characteristic: External Id

text: unspecified

characteristic: INSDC center name

text: public

characteristic: age

text: ArrayExpress

characteristic: broker name

text: medullary thymic epithelial cells

characteristic: cell type

text: house mouse

characteristic: common name

text: Protocols: Thymi were collected from 2 and 4 week-old wild-type C57BL/6 male and female mice. Up to 3 thymi were cleaned of fat and connective tissue, finely minced and pooled together. Thymocytes were flushed by gentle agitation with a magnetic stirrer in RPMI-1640 for 30 min, at 4ºC. Thymic fragments were recovered by settling, and the supernatant discarded. After further dispersion, three additional washes were performed. Fragments were then incubated in 5 mL of 0.125% (w/v) Collagenase D and 0.1% (w/v) DNAse I (both from Roche) in RPMI-1640, at 37ºC for 15 min, with gentle pipetting every 5 min. The supernatant was collected and kept on ice, while the thymic fragments were subject to two further incubations. The remaining fragments were finally resuspended in 5ml of 0.125%(w/v) Collagenase/Dispase (Roche) and 0.1%(w/v) DNaseI in RPMI-1640 for 30 min at 37ºC, with gentle agitation every 15 min. All the collected fractions were pooled, centrifuged at 450x g for 5 min and incubated in 5 mM EDTA, 1% FCS, 0.02% (w/v) NaN3 in PBS (EDTA/FACS buffer) for 10 min at 4ºC. After filtering through a 100μm-strainer, the resulting cell suspension was depleted of hematopoietic cells by Magnetic-Activated Cell Sorting (MACS) using CD45-MicroBeads (Miltenyi Biotec). For sorting, the recovered fraction was blocked using anti-CD16/CD32 (clone 2.4G2, Tonbo) and then stained using anti-CD45-PerCP-Cy5.5 (clone 30-F11, BioLegend), anti-Ly-51-FITC (clone 6C3, BioLegend), anti-CD326(Ep-CAM)-AF647 (clone G8.8, BioLegend), UEA-1-Biotin and Streptavidin-Pacific Blue. Propidium iodide was used as a viability dye. mTECs (PI−CD45−EpCAM+Ly51−UEA-1+) were sorted with a MoFlo™ XDP (Beckman Coulter, Inc.). Single cell capture and processing for the main dataset was performed using the Fluidigm C1 system. The cell suspension obtained from sorting was loaded onto the Fluidigm C1 platform using medium-sized capture chips (10-17μm cells). 1 μl of a 1:400 or 1:2000 dilution of External RNA Control Consortium (ERCC) spike-ins (Ambion, Life Technologies) were included in the lysis buffer. Reverse transcription and cDNA preamplification were performed using the SMARTer Ultra Low RNA kit (Clontech). The cDNA libraries for sequencing were prepared using Nextera XT DNA Sample Preparation Kit (Illumina), according to the protocol supplied by Fluidigm (PN 100-5950 B1). Libraries from 96 single cells were pooled and purified using AMPure XP beads (Beckman Coulter).

text: wild type genotype

characteristic: genotype

text: Mus musculus

text: Mus musculus

text: thymus

characteristic: organism part

text: Mus musculus

characteristic: strain


status: PUBLIC

text: Leishmania donovani

tag: attribute

characteristic: ArrayExpress-SPECIES

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: SC

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: Leishmania donovani

text: Leishmania donovani

characteristic: organism

text: Leishmania donovani

characteristic: subject id

characteristic: title


text: Leishmania infantum

characteristic: External Id

text: SC

characteristic: INSDC center name

text: public

text: Leishmania infantum

text: Leishmania infantum

text: Leishmania infantum


text: JIC

text: public

characteristic: collection date

text: The objectives of the project is to find out (i) which fungus was associated with wheat blast epidemic in Bangladesh in 2017 (Is it the same as the one that caused epidemic in 2016?), (ii) population of structure of the fungus sampled from different districts in Bangladesh, and (iii) if there are any adaptive mutations in the population of the fungus.

characteristic: description

text: Bangladesh

characteristic: geographic location (country and/or sea)

text: diseased

characteristic: host health state

text: Triticum aestivum

characteristic: host scientific name

text: Field sample

characteristic: isolate

text: wheat plant

characteristic: isolation source

text: Magnaporthe oryzae

text: Magnaporthe oryzae

text: RNA-Seq reads from wheat blast field samples from Bangladesh collected in March, 2017


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: INSDC first public

text: public

tag: Namespace:Erasmus University Medical Center, Cancer Institute, Josephine Nefkens Building, Rotterdam

characteristic: case

text: human

characteristic: common name

text: Ion Torrent PGM

characteristic: instrument model

text: SINGLE

characteristic: library layout

text: Homo sapiens

text: Homo sapiens

characteristic: time biopsy after diagnosis(month)

text: primary TGCT


characteristic: External Id

text: Erasmus University Medical Center, Cancer Institute, Josephine Nefkens Building, Rotterdam

characteristic: INSDC center name

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: human

text: Ion Torrent PGM

text: SINGLE

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: RPLND L

characteristic: title


characteristic: ENA-CHECKLIST

text: public

text: human

text: Ion Torrent PGM

text: SINGLE

text: Homo sapiens

text: Homo sapiens

text: primary TGCT


characteristic: ENA-FIRST-PUBLIC

text: public

text: human

text: Ion Torrent PGM

text: SINGLE

text: Homo sapiens

text: Homo sapiens

text: Peripheral blood leukocytes


characteristic: ENA-LAST-UPDATE

text: public

text: human

text: Ion Torrent PGM

text: SINGLE

text: Homo sapiens

text: Homo sapiens

text: lymphnodes thoracal


characteristic: INSDC first public

text: public

text: human

text: Ion Torrent PGM

text: SINGLE

text: Homo sapiens

text: Homo sapiens

text: paravertebral L


text: public

characteristic: case

text: human

text: Ion Torrent PGM

text: SINGLE

text: Homo sapiens

text: Homo sapiens

text: primary TGCT


text: public

text: human

characteristic: common name

text: Ion Torrent PGM

text: SINGLE

text: Homo sapiens

text: Homo sapiens

text: lung right


text: public

text: human

text: Ion Torrent PGM

characteristic: instrument model

text: SINGLE

text: Homo sapiens

text: Homo sapiens

text: Normal adjacent parenchyma


text: public

text: human

text: Ion Torrent PGM

text: SINGLE

characteristic: library layout

text: Homo sapiens

text: Homo sapiens

text: Normal testis tissue


text: MPI-EVA

text: public

text: Denisova hominin

text: Homo sapiens ssp. Denisova

text: Homo sapiens ssp. Denisova

text: Indexed ssDNA library


text: MPI-EVA

text: public

text: Denisova hominin

text: Homo sapiens ssp. Denisova

text: Homo sapiens ssp. Denisova

text: Indexed 3'-Uselected library-i


text: MPI-EVA

text: public

text: Denisova hominin

text: Homo sapiens ssp. Denisova

text: Homo sapiens ssp. Denisova

text: Indexed 3'-Uselected library-ii


text: MPI-EVA

text: public

text: Denisova hominin

text: Homo sapiens ssp. Denisova

text: Homo sapiens ssp. Denisova

text: Indexed 3'-Uselected library-iii


text: MPI-EVA

text: public

text: Denisova hominin

text: Homo sapiens ssp. Denisova

text: Homo sapiens ssp. Denisova

text: Indexed 3'-Uselected library-iv


text: MPI-EVA

text: public

text: Denisova hominin

text: Homo sapiens ssp. Denisova

text: Homo sapiens ssp. Denisova

text: Indexed ssDNA library_Mtcapture


text: public

tag: Namespace:ALFRED WEGENER INSTITUTE FOR POLAR AND MARINE RESEARCH

characteristic: collection date

text: ocean metagenome

text: arctic seawater - ice - meltpond water

characteristic: description

text: ocean biome

characteristic: environment (biome)

text: sea ice

characteristic: environment (feature)

text: sea ice

characteristic: environment (material)

text: Arctic Ocean

characteristic: geographic location (country and/or sea)

unit: m

characteristic: geographic location (depth)

unit: DD

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: mimarks-survey

characteristic: investigation type

text: marine metagenome

text: F-CCAGCASCYGCGGTAATTCC R-ACTTTCGTTCTTGATYRA

characteristic: pcr primers

text: TransIceArk

characteristic: project name

text: marine metagenome

text: Illumina

characteristic: sequencing method

characteristic: target gene

characteristic: target subfragment

text: DNA based Arctic sea ice and water biodiversity

text: water

characteristic: water environmental package


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: ALFRED WEGENER INSTITUTE FOR POLAR AND MARINE RESEARCH

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: ocean metagenome

characteristic: common name

text: arctic seawater - ice - meltpond water

text: ocean biome

text: sea ice

text: sea ice

text: Arctic Ocean

text: mimarks-survey

text: marine metagenome

characteristic: organism

text: TransIceArk

text: marine metagenome

text: Illumina

characteristic: title

text: water


text: public

characteristic: collection date

text: ocean metagenome

text: arctic seawater - ice - meltpond water

characteristic: description

text: ocean biome

characteristic: environment (biome)

text: sea water

characteristic: environment (feature)

text: sea water

characteristic: environment (material)

text: Arctic Ocean

characteristic: geographic location (country and/or sea)

characteristic: geographic location (depth)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: mimarks-survey

characteristic: investigation type

text: marine metagenome

characteristic: pcr primers

text: TransIceArk

characteristic: project name

text: marine metagenome

text: Illumina

characteristic: sequencing method

text: water


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: ocean metagenome

text: arctic seawater - ice - meltpond water

text: ocean biome

text: melt pond water

text: melt pond water

text: Arctic Ocean

text: mimarks-survey

text: marine metagenome

text: TransIceArk

text: marine metagenome

text: Illumina

characteristic: target gene

characteristic: target subfragment

text: water

characteristic: water environmental package


text: public

characteristic: collection date

text: ocean metagenome

characteristic: common name

text: arctic seawater - ice - meltpond water

characteristic: description

text: ocean biome

characteristic: environment (biome)

text: melt pond aggregate

characteristic: environment (feature)

text: melt pond aggregate

characteristic: environment (material)

text: Arctic Ocean

characteristic: geographic location (country and/or sea)

characteristic: geographic location (depth)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: mimarks-survey

characteristic: investigation type

text: marine metagenome

characteristic: organism

text: TransIceArk

text: marine metagenome

text: Illumina

characteristic: title

text: water


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: ocean metagenome

text: arctic seawater - ice - meltpond water

text: ocean biome

text: ice aggregate

text: ice aggregate

text: Arctic Ocean

text: mimarks-survey

text: marine metagenome

characteristic: pcr primers

text: TransIceArk

characteristic: project name

text: marine metagenome

text: Illumina

characteristic: sequencing method

text: water


text: CBMSO

text: public

text: This Project aims to determinate the microbial diversity at different sampling points affected by the blossoming of harmful microorganisms in the Alalay lagoon (Bolivia). For that, samples were collected at a depth between 5 and 10 cm below the water.

characteristic: description

text: metagenome

text: metagenome

text: Metagenomic study in the Alalay lagoon (Bolivia).


