text: WW0623/22 P-EL

characteristic: Contains RNA extracts (sample codes)

characteristic: Cq (N1)

characteristic: Cq (N2)

characteristic: Date of amplification (ARTIC)

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: National Institute of Biology

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: INEXTVIR -20

characteristic: Submitter Id

text: Sequenced wastewater sample from Central WWTP Koper 2

characteristic: description

text: wastewater treatment plant influent

text: wastewater treatment plant

text: wastewater treatment plant influent

text: Slovenia

text: virus

characteristic: organism

text: Illumina

characteristic: title

text: wastewater/sludge


status: PUBLIC

text: WW0627/22 P-EL

tag: attribute

characteristic: ENA-CHECKLIST

characteristic: Forward file name

text: National Institute of Biology

text: public

characteristic: No. replicate

characteristic: Reverse file name

text: Department of Endocrinology, Diabetes and Metabolism, University Children's Hospital, University Medical Centre Ljubljana

characteristic: Sequenced where/how

text: INEXTVIR -20

characteristic: Storage location at NIB

tag: Namespace:National Institute of Biology

text: Sequenced wastewater sample from Central WWTP Maribor 1

text: wastewater treatment plant influent

characteristic: environment (biome)

text: wastewater treatment plant

characteristic: environment (feature)

text: wastewater treatment plant influent

characteristic: environment (material)

text: Slovenia

characteristic: geographic location (country and/or sea)

unit: DD

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: virus

characteristic: investigation type

text: Severe acute respiratory syndrome coronavirus 2

text: Sequencing of Slovenian WW samples for SARS-CoV-2 variant detection

characteristic: project name

text: Illumina

characteristic: sequencing method

text: wastewater/sludge

characteristic: wastewater/sludge environmental package


text: WW0627/22 P-EL

characteristic: Contains RNA extracts (sample codes)

characteristic: Cq (N1)

characteristic: Cq (N2)

characteristic: Date of amplification (ARTIC)

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: National Institute of Biology

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: INEXTVIR -20

characteristic: Submitter Id

text: Sequenced wastewater sample from Central WWTP Maribor 2

characteristic: description

text: wastewater treatment plant influent

text: wastewater treatment plant

text: wastewater treatment plant influent

text: Slovenia

text: virus

characteristic: organism

text: Illumina

characteristic: title

text: wastewater/sludge


characteristic: ENA-CHECKLIST

text: The Hospital for Sick Children

text: public

tag: Namespace:The Hospital for Sick Children

unit: day

characteristic: age

text: ArrayExpress

characteristic: broker name

text: sheep

characteristic: common name

text: Protocols: Under maternal general anesthesia and after fetal echocardiography, fetal lambs were delivered by hysterotomy. The umbilical cord was clamped and the lamb was euthanized with IV sodium pentobarbital (BimedaMTC, Cambridge, Canada). A median sternotomy was used to harvest the heart, then samples were taken from the LV, RV, AAo and main PA. Tissue was snap frozen with liquid N2 and stored at -80°C. At gestational age 76 days, coils were implanted in the left heart under continuous ultrasound guidance (Philips HDI 5000), using a completely percutaneous approach under strict aseptic conditions. A 20G needle (6” Quincke; Beckton-Dickinson) was used to deliver platinum coils (0.018” IDC, Boston Scientific) above the mitral valve until the LV appeared underfilled and the ascending aortic flow decreased or became retrograde. RNA was extracted using the miRNeasy Mini Kit (QIAGEN). Small RNA library preparation was performed following the NEBNext Small RNA Library Prep Set for Illumina protocol. Briefly, 600 ng of total RNA was used to ligate 3’ end Illumina-compatible adaptors, followed by hybridization with the reverse transcription primer that prevents formation of adaptor dimers; then 5’ end adaptors were ligated to the small RNA, and adapter-ligated small RNA molecules were reverse transcribed and amplified by PCR with an initial denaturation at 94°C for 30 seconds, followed by 15 cycles of 94°C for 15 seconds, 62°C for 30 seconds and 70°C for 15 seconds, and a final extension step for 5 minutes at 70°C. At the amplification step, each sample was amplified with a different barcoded adapter to allow for multiplex sequencing.

text: embryo

characteristic: developmental stage

text: normal

characteristic: disease

text: wild type genotype

characteristic: genotype

characteristic: individual

text: coil implant in the left heart ventricle

characteristic: injury

text: not applicable

characteristic: isolate

text: Ovis aries

text: Ovis aries

text: pulmonary artery

characteristic: organism part

text: wild type phenotype

characteristic: phenotype

text: Ovis aries

text: Dorset x Rideau Arcott

characteristic: strain


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: The Hospital for Sick Children

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: ArrayExpress

text: sheep

text: embryo

text: normal

text: wild type genotype

text: not applicable

text: Ovis aries

text: Ovis aries

text: heart right ventricle

text: wild type phenotype

text: Ovis aries

text: Dorset x Rideau Arcott


characteristic: ENA-CHECKLIST

text: The Hospital for Sick Children

text: public

characteristic: age

text: ArrayExpress

characteristic: broker name

text: sheep

characteristic: common name

characteristic: description

text: embryo

characteristic: developmental stage

text: normal

characteristic: disease

text: wild type genotype

text: not applicable

text: Ovis aries

characteristic: organism

text: Ovis aries

text: ascending aorta

text: wild type phenotype

text: Ovis aries

text: Dorset x Rideau Arcott

characteristic: title


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: The Hospital for Sick Children

text: public

text: ArrayExpress

text: sheep

text: embryo

text: normal

text: wild type genotype

characteristic: genotype

characteristic: individual

characteristic: injury

text: not applicable

characteristic: isolate

text: Ovis aries

text: Ovis aries

text: heart left ventricle

characteristic: organism part

text: wild type phenotype

characteristic: phenotype

text: Ovis aries

text: Dorset x Rideau Arcott

characteristic: strain


characteristic: ENA-CHECKLIST

characteristic: External Id

text: The Hospital for Sick Children

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

characteristic: age

text: ArrayExpress

text: sheep

text: embryo

text: normal

text: wild type genotype

text: not applicable

text: Ovis aries

text: Ovis aries

text: pulmonary artery

text: wild type phenotype

text: Ovis aries

text: Dorset x Rideau Arcott


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: The Hospital for Sick Children

text: public

text: ArrayExpress

characteristic: broker name

text: sheep

characteristic: common name

characteristic: description

text: embryo

characteristic: developmental stage

text: normal

characteristic: disease

text: wild type genotype

text: not applicable

text: Ovis aries

characteristic: organism

text: Ovis aries

text: heart right ventricle

text: wild type phenotype

text: Ovis aries

text: Dorset x Rideau Arcott

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: External Id

text: The Hospital for Sick Children

text: public

text: ArrayExpress

text: sheep

text: embryo

text: hypoplastic left heart syndrome

text: wild type genotype

characteristic: genotype

characteristic: individual

characteristic: injury

text: not applicable

characteristic: isolate

text: Ovis aries

text: Ovis aries

text: ascending aorta

characteristic: organism part

text: hypoplasia

characteristic: phenotype

text: Ovis aries

text: Dorset x Rideau Arcott

characteristic: strain


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: The Hospital for Sick Children

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

characteristic: age

text: ArrayExpress

text: sheep

text: embryo

text: hypoplastic left heart syndrome

text: wild type genotype

text: not applicable

text: Ovis aries

text: Ovis aries

text: heart left ventricle

text: hypoplasia

text: Ovis aries

text: Dorset x Rideau Arcott


characteristic: ENA-CHECKLIST

characteristic: External Id

text: The Hospital for Sick Children

text: public

text: ArrayExpress

characteristic: broker name

text: sheep

characteristic: common name

characteristic: description

text: embryo

characteristic: developmental stage

text: hypoplastic left heart syndrome

characteristic: disease

text: wild type genotype

text: not applicable

text: Ovis aries

characteristic: organism

text: Ovis aries

text: ascending aorta

text: moderate hypoplasia

text: Ovis aries

text: Dorset x Rideau Arcott

characteristic: title


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: The Hospital for Sick Children

text: public

text: ArrayExpress

text: sheep

text: embryo

text: hypoplastic left heart syndrome

text: wild type genotype

characteristic: genotype

characteristic: individual

characteristic: injury

text: not applicable

characteristic: isolate

text: Ovis aries

text: Ovis aries

text: heart left ventricle

characteristic: organism part

text: moderate hypoplasia

characteristic: phenotype

text: Ovis aries

text: Dorset x Rideau Arcott

characteristic: strain


characteristic: ENA-CHECKLIST

characteristic: External Id

text: The Hospital for Sick Children

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

characteristic: age

text: ArrayExpress

text: sheep

text: embryo

text: hypoplastic left heart syndrome

text: wild type genotype

text: not applicable

text: Ovis aries

text: Ovis aries

text: ascending aorta

text: moderate hypoplasia

text: Ovis aries

text: Dorset x Rideau Arcott


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: The Hospital for Sick Children

text: public

text: ArrayExpress

characteristic: broker name

text: sheep

characteristic: common name

characteristic: description

text: embryo

characteristic: developmental stage

text: hypoplastic left heart syndrome

characteristic: disease

text: wild type genotype

text: not applicable

text: Ovis aries

characteristic: organism

text: Ovis aries

text: heart left ventricle

text: moderate hypoplasia

text: Ovis aries

text: Dorset x Rideau Arcott

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: External Id

text: public

tag: Namespace:Fraunhofer Institute for Molecular Biology and Applied Ecology IME

