard protocol of the Chromium single cell 5'V1 kit. CD45+ cells were thawed and counted, assessing viability using Trypan Blue. Cells were stained using the TotalSeq™- C antibody panel (Biolegend) where possible (some samples were not stained), prior to immediate processing for 10x 5’ single-cell capture using the Chromium Next GEM Single Cell V(D)J Reagent Kit, v 1.1, according to the manufacturer’s protocol. The Chromium Next GEM Single Cell V(D)J Reagent Kit, v 1.1 was used for scRNAseq library construction for unstained samples.  abTCR or BCR enrichment

text: embryo stage

characteristic: developmental stage

text: normal

characteristic: disease

text: not collected

characteristic: growth condition

characteristic: individual

text: not applicable

characteristic: isolate

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: lung

characteristic: organism part

text: 10x 5' v1

characteristic: protocol

text: Homo sapiens

text: male

characteristic: sex


characteristic: ENA first public

characteristic: ENA-CHECKLIST

text: UCL

characteristic: INSDC center name

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: ArrayExpress

text: not collected

characteristic: collection date

text: human

characteristic: description

text: embryo stage

text: normal

text: not collected

characteristic: geographic location (country and/or sea)

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: lung

text: 10x 5' v1

text: Homo sapiens

text: male

characteristic: title


text: UCL

text: public

characteristic: age

text: ArrayExpress

characteristic: broker name

text: not collected

text: human

characteristic: common name

text: embryo stage

characteristic: developmental stage

text: normal

characteristic: disease

text: not collected

characteristic: growth condition

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: lung

text: 10x 5' v1

text: Homo sapiens

text: Mixed


text: UCL

text: public

text: ArrayExpress

text: not collected

text: human

text: embryo stage

text: normal

text: not collected

characteristic: individual

text: not applicable

characteristic: isolate

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: lung

characteristic: organism part

text: 10x 5' v1

characteristic: protocol

text: Homo sapiens

text: female

characteristic: sex


characteristic: ENA first public

characteristic: ENA-CHECKLIST

text: UCL

characteristic: INSDC center name

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: 9 pcw

text: ArrayExpress

text: not collected

text: human

text: embryo stage

text: normal

text: not collected

text: HDBR 15503

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: lung

text: 10x 5' v1

text: Homo sapiens


text: UCL

text: public

text: 20 pcw

characteristic: age

text: ArrayExpress

characteristic: broker name

text: not collected

characteristic: collection date

text: human

characteristic: description

text: embryo stage

text: normal

text: not collected

characteristic: geographic location (country and/or sea)

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: lung

text: 10x 5' v1

text: Homo sapiens

text: female

characteristic: title


text: UCL

text: public

text: 12 pcw

text: ArrayExpress

text: not collected

text: human

characteristic: common name

text: embryo stage

characteristic: developmental stage

text: normal

characteristic: disease

text: not collected

characteristic: growth condition

characteristic: individual

text: not applicable

characteristic: isolate

text: Homo sapiens

text: Homo sapiens

text: lung

text: 10x 5' v1

text: Homo sapiens

text: female


characteristic: ENA first public

characteristic: ENA-CHECKLIST

text: UCL

text: public

text: 12 pcw

text: ArrayExpress

text: not collected

text: human

text: embryo stage

text: normal

text: not collected

text: not applicable

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: lung

characteristic: organism part

text: 10x 5' v1

characteristic: protocol

text: Homo sapiens

characteristic: sex


text: UCL

characteristic: INSDC center name

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: 20 pcw

characteristic: age

text: ArrayExpress

characteristic: broker name

text: not collected

text: human

text: embryo stage

text: normal

text: not collected

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: lung

text: 10x 5' v1

text: Homo sapiens

text: Mixed


text: UCL

text: public

text: 20 pcw

text: ArrayExpress

text: not collected

characteristic: collection date

text: human

characteristic: common name

characteristic: description

text: embryo stage

characteristic: developmental stage

text: normal

text: not collected

characteristic: geographic location (country and/or sea)

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: lung

text: 10x 5' v1

text: Homo sapiens

text: male

characteristic: title