text: public

tag: Namespace:XINJIANG INSTITUTE OF ECOLOGY AND GEOGRAPHY

characteristic: collection date

text: Gurbantunggut Desert

characteristic: environment (biome)

text: desert soil

characteristic: environment (feature)

text: soil

characteristic: environment (material)

text: China

characteristic: geographic location (country and/or sea)

characteristic: geographic location (depth)

characteristic: geographic location (elevation)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: metagenome

characteristic: investigation type

text: soil metagenome

text: Fungi of desert soil

text: soil metagenome

text: Miseq

text: soil

characteristic: soil environmental package

text: Fungi of desert soil


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: XINJIANG INSTITUTE OF ECOLOGY AND GEOGRAPHY

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: Gurbantunggut Desert

text: desert soil

text: soil

text: China

text: metagenome

text: soil metagenome

characteristic: organism

text: Fungi of desert soil

text: soil metagenome

text: Miseq

text: soil

text: Fungi of desert soil

characteristic: title


text: public

characteristic: Submitter Id

characteristic: collection date

text: Gurbantunggut Desert

characteristic: environment (biome)

text: desert soil

characteristic: environment (feature)

text: soil

characteristic: environment (material)

text: China

characteristic: geographic location (country and/or sea)

characteristic: geographic location (depth)

text: metagenome

text: soil metagenome

text: C

characteristic: project name

text: soil metagenome

text: Miseq

characteristic: sequencing method

text: soil

text: Fungi of desert soil


text: Plasmodium falciparum

characteristic: ArrayExpress-SPECIES

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: SC

text: public

text: malaria parasite P. falciparum

characteristic: common name

text: Plasmodium falciparum

text: Plasmodium falciparum

characteristic: subject id


text: unspecified

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

unit: month

characteristic: age

text: ArrayExpress

characteristic: broker name

text: house mouse

text: Protocols: Upon isofluorane anesthetization, two months-old transgenic C57BL/6 female mice of around 20-25 gr were locally injected with α-LTx close to the LAL muscles. Animals were randomized in the experimental groups based on their body weight. The toxin (5 μg/kg) was diluted in 15 μl of physiological saline (0.9% w/v NaCl in distilled water). Control animals were injected with saline. At different time points (0, 4, 24 and 96 h) treated mice were sacrificed by anesthetic overdose followed by cervical dislocation and LAL muscles were immediately fixed with a local injection PFA 4% for 10 min. Muscles were collected, incubated with fluorescent α-BTx in sterile PBS for 30 10 min at 37°C and then frozen in liquid nitrogen. Cryo-sections (7 μm thick) were transferred to UV treated microscope glass slides. Microdissection was performed under direct microscopic visualization Total RNA was isolated from the microdissected samples by incubation with 50 μl of lysis buffer PKD (Qiagen, Venlo, Netherlands) and 10 μl of proteinase K solution (Promega, Madison, WI, USA) at 55 °C over night with the sample upside down. The day after samples were centrifuged for 10 min at 10000 rpm and RNA extracted using the Maxwell® 16 LEV RNA FFPE Purification Kit (Promega, Madison, WI, USA) following manufacturer’s instructions. To prepare cDNA from RNA samples, the SMARTer Universal Low Input RNA kit (Clontech Laboratories) was employed following manufacturer’s instructions Libraries were prepared using the Ion TargetSeq Exome Enrichment kit, following the manufacturer’s guidelines.

characteristic: description

characteristic: genotype

text: Mus musculus

characteristic: organism

text: Mus musculus

text: neuromuscular junction

characteristic: organism part

text: levator auris longus muscle

characteristic: sampling site

text: Mus musculus

text: female

characteristic: sex

characteristic: strain

characteristic: title

type: has member


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: FONDAZIONE EDMUND MACH

text: public

tag: Namespace:FONDAZIONE EDMUND MACH

characteristic: Submitter Id

characteristic: collection date

text: rainbow trout

characteristic: common name

text: rainbow trout

characteristic: environment (biome)

text: intestine

characteristic: environment (feature)

text: intestinal microbiota

characteristic: environment (material)

text: Italy

characteristic: geographic location (country and/or sea)

text: 46° 11' 22.81 N

characteristic: geographic location (latitude)

text: 11° 07' 55.63 E

characteristic: geographic location (longitude)

text: host-associated

characteristic: host-associated environmental package

text: metagenome

characteristic: investigation type

text: Oncorhynchus mykiss

text: rainbow trout and essential oil supplementation: microbiota and fillet quality analysis