unit: hour

text: ArrayExpress

text: zebrafish

text: Protocols: Flutamide (CAS: 13311-84-7) was purchased from Merck KGgA (Darmstadt, Germany). For the test solution preparation, first a high concentrated stock solution was prepared in water. From this stock, respective volumes for each testing concentration were added to a 250 ml DURAN glass bottle. Then 200 ml of Cu reduced water were added and solutions were stirred in the dark for 3 hours at room temperature. The solutions were freshly prepared one day prior the start of the experiment and stored at room temperature. They were constantly aerated and used over the course of the 96 hours exposure experiment. The glass wells for the incubation of the embryos were pre-saturated with the respective test solution overnight and renewed at the beginning of the experiment. Per sample, about 40 - 50 fertilized fish eggs were pre-picked in glass petri dishes (10 cm diameter) filled with 30 ml of the testing solution. Using an optical binocular microscope, 15 embryos of the same early blastula stage were transferred from the pre-picking plate into the test glass wells filled with 8 ml of the test solution. Embryos were then incubated as described in the “growth protocol”. Adult animal husbandry: Wild-type zebrafish (Danio rerio, Strain AB) broodstocks were maintained under flow-through conditions in 150 L tanks at 26 +/- 2°C on a 12:12 h light/dark cycle. They were fed daily with TetraMin® (Tetra Werke, Melle, Germany) main feed ad libitum and nauplii of Artemia salina. The day before test start, glass spawning-trays with artificial substrate (green glass beads stringed on stainless steel wire) were placed at the bottom of each tank. After mating and spawning in the morning hours eggs were rinsed with clear Cu-reduced water and placed into glass dishes for pre-picking. Fish embryo incubation: For each sample 15 fertilized eggs in the early blastula stage were placed in glass petri dishes (diameter 6 cm) filled with 8 ml of the respective testing solution (Control, Low exposure, High exposure). Embryos were incubated at 27 ± 1°C on a 14:10 h light/dark cycle. At 24 hours post fertilization (hpf), eggs were inspected visually and single coagulated eggs were recorded and removed. At 48 hpf, overall survival, hatching rates, morphological malformations and physiological changes were recorded and aged solutions were replaced by fresh, aerated test solutions. At 96 hpf again, overall survival, hatching rates, morphological malformations and physiological changes were recorded before RNA and protein extraction. Total RNA and Protein was extracted from the tissue lysate using the NucleoSpin RNA Protein kit (Macherey-Nagel, 740933.250) according to the manufacturer’s protocol. RNA concentration (>100 ng/µl) was measured using a Nanodrop 2000 spectrophotometer (Thermo Scientific). The sample’s overall RNA quality and corresponding RIN value was fluorometrically determined with a 2100 Bioanalyzer© Instrument system (Agilent, G2939BA) using the Agilent RNA 6000 Nano Kit© (Agilent, 5067-1511) according to the manufacturer’s protocol. Only samples with a RIN > 8 were used for downstream analysis. Samples were stored at -80°C until they were send to the sequencing facility on dry ice. For each sample, 10 4-day old zebrafish larvae were randomly picked from the glass well and carefully transferred to a 1.5 ml low binding Eppendorf tube. Once individuals were collected for all samples, they were euthanized at the same time by placing the tubes simultaneously on ice for 10 minutes. Supernatant from the test solutions was then carefully removed without injuring the larvae before adding 350µl of RP1 buffer (NucleoSpin RNA Protein kit; Macherey-Nagel 740933.250) for tissue homogenization. RP1 buffer was freshly prepared with TCEP as reducing agent prior extraction. For detailed information about embryonic incubation conditions and husbandry of adult broodstock please refer to the “Growth protocol”. For detailed information about exposure duration and conditions please refer to the “Treatment protocol”. Adapter sequences were removed using trimmomatic (v0.39) and library’s sequence quality was assessed with FastQC (v0.11.5). Reads were checked for potential contaminations with FastQ Screen (v0.14.1) using bowtie2 (v2.3.2) against the following genomes: Daphnia magna (ftp://ftp.ensemblgenomes.org/pub/metazoa/release-48/fasta/daphnia_magna/dna/Daphnia_magna.daphmag2.4.dna.toplevel.fa.gz), Homo sapiens, Mus musculus, Drosophila melanogaster, Saccharomyces cerevisiae, Eschericia coli as well as custom build human rRNA database. With the exception of D. magna, pre-built Bowtie2 indices for those genomes were directly downloaded from Babraham Bioinformatics with the built-in function ‘fastq_screen --get_genomes’.

text: larval day 4

text: wild type genotype

characteristic: genotype

text: mixed pool of 10 larvae

characteristic: individual

text: Danio rerio

text: Danio rerio

text: whole organism

characteristic: organism part

text: Danio rerio

text: mixed

characteristic: sex


text: Fraunhofer Institute for Molecular Biology and Applied Ecology IME

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: ArrayExpress

text: zebrafish

text: larval day 4

text: wild type genotype

text: mixed pool of 10 larvae

text: Danio rerio

text: Danio rerio

text: whole organism

text: Danio rerio

text: mixed


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: University of Padova

text: public

tag: Namespace:University of Padova

text: M-NR-C org:2 - s.1

characteristic: description

text: metagenome

text: metagenome


text: University of Padova

text: public

text: P-NR-C org:3 - s.2

text: metagenome

characteristic: organism

text: metagenome


text: University of Padova

text: public

text: M-NR-C org:3 - s.3

text: metagenome

text: metagenome

characteristic: title


characteristic: ENA-CHECKLIST

text: University of Padova

text: public

text: M-NR-C org:4 - s.4

text: metagenome

text: metagenome


characteristic: External Id

text: University of Padova

text: public

text: P-NR-C org:3 - s.5

text: metagenome

text: metagenome


text: University of Padova

text: public

text: P-NR-C org:2 - s.6

text: metagenome

text: metagenome


text: University of Padova

text: public

text: P-NR-C org:2 - s.8

text: metagenome

text: metagenome


text: University of Padova

text: public

text: P-NR-C org:3 - s.9

text: metagenome

text: metagenome


text: University of Padova

text: public

text: P-NR-C org:4 - s.10

text: metagenome

text: metagenome


text: University of Padova

text: public

text: P-NR-C org:4 - s.11

text: metagenome

text: metagenome


text: University of Padova

text: public

text: M-NR-C org:3 - s.12

text: metagenome

text: metagenome


text: University of Padova

text: public

text: M-NR-C org:2 - s.13

text: metagenome

text: metagenome


text: University of Padova

text: public

text: M-IT-C org:3 - s.14

text: metagenome

text: metagenome


text: University of Padova

text: public

text: M-IT-C org:4 - s.15

text: metagenome

text: metagenome


text: University of Padova

text: public

text: P-IT-C org:3 - s.16

text: metagenome

text: metagenome


text: University of Padova

text: public

text: P-IT-C org:4 - s.17

text: metagenome

text: metagenome


text: University of Padova

text: public

text: M-IT-C org:3 - s.18

text: metagenome

text: metagenome


text: University of Padova

text: public

text: P-IT-C org:4 - s.19

text: metagenome

text: metagenome


text: University of Padova

text: public

text: M-IT-C org:3 - s.20

text: metagenome

text: metagenome


text: University of Padova

text: public

text: P-IT-C org:3 - s.21

text: metagenome

text: metagenome


text: University of Padova

text: public

text: M-IT-C org:2 - s.22

text: metagenome

text: metagenome


text: University of Padova

text: public

text: P-IT-C org:2 - s.23

text: metagenome

text: metagenome


text: University of Padova

text: public

text: P-FR-C org:4 - s.24

text: metagenome

text: metagenome


text: University of Padova

text: public

text: M-FR-C org:4 - s.25

text: metagenome

text: metagenome


text: University of Padova

text: public

text: P-FR-C org:4 - s.26

text: metagenome

text: metagenome


text: University of Padova

text: public

text: M-FR-C org:4 - s.27

text: metagenome

text: metagenome


E-MTAB-12233:HCC1143 HX_1

text: LACDR, Leiden University

text: public

text: E-MTAB-12233:HCC1143 HX_1

tag: Namespace:LACDR, Leiden University

text: ArrayExpress

characteristic: broker name

text: human

characteristic: common name

text: Protocols: Washed once with cold PBS and lysed using TempO-Seq lysis buffer for 15 min at RT. Samples were stored at −80 °C before shipping to BioClavis for whole genome TempO-Seq analysis. All the processes were according to BioSpyder-BioClavis protocol. All the processes were according to BioSpyder-BioClavis protocol.