characteristic: project name

text: Oncorhynchus mykiss

text: pyrosequencing

characteristic: sequencing method

text: Microbiota in Rainbow trout after essential oil supplementation


characteristic: ENA-CHECKLIST

text: IPK-Gatersleben

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: parental line FBB1

characteristic: description

text: Hordeum bulbosum

characteristic: organism

text: Hordeum bulbosum

text: H. bulbosum GBS sequences

characteristic: title


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: IPK-Gatersleben

text: public

characteristic: Submitter Id

text: F1 populations of accessions FBB1xPB1

text: Hordeum bulbosum

text: Hordeum bulbosum

text: H. bulbosum GBS sequences


text: IPK-Gatersleben

text: public

text: parental line FBC_3

text: Hordeum bulbosum

text: Hordeum bulbosum

text: H. bulbosum GBS sequences


text: IPK-Gatersleben

text: public

text: parental line FBC_5

text: Hordeum bulbosum

text: Hordeum bulbosum

text: H. bulbosum GBS sequences


text: IPK-Gatersleben

text: public

text: F1 populations of accessions FBC_3xFBC_5

text: Hordeum bulbosum

text: Hordeum bulbosum

text: H. bulbosum GBS sequences


text: IPK-Gatersleben

text: public

text: parental line PB1

text: Hordeum bulbosum

text: Hordeum bulbosum

text: H. bulbosum GBS sequences


text: UPPSALA UNIVERSITY, IEG, LIMNOLOGY

text: public

tag: Namespace:UPPSALA UNIVERSITY, IEG, LIMNOLOGY

text: marine metagenome

text: marine metagenome

text: 0.2-3 um size fraction, kit extraction, replicate A, 18s


text: UPPSALA UNIVERSITY, IEG, LIMNOLOGY

text: public

text: marine metagenome

text: marine metagenome

text: 0.2-3 um size fraction, kit extraction, replicate B, 18s


text: UPPSALA UNIVERSITY, IEG, LIMNOLOGY

text: public

text: marine metagenome

text: marine metagenome

text: 0.2-3 um size fraction, kit extraction, replicate C, 18s


text: UPPSALA UNIVERSITY, IEG, LIMNOLOGY

text: public

text: marine metagenome

text: marine metagenome

text: 0.2-3 um size fraction, phenol extraction, replicate A, 18s


text: UPPSALA UNIVERSITY, IEG, LIMNOLOGY

text: public

text: marine metagenome

text: marine metagenome

text: 0.2-3 um size fraction, phenol extraction, replicate B,18s


text: UPPSALA UNIVERSITY, IEG, LIMNOLOGY

text: public

text: marine metagenome

text: marine metagenome

text: 0.2-3 um size fraction, phenol extraction, replicate C, 18s


text: UPPSALA UNIVERSITY, IEG, LIMNOLOGY

text: public

text: marine metagenome

text: marine metagenome

text: >0.45 um size fraction, kit extraction, replicate A, 18s


text: UPPSALA UNIVERSITY, IEG, LIMNOLOGY

text: public

text: marine metagenome

text: marine metagenome

text: >0.45 um size fraction, kit extraction, replicate B, 18s


text: UPPSALA UNIVERSITY, IEG, LIMNOLOGY

text: public

text: marine metagenome

text: marine metagenome

text: 0.45 um size fraction, kit extraction, replicate C, 18s


text: UPPSALA UNIVERSITY, IEG, LIMNOLOGY

text: public

text: marine metagenome

text: marine metagenome

text: 0.45 um size fraction, phenol extraction, replicate A, 18s


text: UPPSALA UNIVERSITY, IEG, LIMNOLOGY

text: public

text: marine metagenome

text: marine metagenome

text: >0.45 um size fraction, phenol extraction, replicate B, 18s


text: UPPSALA UNIVERSITY, IEG, LIMNOLOGY

text: public

text: marine metagenome

text: marine metagenome

text: >0.45 um size fraction, phenol extraction, replicate C, 18s


text: UPPSALA UNIVERSITY, IEG, LIMNOLOGY

text: public

text: marine metagenome

text: marine metagenome

text: 3-10um size fraction, kit extraction, replicate A, 18s


text: UPPSALA UNIVERSITY, IEG, LIMNOLOGY

text: public

text: marine metagenome

text: marine metagenome

text: 3-10 um size fraction, kit extraction, replicate B, 18s


text: UPPSALA UNIVERSITY, IEG, LIMNOLOGY

text: public

text: marine metagenome

text: marine metagenome

text: 3-10 um size fraction, kit extraction, replicate C, 18s


text: UPPSALA UNIVERSITY, IEG, LIMNOLOGY

text: public

text: marine metagenome

text: marine metagenome

text: 3-10 um size fraction, phenol extraction, replicate A, 18s


text: UPPSALA UNIVERSITY, IEG, LIMNOLOGY

text: public

text: marine metagenome

text: marine metagenome

text: 3-10 um size fraction, phenol extraction, replicate B, 18s


text: UPPSALA UNIVERSITY, IEG, LIMNOLOGY

text: public

text: marine metagenome

text: marine metagenome

text: 3-10 um size fraction, phenol extraction, replicate C, 18s


text: UPPSALA UNIVERSITY, IEG, LIMNOLOGY

text: public

text: marine metagenome

text: marine metagenome

text: 10-63 um size fraction, kit extraction, replicate A, 18s


text: UPPSALA UNIVERSITY, IEG, LIMNOLOGY

text: public

text: marine metagenome

text: marine metagenome

text: 10-63 um size fraction, kit extraction, replicate B, 18s


text: UPPSALA UNIVERSITY, IEG, LIMNOLOGY

text: public

text: marine metagenome

text: marine metagenome

text: 10-63 um size fraction, kit extraction, replicate C, 18s


text: UPPSALA UNIVERSITY, IEG, LIMNOLOGY

text: public

text: marine metagenome

text: marine metagenome

text: 1063 um size fraction, phenol extraction, replicate A, 18s


text: UPPSALA UNIVERSITY, IEG, LIMNOLOGY

text: public

text: marine metagenome

text: marine metagenome

text: 10-63 um size fraction, phenol extraction, replicate B, 18s


text: UPPSALA UNIVERSITY, IEG, LIMNOLOGY

text: public

text: marine metagenome

text: marine metagenome

text: 10-63 um size fraction, phenol extraction, replicate C, 18s


text: UPPSALA UNIVERSITY, IEG, LIMNOLOGY

text: public

text: marine metagenome

text: marine metagenome

text: 0.45-63 um size fraction, kit extraction, replicate A, 18s


text: UPPSALA UNIVERSITY, IEG, LIMNOLOGY

text: public

text: marine metagenome

text: marine metagenome

text: 0.45-63 um size fraction, kit extraction, replicate B, 18s


text: UPPSALA UNIVERSITY, IEG, LIMNOLOGY

text: public

text: marine metagenome

text: marine metagenome

text: 0.45-63 um size fraction, kit extraction, replicate C, 18s


text: UPPSALA UNIVERSITY, IEG, LIMNOLOGY

text: public

text: marine metagenome

text: marine metagenome

text: 0.45-63 um size fraction, Phenol extraction, replicate A, 18s


text: UPPSALA UNIVERSITY, IEG, LIMNOLOGY

text: public

text: marine metagenome

text: marine metagenome

text: 0.45-63 um size fraction, Phenol extraction, replicate B, 18s


text: UPPSALA UNIVERSITY, IEG, LIMNOLOGY

text: public

text: marine metagenome

text: marine metagenome

text: 0.45-63 um size fraction, Phenol extraction, replicate C, 18s


text: UPPSALA UNIVERSITY, IEG, LIMNOLOGY

text: public

text: marine metagenome

text: marine metagenome

text: 0.2-3 um size fraction, kit extraction, replicate A, 16s


text: UPPSALA UNIVERSITY, IEG, LIMNOLOGY

text: public

text: marine metagenome

text: marine metagenome

text: 0.2-3 um size fraction, kit extraction, replicate B, 16s


text: UPPSALA UNIVERSITY, IEG, LIMNOLOGY

text: public

text: marine metagenome

text: marine metagenome

text: 0.2-3 um size fraction, kit extraction, replicate C, 16s


text: UPPSALA UNIVERSITY, IEG, LIMNOLOGY

text: public

text: marine metagenome

text: marine metagenome

text: 0.2-3 um size fraction, phenol extraction, replicate A, 16s


text: UPPSALA UNIVERSITY, IEG, LIMNOLOGY

text: public

text: marine metagenome

text: marine metagenome

text: 0.2-3 um size fraction, phenol extraction, replicate B,16s


text: UPPSALA UNIVERSITY, IEG, LIMNOLOGY

text: public

text: marine metagenome

text: marine metagenome

text: 0.2-3 um size fraction, phenol extraction, replicate C, 16s


text: UPPSALA UNIVERSITY, IEG, LIMNOLOGY

text: public

text: marine metagenome

text: marine metagenome

text: >0.45 um size fraction, kit extraction, replicate A, 16s


text: UPPSALA UNIVERSITY, IEG, LIMNOLOGY

text: public

text: marine metagenome

text: marine metagenome

text: >0.45 um size fraction, kit extraction, replicate B, 16s


text: UPPSALA UNIVERSITY, IEG, LIMNOLOGY

text: public

text: marine metagenome

text: marine metagenome

text: 0.45 um size fraction, kit extraction, replicate C, 16s


text: UPPSALA UNIVERSITY, IEG, LIMNOLOGY

text: public

text: marine metagenome

text: marine metagenome

text: 0.45 um size fraction, phenol extraction, replicate A, 16s


text: UPPSALA UNIVERSITY, IEG, LIMNOLOGY

text: public

text: marine metagenome

text: marine metagenome

text: >0.45 um size fraction, phenol extraction, replicate B, 16s


text: UPPSALA UNIVERSITY, IEG, LIMNOLOGY

text: public

text: marine metagenome

text: marine metagenome

text: >0.45 um size fraction, phenol extraction, replicate C, 16s


text: UPPSALA UNIVERSITY, IEG, LIMNOLOGY

text: public

text: marine metagenome

text: marine metagenome

text: 3-10um size fraction, kit extraction, replicate A, 16s


text: UPPSALA UNIVERSITY, IEG, LIMNOLOGY

text: public

text: marine metagenome

text: marine metagenome

text: 3-10 um size fraction, kit extraction, replicate B, 16s


text: UPPSALA UNIVERSITY, IEG, LIMNOLOGY

text: public

text: marine metagenome

text: marine metagenome

text: 3-10 um size fraction, kit extraction, replicate C, 16s


text: UPPSALA UNIVERSITY, IEG, LIMNOLOGY

text: public

text: marine metagenome

text: marine metagenome

text: 3-10 um size fraction, phenol extraction, replicate A, 16s


text: UPPSALA UNIVERSITY, IEG, LIMNOLOGY

text: public

text: marine metagenome

text: marine metagenome

text: 3-10 um size fraction, phenol extraction, replicate B, 16s


text: UPPSALA UNIVERSITY, IEG, LIMNOLOGY

text: public

text: marine metagenome

text: marine metagenome

text: 3-10 um size fraction, phenol extraction, replicate C, 16s


text: UPPSALA UNIVERSITY, IEG, LIMNOLOGY

text: public

text: marine metagenome

text: marine metagenome

text: 10-63 um size fraction, kit extraction, replicate A, 16s


text: UPPSALA UNIVERSITY, IEG, LIMNOLOGY

text: public

text: marine metagenome

text: marine metagenome

text: 10-63 um size fraction, kit extraction, replicate B, 16s


text: UPPSALA UNIVERSITY, IEG, LIMNOLOGY

text: public

text: marine metagenome

text: marine metagenome

text: 10-63 um size fraction, kit extraction, replicate C, 16s


text: UPPSALA UNIVERSITY, IEG, LIMNOLOGY

text: public

text: marine metagenome

text: marine metagenome

text: 1063 um size fraction, phenol extraction, replicate A, 16s


text: UPPSALA UNIVERSITY, IEG, LIMNOLOGY

text: public

text: marine metagenome

text: marine metagenome

text: 10-63 um size fraction, phenol extraction, replicate B, 16s


text: UPPSALA UNIVERSITY, IEG, LIMNOLOGY

text: public

text: marine metagenome

text: marine metagenome

text: 10-63 um size fraction, phenol extraction, replicate C, 16s


text: UPPSALA UNIVERSITY, IEG, LIMNOLOGY

text: public

text: marine metagenome

text: marine metagenome

text: 0.45-63 um size fraction, kit extraction, replicate A, 16s


text: UPPSALA UNIVERSITY, IEG, LIMNOLOGY

text: public

text: marine metagenome

text: marine metagenome

text: 0.45-63 um size fraction, kit extraction, replicate B, 16s


text: UPPSALA UNIVERSITY, IEG, LIMNOLOGY

text: public

text: marine metagenome

text: marine metagenome

text: 0.45-63 um size fraction, kit extraction, replicate C, 16s


text: UPPSALA UNIVERSITY, IEG, LIMNOLOGY

text: public

text: marine metagenome

text: marine metagenome

text: 0.45-63 um size fraction, Phenol extraction, replicate A, 16s


text: UPPSALA UNIVERSITY, IEG, LIMNOLOGY

text: public

text: marine metagenome

text: marine metagenome

text: 0.45-63 um size fraction, Phenol extraction, replicate B, 16s


text: UPPSALA UNIVERSITY, IEG, LIMNOLOGY

text: public

text: marine metagenome

text: marine metagenome

text: 0.45-63 um size fraction, Phenol extraction, replicate C, 16s


text: Streptococcus pneumoniae

characteristic: ArrayExpress-SPECIES

text: SC

text: public

text: Streptococcus pneumoniae

characteristic: common name

text: Streptococcus pneumoniae

text: Streptococcus pneumoniae

characteristic: subject id


text: HELMHOLTZ CENTRE FOR INFECTION RESEARCH

text: public

tag: Namespace:HELMHOLTZ CENTRE FOR INFECTION RESEARCH

text: harvested from mid-exponential phase D. shibae wild-type for transcriptomics

text: Dinoroseobacter shibae

text: Dinoroseobacter shibae

text: wild-type

characteristic: strain

text: Dinoroseobacter shibae Gene Transfer Agent study


characteristic: ENA-CHECKLIST

text: HELMHOLTZ CENTRE FOR INFECTION RESEARCH

text: public

text: harvested from mid-exponential phase D. shibae delta luxI1for transcriptomics

text: Dinoroseobacter shibae

text: Dinoroseobacter shibae


text: HELMHOLTZ CENTRE FOR INFECTION RESEARCH

characteristic: INSDC center name

text: public

text: harvested from mid-exponential phase D. shibae delta luxI2for transcriptomics

text: Dinoroseobacter shibae

text: Dinoroseobacter shibae


text: HELMHOLTZ CENTRE FOR INFECTION RESEARCH

characteristic: INSDC first public

text: public

text: harvested from early stationary phase D. shibae delta luxI2 for isolation of GTA DNA from supernatants

text: Dinoroseobacter shibae

text: Dinoroseobacter shibae


text: HELMHOLTZ CENTRE FOR INFECTION RESEARCH

characteristic: INSDC last update

text: public

text: harvested from early stationary phase D. shibae delta luxI2 for isolation of genomic DNA and RNA from cells and GTA DNA from supernatants

text: Dinoroseobacter shibae

text: Dinoroseobacter shibae


text: CANCER RESEARCH UK CAMBRIDGE INSTITUTE

text: public

characteristic: INSDC status

tag: Namespace:CANCER RESEARCH UK CAMBRIDGE INSTITUTE

text: southeastern Asian house mouse

characteristic: date of birth

characteristic: date of death

text: liver sample 92055_N3 from DEN treated individual 92055. This sample is a unique specimen from this individual.

characteristic: individual name

text: Mus musculus castaneus

characteristic: sample name

text: Mus musculus castaneus

text: male

characteristic: sex

text: CAST/EiJ

text: liver

characteristic: tissue type

text: DEN

characteristic: treatment agent

characteristic: treatment date

unit: ug/g body weight

characteristic: treatment dose


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: unspecified

text: public

characteristic: SRA accession

characteristic: Submitter Id

text: ArrayExpress

characteristic: broker name

characteristic: cell line

text: epithelial lung carcinoma cell

characteristic: cell type

text: human

characteristic: common name

text: Protocols: A549 cells were purchased from ATCC (VA, USA). A549 is an epithelial lung adenocarcinoma cell line established in 1972 (Giard et al., 1973). The cells were cultured in tissue culture flasks (75 cm2 and 275 cm2) in RPMI 1640 medium with Glutamax (Gibco, ThermoFisher Scientific Inc., Landsmeer, the Netherlands) supplemented with 10% Fetal Bovine Serum (FBS, Greiner BioOne Serum, Greiner BioOne BV, Alphen aan de Rijn, the Netherlands) and 1% penicillin/streptomycin (Gibco, 100 IU penicillin per mL, 100 µg streptomycin per mL). Cells were culture at 37oC in a humidified atmosphere of 5% CO2 in air. The adherent cells were harvested by a short incubation with 0.5% EDTA trypsin in Ca/Mg free Dulbecco’s Phosphate Buffered Saline (Gibco). 8x10 to the 5 cells were seeded and cultured in wells of a 6 well plate for 18 hours, after which the cells were exposed ZnCl2 1h : A549 cells were exposed to ZnCl2 at 24.6 micrograms per ml for 1 hours. After this, the cells (approximately 2 million per well) were quickly washed with PBS (phosphate buffered saline) twice at room temperature after which the 6 well plates were deep frozen by quenching on liquid nitrogen (-196oC) and stored at -80oC until extraction for omics evaluation Total RNA was extracted from A549 cells using a micro RNeasy Kit (Qiagen, Crawley, UK) according to the manufacturer’s protocol. RNA was quantified with a NanoDrop 8000 spectrophotometer (Thermo Scientific, Waltham, MA), and the integrity of RNA was evaluated with a Agilent 2200 Tapestation (Agilent Technologies, Santa Clara, CA). Only RNA with integrity numbers (RINs) greater than 7.0 were used for subsequent RNA-seq experiments. All RNA libraries were produced using the Biomek FxP (Beckman Coulter A31842) with Ultra Directional RNA Library Prep Kit (New England Biolab E7420L) and NEBnext Multiplex Oligos for Illumina Dual Index Primers (New England Biolabs E7600S), using provided protocols and 500ng of total RNA. Constructed libraries were assessed for quality using the Tapestation 2200 (Agilent G2964AA) with High Sensitivity D1000 DNA screentape (5067-5584), and quantified using Kapa Library Quantification Kit (Kapa Biosystems KK4824) on an AriaMx Realtime PCR System (Agilent G8830A).

characteristic: description

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: Homo sapiens

characteristic: title


characteristic: ENA-CHECKLIST

text: unspecified

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: ArrayExpress

text: epithelial lung carcinoma cell

text: human

text: Protocols: A549 cells were purchased from ATCC (VA, USA). A549 is an epithelial lung adenocarcinoma cell line established in 1972 (Giard et al., 1973). The cells were cultured in tissue culture flasks (75 cm2 and 275 cm2) in RPMI 1640 medium with Glutamax (Gibco, ThermoFisher Scientific Inc., Landsmeer, the Netherlands) supplemented with 10% Fetal Bovine Serum (FBS, Greiner BioOne Serum, Greiner BioOne BV, Alphen aan de Rijn, the Netherlands) and 1% penicillin/streptomycin (Gibco, 100 IU penicillin per mL, 100 µg streptomycin per mL). Cells were culture at 37oC in a humidified atmosphere of 5% CO2 in air. The adherent cells were harvested by a short incubation with 0.5% EDTA trypsin in Ca/Mg free Dulbecco’s Phosphate Buffered Saline (Gibco). 8x10 to the 5 cells were seeded and cultured in wells of a 6 well plate for 18 hours, after which the cells were exposed Control 1h : A549 cells were grown for 1 hours. After this, the cells (approximately 2 million per well) were quickly washed with PBS (phosphate buffered saline) twice at room temperature after which the 6 well plates were deep frozen by quenching on liquid nitrogen (-196oC) and stored at -80oC until extraction for omics evaluation Total RNA was extracted from A549 cells using a micro RNeasy Kit (Qiagen, Crawley, UK) according to the manufacturer’s protocol. RNA was quantified with a NanoDrop 8000 spectrophotometer (Thermo Scientific, Waltham, MA), and the integrity of RNA was evaluated with a Agilent 2200 Tapestation (Agilent Technologies, Santa Clara, CA). Only RNA with integrity numbers (RINs) greater than 7.0 were used for subsequent RNA-seq experiments. All RNA libraries were produced using the Biomek FxP (Beckman Coulter A31842) with Ultra Directional RNA Library Prep Kit (New England Biolab E7420L) and NEBnext Multiplex Oligos for Illumina Dual Index Primers (New England Biolabs E7600S), using provided protocols and 500ng of total RNA. Constructed libraries were assessed for quality using the Tapestation 2200 (Agilent G2964AA) with High Sensitivity D1000 DNA screentape (5067-5584), and quantified using Kapa Library Quantification Kit (Kapa Biosystems KK4824) on an AriaMx Realtime PCR System (Agilent G8830A).

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens


characteristic: ENA-FIRST-PUBLIC

text: unspecified

text: public

text: ArrayExpress

text: epithelial lung carcinoma cell

text: human

text: Protocols: A549 cells were purchased from ATCC (VA, USA). A549 is an epithelial lung adenocarcinoma cell line established in 1972 (Giard et al., 1973). The cells were cultured in tissue culture flasks (75 cm2 and 275 cm2) in RPMI 1640 medium with Glutamax (Gibco, ThermoFisher Scientific Inc., Landsmeer, the Netherlands) supplemented with 10% Fetal Bovine Serum (FBS, Greiner BioOne Serum, Greiner BioOne BV, Alphen aan de Rijn, the Netherlands) and 1% penicillin/streptomycin (Gibco, 100 IU penicillin per mL, 100 µg streptomycin per mL). Cells were culture at 37oC in a humidified atmosphere of 5% CO2 in air. The adherent cells were harvested by a short incubation with 0.5% EDTA trypsin in Ca/Mg free Dulbecco’s Phosphate Buffered Saline (Gibco). 8x10 to the 5 cells were seeded and cultured in wells of a 6 well plate for 18 hours, after which the cells were exposed ZnCl2 6h : A549 cells were exposed to ZnCl2 at 24.6 micrograms per ml for 6 hours. After this, the cells (approximately 2 million per well) were quickly washed with PBS (phosphate buffered saline) twice at room temperature after which the 6 well plates were deep frozen by quenching on liquid nitrogen (-196oC) and stored at -80oC until extraction for omics evaluation Total RNA was extracted from A549 cells using a micro RNeasy Kit (Qiagen, Crawley, UK) according to the manufacturer’s protocol. RNA was quantified with a NanoDrop 8000 spectrophotometer (Thermo Scientific, Waltham, MA), and the integrity of RNA was evaluated with a Agilent 2200 Tapestation (Agilent Technologies, Santa Clara, CA). Only RNA with integrity numbers (RINs) greater than 7.0 were used for subsequent RNA-seq experiments. All RNA libraries were produced using the Biomek FxP (Beckman Coulter A31842) with Ultra Directional RNA Library Prep Kit (New England Biolab E7420L) and NEBnext Multiplex Oligos for Illumina Dual Index Primers (New England Biolabs E7600S), using provided protocols and 500ng of total RNA. Constructed libraries were assessed for quality using the Tapestation 2200 (Agilent G2964AA) with High Sensitivity D1000 DNA screentape (5067-5584), and quantified using Kapa Library Quantification Kit (Kapa Biosystems KK4824) on an AriaMx Realtime PCR System (Agilent G8830A).

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens


characteristic: ENA-LAST-UPDATE

text: unspecified

text: public

text: ArrayExpress

text: epithelial lung carcinoma cell

text: human

text: Protocols: A549 cells were purchased from ATCC (VA, USA). A549 is an epithelial lung adenocarcinoma cell line established in 1972 (Giard et al., 1973). The cells were cultured in tissue culture flasks (75 cm2 and 275 cm2) in RPMI 1640 medium with Glutamax (Gibco, ThermoFisher Scientific Inc., Landsmeer, the Netherlands) supplemented with 10% Fetal Bovine Serum (FBS, Greiner BioOne Serum, Greiner BioOne BV, Alphen aan de Rijn, the Netherlands) and 1% penicillin/streptomycin (Gibco, 100 IU penicillin per mL, 100 µg streptomycin per mL). Cells were culture at 37oC in a humidified atmosphere of 5% CO2 in air. The adherent cells were harvested by a short incubation with 0.5% EDTA trypsin in Ca/Mg free Dulbecco’s Phosphate Buffered Saline (Gibco). 8x10 to the 5 cells were seeded and cultured in wells of a 6 well plate for 18 hours, after which the cells were exposed Control 6h : A549 cells were grown for 6 hours. After this, the cells (approximately 2 million per well) were quickly washed with PBS (phosphate buffered saline) twice at room temperature after which the 6 well plates were deep frozen by quenching on liquid nitrogen (-196oC) and stored at -80oC until extraction for omics evaluation Total RNA was extracted from A549 cells using a micro RNeasy Kit (Qiagen, Crawley, UK) according to the manufacturer’s protocol. RNA was quantified with a NanoDrop 8000 spectrophotometer (Thermo Scientific, Waltham, MA), and the integrity of RNA was evaluated with a Agilent 2200 Tapestation (Agilent Technologies, Santa Clara, CA). Only RNA with integrity numbers (RINs) greater than 7.0 were used for subsequent RNA-seq experiments. All RNA libraries were produced using the Biomek FxP (Beckman Coulter A31842) with Ultra Directional RNA Library Prep Kit (New England Biolab E7420L) and NEBnext Multiplex Oligos for Illumina Dual Index Primers (New England Biolabs E7600S), using provided protocols and 500ng of total RNA. Constructed libraries were assessed for quality using the Tapestation 2200 (Agilent G2964AA) with High Sensitivity D1000 DNA screentape (5067-5584), and quantified using Kapa Library Quantification Kit (Kapa Biosystems KK4824) on an AriaMx Realtime PCR System (Agilent G8830A).

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens


characteristic: External Id

text: unspecified

text: public

text: ArrayExpress

text: epithelial lung carcinoma cell

text: human

text: Protocols: A549 cells were purchased from ATCC (VA, USA). A549 is an epithelial lung adenocarcinoma cell line established in 1972 (Giard et al., 1973). The cells were cultured in tissue culture flasks (75 cm2 and 275 cm2) in RPMI 1640 medium with Glutamax (Gibco, ThermoFisher Scientific Inc., Landsmeer, the Netherlands) supplemented with 10% Fetal Bovine Serum (FBS, Greiner BioOne Serum, Greiner BioOne BV, Alphen aan de Rijn, the Netherlands) and 1% penicillin/streptomycin (Gibco, 100 IU penicillin per mL, 100 µg streptomycin per mL). Cells were culture at 37oC in a humidified atmosphere of 5% CO2 in air. The adherent cells were harvested by a short incubation with 0.5% EDTA trypsin in Ca/Mg free Dulbecco’s Phosphate Buffered Saline (Gibco). 8x10 to the 5 cells were seeded and cultured in wells of a 6 well plate for 18 hours, after which the cells were exposed ZnCl2 24h : A549 cells were exposed to ZnCl2 at 24.6 micrograms per ml for 24 hours. After this, the cells (approximately 2 million per well) were quickly washed with PBS (phosphate buffered saline) twice at room temperature after which the 6 well plates were deep frozen by quenching on liquid nitrogen (-196oC) and stored at -80oC until extraction for omics evaluation Total RNA was extracted from A549 cells using a micro RNeasy Kit (Qiagen, Crawley, UK) according to the manufacturer’s protocol. RNA was quantified with a NanoDrop 8000 spectrophotometer (Thermo Scientific, Waltham, MA), and the integrity of RNA was evaluated with a Agilent 2200 Tapestation (Agilent Technologies, Santa Clara, CA). Only RNA with integrity numbers (RINs) greater than 7.0 were used for subsequent RNA-seq experiments. All RNA libraries were produced using the Biomek FxP (Beckman Coulter A31842) with Ultra Directional RNA Library Prep Kit (New England Biolab E7420L) and NEBnext Multiplex Oligos for Illumina Dual Index Primers (New England Biolabs E7600S), using provided protocols and 500ng of total RNA. Constructed libraries were assessed for quality using the Tapestation 2200 (Agilent G2964AA) with High Sensitivity D1000 DNA screentape (5067-5584), and quantified using Kapa Library Quantification Kit (Kapa Biosystems KK4824) on an AriaMx Realtime PCR System (Agilent G8830A).

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens


text: unspecified

text: public

characteristic: SRA accession

text: ArrayExpress

text: epithelial lung carcinoma cell

text: human

text: Protocols: A549 cells were purchased from ATCC (VA, USA). A549 is an epithelial lung adenocarcinoma cell line established in 1972 (Giard et al., 1973). The cells were cultured in tissue culture flasks (75 cm2 and 275 cm2) in RPMI 1640 medium with Glutamax (Gibco, ThermoFisher Scientific Inc., Landsmeer, the Netherlands) supplemented with 10% Fetal Bovine Serum (FBS, Greiner BioOne Serum, Greiner BioOne BV, Alphen aan de Rijn, the Netherlands) and 1% penicillin/streptomycin (Gibco, 100 IU penicillin per mL, 100 µg streptomycin per mL). Cells were culture at 37oC in a humidified atmosphere of 5% CO2 in air. The adherent cells were harvested by a short incubation with 0.5% EDTA trypsin in Ca/Mg free Dulbecco’s Phosphate Buffered Saline (Gibco). 8x10 to the 5 cells were seeded and cultured in wells of a 6 well plate for 18 hours, after which the cells were exposed Control 24h : A549 cells were grown for 24 hours. After this, the cells (approximately 2 million per well) were quickly washed with PBS (phosphate buffered saline) twice at room temperature after which the 6 well plates were deep frozen by quenching on liquid nitrogen (-196oC) and stored at -80oC until extraction for omics evaluation Total RNA was extracted from A549 cells using a micro RNeasy Kit (Qiagen, Crawley, UK) according to the manufacturer’s protocol. RNA was quantified with a NanoDrop 8000 spectrophotometer (Thermo Scientific, Waltham, MA), and the integrity of RNA was evaluated with a Agilent 2200 Tapestation (Agilent Technologies, Santa Clara, CA). Only RNA with integrity numbers (RINs) greater than 7.0 were used for subsequent RNA-seq experiments. All RNA libraries were produced using the Biomek FxP (Beckman Coulter A31842) with Ultra Directional RNA Library Prep Kit (New England Biolab E7420L) and NEBnext Multiplex Oligos for Illumina Dual Index Primers (New England Biolabs E7600S), using provided protocols and 500ng of total RNA. Constructed libraries were assessed for quality using the Tapestation 2200 (Agilent G2964AA) with High Sensitivity D1000 DNA screentape (5067-5584), and quantified using Kapa Library Quantification Kit (Kapa Biosystems KK4824) on an AriaMx Realtime PCR System (Agilent G8830A).

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens


text: unspecified

text: public

characteristic: Submitter Id

text: ArrayExpress

text: epithelial lung carcinoma cell

text: human

text: Protocols: A549 cells were purchased from ATCC (VA, USA). A549 is an epithelial lung adenocarcinoma cell line established in 1972 (Giard et al., 1973). The cells were cultured in tissue culture flasks (75 cm2 and 275 cm2) in RPMI 1640 medium with Glutamax (Gibco, ThermoFisher Scientific Inc., Landsmeer, the Netherlands) supplemented with 10% Fetal Bovine Serum (FBS, Greiner BioOne Serum, Greiner BioOne BV, Alphen aan de Rijn, the Netherlands) and 1% penicillin/streptomycin (Gibco, 100 IU penicillin per mL, 100 µg streptomycin per mL). Cells were culture at 37oC in a humidified atmosphere of 5% CO2 in air. The adherent cells were harvested by a short incubation with 0.5% EDTA trypsin in Ca/Mg free Dulbecco’s Phosphate Buffered Saline (Gibco). 8x10 to the 5 cells were seeded and cultured in wells of a 6 well plate for 18 hours, after which the cells were exposed ZnO 5 micron 1h : A549 cells were exposed to ZnO microparticles at 30 micrograms per ml for 1 hours. After this, the cells (approximately 2 million per well) were quickly washed with PBS (phosphate buffered saline) twice at room temperature after which the 6 well plates were deep frozen by quenching on liquid nitrogen (-196oC) and stored at -80oC until extraction for omics evaluation Total RNA was extracted from A549 cells using a micro RNeasy Kit (Qiagen, Crawley, UK) according to the manufacturer’s protocol. RNA was quantified with a NanoDrop 8000 spectrophotometer (Thermo Scientific, Waltham, MA), and the integrity of RNA was evaluated with a Agilent 2200 Tapestation (Agilent Technologies, Santa Clara, CA). Only RNA with integrity numbers (RINs) greater than 7.0 were used for subsequent RNA-seq experiments. All RNA libraries were produced using the Biomek FxP (Beckman Coulter A31842) with Ultra Directional RNA Library Prep Kit (New England Biolab E7420L) and NEBnext Multiplex Oligos for Illumina Dual Index Primers (New England Biolabs E7600S), using provided protocols and 500ng of total RNA. Constructed libraries were assessed for quality using the Tapestation 2200 (Agilent G2964AA) with High Sensitivity D1000 DNA screentape (5067-5584), and quantified using Kapa Library Quantification Kit (Kapa Biosystems KK4824) on an AriaMx Realtime PCR System (Agilent G8830A).