text: invasive breast ductal carcinoma

characteristic: disease

text: hypoxia

characteristic: environmental stress

text: wild type genotype

characteristic: genotype

text: 1 percent oxygen

characteristic: growth condition

text: not applicable

characteristic: isolate

text: Homo sapiens

text: Homo sapiens

text: mammary gland

text: basal cell

characteristic: phenotype

text: Homo sapiens

text: HCC1143 HX_1


E-MTAB-12233:HCC1143 HX_2

text: LACDR, Leiden University

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-12233:HCC1143 HX_2

text: ArrayExpress

text: human

text: invasive breast ductal carcinoma

text: hypoxia

text: wild type genotype

text: 1 percent oxygen

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: mammary gland

characteristic: organism part

text: basal cell

text: Homo sapiens

text: HCC1143 HX_2


E-MTAB-12233:HCC1143 HX_3

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: LACDR, Leiden University

text: public

text: E-MTAB-12233:HCC1143 HX_3

characteristic: Submitter Id

text: ArrayExpress

text: human

characteristic: description

text: invasive breast ductal carcinoma

text: hypoxia

text: wild type genotype

text: 1 percent oxygen

text: not applicable

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: mammary gland

text: basal cell

text: Homo sapiens

text: HCC1143 HX_3

characteristic: title


E-MTAB-12233:MCF-7 HX_1

characteristic: ENA-CHECKLIST

characteristic: External Id

text: LACDR, Leiden University

text: public

text: E-MTAB-12233:MCF-7 HX_1

text: ArrayExpress

characteristic: broker name

text: human

characteristic: common name

text: breast adenocarcinoma

characteristic: disease

text: hypoxia

characteristic: environmental stress

text: wild type genotype

text: 1 percent oxygen

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: mammary gland

text: luminal

text: Homo sapiens

text: MCF-7 HX_1


E-MTAB-12233:MCF-7 HX_2

text: LACDR, Leiden University

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: E-MTAB-12233:MCF-7 HX_2

text: ArrayExpress

text: human

text: breast adenocarcinoma

text: hypoxia

text: wild type genotype

characteristic: genotype

text: 1 percent oxygen

characteristic: growth condition

text: not applicable

characteristic: isolate

text: Homo sapiens

text: Homo sapiens

text: mammary gland

text: luminal

characteristic: phenotype

text: Homo sapiens

text: MCF-7 HX_2


E-MTAB-12233:MCF-7 HX_3

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: LACDR, Leiden University

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-12233:MCF-7 HX_3

text: ArrayExpress

text: human

text: breast adenocarcinoma

text: hypoxia

text: wild type genotype

text: 1 percent oxygen

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: mammary gland

characteristic: organism part

text: luminal

text: Homo sapiens

text: MCF-7 HX_3


E-MTAB-12233:HCC1143 NX_1

characteristic: ENA-CHECKLIST

characteristic: External Id

text: LACDR, Leiden University

text: public

text: E-MTAB-12233:HCC1143 NX_1

characteristic: Submitter Id

text: ArrayExpress

text: human

characteristic: description

text: invasive breast ductal carcinoma

text: normoxia

text: wild type genotype

text: 21 percent oxygen

text: not applicable

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: mammary gland

text: basal cell

text: Homo sapiens

text: HCC1143 NX_1

characteristic: title


E-MTAB-12233:HCC1143 NX_2

text: LACDR, Leiden University

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: E-MTAB-12233:HCC1143 NX_2

text: ArrayExpress

characteristic: broker name

text: human

characteristic: common name

text: invasive breast ductal carcinoma

characteristic: disease

text: normoxia

characteristic: environmental stress

text: wild type genotype

text: 21 percent oxygen

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: mammary gland

text: basal cell

text: Homo sapiens

text: HCC1143 NX_2


E-MTAB-12233:HCC1143 NX_3

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: LACDR, Leiden University

text: public

text: E-MTAB-12233:HCC1143 NX_3

text: ArrayExpress

text: human

text: invasive breast ductal carcinoma

text: normoxia

text: wild type genotype

characteristic: genotype

text: 21 percent oxygen

characteristic: growth condition

text: not applicable

characteristic: isolate

text: Homo sapiens

text: Homo sapiens

text: mammary gland

text: basal cell

characteristic: phenotype

text: Homo sapiens

text: HCC1143 NX_3


E-MTAB-12233:MCF-7 NX_1

characteristic: ENA-CHECKLIST

characteristic: External Id

text: LACDR, Leiden University

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-12233:MCF-7 NX_1

text: ArrayExpress

text: human

text: breast adenocarcinoma

text: normoxia

text: wild type genotype

text: 21 percent oxygen

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: mammary gland

characteristic: organism part

text: luminal

text: Homo sapiens

text: MCF-7 NX_1


E-MTAB-12233:MCF-7 NX_2

text: LACDR, Leiden University

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: E-MTAB-12233:MCF-7 NX_2

characteristic: Submitter Id

text: ArrayExpress

text: human

characteristic: description

text: breast adenocarcinoma

text: normoxia

text: wild type genotype

text: 21 percent oxygen

text: not applicable

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: mammary gland

text: luminal

text: Homo sapiens

text: MCF-7 NX_2

characteristic: title


E-MTAB-12233:MCF-7 NX_3

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: LACDR, Leiden University

text: public

text: E-MTAB-12233:MCF-7 NX_3

text: ArrayExpress

characteristic: broker name

text: human

characteristic: common name

text: breast adenocarcinoma

characteristic: disease

text: normoxia

characteristic: environmental stress

text: wild type genotype

text: 21 percent oxygen

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: mammary gland

text: luminal

text: Homo sapiens

text: MCF-7 NX_3


E-MTAB-12234:HCC1143 HX _1

characteristic: ENA-CHECKLIST

characteristic: External Id

text: LACDR, Leiden University

text: public

text: E-MTAB-12234:HCC1143 HX _1

text: ArrayExpress

text: human

text: invasive breast ductal carcinoma

text: wild type genotype

characteristic: genotype

text: 1 percent oxygen

characteristic: growth condition

text: not applicable

characteristic: isolate

text: Homo sapiens

text: Homo sapiens

text: breast

text: basal cell

characteristic: phenotype

text: Homo sapiens

text: HCC1143 HX _1


E-MTAB-12234:HCC1143 HX _2

text: LACDR, Leiden University

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-12234:HCC1143 HX _2

text: ArrayExpress

text: human

text: invasive breast ductal carcinoma

text: wild type genotype

text: 1 percent oxygen

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: breast

characteristic: organism part

text: basal cell

text: Homo sapiens

text: HCC1143 HX _2


E-MTAB-12234:HCC1143 HX _3

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: LACDR, Leiden University

text: public

text: E-MTAB-12234:HCC1143 HX _3

characteristic: Submitter Id

text: ArrayExpress

text: human

characteristic: description

text: invasive breast ductal carcinoma

text: wild type genotype

text: 1 percent oxygen

text: not applicable

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: breast

text: basal cell

text: Homo sapiens

text: HCC1143 HX _3

characteristic: title


E-MTAB-12234:HCC1143 NX _1

characteristic: ENA-CHECKLIST

characteristic: External Id

text: LACDR, Leiden University

text: public

text: E-MTAB-12234:HCC1143 NX _1

text: ArrayExpress

characteristic: broker name

text: human

characteristic: common name

text: invasive breast ductal carcinoma

characteristic: disease

text: wild type genotype

text: 21 percent oxygen

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: breast

text: basal cell

text: Homo sapiens

text: HCC1143 NX _1


E-MTAB-12234:HCC1143 NX _2

text: LACDR, Leiden University

characteristic: INSDC center name

text: public

text: E-MTAB-12234:HCC1143 NX _2

text: ArrayExpress

text: human

text: invasive breast ductal carcinoma

text: wild type genotype

characteristic: genotype

text: 21 percent oxygen

characteristic: growth condition

text: not applicable

characteristic: isolate

text: Homo sapiens

text: Homo sapiens

text: breast

text: basal cell

characteristic: phenotype

text: Homo sapiens

text: HCC1143 NX _2


E-MTAB-12234:HCC1143 NX _3

text: LACDR, Leiden University

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-12234:HCC1143 NX _3

text: ArrayExpress

text: human

text: invasive breast ductal carcinoma

text: wild type genotype

text: 21 percent oxygen

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: breast

characteristic: organism part

text: basal cell

text: Homo sapiens

text: HCC1143 NX _3


E-MTAB-12234:MCF-7 HX _1

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: LACDR, Leiden University

text: public

text: E-MTAB-12234:MCF-7 HX _1

characteristic: Submitter Id

text: ArrayExpress

text: human

characteristic: description

text: breast adenocarcinoma

text: wild type genotype

text: 1 percent oxygen

text: not applicable

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: breast

text: luminal

text: Homo sapiens

text: MCF-7 HX _1


E-MTAB-12234:MCF-7 HX _2

characteristic: ENA-CHECKLIST

characteristic: External Id

text: LACDR, Leiden University

text: public

text: E-MTAB-12234:MCF-7 HX _2

text: ArrayExpress

characteristic: broker name

text: human

characteristic: common name

text: breast adenocarcinoma

text: wild type genotype

text: 1 percent oxygen

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: breast

text: luminal

text: Homo sapiens

text: MCF-7 HX _2

characteristic: title


E-MTAB-12234:MCF-7 HX _3

text: LACDR, Leiden University

characteristic: INSDC center name

text: public

text: E-MTAB-12234:MCF-7 HX _3

text: ArrayExpress

text: human

text: breast adenocarcinoma

characteristic: disease

text: wild type genotype

characteristic: genotype

text: 1 percent oxygen

characteristic: growth condition

text: not applicable

characteristic: isolate

text: Homo sapiens

text: Homo sapiens

text: breast

text: luminal

text: Homo sapiens

text: MCF-7 HX _3


E-MTAB-12234:MCF-7 NX _1

text: LACDR, Leiden University

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-12234:MCF-7 NX _1

text: ArrayExpress

text: human

text: breast adenocarcinoma

text: wild type genotype

text: 21 percent oxygen

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: breast

text: luminal

characteristic: phenotype

text: Homo sapiens

text: MCF-7 NX _1


E-MTAB-12234:MCF-7 NX _2

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: LACDR, Leiden University

text: public

text: E-MTAB-12234:MCF-7 NX _2

characteristic: Submitter Id

text: ArrayExpress

text: human

characteristic: description

text: breast adenocarcinoma

text: wild type genotype

text: 21 percent oxygen

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: breast

characteristic: organism part

text: luminal

text: Homo sapiens

text: MCF-7 NX _2


E-MTAB-12234:MCF-7 NX _3

characteristic: ENA-CHECKLIST

characteristic: External Id

text: LACDR, Leiden University

text: public

text: E-MTAB-12234:MCF-7 NX _3

text: ArrayExpress

characteristic: broker name

text: human

characteristic: common name

text: breast adenocarcinoma

text: wild type genotype

text: 21 percent oxygen

text: not applicable

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: breast

text: luminal

text: Homo sapiens

text: MCF-7 NX _3


characteristic: INSDC center name

text: public

tag: Namespace:Laboratory of Traslational Research. Azienda USL-IRCCS di Reggio Emilia

text: ArrayExpress

text: human

text: Protocols: 40M cells were collected for Chromatin Immunoprecipitation. Cells were cultured in DMEM medium supplemented with 10% FBS and 1% P/S. ChIP samples were purified with PCR Purification Kit (Qiagen) and eluted in 50ul of Elution Buffer. Libraries were obtained starting from 1ng of ChIP and Input samples following the NEBNext Ultra II DNA Library Prep Kit for Illumina (New England BioLabs) protocol.

text: adult

characteristic: developmental stage

text: thyroid anaplastic carcinoma

characteristic: disease

text: wild type genotype

characteristic: genotype

text: Homo sapiens

text: Homo sapiens

text: thyroid gland

text: Homo sapiens

characteristic: title


text: Laboratory of Traslational Research. Azienda USL-IRCCS di Reggio Emilia

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: ArrayExpress

text: human

text: adult

text: thyroid anaplastic carcinoma

text: wild type genotype

text: Homo sapiens

text: Homo sapiens

text: thyroid gland

text: Homo sapiens


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: public

characteristic: Submitter Id

text: ArrayExpress

text: human

text: adult

text: thyroid anaplastic carcinoma

text: wild type genotype

text: Homo sapiens

text: Homo sapiens

text: thyroid gland

text: Homo sapiens

text: INPUT


characteristic: ENA-CHECKLIST

text: PUBLIC HEALTH ENGLAND

text: public

tag: Namespace:PUBLIC HEALTH ENGLAND

characteristic: collection date

text: Blood culture

characteristic: description

text: United Kingdom

characteristic: geographic location (country and/or sea)

text: not provided

characteristic: host health state

text: Homo Sapien

characteristic: host scientific name

characteristic: isolate

text: Blood culture

text: Streptococcus agalactiae

text: Streptococcus agalactiae

text: capsular

characteristic: serovar

text: Antimicrobial resistant GBS culture


characteristic: External Id

text: PUBLIC HEALTH ENGLAND

characteristic: INSDC center name

text: public

text: Blood

text: United Kingdom

text: not provided

text: Homo Sapien

text: Blood

text: Streptococcus agalactiae

characteristic: organism

text: Streptococcus agalactiae

text: capsular

text: Antimicrobial resistant GBS culture


text: PUBLIC HEALTH ENGLAND

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: Csf

text: United Kingdom

text: not provided

text: Homo Sapien

text: Csf

text: Streptococcus agalactiae

text: Streptococcus agalactiae

text: capsular

text: Antimicrobial resistant GBS culture

characteristic: title


characteristic: ENA-FIRST-PUBLIC

text: PUBLIC HEALTH ENGLAND

text: public

characteristic: INSDC status

characteristic: SRA accession

text: Other

text: United Kingdom

text: not provided

text: Homo Sapien

text: Other

text: Streptococcus agalactiae

text: Streptococcus agalactiae

text: capsular

text: Antimicrobial resistant GBS culture


characteristic: ENA-CHECKLIST

characteristic: ENA-LAST-UPDATE

text: PUBLIC HEALTH ENGLAND

text: public

characteristic: Submitter Id

text: Eye swab

text: United Kingdom

text: not provided

text: Homo Sapien

text: Eye swab

text: Streptococcus agalactiae

text: Streptococcus agalactiae

text: capsular

text: Antimicrobial resistant GBS culture


text: PUBLIC HEALTH ENGLAND

text: public

characteristic: collection date

text: Swab

characteristic: description

text: United Kingdom

characteristic: geographic location (country and/or sea)