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens


text: unspecified

text: public

text: ArrayExpress

characteristic: broker name

text: epithelial lung carcinoma cell

text: human

text: Protocols: A549 cells were purchased from ATCC (VA, USA). A549 is an epithelial lung adenocarcinoma cell line established in 1972 (Giard et al., 1973). The cells were cultured in tissue culture flasks (75 cm2 and 275 cm2) in RPMI 1640 medium with Glutamax (Gibco, ThermoFisher Scientific Inc., Landsmeer, the Netherlands) supplemented with 10% Fetal Bovine Serum (FBS, Greiner BioOne Serum, Greiner BioOne BV, Alphen aan de Rijn, the Netherlands) and 1% penicillin/streptomycin (Gibco, 100 IU penicillin per mL, 100 µg streptomycin per mL). Cells were culture at 37oC in a humidified atmosphere of 5% CO2 in air. The adherent cells were harvested by a short incubation with 0.5% EDTA trypsin in Ca/Mg free Dulbecco’s Phosphate Buffered Saline (Gibco). 8x10 to the 5 cells were seeded and cultured in wells of a 6 well plate for 18 hours, after which the cells were exposed ZnO 5 micron 6h : A549 cells were exposed to ZnO microparticles at 30 micrograms per ml for 6 hours. After this, the cells (approximately 2 million per well) were quickly washed with PBS (phosphate buffered saline) twice at room temperature after which the 6 well plates were deep frozen by quenching on liquid nitrogen (-196oC) and stored at -80oC until extraction for omics evaluation Total RNA was extracted from A549 cells using a micro RNeasy Kit (Qiagen, Crawley, UK) according to the manufacturer’s protocol. RNA was quantified with a NanoDrop 8000 spectrophotometer (Thermo Scientific, Waltham, MA), and the integrity of RNA was evaluated with a Agilent 2200 Tapestation (Agilent Technologies, Santa Clara, CA). Only RNA with integrity numbers (RINs) greater than 7.0 were used for subsequent RNA-seq experiments. All RNA libraries were produced using the Biomek FxP (Beckman Coulter A31842) with Ultra Directional RNA Library Prep Kit (New England Biolab E7420L) and NEBnext Multiplex Oligos for Illumina Dual Index Primers (New England Biolabs E7600S), using provided protocols and 500ng of total RNA. Constructed libraries were assessed for quality using the Tapestation 2200 (Agilent G2964AA) with High Sensitivity D1000 DNA screentape (5067-5584), and quantified using Kapa Library Quantification Kit (Kapa Biosystems KK4824) on an AriaMx Realtime PCR System (Agilent G8830A).

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens


text: unspecified

text: public

text: ArrayExpress

characteristic: cell line

text: epithelial lung carcinoma cell

text: human

text: Protocols: A549 cells were purchased from ATCC (VA, USA). A549 is an epithelial lung adenocarcinoma cell line established in 1972 (Giard et al., 1973). The cells were cultured in tissue culture flasks (75 cm2 and 275 cm2) in RPMI 1640 medium with Glutamax (Gibco, ThermoFisher Scientific Inc., Landsmeer, the Netherlands) supplemented with 10% Fetal Bovine Serum (FBS, Greiner BioOne Serum, Greiner BioOne BV, Alphen aan de Rijn, the Netherlands) and 1% penicillin/streptomycin (Gibco, 100 IU penicillin per mL, 100 µg streptomycin per mL). Cells were culture at 37oC in a humidified atmosphere of 5% CO2 in air. The adherent cells were harvested by a short incubation with 0.5% EDTA trypsin in Ca/Mg free Dulbecco’s Phosphate Buffered Saline (Gibco). 8x10 to the 5 cells were seeded and cultured in wells of a 6 well plate for 18 hours, after which the cells were exposed ZnO 5 micron 24h : A549 cells were exposed to ZnO microparticles at 30 micrograms per ml for 24 hours. After this, the cells (approximately 2 million per well) were quickly washed with PBS (phosphate buffered saline) twice at room temperature after which the 6 well plates were deep frozen by quenching on liquid nitrogen (-196oC) and stored at -80oC until extraction for omics evaluation Total RNA was extracted from A549 cells using a micro RNeasy Kit (Qiagen, Crawley, UK) according to the manufacturer’s protocol. RNA was quantified with a NanoDrop 8000 spectrophotometer (Thermo Scientific, Waltham, MA), and the integrity of RNA was evaluated with a Agilent 2200 Tapestation (Agilent Technologies, Santa Clara, CA). Only RNA with integrity numbers (RINs) greater than 7.0 were used for subsequent RNA-seq experiments. All RNA libraries were produced using the Biomek FxP (Beckman Coulter A31842) with Ultra Directional RNA Library Prep Kit (New England Biolab E7420L) and NEBnext Multiplex Oligos for Illumina Dual Index Primers (New England Biolabs E7600S), using provided protocols and 500ng of total RNA. Constructed libraries were assessed for quality using the Tapestation 2200 (Agilent G2964AA) with High Sensitivity D1000 DNA screentape (5067-5584), and quantified using Kapa Library Quantification Kit (Kapa Biosystems KK4824) on an AriaMx Realtime PCR System (Agilent G8830A).

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens


text: unspecified

text: public

text: ArrayExpress

text: epithelial lung carcinoma cell

characteristic: cell type

text: human

text: Protocols: A549 cells were purchased from ATCC (VA, USA). A549 is an epithelial lung adenocarcinoma cell line established in 1972 (Giard et al., 1973). The cells were cultured in tissue culture flasks (75 cm2 and 275 cm2) in RPMI 1640 medium with Glutamax (Gibco, ThermoFisher Scientific Inc., Landsmeer, the Netherlands) supplemented with 10% Fetal Bovine Serum (FBS, Greiner BioOne Serum, Greiner BioOne BV, Alphen aan de Rijn, the Netherlands) and 1% penicillin/streptomycin (Gibco, 100 IU penicillin per mL, 100 µg streptomycin per mL). Cells were culture at 37oC in a humidified atmosphere of 5% CO2 in air. The adherent cells were harvested by a short incubation with 0.5% EDTA trypsin in Ca/Mg free Dulbecco’s Phosphate Buffered Saline (Gibco). 8x10 to the 5 cells were seeded and cultured in wells of a 6 well plate for 18 hours, after which the cells were exposed NM-110 1h : A549 cells were exposed to uncoated ZnO NPs NM110 at 15 micrograms per ml for 1 hours. After this, the cells (approximately 2 million per well) were quickly washed with PBS (phosphate buffered saline) twice at room temperature after which the 6 well plates were deep frozen by quenching on liquid nitrogen (-196oC) and stored at -80oC until extraction for omics evaluation Total RNA was extracted from A549 cells using a micro RNeasy Kit (Qiagen, Crawley, UK) according to the manufacturer’s protocol. RNA was quantified with a NanoDrop 8000 spectrophotometer (Thermo Scientific, Waltham, MA), and the integrity of RNA was evaluated with a Agilent 2200 Tapestation (Agilent Technologies, Santa Clara, CA). Only RNA with integrity numbers (RINs) greater than 7.0 were used for subsequent RNA-seq experiments. All RNA libraries were produced using the Biomek FxP (Beckman Coulter A31842) with Ultra Directional RNA Library Prep Kit (New England Biolab E7420L) and NEBnext Multiplex Oligos for Illumina Dual Index Primers (New England Biolabs E7600S), using provided protocols and 500ng of total RNA. Constructed libraries were assessed for quality using the Tapestation 2200 (Agilent G2964AA) with High Sensitivity D1000 DNA screentape (5067-5584), and quantified using Kapa Library Quantification Kit (Kapa Biosystems KK4824) on an AriaMx Realtime PCR System (Agilent G8830A).

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens


text: unspecified

text: public

text: ArrayExpress

text: epithelial lung carcinoma cell

text: human

characteristic: common name

text: Protocols: A549 cells were purchased from ATCC (VA, USA). A549 is an epithelial lung adenocarcinoma cell line established in 1972 (Giard et al., 1973). The cells were cultured in tissue culture flasks (75 cm2 and 275 cm2) in RPMI 1640 medium with Glutamax (Gibco, ThermoFisher Scientific Inc., Landsmeer, the Netherlands) supplemented with 10% Fetal Bovine Serum (FBS, Greiner BioOne Serum, Greiner BioOne BV, Alphen aan de Rijn, the Netherlands) and 1% penicillin/streptomycin (Gibco, 100 IU penicillin per mL, 100 µg streptomycin per mL). Cells were culture at 37oC in a humidified atmosphere of 5% CO2 in air. The adherent cells were harvested by a short incubation with 0.5% EDTA trypsin in Ca/Mg free Dulbecco’s Phosphate Buffered Saline (Gibco). 8x10 to the 5 cells were seeded and cultured in wells of a 6 well plate for 18 hours, after which the cells were exposed NM-110 6h : A549 cells were exposed to uncoated ZnO NPs NM110 at 15 micrograms per ml for 6 hours. After this, the cells (approximately 2 million per well) were quickly washed with PBS (phosphate buffered saline) twice at room temperature after which the 6 well plates were deep frozen by quenching on liquid nitrogen (-196oC) and stored at -80oC until extraction for omics evaluation Total RNA was extracted from A549 cells using a micro RNeasy Kit (Qiagen, Crawley, UK) according to the manufacturer’s protocol. RNA was quantified with a NanoDrop 8000 spectrophotometer (Thermo Scientific, Waltham, MA), and the integrity of RNA was evaluated with a Agilent 2200 Tapestation (Agilent Technologies, Santa Clara, CA). Only RNA with integrity numbers (RINs) greater than 7.0 were used for subsequent RNA-seq experiments. All RNA libraries were produced using the Biomek FxP (Beckman Coulter A31842) with Ultra Directional RNA Library Prep Kit (New England Biolab E7420L) and NEBnext Multiplex Oligos for Illumina Dual Index Primers (New England Biolabs E7600S), using provided protocols and 500ng of total RNA. Constructed libraries were assessed for quality using the Tapestation 2200 (Agilent G2964AA) with High Sensitivity D1000 DNA screentape (5067-5584), and quantified using Kapa Library Quantification Kit (Kapa Biosystems KK4824) on an AriaMx Realtime PCR System (Agilent G8830A).

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens


text: unspecified

text: public

text: ArrayExpress

text: epithelial lung carcinoma cell

text: human

text: Protocols: A549 cells were purchased from ATCC (VA, USA). A549 is an epithelial lung adenocarcinoma cell line established in 1972 (Giard et al., 1973). The cells were cultured in tissue culture flasks (75 cm2 and 275 cm2) in RPMI 1640 medium with Glutamax (Gibco, ThermoFisher Scientific Inc., Landsmeer, the Netherlands) supplemented with 10% Fetal Bovine Serum (FBS, Greiner BioOne Serum, Greiner BioOne BV, Alphen aan de Rijn, the Netherlands) and 1% penicillin/streptomycin (Gibco, 100 IU penicillin per mL, 100 µg streptomycin per mL). Cells were culture at 37oC in a humidified atmosphere of 5% CO2 in air. The adherent cells were harvested by a short incubation with 0.5% EDTA trypsin in Ca/Mg free Dulbecco’s Phosphate Buffered Saline (Gibco). 8x10 to the 5 cells were seeded and cultured in wells of a 6 well plate for 18 hours, after which the cells were exposed NM-110 24h : A549 cells were exposed to uncoated ZnO NPs NM110 at 15 micrograms per ml for 24 hours. After this, the cells (approximately 2 million per well) were quickly washed with PBS (phosphate buffered saline) twice at room temperature after which the 6 well plates were deep frozen by quenching on liquid nitrogen (-196oC) and stored at -80oC until extraction for omics evaluation Total RNA was extracted from A549 cells using a micro RNeasy Kit (Qiagen, Crawley, UK) according to the manufacturer’s protocol. RNA was quantified with a NanoDrop 8000 spectrophotometer (Thermo Scientific, Waltham, MA), and the integrity of RNA was evaluated with a Agilent 2200 Tapestation (Agilent Technologies, Santa Clara, CA). Only RNA with integrity numbers (RINs) greater than 7.0 were used for subsequent RNA-seq experiments. All RNA libraries were produced using the Biomek FxP (Beckman Coulter A31842) with Ultra Directional RNA Library Prep Kit (New England Biolab E7420L) and NEBnext Multiplex Oligos for Illumina Dual Index Primers (New England Biolabs E7600S), using provided protocols and 500ng of total RNA. Constructed libraries were assessed for quality using the Tapestation 2200 (Agilent G2964AA) with High Sensitivity D1000 DNA screentape (5067-5584), and quantified using Kapa Library Quantification Kit (Kapa Biosystems KK4824) on an AriaMx Realtime PCR System (Agilent G8830A).

characteristic: description

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens


text: unspecified

text: public

text: ArrayExpress

text: epithelial lung carcinoma cell

text: human

text: Protocols: A549 cells were purchased from ATCC (VA, USA). A549 is an epithelial lung adenocarcinoma cell line established in 1972 (Giard et al., 1973). The cells were cultured in tissue culture flasks (75 cm2 and 275 cm2) in RPMI 1640 medium with Glutamax (Gibco, ThermoFisher Scientific Inc., Landsmeer, the Netherlands) supplemented with 10% Fetal Bovine Serum (FBS, Greiner BioOne Serum, Greiner BioOne BV, Alphen aan de Rijn, the Netherlands) and 1% penicillin/streptomycin (Gibco, 100 IU penicillin per mL, 100 µg streptomycin per mL). Cells were culture at 37oC in a humidified atmosphere of 5% CO2 in air. The adherent cells were harvested by a short incubation with 0.5% EDTA trypsin in Ca/Mg free Dulbecco’s Phosphate Buffered Saline (Gibco). 8x10 to the 5 cells were seeded and cultured in wells of a 6 well plate for 18 hours, after which the cells were exposed NM-111 1h : A549 cells were exposed to ZnO NPs coated with triethoxycaprylsilane NM111 at 10 micrograms per ml for 1 hours. After this, the cells (approximately 2 million per well) were quickly washed with PBS (phosphate buffered saline) twice at room temperature after which the 6 well plates were deep frozen by quenching on liquid nitrogen (-196oC) and stored at -80oC until extraction for omics evaluation Total RNA was extracted from A549 cells using a micro RNeasy Kit (Qiagen, Crawley, UK) according to the manufacturer’s protocol. RNA was quantified with a NanoDrop 8000 spectrophotometer (Thermo Scientific, Waltham, MA), and the integrity of RNA was evaluated with a Agilent 2200 Tapestation (Agilent Technologies, Santa Clara, CA). Only RNA with integrity numbers (RINs) greater than 7.0 were used for subsequent RNA-seq experiments. All RNA libraries were produced using the Biomek FxP (Beckman Coulter A31842) with Ultra Directional RNA Library Prep Kit (New England Biolab E7420L) and NEBnext Multiplex Oligos for Illumina Dual Index Primers (New England Biolabs E7600S), using provided protocols and 500ng of total RNA. Constructed libraries were assessed for quality using the Tapestation 2200 (Agilent G2964AA) with High Sensitivity D1000 DNA screentape (5067-5584), and quantified using Kapa Library Quantification Kit (Kapa Biosystems KK4824) on an AriaMx Realtime PCR System (Agilent G8830A).

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: Homo sapiens


text: unspecified

text: public

text: ArrayExpress

text: epithelial lung carcinoma cell

text: human

text: Protocols: A549 cells were purchased from ATCC (VA, USA). A549 is an epithelial lung adenocarcinoma cell line established in 1972 (Giard et al., 1973). The cells were cultured in tissue culture flasks (75 cm2 and 275 cm2) in RPMI 1640 medium with Glutamax (Gibco, ThermoFisher Scientific Inc., Landsmeer, the Netherlands) supplemented with 10% Fetal Bovine Serum (FBS, Greiner BioOne Serum, Greiner BioOne BV, Alphen aan de Rijn, the Netherlands) and 1% penicillin/streptomycin (Gibco, 100 IU penicillin per mL, 100 µg streptomycin per mL). Cells were culture at 37oC in a humidified atmosphere of 5% CO2 in air. The adherent cells were harvested by a short incubation with 0.5% EDTA trypsin in Ca/Mg free Dulbecco’s Phosphate Buffered Saline (Gibco). 8x10 to the 5 cells were seeded and cultured in wells of a 6 well plate for 18 hours, after which the cells were exposed NM-111 6h : A549 cells were exposed to ZnO NPs coated with triethoxycaprylsilane NM111 at 10 micrograms per ml for 6 hours. After this, the cells (approximately 2 million per well) were quickly washed with PBS (phosphate buffered saline) twice at room temperature after which the 6 well plates were deep frozen by quenching on liquid nitrogen (-196oC) and stored at -80oC until extraction for omics evaluation Total RNA was extracted from A549 cells using a micro RNeasy Kit (Qiagen, Crawley, UK) according to the manufacturer’s protocol. RNA was quantified with a NanoDrop 8000 spectrophotometer (Thermo Scientific, Waltham, MA), and the integrity of RNA was evaluated with a Agilent 2200 Tapestation (Agilent Technologies, Santa Clara, CA). Only RNA with integrity numbers (RINs) greater than 7.0 were used for subsequent RNA-seq experiments. All RNA libraries were produced using the Biomek FxP (Beckman Coulter A31842) with Ultra Directional RNA Library Prep Kit (New England Biolab E7420L) and NEBnext Multiplex Oligos for Illumina Dual Index Primers (New England Biolabs E7600S), using provided protocols and 500ng of total RNA. Constructed libraries were assessed for quality using the Tapestation 2200 (Agilent G2964AA) with High Sensitivity D1000 DNA screentape (5067-5584), and quantified using Kapa Library Quantification Kit (Kapa Biosystems KK4824) on an AriaMx Realtime PCR System (Agilent G8830A).

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens

characteristic: title


characteristic: ENA-CHECKLIST

text: unspecified

text: public

text: ArrayExpress

text: epithelial lung carcinoma cell

text: human

text: Protocols: A549 cells were purchased from ATCC (VA, USA). A549 is an epithelial lung adenocarcinoma cell line established in 1972 (Giard et al., 1973). The cells were cultured in tissue culture flasks (75 cm2 and 275 cm2) in RPMI 1640 medium with Glutamax (Gibco, ThermoFisher Scientific Inc., Landsmeer, the Netherlands) supplemented with 10% Fetal Bovine Serum (FBS, Greiner BioOne Serum, Greiner BioOne BV, Alphen aan de Rijn, the Netherlands) and 1% penicillin/streptomycin (Gibco, 100 IU penicillin per mL, 100 µg streptomycin per mL). Cells were culture at 37oC in a humidified atmosphere of 5% CO2 in air. The adherent cells were harvested by a short incubation with 0.5% EDTA trypsin in Ca/Mg free Dulbecco’s Phosphate Buffered Saline (Gibco). 8x10 to the 5 cells were seeded and cultured in wells of a 6 well plate for 18 hours, after which the cells were exposed NM-111 24h : A549 cells were exposed to ZnO NPs coated with triethoxycaprylsilane NM111 at 10 micrograms per ml for 24 hours. After this, the cells (approximately 2 million per well) were quickly washed with PBS (phosphate buffered saline) twice at room temperature after which the 6 well plates were deep frozen by quenching on liquid nitrogen (-196oC) and stored at -80oC until extraction for omics evaluation Total RNA was extracted from A549 cells using a micro RNeasy Kit (Qiagen, Crawley, UK) according to the manufacturer’s protocol. RNA was quantified with a NanoDrop 8000 spectrophotometer (Thermo Scientific, Waltham, MA), and the integrity of RNA was evaluated with a Agilent 2200 Tapestation (Agilent Technologies, Santa Clara, CA). Only RNA with integrity numbers (RINs) greater than 7.0 were used for subsequent RNA-seq experiments. All RNA libraries were produced using the Biomek FxP (Beckman Coulter A31842) with Ultra Directional RNA Library Prep Kit (New England Biolab E7420L) and NEBnext Multiplex Oligos for Illumina Dual Index Primers (New England Biolabs E7600S), using provided protocols and 500ng of total RNA. Constructed libraries were assessed for quality using the Tapestation 2200 (Agilent G2964AA) with High Sensitivity D1000 DNA screentape (5067-5584), and quantified using Kapa Library Quantification Kit (Kapa Biosystems KK4824) on an AriaMx Realtime PCR System (Agilent G8830A).

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens


text: unspecified

characteristic: INSDC center name

text: public

text: ArrayExpress

text: epithelial lung carcinoma cell

text: human

text: Protocols: A549 cells were purchased from ATCC (VA, USA). A549 is an epithelial lung adenocarcinoma cell line established in 1972 (Giard et al., 1973). The cells were cultured in tissue culture flasks (75 cm2 and 275 cm2) in RPMI 1640 medium with Glutamax (Gibco, ThermoFisher Scientific Inc., Landsmeer, the Netherlands) supplemented with 10% Fetal Bovine Serum (FBS, Greiner BioOne Serum, Greiner BioOne BV, Alphen aan de Rijn, the Netherlands) and 1% penicillin/streptomycin (Gibco, 100 IU penicillin per mL, 100 µg streptomycin per mL). Cells were culture at 37oC in a humidified atmosphere of 5% CO2 in air. The adherent cells were harvested by a short incubation with 0.5% EDTA trypsin in Ca/Mg free Dulbecco’s Phosphate Buffered Saline (Gibco). 8x10 to the 5 cells were seeded and cultured in wells of a 6 well plate for 18 hours, after which the cells were exposed AgNO3 1h : A549 cells were exposed to AgNO3 at 8 micrograms per ml for 1 hours. After this, the cells (approximately 2 million per well) were quickly washed with PBS (phosphate buffered saline) twice at room temperature after which the 6 well plates were deep frozen by quenching on liquid nitrogen (-196oC) and stored at -80oC until extraction for omics evaluation Total RNA was extracted from A549 cells using a micro RNeasy Kit (Qiagen, Crawley, UK) according to the manufacturer’s protocol. RNA was quantified with a NanoDrop 8000 spectrophotometer (Thermo Scientific, Waltham, MA), and the integrity of RNA was evaluated with a Agilent 2200 Tapestation (Agilent Technologies, Santa Clara, CA). Only RNA with integrity numbers (RINs) greater than 7.0 were used for subsequent RNA-seq experiments. All RNA libraries were produced using the Biomek FxP (Beckman Coulter A31842) with Ultra Directional RNA Library Prep Kit (New England Biolab E7420L) and NEBnext Multiplex Oligos for Illumina Dual Index Primers (New England Biolabs E7600S), using provided protocols and 500ng of total RNA. Constructed libraries were assessed for quality using the Tapestation 2200 (Agilent G2964AA) with High Sensitivity D1000 DNA screentape (5067-5584), and quantified using Kapa Library Quantification Kit (Kapa Biosystems KK4824) on an AriaMx Realtime PCR System (Agilent G8830A).

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens


text: unspecified

characteristic: INSDC first public

text: public

text: ArrayExpress

text: epithelial lung carcinoma cell

text: human

text: Protocols: A549 cells were purchased from ATCC (VA, USA). A549 is an epithelial lung adenocarcinoma cell line established in 1972 (Giard et al., 1973). The cells were cultured in tissue culture flasks (75 cm2 and 275 cm2) in RPMI 1640 medium with Glutamax (Gibco, ThermoFisher Scientific Inc., Landsmeer, the Netherlands) supplemented with 10% Fetal Bovine Serum (FBS, Greiner BioOne Serum, Greiner BioOne BV, Alphen aan de Rijn, the Netherlands) and 1% penicillin/streptomycin (Gibco, 100 IU penicillin per mL, 100 µg streptomycin per mL). Cells were culture at 37oC in a humidified atmosphere of 5% CO2 in air. The adherent cells were harvested by a short incubation with 0.5% EDTA trypsin in Ca/Mg free Dulbecco’s Phosphate Buffered Saline (Gibco). 8x10 to the 5 cells were seeded and cultured in wells of a 6 well plate for 18 hours, after which the cells were exposed AgNO3 6h : A549 cells were exposed to AgNO3 at 8 micrograms per ml for 6 hours. After this, the cells (approximately 2 million per well) were quickly washed with PBS (phosphate buffered saline) twice at room temperature after which the 6 well plates were deep frozen by quenching on liquid nitrogen (-196oC) and stored at -80oC until extraction for omics evaluation Total RNA was extracted from A549 cells using a micro RNeasy Kit (Qiagen, Crawley, UK) according to the manufacturer’s protocol. RNA was quantified with a NanoDrop 8000 spectrophotometer (Thermo Scientific, Waltham, MA), and the integrity of RNA was evaluated with a Agilent 2200 Tapestation (Agilent Technologies, Santa Clara, CA). Only RNA with integrity numbers (RINs) greater than 7.0 were used for subsequent RNA-seq experiments. All RNA libraries were produced using the Biomek FxP (Beckman Coulter A31842) with Ultra Directional RNA Library Prep Kit (New England Biolab E7420L) and NEBnext Multiplex Oligos for Illumina Dual Index Primers (New England Biolabs E7600S), using provided protocols and 500ng of total RNA. Constructed libraries were assessed for quality using the Tapestation 2200 (Agilent G2964AA) with High Sensitivity D1000 DNA screentape (5067-5584), and quantified using Kapa Library Quantification Kit (Kapa Biosystems KK4824) on an AriaMx Realtime PCR System (Agilent G8830A).