text: diseased

text: Homo Sapien

text: Swab

text: Streptococcus agalactiae

text: Streptococcus agalactiae

text: capsular

text: Penicillin resistant GBS Culture from bacterial swab collected from chronic discarhign snius overlying a prosthetic joint


text: PUBLIC HEALTH ENGLAND

text: public

text: Information not provided

text: United Kingdom

text: not provided

characteristic: host health state

text: Homo Sapien

characteristic: host scientific name

characteristic: isolate

text: Information not provided

text: Streptococcus agalactiae

text: Streptococcus agalactiae

text: capsular

text: Antimicrobial resistant GBS culture


characteristic: External Id

text: PUBLIC HEALTH ENGLAND

characteristic: INSDC center name

text: public

text: Blood culture

text: United Kingdom

text: not provided

text: Homo Sapien

text: Blood culture

text: Streptococcus agalactiae

text: Streptococcus agalactiae

text: capsular

characteristic: serovar

characteristic: strain

text: Antimicrobial resistant GBS culture


E-MTAB-12293:SUMO2 starved U2OS

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: E-MTAB-12293:SUMO2 starved U2OS

tag: Namespace:Faculty of Biology, Medicine and Health, University of Manchester

text: ArrayExpress

characteristic: broker name

text: human

characteristic: common name

text: Protocols: U2OS cells were grown in DMEM medium containing 10% foetal bovine serum at 37°C incubator with 5% CO2. After reverse cross-link and protein digestion with Proteinase K (Roche), DNA was purified using Qiaquick, PCR purification kit (Qiagen) following the manufacturer’s. ChIP-seq was performed as described in Schmidt et al., 2009, using 3 x 10^6 U2OS. Immuno-precipitation was performed overnight at 4° C by incubating the shared DNA-protein complex with3 micro-gram of anti-SUMO2 (Life technologies) antibody previously coupled to Dynabeads protein A (Invitrogen). Schmidt D, Wilson MD, Spyrou C, Brown GD, Hadfield J, Odom DT. (2009) ChIP-seq: using high-throughput sequencing to discover protein-DNA interactions. Methods 48: 240–248. Libraries were generated following manufacturer's protocol.

text: juvenile stage

characteristic: developmental stage

text: osteosarcoma

characteristic: disease

text: nutrient starvation

characteristic: environmental stress

text: wild type genotype

characteristic: genotype

text: not applicable

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: tibia

characteristic: organism part

text: Homo sapiens

text: SUMO2 starved U2OS

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: Faculty of Biology, Medicine and Health, University of Manchester

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: ArrayExpress

text: human

text: Protocols: U2OS cells were grown in DMEM medium containing 10% foetal bovine serum at 37°C incubator with 5% CO2. Cells were transfected using ADNP, TRIM28 or ZMYM2 siRNA or non-target control siRNA for 48 hours, followed by second siRNA transfection. Total RNA was extracted using an RNeasy plus kit (Qiagen, 74134) with DNase treatment according to the manufacturer’s protocol. RNA-seq libraries were constructed following the TruSeq Stranded mRNA sample preparation protocol (Illumina).

characteristic: description

text: juvenile stage

text: osteosarcoma

text: wild type genotype

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: tibia

text: Homo sapiens


characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: E-MTAB-12291:siNT_forZMYM2andTRIM28_rep1

text: ArrayExpress

text: human

text: juvenile stage

text: osteosarcoma

text: wild type genotype

text: not applicable

characteristic: isolate

text: Homo sapiens

text: Homo sapiens

text: tibia

text: Homo sapiens


text: public

text: E-MTAB-12291:siNT_forZMYM2andTRIM28_rep2

text: ArrayExpress

characteristic: broker name

text: human

characteristic: common name

text: juvenile stage

characteristic: developmental stage

text: osteosarcoma

characteristic: disease

text: wild type genotype

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: tibia

text: Homo sapiens


text: public

text: E-MTAB-12291:siNT_forZMYM2andTRIM28_rep3

text: ArrayExpress

text: human

text: juvenile stage

text: osteosarcoma

text: wild type genotype

characteristic: genotype

text: not applicable

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: tibia

characteristic: organism part

text: Homo sapiens

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: public

characteristic: INSDC status

tag: Namespace:Leonard Davis School of Gerontology University of Southern California

characteristic: age

text: ArrayExpress

text: Protocols: For RNA isolation, all RNa collection was performed at day 1 of adulthood. ~1000 animals were harvested from RNAi plates using M9. Animals were pelleted by gravity by allowing adult worms to settle to the bottom of the tube and aspirating off eggs and L1. Animals were washed and gravity settled 3x to remove a majority of progeny, then animals were placed into Trizol solution and worms were freeze/thawed 3x with liquid nitrogen with a 30 sec vortexing step between each freeze cycle. Standard bleaching protocol was used to synchronize animal populations. Animals were L1 arrested for a maximum of 16 hours to further synchronize populations. Animals were grown on RNAi indicated from L1 until Day 1 of adulthood and material was collected on Day 1. After the final thaw, chloroform was added at a 1:5 chlorform/trizol ratio and aqueous separation of RNA was performed via centrifugation in a heavy gel phase-lock tube (VWR, 10847-802). The aqueous phase was mixed 1:1 with isopropanol then applied to a Qiagen RNeasy Mini Kit (74106) and RNA purification was performed as per manufacturer’s directions. Library preparation was performed using a Kapa Biosystems mRNA Hyper Prep Kit.

text: adult

text: bet-1A overexpression

text: not applicable

text: Caenorhabditis elegans

text: Caenorhabditis elegans

text: whole organism

text: Caenorhabditis elegans

text: hermaphrodite

characteristic: sex

characteristic: strain


characteristic: External Id

text: Leonard Davis School of Gerontology University of Southern California

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: SRA accession

characteristic: Submitter Id

text: ArrayExpress

characteristic: description

text: adult

text: bet-1A overexpression

text: not applicable

text: Caenorhabditis elegans

text: Caenorhabditis elegans

text: whole organism

text: Caenorhabditis elegans

text: hermaphrodite


text: public

text: ArrayExpress

characteristic: broker name

text: adult

characteristic: developmental stage

text: wild type genotype

characteristic: genotype

text: not applicable

characteristic: isolate

text: Caenorhabditis elegans

characteristic: organism

text: Caenorhabditis elegans

text: whole organism

text: Caenorhabditis elegans

text: hermaphrodite


E-MTAB-12292:ADNP rep1

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: public

text: E-MTAB-12292:ADNP rep1

text: ArrayExpress

text: human

characteristic: common name

text: Protocols: U2OS cells were grown in DMEM medium containing 10% foetal bovine serum at 37°C incubator with 5% CO2. After reverse cross-link and protein digestion with Proteinase K (Roche), DNA was purified using QIAquick PCR purification kit (Qiagen) following the manufacturer's instructions. ChIP-seq was performed as described in Schmidt et al., 2009 with modifications, using 5 x 10^7 U2OS. Immuno-precipitation was performed overnight at 4°C by incubating the shared DNA-protein complex with 10 µg of anti-ADNP or anti-TRIM28 antibody, followed by adding Dynabeads protein A (Invitrogen) and incubating for further 2 hours. Schmidt D, Wilson MD, Spyrou C, Brown GD, Hadfield J, Odom DT. (2009) ChIP-seq: using high-throughput sequencing to discover protein-DNA interactions. Methods 48: 240-248.

text: juvenile stage

text: osteosarcoma

characteristic: disease

text: wild type genotype

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: tibia

characteristic: organism part

text: Homo sapiens

text: ADNP rep1

characteristic: title


E-MTAB-12292:ADNP rep2

characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC first public

text: public

characteristic: INSDC status

text: E-MTAB-12292:ADNP rep2

text: ArrayExpress

text: human

text: juvenile stage

text: osteosarcoma

text: wild type genotype

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: tibia

text: Homo sapiens

text: ADNP rep2


E-MTAB-12292:TRIM28 rep1

characteristic: INSDC last update

text: public

characteristic: SRA accession

text: E-MTAB-12292:TRIM28 rep1

characteristic: Submitter Id

text: ArrayExpress

text: human

characteristic: description

text: juvenile stage

text: osteosarcoma

text: wild type genotype

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: tibia

text: Homo sapiens

text: TRIM28 rep1


E-MTAB-12292:TRIM28 rep2

text: public

text: E-MTAB-12292:TRIM28 rep2

text: ArrayExpress

characteristic: broker name

text: human

text: juvenile stage

characteristic: developmental stage

text: osteosarcoma

text: wild type genotype

characteristic: genotype

text: not applicable

characteristic: isolate

text: Homo sapiens

text: Homo sapiens

text: tibia

text: Homo sapiens

text: TRIM28 rep2


E-MTAB-12294:ATACseq U2OS

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: public

text: E-MTAB-12294:ATACseq U2OS

text: ArrayExpress

text: human

text: Protocols: Cells were lysed 48 h after transfection in cold lysis buffer (10mM Tris-HCL, pH 7.4, 10mMNaCl, 3mM MgCl2 and 0.1% Igepal). DNA was purified using Qiagen mini elute kit and using Ampure XP beads following the manufacturer’s instructions. Nuclei was concentrated by centrifugation at 500 g for 10 minutes at 4°C. The nuclei pellet was resuspended in nuclease free water, diluted 1:10 and quantified. The equivalent volume for 50,000 nuclei was made up to 22.5 ul with nuclease free water. Nuclei were incubated for 30 minutes at 37°C, 300 rpm, with 25 ul of 2x TD buffer and 2.5 ul tagmentation ezyme (Illumina transposase FC-121-1030). Library fragments were amplified using standard PCR and Nextera primers (Illumina) by adding 25 ul of 2x NEBnext master mix, 2.5 ul forward primer, 2.5 ul reverse primer and 20 ul transposased DNA. PCR was run for 5 cycles, 72°C, 5 minutes; 98°C 30 seconds; cycle of 98°C 10 seconds, 63°C 30 seconds, 72°C 1 minute, paused at 4°C. To determine the total number of cycles needed for the amplified library, 5 ul of the PCR mix were taken and added to a new mix containing 5 ul 2X master mix, 1 ul of each primer, 0.6 ul of 10X SYBR green and 2.4 ul H2O. In a qPCR machine, 20 cycles were run, the total number of cycles for the ATAC library was chosen according to qPCR cycle that gave 1/3 of saturation.

text: juvenile stage

text: osteosarcoma

text: wild type genotype

text: not applicable

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: tibia

text: Homo sapiens

text: ATACseq U2OS


text: Bee

characteristic: ArrayExpress-Phenotype

text: Apis mellifera

characteristic: ArrayExpress-Species

text: SC

text: public

text: honey bee

characteristic: common name

text: Apis mellifera

text: Study 6320

text: Apis mellifera

characteristic: title


text: WW0647/22 p-EL

characteristic: Contains RNA extracts (sample codes)

characteristic: Cq (N1)

characteristic: Cq (N2)

characteristic: Date of amplification (ARTIC)

characteristic: External Id

characteristic: Forward file name

text: National Institute of Biology

characteristic: INSDC center name

characteristic: INSDC first public

text: public

characteristic: INSDC status

characteristic: No. replicate

characteristic: Reverse file name

text: Department of Endocrinology, Diabetes and Metabolism, University Children's Hospital, University Medical Centre Ljubljana

characteristic: Sequenced where/how

text: INEXTVIR -20

characteristic: Storage location at NIB

text: Sequenced wastewater sample from Central WWTP Ljubljana 1

text: wastewater treatment plant influent

characteristic: environment (biome)

text: wastewater treatment plant

characteristic: environment (feature)

text: wastewater treatment plant influent

characteristic: environment (material)

text: Slovenia

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: virus

characteristic: investigation type

text: Severe acute respiratory syndrome coronavirus 2

text: Sequencing of Slovenian WW samples for SARS-CoV-2 variant detection

characteristic: project name

text: Illumina

characteristic: sequencing method

text: wastewater/sludge

characteristic: wastewater/sludge environmental package


text: WW0647/22 p-EL

characteristic: Contains RNA extracts (sample codes)

characteristic: Cq (N1)

characteristic: Cq (N2)

characteristic: Date of amplification (ARTIC)

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: Forward file name

text: National Institute of Biology

characteristic: INSDC center name

characteristic: INSDC last update

text: public

characteristic: SRA accession

text: INEXTVIR -20

characteristic: Submitter Id

text: Sequenced wastewater sample from Central WWTP Ljubljana 2

characteristic: description

text: wastewater treatment plant influent

text: wastewater treatment plant

text: wastewater treatment plant influent

text: Slovenia

text: virus

characteristic: organism

text: Illumina

characteristic: title

text: wastewater/sludge


text: WW0651/22 p-EL

text: National Institute of Biology

characteristic: INSDC first public

text: public

characteristic: INSDC status

characteristic: No. replicate

characteristic: Reverse file name

characteristic: Sequenced where/how

text: INEXTVIR -20

characteristic: Storage location at NIB

text: Sequenced wastewater sample from Central WWTP Koper 1

text: wastewater treatment plant influent

characteristic: environment (biome)

text: wastewater treatment plant

characteristic: environment (feature)

text: wastewater treatment plant influent

characteristic: environment (material)

text: Slovenia

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: virus

characteristic: investigation type

characteristic: project name

text: Illumina

characteristic: sequencing method

text: wastewater/sludge

characteristic: wastewater/sludge environmental package


text: WW0651/22 p-EL

characteristic: Contains RNA extracts (sample codes)

characteristic: Cq (N1)

characteristic: Cq (N2)

characteristic: Date of amplification (ARTIC)

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: Forward file name

text: National Institute of Biology

characteristic: INSDC center name

characteristic: INSDC last update

text: public

characteristic: SRA accession

text: INEXTVIR -20

characteristic: Submitter Id

text: Sequenced wastewater sample from Central WWTP Koper 2

characteristic: description

text: wastewater treatment plant influent

text: wastewater treatment plant

text: wastewater treatment plant influent

text: Slovenia

text: virus

characteristic: organism

text: Illumina

characteristic: title

text: wastewater/sludge


text: WW0655/22 p-EL

text: National Institute of Biology

characteristic: INSDC first public

text: public

characteristic: INSDC status

characteristic: No. replicate

characteristic: Reverse file name

characteristic: Sequenced where/how

text: INEXTVIR -20

characteristic: Storage location at NIB

text: Sequenced wastewater sample from Central WWTP Maribor 1

text: wastewater treatment plant influent

characteristic: environment (biome)

text: wastewater treatment plant

characteristic: environment (feature)

text: wastewater treatment plant influent

characteristic: environment (material)

text: Slovenia

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: virus

characteristic: investigation type

characteristic: project name

text: Illumina

characteristic: sequencing method

text: wastewater/sludge

characteristic: wastewater/sludge environmental package


text: WW0655/22 p-EL

characteristic: Contains RNA extracts (sample codes)

characteristic: Cq (N1)

characteristic: Cq (N2)

characteristic: Date of amplification (ARTIC)

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: Forward file name

text: National Institute of Biology

characteristic: INSDC center name

characteristic: INSDC last update

text: public

characteristic: SRA accession

text: INEXTVIR -20

characteristic: Submitter Id

text: Sequenced wastewater sample from Central WWTP Maribor 2

characteristic: description

text: wastewater treatment plant influent

text: wastewater treatment plant

text: wastewater treatment plant influent

text: Slovenia

text: virus

characteristic: organism

text: Illumina

characteristic: title

text: wastewater/sludge


text: University College Dublin

characteristic: INSDC first public

text: public

characteristic: INSDC status

text: ena-SAMPLE-TAB-18-10-2022-09:29:23:250-788

tag: Namespace:University College Dublin

text: cattle

characteristic: common name

text: Bos taurus

text: Bos taurus


text: University College Dublin

text: public

text: ena-SAMPLE-TAB-18-10-2022-09:29:23:250-789

text: cattle

text: Bos taurus

text: Bos taurus


text: University College Dublin

text: public

text: ena-SAMPLE-TAB-18-10-2022-09:29:23:250-790

text: cattle

text: Bos taurus

text: Bos taurus


text: University College Dublin

text: public

text: ena-SAMPLE-TAB-18-10-2022-09:29:23:250-791

text: cattle

text: Bos taurus

text: Bos taurus


text: University College Dublin

text: public

text: ena-SAMPLE-TAB-18-10-2022-09:29:23:250-792

text: cattle

text: Bos taurus

text: Bos taurus


text: University College Dublin

text: public

text: ena-SAMPLE-TAB-18-10-2022-09:29:23:250-793

text: cattle

text: Bos taurus

text: Bos taurus


text: University College Dublin

text: public

text: ena-SAMPLE-TAB-18-10-2022-09:29:23:250-794

text: cattle

text: Bos taurus

text: Bos taurus


text: University College Dublin

text: public

text: ena-SAMPLE-TAB-18-10-2022-09:29:23:250-795

text: cattle

text: Bos taurus

text: Bos taurus


text: University College Dublin

text: public

text: ena-SAMPLE-TAB-18-10-2022-09:29:23:250-796

text: cattle

text: Bos taurus

text: Bos taurus


text: University College Dublin

text: public

text: ena-SAMPLE-TAB-18-10-2022-09:29:23:250-797

text: cattle

text: Bos taurus

text: Bos taurus


text: University College Dublin

text: public

text: ena-SAMPLE-TAB-18-10-2022-09:29:23:250-798

text: cattle

text: Bos taurus

text: Bos taurus


text: University College Dublin

text: public

text: ena-SAMPLE-TAB-18-10-2022-09:29:23:250-799

text: cattle

text: Bos taurus

text: Bos taurus


text: University College Dublin

text: public

text: ena-SAMPLE-TAB-18-10-2022-09:29:23:250-800

text: cattle

text: Bos taurus

text: Bos taurus


text: University College Dublin

text: public

text: ena-SAMPLE-TAB-18-10-2022-09:29:23:250-801

text: cattle

text: Bos taurus

text: Bos taurus


text: University College Dublin

text: public

text: ena-SAMPLE-TAB-18-10-2022-09:29:23:251-802

text: cattle

text: Bos taurus

text: Bos taurus


text: University College Dublin

text: public

text: ena-SAMPLE-TAB-18-10-2022-09:29:23:251-803

text: cattle

text: Bos taurus

text: Bos taurus


text: University College Dublin

text: public

text: ena-SAMPLE-TAB-18-10-2022-09:29:23:251-804

text: cattle

text: Bos taurus

text: Bos taurus


text: University College Dublin

text: public

text: ena-SAMPLE-TAB-18-10-2022-09:29:23:251-805

text: cattle

text: Bos taurus

text: Bos taurus


text: University College Dublin

text: public

text: ena-SAMPLE-TAB-18-10-2022-09:29:23:251-806

text: cattle

text: Bos taurus

text: Bos taurus


text: University College Dublin

text: public

text: ena-SAMPLE-TAB-18-10-2022-09:29:23:251-807

text: cattle

text: Bos taurus

text: Bos taurus


text: University College Dublin

text: public

text: ena-SAMPLE-TAB-18-10-2022-09:29:23:251-808

text: cattle

text: Bos taurus

text: Bos taurus


text: University College Dublin

text: public

text: ena-SAMPLE-TAB-18-10-2022-09:29:23:251-809

text: cattle

text: Bos taurus

text: Bos taurus


text: University College Dublin

text: public

text: ena-SAMPLE-TAB-18-10-2022-09:29:23:251-810

text: cattle

text: Bos taurus

text: Bos taurus


text: University College Dublin

text: public

text: ena-SAMPLE-TAB-18-10-2022-09:29:23:251-811

text: cattle

text: Bos taurus

text: Bos taurus


text: University College Dublin

text: public

text: ena-SAMPLE-TAB-18-10-2022-09:29:23:251-812

text: cattle

text: Bos taurus

text: Bos taurus


text: University College Dublin

text: public

text: ena-SAMPLE-TAB-18-10-2022-09:29:23:251-813

text: cattle

text: Bos taurus

text: Bos taurus


text: University College Dublin

text: public

text: ena-SAMPLE-TAB-18-10-2022-09:29:23:251-814

text: cattle

text: Bos taurus

text: Bos taurus


text: University College Dublin

text: public

text: ena-SAMPLE-TAB-18-10-2022-09:29:23:251-815

text: cattle

text: Bos taurus

text: Bos taurus


text: University College Dublin

text: public

text: ena-SAMPLE-TAB-18-10-2022-09:29:23:251-816

text: cattle

text: Bos taurus

text: Bos taurus


text: University College Dublin

text: public

text: ena-SAMPLE-TAB-18-10-2022-09:29:23:251-817

text: cattle

text: Bos taurus

text: Bos taurus


text: University College Dublin

text: public

text: ena-SAMPLE-TAB-18-10-2022-09:29:23:251-818

text: cattle

text: Bos taurus

text: Bos taurus


text: University College Dublin

text: public

text: ena-SAMPLE-TAB-18-10-2022-09:29:23:252-819

text: cattle

text: Bos taurus

text: Bos taurus


text: University College Dublin

text: public

text: ena-SAMPLE-TAB-18-10-2022-09:29:23:252-820

text: cattle

text: Bos taurus

text: Bos taurus


text: University College Dublin

text: public

text: ena-SAMPLE-TAB-18-10-2022-09:29:23:252-821

text: cattle

text: Bos taurus

text: Bos taurus


text: University College Dublin

text: public

text: ena-SAMPLE-TAB-18-10-2022-09:29:23:252-822

text: cattle

text: Bos taurus

text: Bos taurus


text: University College Dublin

text: public

text: ena-SAMPLE-TAB-18-10-2022-09:29:23:252-823

text: cattle

text: Bos taurus

text: Bos taurus


text: University College Dublin

text: public

text: ena-SAMPLE-TAB-18-10-2022-09:29:23:252-824

text: cattle

text: Bos taurus

text: Bos taurus


text: University College Dublin

text: public

text: ena-SAMPLE-TAB-18-10-2022-09:29:23:252-825

text: cattle

text: Bos taurus

text: Bos taurus


text: University College Dublin

text: public

text: ena-SAMPLE-TAB-18-10-2022-09:29:23:252-826

text: cattle

text: Bos taurus

text: Bos taurus


text: University College Dublin

text: public

text: ena-SAMPLE-TAB-18-10-2022-09:29:23:252-827

text: cattle

text: Bos taurus

text: Bos taurus


text: University College Dublin

text: public

text: ena-SAMPLE-TAB-18-10-2022-09:29:23:252-828

text: cattle

text: Bos taurus

text: Bos taurus


text: University College Dublin

text: public

text: ena-SAMPLE-TAB-18-10-2022-09:29:23:252-829

text: cattle

text: Bos taurus

text: Bos taurus


text: University College Dublin

text: public

text: ena-SAMPLE-TAB-18-10-2022-09:29:23:252-830

text: cattle

text: Bos taurus

text: Bos taurus


text: University College Dublin

text: public

text: ena-SAMPLE-TAB-18-10-2022-09:29:23:252-831

text: cattle

text: Bos taurus

text: Bos taurus


text: University College Dublin

text: public

text: ena-SAMPLE-TAB-18-10-2022-09:29:23:252-832

text: cattle

text: Bos taurus

text: Bos taurus


text: University College Dublin

text: public

text: ena-SAMPLE-TAB-18-10-2022-09:29:23:252-833

text: cattle

text: Bos taurus

text: Bos taurus


text: The Hospital for Sick Children

text: public

characteristic: age

text: ArrayExpress

characteristic: broker name

text: sheep

text: Protocols: Under maternal general anesthesia and after fetal echocardiography, fetal lambs were delivered by hysterotomy. The umbilical cord was clamped and the lamb was euthanized with IV sodium pentobarbital (BimedaMTC, Cambridge, Canada). A median sternotomy was used to harvest the heart, then samples were taken from the LV, RV, AAo and main PA. Tissue was snap frozen with liquid N2 and stored at -80°C. At gestational age 76 days, coils were implanted in the left heart under continuous ultrasound guidance (Philips HDI 5000), using a completely percutaneous approach under strict aseptic conditions. A 20G needle (6” Quincke; Beckton-Dickinson) was used to deliver platinum coils (0.018” IDC, Boston Scientific) above the mitral valve until the LV appeared underfilled and the ascending aortic flow decreased or became retrograde. RNA was extracted using the miRNeasy Mini Kit (QIAGEN). RNA-Seq library preparation was performed following the TruSeq Stranded Total RNA Library Preparation protocol (Illumina, USA) with the Ribo-Zero Gold rRNA removal kit. Briefly, 600 ng of total RNA was used as the input material and submitted to rRNA depletion using biotinylated beads that contain rRNA-targeting-specific oligos. rRNA-depleted RNA samples were fragmented into ranges of 200-300-bases for 4 minutes at 94°C and converted to double stranded cDNA, end-repaired and adenylated at the 3’ to create an overhang A to allow for ligation of Illumina adapters with an overhang T. Library fragments were amplified under the following conditions: initial denaturation at 98°C for 10 seconds, followed by 12 cycles of 98°C for 10 seconds, 60°C for 30 seconds and 72°C for 30 seconds, and finally an extension step for 5 minutes at 72°C. At the amplification step, each sample was amplified with a different barcoded adapter to allow for multiplex sequencing.

text: embryo

characteristic: developmental stage

text: hypoplastic left heart syndrome

characteristic: disease

text: wild type genotype

characteristic: genotype

characteristic: individual

text: coil implantation in the left atrium

characteristic: injury

text: not applicable

characteristic: isolate

text: Ovis aries

text: Ovis aries

text: ascending aorta

characteristic: organism part

text: hypoplastic left heart syndrome

characteristic: phenotype

text: Ovis aries

text: Dorset x Rideau Arcott

characteristic: strain


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: The Hospital for Sick Children

characteristic: INSDC center name

characteristic: INSDC last update

text: public

characteristic: SRA accession

characteristic: Submitter Id

text: ArrayExpress

text: sheep

characteristic: description

text: embryo

text: hypoplastic left heart syndrome

text: wild type genotype

text: coil implantation in the left atrium

text: not applicable

text: Ovis aries

text: Ovis aries

text: heart left ventricle

text: hypoplastic left heart syndrome

text: Ovis aries

text: Dorset x Rideau Arcott


text: The Hospital for Sick Children

characteristic: INSDC first public

text: public

characteristic: INSDC status

characteristic: age

text: ArrayExpress

characteristic: broker name

text: sheep

characteristic: common name

text: embryo

characteristic: developmental stage

text: hypoplastic left heart syndrome

characteristic: disease

text: wild type genotype

text: coil implantation in the left atrium

text: not applicable

text: Ovis aries

characteristic: organism

text: Ovis aries

text: ascending aorta

text: moderate hypoplasia

text: Ovis aries

text: Dorset x Rideau Arcott

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: The Hospital for Sick Children

text: public

text: ArrayExpress

text: sheep

text: embryo

text: hypoplastic left heart syndrome

text: wild type genotype

characteristic: genotype

characteristic: individual

text: coil implantation in the left atrium

characteristic: injury

text: not applicable

characteristic: isolate

text: Ovis aries

text: Ovis aries

text: heart left ventricle

characteristic: organism part

text: moderate hypoplasia

characteristic: phenotype

text: Ovis aries

text: Dorset x Rideau Arcott

characteristic: strain


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: The Hospital for Sick Children

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: ArrayExpress

text: sheep

characteristic: description

text: embryo

text: hypoplastic left heart syndrome

text: wild type genotype

text: coil implantation in the left atrium

text: not applicable

text: Ovis aries

text: Ovis aries

text: pulmonary artery

text: normal

text: Ovis aries

text: Dorset x Rideau Arcott


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: The Hospital for Sick Children

text: public

characteristic: age

text: ArrayExpress

characteristic: broker name

text: sheep

characteristic: common name

text: embryo

characteristic: developmental stage

text: hypoplastic left heart syndrome

characteristic: disease

text: wild type genotype

text: coil implantation in the left atrium

text: not applicable

text: Ovis aries

characteristic: organism

text: Ovis aries

text: heart right ventricle

text: normal

text: Ovis aries

text: Dorset x Rideau Arcott

characteristic: title


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: The Hospital for Sick Children

text: public

text: ArrayExpress

text: sheep

text: embryo

text: normal

text: wild type genotype

characteristic: genotype

characteristic: individual

text: control

characteristic: injury

text: not applicable

characteristic: isolate

text: Ovis aries

text: Ovis aries

text: ascending aorta

characteristic: organism part

text: normal

characteristic: phenotype

text: Ovis aries

text: Dorset x Rideau Arcott

characteristic: strain


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: The Hospital for Sick Children

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: ArrayExpress

text: sheep

characteristic: description

text: embryo

text: normal

text: wild type genotype

text: control

text: not applicable

text: Ovis aries

text: Ovis aries

text: heart left ventricle

text: normal

text: Ovis aries

text: Dorset x Rideau Arcott


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: The Hospital for Sick Children

text: public

characteristic: age

text: ArrayExpress

characteristic: broker name

text: sheep

characteristic: common name

text: embryo

characteristic: developmental stage

text: normal

characteristic: disease

text: wild type genotype

text: control

text: not applicable

text: Ovis aries

characteristic: organism

text: Ovis aries

text: pulmonary artery

text: normal

text: Ovis aries

text: Dorset x Rideau Arcott

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: The Hospital for Sick Children

text: public

text: ArrayExpress

text: sheep

text: embryo

text: normal

text: wild type genotype

characteristic: genotype

characteristic: individual

text: control

characteristic: injury

text: not applicable

characteristic: isolate

text: Ovis aries

text: Ovis aries

text: heart right ventricle

characteristic: organism part

text: normal

characteristic: phenotype

text: Ovis aries

text: Dorset x Rideau Arcott

characteristic: strain


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Shanghai Tenth People's Hospital

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

tag: Namespace:Shanghai Tenth People's Hospital

characteristic: Submitter Id

text: ArrayExpress

text: Protocols: Strains were maintained at -80˚C. Strains were streaked on YPD plates. The plates were incubated at 37˚C overnight. Then several colonies were picked up and suspended in DDW. Cell density was adjusted to 10,000 cells/ml, then 100µl of cell suspension was plated on YPD plates. The plates were incubated at 37˚C overnight. Colonies were picked up and suspended in DDW, then cell pellets were obtained by centrifuging at highest speed for 1min. We used the phenol-chloroform method to extract Genomic DNA. Cell pellets were suspended in 200µl of lysis buffer, add 100µl of acid washed glass beads, and 0,2ml phenol:chloroform:isoamyl alcohol (25:24:1). Vortex for 30min at 4˚C. Add 200µl TE pH7.5. Centrifuge for 5min at maximum speed. Transfer aqueous layer to a new 1.5ml EP tube. Add 1ml 100% ethanol. Precipitate 1h at -20˚C. Pellet DNA by centrifuging for 10min at maximum speed. Discard the supernatant. Add 400µl TE pH 7.5. Add 3ul of RNase A (10mg/ml). Incubate at 37˚C for 30min. Add 10µl of 3M NaOAc and 1ml of 100% ethanol. Mix by inversion. Precipitate 30min at -20˚C. Pellet DNA by centrifuging for 10min at maximum speed. Discard supernatant. Air-dry the pellet overnight. Resuspend in 50µl water. 1µg Genomic DNA was randomly fragmented by Covaris, followed by fragments selection by Agencourt AMPure XP-Medium kit to an average size of 200~400 bp. Selected fragments were end repaired and 3\adenylate, then the adaptors were ligated to the end of these 3\adenylate fragments. The products were amplified by PCR and purified by the Agencourt AMPure XP-Medium kit. The purified double stranded PCR products were heat denatured to single strand, then circularised by the splint oligo sequence. The single strand circle DNA (ssCirDNA) were formatted as the final library and qualified by QC.

characteristic: description

text: euploid revertant

text: Candida albicans

text: Candida albicans

text: Candida albicans


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: Shanghai Tenth People's Hospital

text: public

text: ArrayExpress

characteristic: broker name

text: euploid

text: Candida albicans

characteristic: organism

text: Candida albicans

text: Candida albicans

characteristic: title


strain 217

text: ETH Zurich

text: public

text: strain 217

tag: Namespace:ETH Zurich

text: mEp235 lysogen

text: Escherichia coli

text: Escherichia coli


strain 154

text: ETH Zurich

text: public

text: strain 154

text: phi80 lysogen

text: Escherichia coli

text: Escherichia coli


text: ETH Zurich

text: public

text: lambda lysogen

text: Escherichia coli

text: Escherichia coli


text: ETH Zurich

text: public

text: HK022 lysogen

text: Escherichia coli

text: Escherichia coli


text: ETH Zurich

text: public

text: Escherichia coli

text: Escherichia coli


text: public

tag: Namespace:Department of Biochemistry, University of Otago

characteristic: age

text: ArrayExpress

text: thale cress

characteristic: common name

text: Columbia

characteristic: cultivar

text: Protocols: Three biological replicates were collected. Whole seedlings were harvested. Wild-type, lsm4-1, LSM4R and LSM4RxK in lsm4-1 background seedlings were grown on Murashige and Skoog (MS) medium containing 0.8% (w/v) agar for 12 days under continuous light at 22°C. Whole seedlings were harvested and total RNA was extracted with RNeasy Plant Mini Kit (QIAGEN) following the manufacturer’s protocols. To estimate RNA concentration NanoDrop 2000c (Thermo Scientific) was used. Libraries were prepared by genome center at the Max Planck-Genome-Centre Cologne (MP-GC).

text: seedling development stage

characteristic: developmental stage

text: wild type genotype

characteristic: genotype

text: not applicable

characteristic: isolate

text: Arabidopsis thaliana

text: Arabidopsis thaliana

text: whole organism

characteristic: organism part

characteristic: replicate

text: Arabidopsis thaliana


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Department of Biochemistry, University of Otago

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: ArrayExpress

text: thale cress

text: Columbia

text: seedling development stage

text: wild type genotype

text: not applicable

text: Arabidopsis thaliana

text: Arabidopsis thaliana

text: whole organism

text: Arabidopsis thaliana


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: public

characteristic: SRA accession

characteristic: Submitter Id

text: ArrayExpress

characteristic: broker name

text: thale cress

text: Columbia

characteristic: description

text: seedling development stage

text: LSM4R in lsm4-1

text: not applicable

text: Arabidopsis thaliana

text: Arabidopsis thaliana

text: whole organism

text: Arabidopsis thaliana


text: public

characteristic: age

text: ArrayExpress

text: thale cress

characteristic: common name

text: Columbia

characteristic: cultivar

text: seedling development stage

characteristic: developmental stage

text: LSM4RxK in lsm4-1

text: not applicable

text: Arabidopsis thaliana

characteristic: organism

text: Arabidopsis thaliana

text: whole organism

text: Arabidopsis thaliana

characteristic: title


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: public

text: ArrayExpress

text: thale cress

text: Columbia

text: seedling development stage

characteristic: genotype

text: not applicable

characteristic: isolate

text: Arabidopsis thaliana

text: Arabidopsis thaliana

text: whole organism

characteristic: organism part

characteristic: replicate

text: Arabidopsis thaliana


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: 70769:99b6174d-caa9-4f10-9ecd-22dea2a6a027

tag: Namespace:Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research

text: GFBIO

text: not collected

text: Negative Control

text: laboratory environment [ENVO:01001405

characteristic: environment (biome)

text: marine benthic feature [ENVO:01000105]

characteristic: environment (feature)

text: marine sediment [ENVO:03000033]

characteristic: environment (material)

text: not collected

characteristic: environmental package

text: not collected

characteristic: geographic location (country and/or sea)

text: not collected

unit: m

characteristic: geographic location (depth)

text: not collected

characteristic: geographic location (elevation)

text: not collected

characteristic: geographic location (latitude)

text: not collected

characteristic: geographic location (longitude)

text: not collected

characteristic: geographic location (region and locality)

text: not collected

characteristic: investigation type

text: not collected

characteristic: not collected environmental package

text: marine sediment metagenome

text: Benthic carbon turnover on the Antarctic continental shelf: this study was funded by the AWI Grant-No. AWI_PS118_118

characteristic: project name

text: Negative Control

text: marine sediment metagenome

text: Illumina MiSeq

characteristic: sequencing method

text: true

characteristic: submitted to insdc

text: not collected

characteristic: total depth of water column


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Alfred Wegener Institute Helmholtz Centre 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

text: 70767:99b6174d-caa9-4f10-9ecd-22dea2a6a027

characteristic: Submitter Id

text: marine biome [ENVO:00000447]

characteristic: broad-scale environmental context

text: GFBIO

characteristic: broker name

characteristic: collection date

characteristic: depth

text: surface sediment (0-1 cm) collected under ice free station

characteristic: description

characteristic: elevation

text: marine sediment [ENVO:03000033]

characteristic: environmental medium

text: sediment

text: Southern Ocean

text: microbial communities from surface sediment along the eastern coast of Antarctic Peninsula

text: mimarks-survey

text: marine benthic feature [ENVO:01000105]

characteristic: local environmental context

text: marine sediment metagenome

characteristic: organism

text: Benthic carbon turnover on the Antarctic continental shelf: this study was funded by the AWI Grant-No. AWI_PS118_101

text: marine sediment metagenome

text: sediment

characteristic: sediment environmental package

text: Illumina MiSeq

text: true

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC center name

text: public

text: 70766:99b6174d-caa9-4f10-9ecd-22dea2a6a027

text: marine biome [ENVO:00000447]

text: GFBIO

text: surface sediment (0-1 cm) collected under marginal ice zone station

text: marine sediment [ENVO:03000033]

text: sediment

characteristic: environmental package

text: Southern Ocean

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

characteristic: geographic location (region and locality)

text: mimarks-survey

characteristic: investigation type

text: marine benthic feature [ENVO:01000105]

text: marine sediment metagenome

text: Benthic carbon turnover on the Antarctic continental shelf: this study was funded by the AWI Grant-No. AWI_PS118_59

characteristic: project name

text: marine sediment metagenome

text: sediment

text: Illumina MiSeq

characteristic: sequencing method

text: true

characteristic: submitted to insdc

characteristic: total depth of water column


characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: 70765:99b6174d-caa9-4f10-9ecd-22dea2a6a027

characteristic: Submitter Id

text: marine biome [ENVO:00000447]

characteristic: broad-scale environmental context

text: GFBIO

characteristic: broker name

characteristic: collection date

characteristic: depth

characteristic: description

characteristic: elevation

text: marine sediment [ENVO:03000033]

characteristic: environmental medium

text: sediment

text: Southern Ocean

text: mimarks-survey

text: marine benthic feature [ENVO:01000105]

characteristic: local environmental context

text: marine sediment metagenome

characteristic: organism

text: Benthic carbon turnover on the Antarctic continental shelf: this study was funded by the AWI Grant-No. AWI_PS118_53

text: marine sediment metagenome

text: sediment

characteristic: sediment environmental package

text: Illumina MiSeq

text: true


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC center name

text: public

text: 70764:99b6174d-caa9-4f10-9ecd-22dea2a6a027

text: marine biome [ENVO:00000447]

text: GFBIO

text: marine sediment [ENVO:03000033]

text: sediment

characteristic: environmental package

text: Southern Ocean

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

characteristic: geographic location (region and locality)

text: mimarks-survey

characteristic: investigation type

text: marine benthic feature [ENVO:01000105]

text: marine sediment metagenome

text: Benthic carbon turnover on the Antarctic continental shelf: this study was funded by the AWI Grant-No. AWI_PS118_41

characteristic: project name

text: marine sediment metagenome

text: sediment

text: Illumina MiSeq

characteristic: sequencing method

text: true

characteristic: submitted to insdc

characteristic: title


characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: 70763:99b6174d-caa9-4f10-9ecd-22dea2a6a027

characteristic: Submitter Id

text: marine biome [ENVO:00000447]

characteristic: broad-scale environmental context

text: GFBIO

characteristic: broker name

characteristic: collection date

characteristic: depth

characteristic: description

characteristic: elevation

text: marine sediment [ENVO:03000033]

characteristic: environmental medium

text: sediment

text: Southern Ocean

text: mimarks-survey

text: marine benthic feature [ENVO:01000105]

characteristic: local environmental context

text: marine sediment metagenome

characteristic: organism

text: Benthic carbon turnover on the Antarctic continental shelf: this study was funded by the AWI Grant-No. AWI_PS118_35

text: marine sediment metagenome

text: sediment

text: Illumina MiSeq

text: true

characteristic: total depth of water column


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC center name

text: public

text: 70762:99b6174d-caa9-4f10-9ecd-22dea2a6a027

text: marine biome [ENVO:00000447]

text: GFBIO

text: marine sediment [ENVO:03000033]

text: sediment

characteristic: environmental package

text: Southern Ocean

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

characteristic: geographic location (region and locality)

text: mimarks-survey

characteristic: investigation type

text: marine benthic feature [ENVO:01000105]

text: marine sediment metagenome

text: Benthic carbon turnover on the Antarctic continental shelf: this study was funded by the AWI Grant-No. AWI_PS118_29

characteristic: project name

text: marine sediment metagenome

text: sediment

characteristic: sediment environmental package

text: Illumina MiSeq

characteristic: sequencing method

text: true

characteristic: submitted to insdc


characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: 70761:99b6174d-caa9-4f10-9ecd-22dea2a6a027

characteristic: Submitter Id

text: marine biome [ENVO:00000447]

characteristic: broad-scale environmental context

text: GFBIO

characteristic: broker name

characteristic: collection date

characteristic: depth

characteristic: description

characteristic: elevation

text: marine sediment [ENVO:03000033]

characteristic: environmental medium

text: sediment

text: Southern Ocean

text: mimarks-survey

text: marine benthic feature [ENVO:01000105]

characteristic: local environmental context

text: marine sediment metagenome

characteristic: organism

text: Benthic carbon turnover on the Antarctic continental shelf: this study was funded by the AWI Grant-No. AWI_PS118_23

text: marine sediment metagenome

text: sediment

text: Illumina MiSeq

text: true

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research

characteristic: INSDC center name

text: public

text: 70760:99b6174d-caa9-4f10-9ecd-22dea2a6a027

text: marine biome [ENVO:00000447]

text: GFBIO

text: surface sediment (0-1 cm) collected under heavy ice covered station

text: marine sediment [ENVO:03000033]

text: sediment

characteristic: environmental package

text: Southern Ocean

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

characteristic: geographic location (region and locality)

text: mimarks-survey

characteristic: investigation type

text: marine benthic feature [ENVO:01000105]

text: marine sediment metagenome

text: Benthic carbon turnover on the Antarctic continental shelf: this study was funded by the AWI Grant-No. AWI_PS118_11

characteristic: project name

text: marine sediment metagenome

text: sediment

characteristic: sediment environmental package

text: Illumina MiSeq

characteristic: sequencing method

text: true

characteristic: total depth of water column


characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: 70759:99b6174d-caa9-4f10-9ecd-22dea2a6a027

characteristic: Submitter Id

text: marine biome [ENVO:00000447]

characteristic: broad-scale environmental context

text: GFBIO

characteristic: broker name

characteristic: collection date

characteristic: depth

characteristic: description

characteristic: elevation

text: marine sediment [ENVO:03000033]

characteristic: environmental medium

text: sediment

text: Southern Ocean

text: microbial communities from surface sediment along the eastern coast of Antarctic Peninsula

text: mimarks-survey

text: marine benthic feature [ENVO:01000105]

characteristic: local environmental context

text: marine sediment metagenome

characteristic: organism

text: Benthic carbon turnover on the Antarctic continental shelf: this study was funded by the AWI Grant-No. AWI_PS118_05

text: marine sediment metagenome

text: sediment

text: Illumina MiSeq

text: true

characteristic: submitted to insdc


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC center name

text: public

text: ena-SAMPLE-TAB-14-11-2022-09:26:50:990-116347

tag: Namespace:UNIVERSITY OF NATURAL RESOURCES AND LIFE SCIENCES,

text: Chinese hamster

characteristic: common name

text: nCats of the B4GALT1 gene

text: Cricetulus griseus

text: Cricetulus griseus

text: run ID 1

characteristic: title


text: UNIVERSITY OF NATURAL RESOURCES AND LIFE SCIENCES,

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: ena-SAMPLE-TAB-14-11-2022-09:26:50:990-116348

characteristic: Submitter Id

text: Chinese hamster

text: nCats of the unmethylated Fut8 promoter

text: Cricetulus griseus

text: Cricetulus griseus

text: run ID 2


text: public

text: ena-SAMPLE-TAB-14-11-2022-09:26:50:990-116349

text: Chinese hamster

text: nCats of the methylated Fut8 promoter

characteristic: description

text: Cricetulus griseus

text: Cricetulus griseus

text: run ID 3


text: public

text: ena-SAMPLE-TAB-14-11-2022-09:26:50:990-116350

text: Chinese hamster

text: nCats for junction site detection of the CD4 expression vector

text: Cricetulus griseus

text: Cricetulus griseus

text: run ID 4


text: public

text: ena-SAMPLE-TAB-14-11-2022-09:26:50:990-116351

text: Chinese hamster

text: Cricetulus griseus

text: Cricetulus griseus

text: run ID 5


text: public

text: ena-SAMPLE-TAB-14-11-2022-09:26:50:990-116352

text: CHO-Herc

text: Chinese hamster

text: nCats for junction site detection of the Herceptin expression vector

text: Cricetulus griseus

text: Cricetulus griseus

text: run ID 6


text: public

text: ena-SAMPLE-TAB-14-11-2022-09:26:50:990-116353

text: Chinese hamster

text: nCats to determine the structure of the integrated the CD4 expression vector

text: Cricetulus griseus

text: Cricetulus griseus

text: run ID 7


text: public

text: ena-SAMPLE-TAB-14-11-2022-09:26:50:990-116354

text: Chinese hamster

text: Cricetulus griseus

text: Cricetulus griseus

text: run ID 8


text: public

text: ena-SAMPLE-TAB-14-11-2022-09:26:50:990-116355

text: CHO-Herc

text: Chinese hamster

text: nCats to determine the structure of the integrated the Herceptin expression vector

text: Cricetulus griseus

text: Cricetulus griseus

text: run ID 9


text: Department of Biochemistry, University of Otago

text: public

characteristic: age

text: ArrayExpress

characteristic: broker name

text: thale cress

text: Columbia

characteristic: cultivar

text: Protocols: Plants grown in MS plates in continuous light (LL) for 12 days were vacuum-infiltrated with 1% formaldehyde for 15 min followed by quenching with 125 mM glycine. A whole-cell extract was prepared in RIP-lysis buffer. The extract was pre-cleared with Sepharose beads and subjected to immunoprecipitation with GFP-Trap beads (Chromotek). After extensive washing with RIP washing buffer, co-precipitated RNAs were extracted with Trizol (Invitrogen) and treated with DNase (Promega). RNAs were extracted with Trizol (Invitrogen) and treated with DNase (Promega). Libraries were prepared by genome center at the Max Planck-Genome-Centre Cologne (MP-GC).

text: seedling development stage

characteristic: developmental stage

text: 35S-LSM4-YFP in lsm4-1

characteristic: genotype

text: not applicable

characteristic: isolate

text: Arabidopsis thaliana

text: Arabidopsis thaliana

text: whole organism

characteristic: organism part

text: Arabidopsis thaliana


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: public

text: ArrayExpress

text: thale cress

text: Columbia

text: seedling development stage

text: not applicable

text: Arabidopsis thaliana

characteristic: organism

text: Arabidopsis thaliana

text: whole organism

text: Arabidopsis thaliana


text: Addis Ababa University

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

tag: Namespace:Addis Ababa University

text: metagenome

characteristic: common name

text: Shotgun metagenomic sequences for chicken sample Batambie_A1

text: Gallus gallus

characteristic: environment (biome)

characteristic: environment (feature)

characteristic: environment (material)

text: Ethiopia

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: host-associated

characteristic: host-associated environmental package

text: metagenome

characteristic: investigation type

text: metagenome

text: Ethiopian chicken caecal microbiota

characteristic: project name

text: metagenome

characteristic: sequencing method

characteristic: title


tag: attribute

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Addis Ababa University

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: metagenome

text: Shotgun metagenomic sequences for chicken sample Tsion_Teguaz_A10

characteristic: description

text: Gallus gallus

text: Ethiopia

text: host-associated

text: metagenome

text: metagenome

text: Ethiopian chicken caecal microbiota

text: metagenome


text: Addis Ababa University

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: metagenome

characteristic: common name

text: Shotgun metagenomic sequences for chicken sample Kefis_A100

text: Gallus gallus

characteristic: environment (biome)

characteristic: environment (feature)

characteristic: environment (material)

text: Ethiopia

text: host-associated

text: metagenome

text: metagenome

characteristic: organism

text: Ethiopian chicken caecal microbiota

text: metagenome


text: Addis Ababa University

text: public

text: metagenome

text: Shotgun metagenomic sequences for chicken sample Kefis_A101

text: Gallus gallus

text: Ethiopia

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: host-associated

characteristic: host-associated environmental package

text: metagenome

characteristic: investigation type

text: metagenome

text: Ethiopian chicken caecal microbiota

characteristic: project name

text: metagenome

characteristic: sequencing method

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Addis Ababa University

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: metagenome

text: Shotgun metagenomic sequences for chicken sample Kefis_A102

characteristic: description

text: Gallus gallus

text: Ethiopia

text: host-associated

text: metagenome

text: metagenome

text: Ethiopian chicken caecal microbiota

text: metagenome


text: Addis Ababa University

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: metagenome

characteristic: common name

text: Shotgun metagenomic sequences for chicken sample Kefis_A103

text: Gallus gallus

characteristic: environment (biome)

characteristic: environment (feature)

characteristic: environment (material)

text: Ethiopia

text: host-associated

text: metagenome

text: metagenome

characteristic: organism

text: Ethiopian chicken caecal microbiota

text: metagenome


text: Addis Ababa University

text: public

text: metagenome

text: Shotgun metagenomic sequences for chicken sample Kefis_A104

text: Gallus gallus

text: Ethiopia

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: host-associated

characteristic: host-associated environmental package

text: metagenome

characteristic: investigation type

text: metagenome

text: Ethiopian chicken caecal microbiota

characteristic: project name

text: metagenome

characteristic: sequencing method

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Addis Ababa University

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: metagenome

text: Shotgun metagenomic sequences for chicken sample Kefis_A105

characteristic: description

text: Gallus gallus

text: Ethiopia

text: host-associated

text: metagenome

text: metagenome

text: Ethiopian chicken caecal microbiota

text: metagenome


text: Addis Ababa University

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: metagenome

characteristic: common name

text: Shotgun metagenomic sequences for chicken sample Kefis_A106

text: Gallus gallus

characteristic: environment (biome)

characteristic: environment (feature)

characteristic: environment (material)

text: Ethiopia

text: host-associated

text: metagenome

text: metagenome

characteristic: organism

text: Ethiopian chicken caecal microbiota

text: metagenome


text: Addis Ababa University

text: public

text: metagenome

text: Shotgun metagenomic sequences for chicken sample Kefis_A107

text: Gallus gallus

text: Ethiopia

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: host-associated

characteristic: host-associated environmental package

text: metagenome

characteristic: investigation type

text: metagenome

text: Ethiopian chicken caecal microbiota

characteristic: project name

text: metagenome

characteristic: sequencing method

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Addis Ababa University

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: metagenome

text: Shotgun metagenomic sequences for chicken sample Tsion_Teguaz_A11

characteristic: description

text: Gallus gallus

text: Ethiopia

text: host-associated

text: metagenome

text: metagenome

text: Ethiopian chicken caecal microbiota

text: metagenome


text: Addis Ababa University

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: metagenome

characteristic: common name

text: Shotgun metagenomic sequences for chicken sample Tsion_Teguaz_A12

text: Gallus gallus

characteristic: environment (biome)

characteristic: environment (feature)

characteristic: environment (material)

text: Ethiopia

text: host-associated

text: metagenome

text: metagenome

characteristic: organism

text: Ethiopian chicken caecal microbiota

text: metagenome