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens


text: unspecified

characteristic: INSDC last update

text: public

text: ArrayExpress

text: epithelial lung carcinoma cell

text: human

text: Protocols: A549 cells were purchased from ATCC (VA, USA). A549 is an epithelial lung adenocarcinoma cell line established in 1972 (Giard et al., 1973). The cells were cultured in tissue culture flasks (75 cm2 and 275 cm2) in RPMI 1640 medium with Glutamax (Gibco, ThermoFisher Scientific Inc., Landsmeer, the Netherlands) supplemented with 10% Fetal Bovine Serum (FBS, Greiner BioOne Serum, Greiner BioOne BV, Alphen aan de Rijn, the Netherlands) and 1% penicillin/streptomycin (Gibco, 100 IU penicillin per mL, 100 µg streptomycin per mL). Cells were culture at 37oC in a humidified atmosphere of 5% CO2 in air. The adherent cells were harvested by a short incubation with 0.5% EDTA trypsin in Ca/Mg free Dulbecco’s Phosphate Buffered Saline (Gibco). 8x10 to the 5 cells were seeded and cultured in wells of a 6 well plate for 18 hours, after which the cells were exposed AgNO3 24h : A549 cells were exposed to AgNO3 at 8 micrograms per ml for 24 hours. After this, the cells (approximately 2 million per well) were quickly washed with PBS (phosphate buffered saline) twice at room temperature after which the 6 well plates were deep frozen by quenching on liquid nitrogen (-196oC) and stored at -80oC until extraction for omics evaluation Total RNA was extracted from A549 cells using a micro RNeasy Kit (Qiagen, Crawley, UK) according to the manufacturer’s protocol. RNA was quantified with a NanoDrop 8000 spectrophotometer (Thermo Scientific, Waltham, MA), and the integrity of RNA was evaluated with a Agilent 2200 Tapestation (Agilent Technologies, Santa Clara, CA). Only RNA with integrity numbers (RINs) greater than 7.0 were used for subsequent RNA-seq experiments. All RNA libraries were produced using the Biomek FxP (Beckman Coulter A31842) with Ultra Directional RNA Library Prep Kit (New England Biolab E7420L) and NEBnext Multiplex Oligos for Illumina Dual Index Primers (New England Biolabs E7600S), using provided protocols and 500ng of total RNA. Constructed libraries were assessed for quality using the Tapestation 2200 (Agilent G2964AA) with High Sensitivity D1000 DNA screentape (5067-5584), and quantified using Kapa Library Quantification Kit (Kapa Biosystems KK4824) on an AriaMx Realtime PCR System (Agilent G8830A).

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens


text: unspecified

text: public

characteristic: INSDC status

text: ArrayExpress

text: epithelial lung carcinoma cell

text: human

text: Protocols: A549 cells were purchased from ATCC (VA, USA). A549 is an epithelial lung adenocarcinoma cell line established in 1972 (Giard et al., 1973). The cells were cultured in tissue culture flasks (75 cm2 and 275 cm2) in RPMI 1640 medium with Glutamax (Gibco, ThermoFisher Scientific Inc., Landsmeer, the Netherlands) supplemented with 10% Fetal Bovine Serum (FBS, Greiner BioOne Serum, Greiner BioOne BV, Alphen aan de Rijn, the Netherlands) and 1% penicillin/streptomycin (Gibco, 100 IU penicillin per mL, 100 µg streptomycin per mL). Cells were culture at 37oC in a humidified atmosphere of 5% CO2 in air. The adherent cells were harvested by a short incubation with 0.5% EDTA trypsin in Ca/Mg free Dulbecco’s Phosphate Buffered Saline (Gibco). 8x10 to the 5 cells were seeded and cultured in wells of a 6 well plate for 18 hours, after which the cells were exposed Ag micron sized 1h : A549 cells were exposed to Silver microparticles at 128 micrograms per ml for 1 hours. After this, the cells (approximately 2 million per well) were quickly washed with PBS (phosphate buffered saline) twice at room temperature after which the 6 well plates were deep frozen by quenching on liquid nitrogen (-196oC) and stored at -80oC until extraction for omics evaluation Total RNA was extracted from A549 cells using a micro RNeasy Kit (Qiagen, Crawley, UK) according to the manufacturer’s protocol. RNA was quantified with a NanoDrop 8000 spectrophotometer (Thermo Scientific, Waltham, MA), and the integrity of RNA was evaluated with a Agilent 2200 Tapestation (Agilent Technologies, Santa Clara, CA). Only RNA with integrity numbers (RINs) greater than 7.0 were used for subsequent RNA-seq experiments. All RNA libraries were produced using the Biomek FxP (Beckman Coulter A31842) with Ultra Directional RNA Library Prep Kit (New England Biolab E7420L) and NEBnext Multiplex Oligos for Illumina Dual Index Primers (New England Biolabs E7600S), using provided protocols and 500ng of total RNA. Constructed libraries were assessed for quality using the Tapestation 2200 (Agilent G2964AA) with High Sensitivity D1000 DNA screentape (5067-5584), and quantified using Kapa Library Quantification Kit (Kapa Biosystems KK4824) on an AriaMx Realtime PCR System (Agilent G8830A).

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens


characteristic: ENA-FIRST-PUBLIC

text: unspecified

text: public

text: ArrayExpress

text: epithelial lung carcinoma cell

text: human

text: Protocols: A549 cells were purchased from ATCC (VA, USA). A549 is an epithelial lung adenocarcinoma cell line established in 1972 (Giard et al., 1973). The cells were cultured in tissue culture flasks (75 cm2 and 275 cm2) in RPMI 1640 medium with Glutamax (Gibco, ThermoFisher Scientific Inc., Landsmeer, the Netherlands) supplemented with 10% Fetal Bovine Serum (FBS, Greiner BioOne Serum, Greiner BioOne BV, Alphen aan de Rijn, the Netherlands) and 1% penicillin/streptomycin (Gibco, 100 IU penicillin per mL, 100 µg streptomycin per mL). Cells were culture at 37oC in a humidified atmosphere of 5% CO2 in air. The adherent cells were harvested by a short incubation with 0.5% EDTA trypsin in Ca/Mg free Dulbecco’s Phosphate Buffered Saline (Gibco). 8x10 to the 5 cells were seeded and cultured in wells of a 6 well plate for 18 hours, after which the cells were exposed Ag micron sized 6h : A549 cells were exposed to Silver microparticles at 128 micrograms per ml for 6 hours. After this, the cells (approximately 2 million per well) were quickly washed with PBS (phosphate buffered saline) twice at room temperature after which the 6 well plates were deep frozen by quenching on liquid nitrogen (-196oC) and stored at -80oC until extraction for omics evaluation Total RNA was extracted from A549 cells using a micro RNeasy Kit (Qiagen, Crawley, UK) according to the manufacturer’s protocol. RNA was quantified with a NanoDrop 8000 spectrophotometer (Thermo Scientific, Waltham, MA), and the integrity of RNA was evaluated with a Agilent 2200 Tapestation (Agilent Technologies, Santa Clara, CA). Only RNA with integrity numbers (RINs) greater than 7.0 were used for subsequent RNA-seq experiments. All RNA libraries were produced using the Biomek FxP (Beckman Coulter A31842) with Ultra Directional RNA Library Prep Kit (New England Biolab E7420L) and NEBnext Multiplex Oligos for Illumina Dual Index Primers (New England Biolabs E7600S), using provided protocols and 500ng of total RNA. Constructed libraries were assessed for quality using the Tapestation 2200 (Agilent G2964AA) with High Sensitivity D1000 DNA screentape (5067-5584), and quantified using Kapa Library Quantification Kit (Kapa Biosystems KK4824) on an AriaMx Realtime PCR System (Agilent G8830A).

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens


characteristic: ENA-LAST-UPDATE

text: unspecified

text: public

text: ArrayExpress

text: epithelial lung carcinoma cell

text: human

text: Protocols: A549 cells were purchased from ATCC (VA, USA). A549 is an epithelial lung adenocarcinoma cell line established in 1972 (Giard et al., 1973). The cells were cultured in tissue culture flasks (75 cm2 and 275 cm2) in RPMI 1640 medium with Glutamax (Gibco, ThermoFisher Scientific Inc., Landsmeer, the Netherlands) supplemented with 10% Fetal Bovine Serum (FBS, Greiner BioOne Serum, Greiner BioOne BV, Alphen aan de Rijn, the Netherlands) and 1% penicillin/streptomycin (Gibco, 100 IU penicillin per mL, 100 µg streptomycin per mL). Cells were culture at 37oC in a humidified atmosphere of 5% CO2 in air. The adherent cells were harvested by a short incubation with 0.5% EDTA trypsin in Ca/Mg free Dulbecco’s Phosphate Buffered Saline (Gibco). 8x10 to the 5 cells were seeded and cultured in wells of a 6 well plate for 18 hours, after which the cells were exposed Ag micron sized 24h : A549 cells were exposed to Silver microparticles at 128 micrograms per ml for 24 hours. After this, the cells (approximately 2 million per well) were quickly washed with PBS (phosphate buffered saline) twice at room temperature after which the 6 well plates were deep frozen by quenching on liquid nitrogen (-196oC) and stored at -80oC until extraction for omics evaluation Total RNA was extracted from A549 cells using a micro RNeasy Kit (Qiagen, Crawley, UK) according to the manufacturer’s protocol. RNA was quantified with a NanoDrop 8000 spectrophotometer (Thermo Scientific, Waltham, MA), and the integrity of RNA was evaluated with a Agilent 2200 Tapestation (Agilent Technologies, Santa Clara, CA). Only RNA with integrity numbers (RINs) greater than 7.0 were used for subsequent RNA-seq experiments. All RNA libraries were produced using the Biomek FxP (Beckman Coulter A31842) with Ultra Directional RNA Library Prep Kit (New England Biolab E7420L) and NEBnext Multiplex Oligos for Illumina Dual Index Primers (New England Biolabs E7600S), using provided protocols and 500ng of total RNA. Constructed libraries were assessed for quality using the Tapestation 2200 (Agilent G2964AA) with High Sensitivity D1000 DNA screentape (5067-5584), and quantified using Kapa Library Quantification Kit (Kapa Biosystems KK4824) on an AriaMx Realtime PCR System (Agilent G8830A).

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens


characteristic: External Id

text: unspecified

text: public

text: ArrayExpress

text: epithelial lung carcinoma cell

text: human

text: Protocols: A549 cells were purchased from ATCC (VA, USA). A549 is an epithelial lung adenocarcinoma cell line established in 1972 (Giard et al., 1973). The cells were cultured in tissue culture flasks (75 cm2 and 275 cm2) in RPMI 1640 medium with Glutamax (Gibco, ThermoFisher Scientific Inc., Landsmeer, the Netherlands) supplemented with 10% Fetal Bovine Serum (FBS, Greiner BioOne Serum, Greiner BioOne BV, Alphen aan de Rijn, the Netherlands) and 1% penicillin/streptomycin (Gibco, 100 IU penicillin per mL, 100 µg streptomycin per mL). Cells were culture at 37oC in a humidified atmosphere of 5% CO2 in air. The adherent cells were harvested by a short incubation with 0.5% EDTA trypsin in Ca/Mg free Dulbecco’s Phosphate Buffered Saline (Gibco). 8x10 to the 5 cells were seeded and cultured in wells of a 6 well plate for 18 hours, after which the cells were exposed Ag 15 nm 1h : A549 cells were exposed to Silver nanoparticles NM300K at 38.6 micrograms per ml for 1 hours. After this, the cells (approximately 2 million per well) were quickly washed with PBS (phosphate buffered saline) twice at room temperature after which the 6 well plates were deep frozen by quenching on liquid nitrogen (-196oC) and stored at -80oC until extraction for omics evaluation Total RNA was extracted from A549 cells using a micro RNeasy Kit (Qiagen, Crawley, UK) according to the manufacturer’s protocol. RNA was quantified with a NanoDrop 8000 spectrophotometer (Thermo Scientific, Waltham, MA), and the integrity of RNA was evaluated with a Agilent 2200 Tapestation (Agilent Technologies, Santa Clara, CA). Only RNA with integrity numbers (RINs) greater than 7.0 were used for subsequent RNA-seq experiments. All RNA libraries were produced using the Biomek FxP (Beckman Coulter A31842) with Ultra Directional RNA Library Prep Kit (New England Biolab E7420L) and NEBnext Multiplex Oligos for Illumina Dual Index Primers (New England Biolabs E7600S), using provided protocols and 500ng of total RNA. Constructed libraries were assessed for quality using the Tapestation 2200 (Agilent G2964AA) with High Sensitivity D1000 DNA screentape (5067-5584), and quantified using Kapa Library Quantification Kit (Kapa Biosystems KK4824) on an AriaMx Realtime PCR System (Agilent G8830A).

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens


text: unspecified

text: public

characteristic: SRA accession

text: ArrayExpress

text: epithelial lung carcinoma cell

text: human

text: Protocols: A549 cells were purchased from ATCC (VA, USA). A549 is an epithelial lung adenocarcinoma cell line established in 1972 (Giard et al., 1973). The cells were cultured in tissue culture flasks (75 cm2 and 275 cm2) in RPMI 1640 medium with Glutamax (Gibco, ThermoFisher Scientific Inc., Landsmeer, the Netherlands) supplemented with 10% Fetal Bovine Serum (FBS, Greiner BioOne Serum, Greiner BioOne BV, Alphen aan de Rijn, the Netherlands) and 1% penicillin/streptomycin (Gibco, 100 IU penicillin per mL, 100 µg streptomycin per mL). Cells were culture at 37oC in a humidified atmosphere of 5% CO2 in air. The adherent cells were harvested by a short incubation with 0.5% EDTA trypsin in Ca/Mg free Dulbecco’s Phosphate Buffered Saline (Gibco). 8x10 to the 5 cells were seeded and cultured in wells of a 6 well plate for 18 hours, after which the cells were exposed Ag 15 nm 6h : A549 cells were exposed to Silver nanoparticles NM300K at 38.6 micrograms per ml for 6 hours. After this, the cells (approximately 2 million per well) were quickly washed with PBS (phosphate buffered saline) twice at room temperature after which the 6 well plates were deep frozen by quenching on liquid nitrogen (-196oC) and stored at -80oC until extraction for omics evaluation Total RNA was extracted from A549 cells using a micro RNeasy Kit (Qiagen, Crawley, UK) according to the manufacturer’s protocol. RNA was quantified with a NanoDrop 8000 spectrophotometer (Thermo Scientific, Waltham, MA), and the integrity of RNA was evaluated with a Agilent 2200 Tapestation (Agilent Technologies, Santa Clara, CA). Only RNA with integrity numbers (RINs) greater than 7.0 were used for subsequent RNA-seq experiments. All RNA libraries were produced using the Biomek FxP (Beckman Coulter A31842) with Ultra Directional RNA Library Prep Kit (New England Biolab E7420L) and NEBnext Multiplex Oligos for Illumina Dual Index Primers (New England Biolabs E7600S), using provided protocols and 500ng of total RNA. Constructed libraries were assessed for quality using the Tapestation 2200 (Agilent G2964AA) with High Sensitivity D1000 DNA screentape (5067-5584), and quantified using Kapa Library Quantification Kit (Kapa Biosystems KK4824) on an AriaMx Realtime PCR System (Agilent G8830A).

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens


text: unspecified

text: public

characteristic: Submitter Id

text: ArrayExpress

text: epithelial lung carcinoma cell

text: human

text: Protocols: A549 cells were purchased from ATCC (VA, USA). A549 is an epithelial lung adenocarcinoma cell line established in 1972 (Giard et al., 1973). The cells were cultured in tissue culture flasks (75 cm2 and 275 cm2) in RPMI 1640 medium with Glutamax (Gibco, ThermoFisher Scientific Inc., Landsmeer, the Netherlands) supplemented with 10% Fetal Bovine Serum (FBS, Greiner BioOne Serum, Greiner BioOne BV, Alphen aan de Rijn, the Netherlands) and 1% penicillin/streptomycin (Gibco, 100 IU penicillin per mL, 100 µg streptomycin per mL). Cells were culture at 37oC in a humidified atmosphere of 5% CO2 in air. The adherent cells were harvested by a short incubation with 0.5% EDTA trypsin in Ca/Mg free Dulbecco’s Phosphate Buffered Saline (Gibco). 8x10 to the 5 cells were seeded and cultured in wells of a 6 well plate for 18 hours, after which the cells were exposed Ag 15 nm 24h : A549 cells were exposed to Silver nanoparticles NM300K at 38.6 micrograms per ml for 24 hours. After this, the cells (approximately 2 million per well) were quickly washed with PBS (phosphate buffered saline) twice at room temperature after which the 6 well plates were deep frozen by quenching on liquid nitrogen (-196oC) and stored at -80oC until extraction for omics evaluation Total RNA was extracted from A549 cells using a micro RNeasy Kit (Qiagen, Crawley, UK) according to the manufacturer’s protocol. RNA was quantified with a NanoDrop 8000 spectrophotometer (Thermo Scientific, Waltham, MA), and the integrity of RNA was evaluated with a Agilent 2200 Tapestation (Agilent Technologies, Santa Clara, CA). Only RNA with integrity numbers (RINs) greater than 7.0 were used for subsequent RNA-seq experiments. All RNA libraries were produced using the Biomek FxP (Beckman Coulter A31842) with Ultra Directional RNA Library Prep Kit (New England Biolab E7420L) and NEBnext Multiplex Oligos for Illumina Dual Index Primers (New England Biolabs E7600S), using provided protocols and 500ng of total RNA. Constructed libraries were assessed for quality using the Tapestation 2200 (Agilent G2964AA) with High Sensitivity D1000 DNA screentape (5067-5584), and quantified using Kapa Library Quantification Kit (Kapa Biosystems KK4824) on an AriaMx Realtime PCR System (Agilent G8830A).

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens


text: unspecified

text: public

text: ArrayExpress

characteristic: broker name

text: epithelial lung carcinoma cell

text: human

text: Protocols: A549 cells were purchased from ATCC (VA, USA). A549 is an epithelial lung adenocarcinoma cell line established in 1972 (Giard et al., 1973). The cells were cultured in tissue culture flasks (75 cm2 and 275 cm2) in RPMI 1640 medium with Glutamax (Gibco, ThermoFisher Scientific Inc., Landsmeer, the Netherlands) supplemented with 10% Fetal Bovine Serum (FBS, Greiner BioOne Serum, Greiner BioOne BV, Alphen aan de Rijn, the Netherlands) and 1% penicillin/streptomycin (Gibco, 100 IU penicillin per mL, 100 µg streptomycin per mL). Cells were culture at 37oC in a humidified atmosphere of 5% CO2 in air. The adherent cells were harvested by a short incubation with 0.5% EDTA trypsin in Ca/Mg free Dulbecco’s Phosphate Buffered Saline (Gibco). 8x10 to the 5 cells were seeded and cultured in wells of a 6 well plate for 18 hours, after which the cells were exposed CeO2 A 1h : A549 cells were exposed to Ceria nanoparticles CeO2 A at 128 micrograms per ml for 1 hours. After this, the cells (approximately 2 million per well) were quickly washed with PBS (phosphate buffered saline) twice at room temperature after which the 6 well plates were deep frozen by quenching on liquid nitrogen (-196oC) and stored at -80oC until extraction for omics evaluation Total RNA was extracted from A549 cells using a micro RNeasy Kit (Qiagen, Crawley, UK) according to the manufacturer’s protocol. RNA was quantified with a NanoDrop 8000 spectrophotometer (Thermo Scientific, Waltham, MA), and the integrity of RNA was evaluated with a Agilent 2200 Tapestation (Agilent Technologies, Santa Clara, CA). Only RNA with integrity numbers (RINs) greater than 7.0 were used for subsequent RNA-seq experiments. All RNA libraries were produced using the Biomek FxP (Beckman Coulter A31842) with Ultra Directional RNA Library Prep Kit (New England Biolab E7420L) and NEBnext Multiplex Oligos for Illumina Dual Index Primers (New England Biolabs E7600S), using provided protocols and 500ng of total RNA. Constructed libraries were assessed for quality using the Tapestation 2200 (Agilent G2964AA) with High Sensitivity D1000 DNA screentape (5067-5584), and quantified using Kapa Library Quantification Kit (Kapa Biosystems KK4824) on an AriaMx Realtime PCR System (Agilent G8830A).

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens


text: unspecified

text: public

text: ArrayExpress

characteristic: cell line

text: epithelial lung carcinoma cell

text: human

text: Protocols: A549 cells were purchased from ATCC (VA, USA). A549 is an epithelial lung adenocarcinoma cell line established in 1972 (Giard et al., 1973). The cells were cultured in tissue culture flasks (75 cm2 and 275 cm2) in RPMI 1640 medium with Glutamax (Gibco, ThermoFisher Scientific Inc., Landsmeer, the Netherlands) supplemented with 10% Fetal Bovine Serum (FBS, Greiner BioOne Serum, Greiner BioOne BV, Alphen aan de Rijn, the Netherlands) and 1% penicillin/streptomycin (Gibco, 100 IU penicillin per mL, 100 µg streptomycin per mL). Cells were culture at 37oC in a humidified atmosphere of 5% CO2 in air. The adherent cells were harvested by a short incubation with 0.5% EDTA trypsin in Ca/Mg free Dulbecco’s Phosphate Buffered Saline (Gibco). 8x10 to the 5 cells were seeded and cultured in wells of a 6 well plate for 18 hours, after which the cells were exposed Control 1h : A549 cells were grown for 1 hours. After this, the cells (approximately 2 million per well) were quickly washed with PBS (phosphate buffered saline) twice at room temperature after which the 6 well plates were deep frozen by quenching on liquid nitrogen (-196oC) and stored at -80oC until extraction for omics evaluation Total RNA was extracted from A549 cells using a micro RNeasy Kit (Qiagen, Crawley, UK) according to the manufacturer’s protocol. RNA was quantified with a NanoDrop 8000 spectrophotometer (Thermo Scientific, Waltham, MA), and the integrity of RNA was evaluated with a Agilent 2200 Tapestation (Agilent Technologies, Santa Clara, CA). Only RNA with integrity numbers (RINs) greater than 7.0 were used for subsequent RNA-seq experiments. All RNA libraries were produced using the Biomek FxP (Beckman Coulter A31842) with Ultra Directional RNA Library Prep Kit (New England Biolab E7420L) and NEBnext Multiplex Oligos for Illumina Dual Index Primers (New England Biolabs E7600S), using provided protocols and 500ng of total RNA. Constructed libraries were assessed for quality using the Tapestation 2200 (Agilent G2964AA) with High Sensitivity D1000 DNA screentape (5067-5584), and quantified using Kapa Library Quantification Kit (Kapa Biosystems KK4824) on an AriaMx Realtime PCR System (Agilent G8830A).

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens


text: unspecified

text: public

text: ArrayExpress

text: epithelial lung carcinoma cell

characteristic: cell type

text: human

text: Protocols: A549 cells were purchased from ATCC (VA, USA). A549 is an epithelial lung adenocarcinoma cell line established in 1972 (Giard et al., 1973). The cells were cultured in tissue culture flasks (75 cm2 and 275 cm2) in RPMI 1640 medium with Glutamax (Gibco, ThermoFisher Scientific Inc., Landsmeer, the Netherlands) supplemented with 10% Fetal Bovine Serum (FBS, Greiner BioOne Serum, Greiner BioOne BV, Alphen aan de Rijn, the Netherlands) and 1% penicillin/streptomycin (Gibco, 100 IU penicillin per mL, 100 µg streptomycin per mL). Cells were culture at 37oC in a humidified atmosphere of 5% CO2 in air. The adherent cells were harvested by a short incubation with 0.5% EDTA trypsin in Ca/Mg free Dulbecco’s Phosphate Buffered Saline (Gibco). 8x10 to the 5 cells were seeded and cultured in wells of a 6 well plate for 18 hours, after which the cells were exposed CeO2 A 6h : A549 cells were exposed to Ceria nanoparticles CeO2 A at 128 micrograms per ml for 6 hours. After this, the cells (approximately 2 million per well) were quickly washed with PBS (phosphate buffered saline) twice at room temperature after which the 6 well plates were deep frozen by quenching on liquid nitrogen (-196oC) and stored at -80oC until extraction for omics evaluation Total RNA was extracted from A549 cells using a micro RNeasy Kit (Qiagen, Crawley, UK) according to the manufacturer’s protocol. RNA was quantified with a NanoDrop 8000 spectrophotometer (Thermo Scientific, Waltham, MA), and the integrity of RNA was evaluated with a Agilent 2200 Tapestation (Agilent Technologies, Santa Clara, CA). Only RNA with integrity numbers (RINs) greater than 7.0 were used for subsequent RNA-seq experiments. All RNA libraries were produced using the Biomek FxP (Beckman Coulter A31842) with Ultra Directional RNA Library Prep Kit (New England Biolab E7420L) and NEBnext Multiplex Oligos for Illumina Dual Index Primers (New England Biolabs E7600S), using provided protocols and 500ng of total RNA. Constructed libraries were assessed for quality using the Tapestation 2200 (Agilent G2964AA) with High Sensitivity D1000 DNA screentape (5067-5584), and quantified using Kapa Library Quantification Kit (Kapa Biosystems KK4824) on an AriaMx Realtime PCR System (Agilent G8830A).

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens