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text: human oral metagenome

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text: terrestrial biome

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text: Human-oral

characteristic: environmental package

text: Spain

characteristic: geographic location (country and/or sea)

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characteristic: geographic location (longitude)

text: metagenome

characteristic: investigation type

text: human oral metagenome

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unit: DD

text: metagenome

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text: 16S rRNA gene amplicons (V3-V4) from sample 16S_EE69S

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text: FISABIO - Public Health

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characteristic: geographic location (country and/or sea)

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characteristic: investigation type

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text: human oral metagenome

text: Oral sample from Elder 71S

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text: metagenome

text: human oral metagenome

text: human oral metagenome

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text: 16S rRNA gene amplicons (V3-V4) from sample 16S_EE71S


text: FISABIO - Public Health

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characteristic: SRA accession

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text: human oral metagenome

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text: Oral sample from Elder 72S

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text: human-associated habitat

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text: metagenome

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characteristic: organism

text: human oral metagenome

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text: 16S rRNA gene amplicons (V3-V4) from sample 16S_EE72S

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text: FISABIO - Public Health

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text: human oral metagenome

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text: terrestrial biome

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characteristic: geographic location (country and/or sea)

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characteristic: investigation type

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text: human oral metagenome

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text: FISABIO - Public Health

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text: human oral metagenome

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characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

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characteristic: investigation type

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text: 16S rRNA gene amplicons (V3-V4) from sample 16S_EE78S

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characteristic: geographic location (country and/or sea)

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text: human oral metagenome

text: Illumina

text: 16S rRNA gene amplicons (V3-V4) from sample 16S_EE80S


text: FISABIO - Public Health

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characteristic: SRA accession

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text: human oral metagenome

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text: Oral sample from Elder 81S

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text: 16S rRNA gene amplicons (V3-V4) from sample 16S_EE81S

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text: FISABIO - Public Health

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text: 16S rRNA gene amplicons (V3-V4) from sample 16S_EE86S


text: FISABIO - Public Health

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text: human oral metagenome

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text: Oral sample from Elder 87S

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text: 16S rRNA gene amplicons (V3-V4) from sample 16S_EE87S

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text: FISABIO - Public Health

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text: Human-oral

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text: 16S rRNA gene amplicons (V3-V4) from sample 16S_EE88S


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text: 16S rRNA gene amplicons (V3-V4) from sample 16S_EE89S


text: FISABIO - Public Health

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text: human oral metagenome

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text: Oral sample from Elder 90S

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text: 16S rRNA gene amplicons (V3-V4) from sample 16S_EE90S

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text: FISABIO - Public Health

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text: human oral metagenome

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text: 16S rRNA gene amplicons (V3-V4) from sample 16S_EE91S


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text: FISABIO - Public Health

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text: public

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text: human oral metagenome

text: Oral sample from Elder 92S

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text: Human-oral

text: Spain

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text: human oral metagenome

text: human oral metagenome

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text: 16S rRNA gene amplicons (V3-V4) from sample 16S_EE92S


text: FISABIO - Public Health

text: public

characteristic: SRA accession

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text: human oral metagenome

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text: Oral sample from Elder 93S

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text: terrestrial biome

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text: human-associated habitat

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text: human-associated habitat

text: Human-oral

text: Spain

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text: human oral metagenome

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text: human oral metagenome

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text: 16S rRNA gene amplicons (V3-V4) from sample 16S_EE93S

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text: FISABIO - Public Health

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text: human oral metagenome

text: Oral sample from Elder 94S

text: terrestrial biome

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characteristic: environment (material)

text: Human-oral

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text: Spain

characteristic: geographic location (country and/or sea)

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characteristic: investigation type

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text: 16S rRNA gene amplicons (V3-V4) from sample 16S_EE94S


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text: FISABIO - Public Health

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text: public

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text: human oral metagenome

text: Oral sample from Elder 95S

text: terrestrial biome

text: human-associated habitat

text: human-associated habitat

text: Human-oral

text: Spain

text: metagenome

text: human oral metagenome

text: human oral metagenome

text: Illumina

text: 16S rRNA gene amplicons (V3-V4) from sample 16S_EE95S


text: FISABIO - Public Health

text: public

characteristic: SRA accession

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text: human oral metagenome

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text: Oral sample from Elder 97S

characteristic: description

text: terrestrial biome

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text: human-associated habitat

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text: human-associated habitat

text: Human-oral

text: Spain

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text: human oral metagenome

characteristic: organism

text: human oral metagenome

text: Illumina

text: 16S rRNA gene amplicons (V3-V4) from sample 16S_EE97S

characteristic: title


text: FISABIO - Public Health

text: public

text: human oral metagenome

text: Oral sample from Elder 98S

text: terrestrial biome

text: human-associated habitat

text: human-associated habitat

characteristic: environment (material)

text: Human-oral

characteristic: environmental package

text: Spain

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: metagenome

characteristic: investigation type

text: human oral metagenome

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text: 16S rRNA gene amplicons (V3-V4) from sample 16S_EE98S


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text: FISABIO - Public Health

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text: public

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text: human oral metagenome

text: Oral sample from Elder 99S

text: terrestrial biome

text: human-associated habitat

text: human-associated habitat

text: Human-oral

text: Spain

text: metagenome

text: human oral metagenome

text: human oral metagenome

text: Illumina

text: 16S rRNA gene amplicons (V3-V4) from sample 16S_EE99S


text: Socheatraksmey

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characteristic: SRA accession

characteristic: Submitter Id

text: human T-cell

text: human

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text: 4-1BBz CAR-T cell after stimulation with target cell for 7 days

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text: Homo sapiens

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text: Homo sapiens

text: 4-1BBz CAR-T cell sample donor 1

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text: Socheatraksmey

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text: human

text: Homo sapiens

text: Homo sapiens

text: 4-1BBz CAR-T cell sample donor 2


text: Socheatraksmey

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text: Homo sapiens

text: Homo sapiens

text: 4-1BBz CAR-T cell sample donor 3


text: Socheatraksmey

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text: human T-cell

text: human

text: CD79A-40 CAR-T cell after stimulation with target cell for 7 days

text: Homo sapiens

text: Homo sapiens

text: CD79A-40 CAR-T cell sample donor 1


text: Socheatraksmey

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text: human T-cell

text: human

text: Homo sapiens

text: Homo sapiens

text: CD79A-40 CAR-T cell sample donor 2


text: Socheatraksmey

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text: human

text: Homo sapiens

text: Homo sapiens

text: CD79A-40 CAR-T cell sample donor 3


text: Socheatraksmey

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text: human T-cell

text: human

text: CD28z CAR-T cell after stimulation with target cell for 7 days

text: Homo sapiens

text: Homo sapiens

text: CD28z CAR-T cell sample donor 1


text: Socheatraksmey

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text: human T-cell

text: human

text: Homo sapiens

text: Homo sapiens

text: CD28z CAR-T cell sample donor 2


text: Socheatraksmey

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text: CD28z CAR-T cell sample donor 3


text: public

tag: Namespace:Department of Agriculture, Food, Environment and Forestry (DAGRI) - University of Florence

unit: year

characteristic: age

text: ArrayExpress

characteristic: broker name

text: Protocols: 10 plants of L. nobilis were planted in pots using commercial soils collected from two different areas of Altopascio (Lucca, Tuscany, Italy). 5 plants were cultivated in a rural area (named \R\) sparsely inhabited, with significant lower levels of PM (control) compared to 5 plants exposed to higher levels of PM (named \T\; “traffic”, close to a traffic light with a high number of moving cars). Plants were irrigated weekly and routinely inspected to determine any eventual symptoms of biotic and abiotic stresses. Plants remain healthy during the three months of the experimental trial. Healthy, fully-expanded, green leaves were sampled from the 5 plants from each zone at the time of planting (T0; 15th March 2021) and three months after planting (T1; 15th June 2021). Leaves were immediately frozen in liquid nitrogen and stored at - 80 °C until RNA extraction. Plants have a height of around 1.5 meters and were bought in the same plant nursery to reduce plants' physiological and agronomic variability at the beginning of the trial. Frozen leaves were ground to a fine powder. A CTAB-modified protocol was used. The pellet obtained from the extraction procedure was resuspended in 130 µL of nuclease-free water, and the RNAs were treated with DNaseI (NEB). Then, RNAs were purified using a silica-based method (Monarch RNA Cleanup kit - NEB) and eluted twice in 15 µL of nuclease-free water. The 16 transcriptomic libraries were prepared using Illumina mRNA Prep kit, following the manufacturers instructions and a unique dual index combinations was used for each sample for barcoding.

text: adult

characteristic: developmental stage

text: normal

characteristic: disease

text: Altopascio, Lucca, Italy

characteristic: environmental history

text: wild type genotype

characteristic: genotype

text: Laurus nobilis

text: Laurus nobilis

text: leaf

characteristic: organism part

text: Laurus nobilis


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Department of Agriculture, Food, Environment and Forestry (DAGRI) - University of Florence

characteristic: INSDC center name

text: public

text: ArrayExpress

text: adult

text: normal

text: Altopascio, Lucca, Italy

text: wild type genotype

text: Laurus nobilis

text: Laurus nobilis

text: leaf

text: Laurus nobilis


characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: ArrayExpress

text: adult

text: normal

text: Altopascio, Lucca, Italy

text: traffic air pollution

characteristic: environmental stress

text: wild type genotype

text: Laurus nobilis

text: Laurus nobilis

text: leaf

text: Laurus nobilis


text: public

tag: Namespace:Hospital General Universitario Gregorio Maranon

characteristic: collection date

text: Mycobacterium caprae as responsible for human tuberculosis

characteristic: description

text: Spain

characteristic: geographic location (country and/or sea)

text: Human

characteristic: host scientific name

characteristic: isolate

text: Mycobacterium tuberculosis variant caprae

characteristic: organism

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: Hospital General Universitario Gregorio Maranon

text: public

text: Spain

text: Human


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: public

text: Spain

text: Goat


characteristic: INSDC center name

characteristic: INSDC first public

text: public

tag: Namespace:(1) Genetics and Genome Biology, SickKids Research Institute, Toronto, ON, Canada (2) Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada

unit: day

characteristic: age

text: ArrayExpress

characteristic: broker name

text: house mouse

characteristic: common name

text: Protocols: Male and female mice were euthanized using automated Euthanex Carbon Dioxide (CO2) lids followed by decapitation between 9:30 am and 11:30 am. Whole hypothalamus were dissected on postnatal days 12, 22, 27, 32 and 37. Collected tissues were directly placed in RNAlater (containing 10% w/v sodium citrate tribasic dihydrate and 60% w/v ammonium sulphate following dissection, and stored at −20 °C until RNA extraction. Total RNA was extracted from mouse hypothalamus with the NucleoSpin® miRNA kit (Macherey Nagel) in combination with TRIzol lysis (Invitrogen) following manufacturers' protocols, allowing for collection of small RNA (< 200 nt) and large RNA (> 200 nt) simultaneously into separate tubes from total RNA. Prior to RNA extraction, tissue samples were placed into bead mill tubes containing six 1.4 mm ceramic beads (MoBio Laboratories), and homogenized for 30 s at 6.5 m/s at 4 °C using Omni Bead Ruptor 24 bead mill. RNA quantity was determined using Nanodrop and the quality was assessed by Agilent 2100 Bioanalyzer. Construction of RNA-seq libraries was automated with QuantSeq 3'mRNA-seq Library Prep Kit (Lexogen GmbH, Vienna) using the Agilent NGS Workstation (Agilent Technologies, Santa Clara) as per manufacturer's protocol. 250 ng of RNA, from the large RNA fraction, was used to generate cDNA. cDNA was amplified with 17 PCR cycles as determined by qPCR analysis using the PCR Add-on kit (Lexogen). The resulting libraries were quantified with Qubit DNA HS (Thermo Fisher, Waltham) and fragment sizes analyzed on the Agilent Bioanalyzer using the High Sensitivity DNA assay prior to sequencing.

text: early postnatal development

characteristic: developmental stage

text: normal

characteristic: disease

text: wild type genotype

characteristic: genotype

characteristic: individual

text: Mus musculus

text: Mus musculus

text: hypothalamus

characteristic: organism part

text: Mus musculus

text: female

characteristic: sex

characteristic: strain


text: (1) Genetics and Genome Biology, SickKids Research Institute, Toronto, ON, Canada (2) Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: ArrayExpress

text: house mouse

characteristic: description

text: early postnatal development

text: normal

text: wild type genotype

text: Mus musculus

characteristic: organism

text: Mus musculus

text: hypothalamus

text: Mus musculus

text: female

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC first public

text: public

characteristic: age

text: ArrayExpress

text: house mouse

text: pre-puberty

text: normal

text: wild type genotype

text: Mus musculus

text: Mus musculus

text: hypothalamus

text: Mus musculus

text: male


text: public

text: ArrayExpress

characteristic: broker name

text: house mouse

characteristic: common name

text: pre-puberty

characteristic: developmental stage

text: normal

characteristic: disease

text: wild type genotype

characteristic: genotype

characteristic: individual

text: Mus musculus

text: Mus musculus

text: hypothalamus

characteristic: organism part

text: Mus musculus

text: female


characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: ArrayExpress

text: house mouse

characteristic: description

text: peri-puberty

text: normal

text: wild type genotype

text: Mus musculus

text: Mus musculus

text: hypothalamus

text: Mus musculus

text: male

characteristic: sex

characteristic: strain


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC center name

text: public

text: ArrayExpress

text: house mouse

text: peri-puberty

text: normal

text: wild type genotype

text: Mus musculus

characteristic: organism

text: Mus musculus

text: hypothalamus

text: Mus musculus

text: female

characteristic: title


characteristic: INSDC first public

text: public

characteristic: age

text: ArrayExpress

characteristic: broker name

text: house mouse

characteristic: common name

text: post-puberty

characteristic: developmental stage

text: normal

characteristic: disease

text: wild type genotype

characteristic: genotype

text: Mus musculus

text: Mus musculus

text: hypothalamus

text: Mus musculus

text: male


characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: ArrayExpress

text: house mouse

characteristic: description

text: post-puberty

text: normal

text: wild type genotype

characteristic: individual

text: Mus musculus

text: Mus musculus

text: hypothalamus

characteristic: organism part

text: Mus musculus

text: female


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC center name

text: public

text: ArrayExpress

text: house mouse

text: early postnatal development

text: normal

text: wild type genotype

text: Mus musculus

text: Mus musculus

text: hypothalamus

text: Mus musculus

text: male

characteristic: sex

characteristic: strain


text: IMEDEA

characteristic: INSDC first public

text: public

text: CNAG-CRG

characteristic: broker name

text: Josep Al�s

text: Institut Mediterrani d'Estudis Avan�ats

characteristic: collecting institution

text: pearly razorfish

characteristic: common name

text: Xyrichtys novacula liver tissue for DNA extraction

text: Spain

characteristic: geographic location (country and/or sea)

characteristic: geographic location (depth)

characteristic: geographic location (elevation)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: Spain | Balearic Islands | Mallorca | Llucmajor | Badia de Palma marine protected area

characteristic: geographic location (region and locality)

text: Littoral zone

characteristic: habitat

text: Josep Al�s Crep�

text: Institut Mediterrani d'Estudis Avan�ats

text: adult

characteristic: lifestage

text: Xyrichtys novacula

characteristic: organism

text: LIVER

characteristic: original collection date

characteristic: original geographic location

text: CBP

characteristic: project name

text: Xyrichtys novacula

text: Female

text: IMEDEA 109264

characteristic: title

characteristic: tolid


characteristic: ENA first public

characteristic: ENA-CHECKLIST

characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

tag: Namespace:Department of Microbial Genetics and Gene Expression, Institute of Microbiology, Czech Academy of Sciences, Prague, Czech Republic

characteristic: Submitter Id

text: ArrayExpress

characteristic: broker name

text: Protocols: 100 ml of bacterial culture was crosslinked with 1% formaldehyde (final conc.), formaldehyde was added directly to the medium) for 30 minutes at 37 °C in the shaker. Formaldehyde was quenched by glycine (0.125 M final conc.) added for 5 minutes at 37 °C in the shaker. Bacterial cultures were centrifuged for 5 min at 9000 rpm, 4 °C, pellet washed with 10 ml of 1x PBS, bacteria centrifuged again and pellet immediately frozen at -80°C. Mycobacterium smegmatis mc2 155 cells (wt, LK865) were grown at 37 °C in Middlebrook 7H9 medium with 0.2% glycerol and 0.05% Tween 80, and harvested in exponential (OD600 ∼0.5) or early stationary phase (OD600 ∼2.5–3, 24 hrs of cultivation). Bacterial pellet was resuspended in 3 ml of ice cold RIPA buffer (150 mM NaCl, 1% Triton X-100, 0.5% dexycholate, 0.1% SDS, 50 mM Tris-Cl pH 8.0, 5 mM EDTA) with protease inhibitors cocktail (Sigma-Aldrich, 5 ul/1 ml) and 0.1 M PMSF (5 ul/1 ml) and sonicated 18x10 seconds with 1 min pauses on ice between cycles. Lysate was centrifuged 9000 rpm at 4 °C for 15 min and pellet discarded. 2 mg (protein) of lysates were incubated for 16-18 hours at 4 °C with 20 μl of Protein G plus agarose beads (Santa Cruz) coated with 5 μg mouse monoclonal anti-beta subunit of RNAP antibody [clone 8RB13] (Biolegend), 5 μg of anti-Sigma70 antibody [clone 2G10] (Biolegend), or 5 μg of mouse nonspecific IgG (Sigma-Aldrich) used as a negative control, respectively. The captured complexes were washed twice with RIPA, four times with 100 mM Tris-HCl, pH 8.5, 500 mM LiCL, 1% Triton X-100, 1% deoxycholic acid. Beads with captured complexes were transfered to new eppendorf tube to reduce the background and washed again two times with RIPA and TE buffer. Protein-DNA complexes were eluted with elution buffer (50 mM Tris-Cl pH 8, 0.66 Mm EDTA, 1% SDS) for 10 minutes at 65°C, decrosslinked in the presence of 200 mM NaCl for 5 h at 65°C, treated with 100 µg/ml RNase A for 1 hour at 37°C and 400 µg/ml proteinase K for 30 min at 45°C. DNA was purified with Qiagen PCR purification kit and eluted into 100 ul EB. 40 ul of immunoprecipitated DNA sample or 10 ng of DNA input were used for library construction according to the NEXTflex™ ChIP-Seq Kit manual including the Size-Selection Cleanup step B2.

characteristic: description

text: exponential phase

characteristic: developmental stage

text: wild type genotype

characteristic: genotype

text: Middlebrook 7H9 medium

characteristic: growth condition

text: not applicable

characteristic: isolate

text: Mycolicibacterium smegmatis MC2 155

text: Mycolicibacterium smegmatis MC2 155

text: Mycolicibacterium smegmatis MC2 155

characteristic: strain


text: Department of Microbial Genetics and Gene Expression, Institute of Microbiology, Czech Academy of Sciences, Prague, Czech Republic

text: public

text: ArrayExpress

text: exponential phase

text: wild type genotype

text: Middlebrook 7H9 medium

text: not applicable

text: Mycolicibacterium smegmatis MC2 155

characteristic: organism

text: Mycolicibacterium smegmatis MC2 155

text: Mycolicibacterium smegmatis MC2 155

characteristic: title


characteristic: ENA first public

text: public

text: ArrayExpress

text: stationary phase

text: wild type genotype

text: Middlebrook 7H9 medium

text: not applicable

text: Mycolicibacterium smegmatis MC2 155

text: Mycolicibacterium smegmatis MC2 155

text: Mycolicibacterium smegmatis MC2 155


E-MTAB-12350:Mtb input

characteristic: ENA-CHECKLIST

text: public

text: E-MTAB-12350:Mtb input

text: ArrayExpress

text: Protocols: 100 ml cells were pelleted and washed in lysis buffer (20 mM Tris–HCl pH 7.9, 150 mM KCl, 1 mM MgCl2, 1 mM dithiothreitol (DTT) and frozen in -70°C. 2-3 loops of M. tuberculosis H37Rv cells (grown on Löwenstein–Jensen agar plates for 21 days) were inoculated into Middlebrook 7H9 medium supplemented 10% (v/v) OADC, 0.2% glycerol and 0.05% Tween 80 and cultivated at 35.5°C for 15 days. Cells resuspended in lysis buffer (20 mM Tris–HCl pH 7.9, 150 mM KCl, 1 mM MgCl2, 1 mM dithiothreitol (DTT), 0.5 mM phenylmethylsulfonyl fluoride (PMSF), supplemented with Calbiochem Protease Inhibitor Cocktail Set III protease inhibitors), disrupted by vortexing with 0.1 mm zirconia beads 7x30s with 1 min pauses on ice and centrifuged. 3 mg (protein) of lysates were incubated for 2 hours at 4°C with 20 μl of Protein G plus agarose beads (Santa Cruz) coated with 5 μg mouse monoclonal anti-beta subunit of RNAP antibody [clone 8RB13] (Biolegend), 2.5 μg of anti-Sigma70 antibody [clone 2G10] (Biolegend), or 5 μg of mouse nonspecific IgG (Sigma-Aldrich) used as a negative control, respectively. The captured complexes were washed four times using 20 mM Tris–HCl pH 7.9, 150 mM KCl, 1 mM MgCl2, finally resuspended in 200 μl 1% SDS, 150 mM KCl, 20 mM Tris–HCl pH 7.9, 1 mM MgCl2 and incubated on a rotating platform with 200 μl acidic phenol (pH∼3):chloroform (1:1) for 15 minutes. Eluted RNA was precipitated with ethanol, dissolved in water and DNase treated (TURBO DNA-free Kit, Ambion). Inputs are total RNA samples isolated from the bacterial lysates. 10% of lysate that was used for one immunoprecipitation was diluted in 1% SDS, 20 mM Tris–HCl pH 7.9, 150 mM KCl, 1 mM MgCl2 to final volume 200 μl and RNA was isolated with the same protocol as the immunoprecipitated RNA. 14 ul of RNA sample was used for library construction according to the NEXTFLEX® Rapid Directional RNA-Seq Kit. For input samples, 100 ng of RNA was used for library construction. DNA concentrations of IgG control libraries were not measurable, therefore these libraries were not sequenced.

text: wild type genotype

text: Middlebrook 7H9 medium

text: not applicable

text: Mycobacterium tuberculosis

text: Mycobacterium tuberculosis

text: whole organism

characteristic: organism part

text: Mycobacterium tuberculosis

text: Mtb input


characteristic: External Id

characteristic: INSDC center name

text: public

text: ArrayExpress

text: wild type genotype

text: Middlebrook 7H9 medium

text: not applicable

text: Mycobacterium tuberculosis

text: Mycobacterium tuberculosis

text: whole organism

text: Mycobacterium tuberculosis


characteristic: INSDC last update

text: public

characteristic: INSDC status

text: ArrayExpress

text: Protocols: 40 ml cells from exponential phase or 35 ml cells from stationary phase were pelleted and washed in lysis buffer (20 mM Tris–HCl pH 7.9, 150 mM KCl, 1 mM MgCl2, 1 mM dithiothreitol (DTT) and frozen in -70°C. Corynebacterium glutamicum ATCC 13032 (wt, LK1100) were grown at 30°C in 2x YT medium and harvested in exponential (OD600 ∼1) or early stationary phase (OD600 >10, ∼26 hrs of cultivation). Cells resuspended in lysis buffer (20 mM Tris–HCl pH 7.9, 150 mM KCl, 1 mM MgCl2, 1 mM dithiothreitol (DTT), 0.5 mM phenylmethylsulfonyl fluoride (PMSF), supplemented with Calbiochem Protease Inhibitor Cocktail Set III protease inhibitors), sonicated 20 × 10 s with 1 minute pauses on ice and centrifuged. 3 mg (protein) of lysates were incubated for 16-18 hours at 4°C with 20 μl of Protein G plus agarose beads (Santa Cruz) coated with 5 μg mouse monoclonal anti-beta subunit of RNAP antibody [clone 8RB13] (Biolegend), 2.5 μg of anti-Sigma70 antibody [clone 2G10] (Biolegend), or 5 μg of mouse nonspecific IgG (Sigma-Aldrich) used as a negative control, respectively. The captured complexes were washed four times using 20 mM Tris–HCl pH 7.9, 150 mM KCl, 1 mM MgCl2, finally resuspended in 200 μl 1% SDS, 150 mM KCl, 20 mM Tris–HCl pH 7.9, 1 mM MgCl2 and incubated on a rotating platform with 200 μl acidic phenol (pH∼3):chloroform (1:1) for 15 minutes. Eluted RNA was precipitated with ethanol, dissolved in water and DNase treated (TURBO DNA-free Kit, Ambion). Inputs are total RNA samples isolated from the bacterial lysates. 10% of lysate that was used for one immunoprecipitation was diluted in 1% SDS, 20 mM Tris–HCl pH 7.9, 150 mM KCl, 1 mM MgCl2 to final volume 200 μl and RNA was isolated with the same protocol as the immunoprecipitated RNA. 14 ul of RNA sample was used for library construction according to the NEXTFLEX® Rapid Directional RNA-Seq Kit. For input samples, 100 ng of RNA was used for library construction. DNA concentrations of IgG control libraries were not measurable, therefore these libraries were not sequenced.

text: exponential phase

text: wild type genotype

text: 2x YT medium

text: not applicable

text: Corynebacterium glutamicum ATCC 13032

text: Corynebacterium glutamicum ATCC 13032

text: whole organism

text: Corynebacterium glutamicum ATCC 13032


text: public

characteristic: SRA accession

characteristic: Submitter Id

text: ArrayExpress

text: stationary phase

text: wild type genotype

text: 2x YT medium

text: not applicable

text: Corynebacterium glutamicum ATCC 13032

text: Corynebacterium glutamicum ATCC 13032

text: whole organism

text: Corynebacterium glutamicum ATCC 13032


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: UNIVERSITY OF COPENHAGEN

characteristic: INSDC first public

text: public

tag: Namespace:UNIVERSITY OF COPENHAGEN

text: Many fragments with little to no review of assembly other than reporting of standard assembly statistics

characteristic: assembly quality

characteristic: assembly software

text: MaxBin2, MetaBat2, Concoct with default parameter of the metaWRAP pipeline. Bin refinement module used from metaWRAP with default parameters.

characteristic: binning parameters

text: MetaWRAP v1.1

characteristic: binning software

text: Chicken digestive system

characteristic: broad-scale environmental context

text: EMG broker account, EMBL-EBI

characteristic: broker name

text: not provided

characteristic: collection date

characteristic: completeness score

text: CheckM

characteristic: completeness software

characteristic: contamination score

text: This sample represents a Metagenome-Assembled Genome (MAG) assembled from the metagenomic runs ERR4647691,ERR4647692,ERR4647693,ERR4647694,ERR4647695,ERR4647696,ERR4647697,ERR4647698,ERR4647699,ERR4647712,ERR4647713,ERR4647716 of study ERP122587.

characteristic: description

text: Ileum

characteristic: environmental medium

text: Spain

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: metagenome-assembled genome

characteristic: investigation type

text: chicken gut metagenome

text: Digestive tube

characteristic: local environmental context

text: chicken gut metagenome

characteristic: metagenomic source

text: uncultured Clostridia bacterium

text: HoloFood Chicken -- MAG Catalogue data

characteristic: project name

text: SAMEA7368185,SAMEA7368180,SAMEA7368178,SAMEA7368184,SAMEA7368182,SAMEA7368179,SAMEA7368183,SAMEA7368186,SAMEA7368188,SAMEA7368177,SAMEA7368181,SAMEA7368187

characteristic: sample derived from

text: uncultured Clostridia bacterium

characteristic: sequencing method

text: The taxonomy of this metagenome-assembled genome was originally computed with GTDBtk, which assigned the following taxonomic annotation: d__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__;g__;s__

characteristic: taxonomic classification

text: multi-marker approach

characteristic: taxonomic identity marker

text: Metagenome-assembled genome: ERR4647all_bin.19_MetaWRAP_v1.1_MAG


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: UNIVERSITY OF COPENHAGEN

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

characteristic: assembly quality

characteristic: assembly software

characteristic: binning parameters

text: MetaWRAP v1.1

characteristic: binning software

text: Chicken digestive system

characteristic: broad-scale environmental context

text: EMG broker account, EMBL-EBI

characteristic: broker name

text: not provided

characteristic: collection date

text: CheckM

text: Ileum

text: Spain

text: metagenome-assembled genome

text: chicken gut metagenome

text: Digestive tube

text: chicken gut metagenome

text: uncultured Enteractinococcus sp.

characteristic: organism

text: HoloFood Chicken -- MAG Catalogue data

text: uncultured Enteractinococcus sp.

text: The taxonomy of this metagenome-assembled genome was originally computed with GTDBtk, which assigned the following taxonomic annotation: d__Bacteria;p__Actinobacteria;c__Actinobacteria;o__Micrococcales;f__Micrococcaceae;g__Enteractinococcus;s__

text: multi-marker approach

text: Metagenome-assembled genome: ERR4647all_bin.32_MetaWRAP_v1.1_MAG

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: UNIVERSITY OF COPENHAGEN

text: public

text: MetaWRAP v1.1

text: Chicken digestive system

text: EMG broker account, EMBL-EBI

text: not provided

characteristic: completeness score

text: CheckM

characteristic: completeness software

characteristic: contamination score

characteristic: description

text: Ileum

characteristic: environmental medium

text: Spain

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: metagenome-assembled genome

characteristic: investigation type

text: chicken gut metagenome

text: Digestive tube

characteristic: local environmental context

text: chicken gut metagenome

characteristic: metagenomic source

text: uncultured Candidatus Arthromitus sp.

text: HoloFood Chicken -- MAG Catalogue data

characteristic: project name

characteristic: sample derived from

text: uncultured Candidatus Arthromitus sp.

characteristic: sequencing method

text: The taxonomy of this metagenome-assembled genome was originally computed with GTDBtk, which assigned the following taxonomic annotation: d__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Candidatus Arthromitus;s__

characteristic: taxonomic classification

text: multi-marker approach

characteristic: taxonomic identity marker

text: Metagenome-assembled genome: ERR4647all_bin.16_MetaWRAP_v1.1_MAG


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: UNIVERSITY OF COPENHAGEN

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

characteristic: assembly quality

characteristic: assembly software

characteristic: binning parameters

text: MetaWRAP v1.1

characteristic: binning software

text: Chicken digestive system

characteristic: broad-scale environmental context

text: EMG broker account, EMBL-EBI

characteristic: broker name

text: not provided

characteristic: collection date

text: CheckM

text: Ileum

text: Spain

text: metagenome-assembled genome

text: chicken gut metagenome

text: Digestive tube

text: chicken gut metagenome

text: uncultured Ruaniaceae bacterium

characteristic: organism

text: HoloFood Chicken -- MAG Catalogue data

text: uncultured Ruaniaceae bacterium

text: The taxonomy of this metagenome-assembled genome was originally computed with GTDBtk, which assigned the following taxonomic annotation: d__Bacteria;p__Actinobacteria;c__Actinobacteria;o__Micrococcales;f__Ruaniaceae;g__Haloactinobacterium;s__

text: multi-marker approach

text: Metagenome-assembled genome: ERR4647all_bin.25_MetaWRAP_v1.1_MAG

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: UNIVERSITY OF COPENHAGEN

text: public

text: MetaWRAP v1.1

text: Chicken digestive system

text: EMG broker account, EMBL-EBI

text: not provided

characteristic: completeness score

text: CheckM

characteristic: completeness software

characteristic: contamination score

characteristic: description

text: Ileum

characteristic: environmental medium

text: Spain

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: metagenome-assembled genome

characteristic: investigation type

text: chicken gut metagenome

text: Digestive tube

characteristic: local environmental context

text: chicken gut metagenome

characteristic: metagenomic source

text: uncultured bacterium

text: HoloFood Chicken -- MAG Catalogue data

characteristic: project name

characteristic: sample derived from

text: uncultured bacterium

characteristic: sequencing method

text: The taxonomy of this metagenome-assembled genome was originally computed with GTDBtk, which assigned the following taxonomic annotation: d__Bacteria;p__;c__;o__;f__;g__;s__

characteristic: taxonomic classification

text: multi-marker approach

characteristic: taxonomic identity marker

text: Metagenome-assembled genome: ERR4647all_bin.26_MetaWRAP_v1.1_MAG


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: UNIVERSITY OF COPENHAGEN

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

characteristic: assembly quality

characteristic: assembly software

characteristic: binning parameters

text: MetaWRAP v1.1

characteristic: binning software

text: Chicken digestive system

characteristic: broad-scale environmental context

text: EMG broker account, EMBL-EBI

characteristic: broker name

text: not provided

characteristic: collection date

text: CheckM

text: Ileum

text: Spain

text: metagenome-assembled genome

text: chicken gut metagenome

text: Digestive tube

text: chicken gut metagenome

text: uncultured Staphylococcus sp.

characteristic: organism

text: HoloFood Chicken -- MAG Catalogue data

text: uncultured Staphylococcus sp.

text: The taxonomy of this metagenome-assembled genome was originally computed with GTDBtk, which assigned the following taxonomic annotation: d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Staphylococcaceae;g__Staphylococcus;s__Staphylococcus lentus

text: multi-marker approach

text: Metagenome-assembled genome: ERR4647all_bin.30_MetaWRAP_v1.1_MAG

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: UNIVERSITY OF COPENHAGEN

text: public

text: MetaWRAP v1.1

text: Chicken digestive system

text: EMG broker account, EMBL-EBI

text: not provided

characteristic: completeness score

text: CheckM

characteristic: completeness software

characteristic: contamination score

text: This sample represents a Metagenome-Assembled Genome (MAG) assembled from the metagenomic runs ERR4304450,ERR4303136,ERR4303150 of study ERP122587.

characteristic: description

text: Caecum

characteristic: environmental medium

text: Spain

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: metagenome-assembled genome

characteristic: investigation type

text: chicken gut metagenome

text: Digestive tube

characteristic: local environmental context

text: chicken gut metagenome

characteristic: metagenomic source

text: Klebsiella pneumoniae

text: HoloFood Chicken -- MAG Catalogue data

characteristic: project name

characteristic: sample derived from

text: Klebsiella pneumoniae

characteristic: sequencing method

text: The taxonomy of this metagenome-assembled genome was originally computed with GTDBtk, which assigned the following taxonomic annotation: d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Klebsiella;s__Klebsiella pneumoniae

characteristic: taxonomic classification

text: multi-marker approach

characteristic: taxonomic identity marker

text: Metagenome-assembled genome: ERR4304450_ERR4303136_ERR4303150_bin.93_MetaWRAP_v1.1_MAG


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: UNIVERSITY OF COPENHAGEN

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: Many fragments with little to no review of assembly other than reporting of standard assembly statistics

characteristic: assembly quality

characteristic: assembly software

text: MaxBin2, MetaBat2, Concoct with default parameter of the metaWRAP pipeline. Bin refinement module used from metaWRAP with default parameters.

characteristic: binning parameters

text: MetaWRAP v1.1

characteristic: binning software

text: Chicken digestive system

characteristic: broad-scale environmental context

text: EMG broker account, EMBL-EBI

characteristic: broker name

text: not provided

characteristic: collection date

text: CheckM

text: Caecum

text: Spain

text: metagenome-assembled genome

text: chicken gut metagenome

text: Digestive tube

text: chicken gut metagenome

text: uncultured Clostridium sp.

characteristic: organism

text: HoloFood Chicken -- MAG Catalogue data

text: uncultured Clostridium sp.

text: The taxonomy of this metagenome-assembled genome was originally computed with GTDBtk, which assigned the following taxonomic annotation: d__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium;s__

text: multi-marker approach

text: Metagenome-assembled genome: ERR4304450_ERR4303136_ERR4303150_bin.29_MetaWRAP_v1.1_MAG

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: UNIVERSITY OF COPENHAGEN

text: public

text: MetaWRAP v1.1

text: Chicken digestive system

text: EMG broker account, EMBL-EBI

text: not provided

characteristic: completeness score

text: CheckM

characteristic: completeness software

characteristic: contamination score

characteristic: description

text: Caecum

characteristic: environmental medium

text: Spain

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: metagenome-assembled genome

characteristic: investigation type

text: chicken gut metagenome

text: Digestive tube

characteristic: local environmental context

text: chicken gut metagenome

characteristic: metagenomic source

text: uncultured Clostridia bacterium

text: HoloFood Chicken -- MAG Catalogue data

characteristic: project name

characteristic: sample derived from

text: uncultured Clostridia bacterium

characteristic: sequencing method

text: The taxonomy of this metagenome-assembled genome was originally computed with GTDBtk, which assigned the following taxonomic annotation: d__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Ruminococcaceae;g__;s__

characteristic: taxonomic classification

text: multi-marker approach

characteristic: taxonomic identity marker

text: Metagenome-assembled genome: ERR4304450_ERR4303136_ERR4303150_bin.49_MetaWRAP_v1.1_MAG


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

tag: Namespace:Senckenber Biodiversity and Climate Research Centre Frankfurt

characteristic: Submitter Id

text: yellow fever mosquito

characteristic: common name

text: Aedes aegypti sample from Chitwan, Nepal - forward

text: Aedes aegypti

characteristic: organism

text: Aedes aegypti

text: Ae. aegypti Chitwan

characteristic: title


text: Senckenber Biodiversity and Climate Research Centre Frankfurt

text: public

text: yellow fever mosquito

text: Aedes aegypti sample from Dhading, Nepal - forward

characteristic: description

text: Aedes aegypti

text: Aedes aegypti

text: Ae. aegypti Dhading


text: public

text: yellow fever mosquito

text: Aedes aegypti sample from Dharke, Nepal - forward

text: Aedes aegypti

text: Aedes aegypti

text: Ae. aegypti Dharke


text: public

text: yellow fever mosquito

text: Aedes aegypti sample from Kathmandu, Nepal - forward

text: Aedes aegypti

text: Aedes aegypti

text: Ae. aegypti Kathmandu


E-MTAB-12354:Control 1

text: public

text: E-MTAB-12354:Control 1

tag: Namespace:Fekadu Yadetie, Department of Biological Sciences University of Bergen, Bergen, Norway

text: ArrayExpress

characteristic: broker name

text: Protocols: Polar cod were collected in Southeastern Hinlopen (78° 55’N, 23° 40’E) and transported to the research facility in Kårvika, Norway (69°23’N, 18°10’E). At the research station, the fish were acclimatized. Polar co average weight 81.48 ± 24.76 g (mean±standard deviation) were selected for the experiment. Each fish was anaesthetized in a Finquel® (Tricaine Methanesulfonate; Sigma Aldrich) solution, sexed using ultrasound (General Electric, LOGIQ XP) based on Karlsen & Holm (1994), and marked with a unique dorsal fin tag. Fish were then randomly transferred to one of twelve 300 L tanks (n=36 per tank, 18 males, and 18 females). The fish were maintained in the experimental tanks for three months, from December 15th to April 24th. This period covered late reproductive development (pre-spwning) until post-spawning. Each of the 12 experimental tanks was randomly assigned an oil exposure and a feed ration. Six tanks were exposed to Goliat crude oil, and sex other tanks were maintained under control conditions (no oil). Exposure to a crude oil water accommodated fraction (WAF) was produced by an oiled-rock-column system (Carls et al. 1999), delivering decreasing aqueous levels of oil compounds over time. Fish in each tank were hand fed once daily, with Calanus finmarchicus (CALANUS AS, Lofoten) either at a high (4 % somatic weight day-1) or low-food (1.5 % somatic weight day-1) ration. Samples were taken when polar cod were estimated to be in a late stage of reproductive development (0 days exposure), during the spawning window (47 days exposure) and during the post-spawning period (131 days exposure). At each sampling event, polar cod (n=6-8) were taken from each tank at a balanced sex ratio. Each polar cod was anesthetized before blood was drawn from the caudal vein (Bender et al. 2016). During the second sampling time-point, all polar cod were stripped before the rest of the samples were taken. Fish were then sacrificed by a sharp blow to the head, and fork length (± 0.1 cm), wet weight (± 0.1 g), gonad weight (± 0.1 g), and somatic weight (± 0.1 g) were measured. Samples were taken from the gonad, liver, and gall bladder of each fish. Liver samples were taken and snap-frozen in liquid nitrogen and stored at -80C for RNA extraction. Total RNA was isolated from frozen liver samples as described before (Yadetie et al., 2021), using TRI Reagent according to the manufacturer’s protocol (Sigma-Aldrich, St. Louis, MO, USA). RNA samples from five high-food control and five high-food-oil-exposed female fish from day 47 were submitted for RNA sequencing (RNA-seq) . Sequenced by Novogene (Novogene, Cambridge, UK) on Illumina NovaSeq 6000 System

text: adult

characteristic: developmental stage

text: Boreogadus saida

text: Boreogadus saida

text: liver

characteristic: organism part

text: Boreogadus saida

text: female

characteristic: sex

text: control

characteristic: stimulus

text: Control 1


E-MTAB-12354:Control 2

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: Fekadu Yadetie, Department of Biological Sciences University of Bergen, Bergen, Norway

text: public

text: E-MTAB-12354:Control 2

text: ArrayExpress

text: adult

text: Boreogadus saida

text: Boreogadus saida

text: liver

text: Boreogadus saida

text: female

text: control

text: Control 2


E-MTAB-12354:Control 3

characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: E-MTAB-12354:Control 3

text: ArrayExpress

text: adult

text: Boreogadus saida

text: Boreogadus saida

text: liver

text: Boreogadus saida

text: female

text: control

text: Control 3


E-MTAB-12354:Control 4

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-12354:Control 4

text: ArrayExpress

text: adult

text: Boreogadus saida

text: Boreogadus saida

text: liver

text: Boreogadus saida

text: female

text: control

text: Control 4


E-MTAB-12354:Control 5

text: public

text: E-MTAB-12354:Control 5

characteristic: Submitter Id

text: ArrayExpress

text: adult

text: Boreogadus saida

characteristic: organism

text: Boreogadus saida

text: liver

text: Boreogadus saida

text: female

text: control

text: Control 5


E-MTAB-12354:Crude oil exposed 1

text: public

text: E-MTAB-12354:Crude oil exposed 1

text: ArrayExpress

characteristic: description

text: adult

text: Boreogadus saida

text: Boreogadus saida

text: liver

text: Boreogadus saida

text: female

text: crude oil

text: Crude oil exposed 1

characteristic: title


E-MTAB-12354:Crude oil exposed 2

text: public

text: E-MTAB-12354:Crude oil exposed 2

text: ArrayExpress

characteristic: broker name

text: adult

characteristic: developmental stage

text: Boreogadus saida

text: Boreogadus saida

text: liver

text: Boreogadus saida

text: female

text: crude oil

text: Crude oil exposed 2


E-MTAB-12354:Crude oil exposed 3

text: public

text: E-MTAB-12354:Crude oil exposed 3

text: ArrayExpress

text: adult

text: Boreogadus saida

text: Boreogadus saida

text: liver

characteristic: organism part

text: Boreogadus saida

text: female

characteristic: sex

text: crude oil

text: Crude oil exposed 3


E-MTAB-12354:Crude oil exposed 4

characteristic: ENA-CHECKLIST

text: public

text: E-MTAB-12354:Crude oil exposed 4

text: ArrayExpress

text: adult

text: Boreogadus saida

text: Boreogadus saida

text: liver

text: Boreogadus saida

text: female

text: crude oil

characteristic: stimulus

text: Crude oil exposed 4


E-MTAB-12354:Crude oil exposed 5

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: public

text: E-MTAB-12354:Crude oil exposed 5

text: ArrayExpress

text: adult

text: Boreogadus saida

text: Boreogadus saida

text: liver

text: Boreogadus saida

text: female

text: crude oil

text: Crude oil exposed 5


E-MTAB-12355:Sample 1

characteristic: External Id

characteristic: INSDC center name

text: public

text: E-MTAB-12355:Sample 1

tag: Namespace:Departamento de Produccion Animal, Facultad de Veterinaria, Universidad de Leon

text: Assaf

characteristic: breed

text: ArrayExpress

text: mammary epithelial cell

text: sheep

characteristic: common name

text: Protocols: Sheep with extreme FEI values (8 high feed efficiency sheep (H-FE), FEI = −0.29 (SD = 0.23), RFI = −0.16 (SD = 0.25), and 8 low feed efficiency sheep (L-FE), FEI = 0.81 (SD = 0.24), RFI = 0.19 (SD = 0.24)) were sampled for RNA-Seq. To summarize, 50 mL of fresh milk was collected from each animal one hour after milking and 10 min after injection of 5 IU of oxytocin/animal (Facilpart, Laboratorios SYVA, León, Spain) to maximize milk somatic cell concentration. To prevent RNA degradation, udders were cleaned with soap and water and disinfected with povidone-iodine, and the nipples were also flushed with RNAseZap (Ambion, Austin, TX, USA). A sterile gauze was used to cover the collection tube to avoid contamination. For RNA extraction, the milk somatic cells (MSC) were pelleted by centrifugation at 650×g for 10 min at 4 °C in the presence of a final concentration of 0.5 mM of EDTA. Then, the pellet was washed twice with 10 and 2 mL of PBS (pH 7.2 and 0.5 mM of EDTA) followed by centrifugation at 650×g for 10 min at 4 °C. The last pellet was kept in RNAlater (Sigma-Aldrich, Madrid, Spain) and stored at −80 ºC until RNA extraction using 500 μL of TRIzol according to the manufacturer’s instructions (Invitrogen, Carlsbad, CA, USA). The RNA sequencing was conducted at CNAG (Centro Nacional de Análisis Genómico, Barcelona, Spain), where the TrueSeq Stranded Total RNA Library Prep Kit (Illumina, San Diego, CA, USA) was used for library preparation.

text: adult

text: Ovis aries

text: Ovis aries

text: mammary gland

text: milk

characteristic: organism substance

text: high feed efficiency

characteristic: phenotype

text: Ovis aries

text: female

text: Sample 1


E-MTAB-12355:Sample 10

text: Departamento de Produccion Animal, Facultad de Veterinaria, Universidad de Leon

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-12355:Sample 10

characteristic: Submitter Id

text: Assaf

text: ArrayExpress

text: mammary epithelial cell

text: sheep

text: adult

text: Ovis aries

characteristic: organism

text: Ovis aries

text: mammary gland

text: milk

text: low feed efficiency

text: Ovis aries

text: female

text: Sample 10


E-MTAB-12355:Sample 11

text: public

text: E-MTAB-12355:Sample 11

text: Assaf

text: ArrayExpress

characteristic: broker name

text: mammary epithelial cell

text: sheep

characteristic: description

text: adult

characteristic: developmental stage

text: Ovis aries

text: Ovis aries

text: mammary gland

characteristic: organism part

text: milk

text: low feed efficiency

text: Ovis aries

text: female

characteristic: sex

text: Sample 11

characteristic: title


E-MTAB-12355:Sample 12

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC center name

text: public

text: E-MTAB-12355:Sample 12

text: Assaf

text: ArrayExpress

text: mammary epithelial cell

text: sheep

text: adult

text: Ovis aries

text: Ovis aries

text: mammary gland

text: milk

text: low feed efficiency

text: Ovis aries

text: female

text: Sample 12


E-MTAB-12355:Sample 13

characteristic: INSDC first public

text: public

text: E-MTAB-12355:Sample 13

text: Assaf

characteristic: breed

text: ArrayExpress

text: mammary epithelial cell

text: sheep

characteristic: common name

text: adult

text: Ovis aries

text: Ovis aries

text: mammary gland

text: milk

characteristic: organism substance

text: low feed efficiency

characteristic: phenotype

text: Ovis aries

text: female

text: Sample 13


E-MTAB-12355:Sample 14

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-12355:Sample 14

characteristic: Submitter Id

text: Assaf

text: ArrayExpress

text: mammary epithelial cell

text: sheep

text: adult

text: Ovis aries

characteristic: organism

text: Ovis aries

text: mammary gland

text: milk

text: low feed efficiency

text: Ovis aries

text: female

text: Sample 14


E-MTAB-12355:Sample 15

text: public

text: E-MTAB-12355:Sample 15

text: Assaf

text: ArrayExpress

characteristic: broker name

text: mammary epithelial cell

text: sheep

characteristic: description

text: adult

characteristic: developmental stage

text: Ovis aries

text: Ovis aries

text: mammary gland

characteristic: organism part

text: milk

text: low feed efficiency

text: Ovis aries

text: female

characteristic: sex

text: Sample 15


E-MTAB-12355:Sample 16

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: public

text: E-MTAB-12355:Sample 16

text: Assaf

text: ArrayExpress

text: mammary epithelial cell

text: sheep

text: adult

text: Ovis aries

text: Ovis aries

text: mammary gland

text: milk

text: low feed efficiency

text: Ovis aries

text: female

text: Sample 16

characteristic: title


E-MTAB-12355:Sample 2

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: E-MTAB-12355:Sample 2

text: Assaf

characteristic: breed

text: ArrayExpress

text: mammary epithelial cell

text: sheep

characteristic: common name

text: adult

text: Ovis aries

text: Ovis aries

text: mammary gland

text: milk

characteristic: organism substance

text: high feed efficiency

text: Ovis aries

text: female

text: Sample 2


E-MTAB-12355:Sample 3

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-12355:Sample 3

characteristic: Submitter Id

text: Assaf

text: ArrayExpress

text: mammary epithelial cell

text: sheep

text: adult

text: Ovis aries

text: Ovis aries

text: mammary gland

text: milk

text: high feed efficiency

characteristic: phenotype

text: Ovis aries

text: female

text: Sample 3


E-MTAB-12355:Sample 4

text: public

text: E-MTAB-12355:Sample 4

text: Assaf

text: ArrayExpress

characteristic: broker name

text: mammary epithelial cell

text: sheep

characteristic: description

text: adult

characteristic: developmental stage

text: Ovis aries

characteristic: organism

text: Ovis aries

text: mammary gland

characteristic: organism part

text: milk

text: high feed efficiency

text: Ovis aries

text: female

text: Sample 4


E-MTAB-12355:Sample 5

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: public

text: E-MTAB-12355:Sample 5

text: Assaf

text: ArrayExpress

text: mammary epithelial cell

text: sheep

text: adult

text: Ovis aries

text: Ovis aries

text: mammary gland

text: milk

text: high feed efficiency

text: Ovis aries

text: female

characteristic: sex

text: Sample 5


E-MTAB-12355:Sample 6

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: E-MTAB-12355:Sample 6

text: Assaf

characteristic: breed

text: ArrayExpress

text: mammary epithelial cell

text: sheep

characteristic: common name

text: adult

text: Ovis aries

text: Ovis aries

text: mammary gland

text: milk

text: high feed efficiency

text: Ovis aries

text: female

text: Sample 6

characteristic: title


E-MTAB-12355:Sample 7

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-12355:Sample 7

characteristic: Submitter Id

text: Assaf

text: ArrayExpress

text: mammary epithelial cell

text: sheep

text: adult

text: Ovis aries

text: Ovis aries

text: mammary gland

text: milk

characteristic: organism substance

text: high feed efficiency

text: Ovis aries

text: female

text: Sample 7


E-MTAB-12355:Sample 8

text: public

text: E-MTAB-12355:Sample 8

text: Assaf

text: ArrayExpress

characteristic: broker name

text: mammary epithelial cell

text: sheep

characteristic: description

text: adult

characteristic: developmental stage

text: Ovis aries

characteristic: organism

text: Ovis aries

text: mammary gland

text: milk

text: high feed efficiency

characteristic: phenotype

text: Ovis aries

text: female

text: Sample 8


E-MTAB-12355:Sample 9

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: public

text: E-MTAB-12355:Sample 9

text: Assaf

text: ArrayExpress

text: mammary epithelial cell

text: sheep

text: adult

text: Ovis aries

text: Ovis aries

text: mammary gland

characteristic: organism part

text: milk

text: low feed efficiency

text: Ovis aries

text: female

text: Sample 9


characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: E-MTAB-115061667384789:ChIP_HEK_dSPOC_PHF3-GFP_br1

tag: Namespace:Bioinformatics and Omics Data Science Group, BIMSB, Berlin

text: ArrayExpress

text: human

characteristic: common name

text: Protocols: Cells were resuspended in 50 mL PBS/108 cells and fixed by adding 1% formaldehyde for 10 min. Formaldehyde was quenched by addition of 0.6 M glycine pH 3 for 15 min. Cells were washed twice in cold PBS. Nuclei were isolated by resuspending the cells in 5 mL cold lysis buffer 1 (50 mM HEPES/KOH pH 7.5, 140 mM NaCl, 1 mM EDTA, 10% glycerol, 0.5% Nonidet P-40, 0.25% Triton X-100, 1x Complete protease inhibitors (Roche)) per 108 cells and rotating at 4°C for 10 min. After centrifugation nuclei were resuspended in 5mL/108 cells cold lysis buffer 2 (10 mM Tris-Cl pH 8, 200 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 1x Complete protease inhibitors (Roche)) and rotated for 10 min at room temperature. The pellet after centrifugation was resuspended in 3 mL lysis buffer 3 (10 mM Tris-Cl pH 8, 100 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 0.1% Na-deoxycholate, 0.5% N-lauroylsarcosine, 1x Complete protease inhibitors (Roche)) and chromatin was sheared to an average size of 200-600 bp by sonication for 20 cycles 30 sec on/30 sec off using Bioruptor Pico (Diagenode). 1% Triton X-100 was added after sonication. 5-10% of chromatin was kept as an input control for qPCR. For ChIP-seq 1.5% spike-in chromatin from a mouse cell line expressing endogenously tagged PHF3-GFP was added. Anti-GFP antiserum (Abcam ab290) was added to sheared chromatin and rotated ON at 4°C. Protein A Dynabeads (Invitrogen) were washed in cold block solution (0.5% BSA in PBS) three times, mixed with antibody-bound chromatin and rotated for 4-6 h at 4°C. Beads were washed in RIPA washing buffer (50 mM Hepes/KOH pH 7.5, 500 mM LiCl, 1 mM EDTA, 1% NP-40, 0.7% Na-deoxycholate) five times and in 50 mM NaCl in TE once. Immunoprecipitated protein-DNA complexes were eluted in 200 µL elution buffer (50 mM Tris-Cl pH 8, 10 mM EDTA, 1% SDS) for 15 min at 65°C. Eluates were incubated ON at 65°C to reverse crosslinks, treated with 0.2 mg/mL RNase A for 2 h at 37°C and 0.2 mg/mL proteinase K and 5.25 mM CaCl2 for 30 min at 55°C. DNA was purified by phenol-chloroform extraction followed by ethanol precipitation and resuspended in 50 µL nuclease free water. ChIP-seq libraries were prepared using NEBNext Ultra II DNA library prep kit for Illumina (New England Biolabs) and NEBNext Multiplex Oligos for Illumina (New England Biolabs) according to the manufacturer’s instructions.

text: embryo

text: normal

characteristic: disease

text: PHF3 dSPOC mutation

characteristic: genotype

text: Homo sapiens

text: Homo sapiens

text: kidney

text: Homo sapiens


text: Bioinformatics and Omics Data Science Group, BIMSB, Berlin

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-115061667384789:ChIP_HEK_dSPOC_PHF3-GFP_br2

characteristic: Submitter Id

text: ArrayExpress

text: human

text: embryo

text: normal

text: PHF3 dSPOC mutation

text: Homo sapiens

text: Homo sapiens

text: kidney

text: Homo sapiens

characteristic: title


text: public

text: E-MTAB-115061667384789:ChIP_HEK_dSPOC_PHF3-GFP_br3

text: ArrayExpress

characteristic: broker name

text: human

characteristic: description

text: embryo

characteristic: developmental stage

text: normal

text: PHF3 dSPOC mutation

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: kidney

text: Homo sapiens


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: public

text: E-MTAB-115061667384789:ChIP_HEK_dSPOC_SHARP-GFP_br1

text: ArrayExpress

text: human

text: embryo

text: normal

text: PHF3 dSPOC mutation

text: Homo sapiens

text: Homo sapiens

text: kidney

text: Homo sapiens


characteristic: External Id

characteristic: INSDC center name

text: public

text: E-MTAB-115061667384789:ChIP_HEK_dSPOC_SHARP-GFP_br2

text: ArrayExpress

text: human

text: embryo

text: normal

text: PHF3 dSPOC mutation

text: Homo sapiens

text: Homo sapiens

text: kidney

characteristic: organism part

text: Homo sapiens


characteristic: INSDC first public

text: public

text: E-MTAB-115061667384789:ChIP_HEK_WT_PHF3-GFP_br1

text: ArrayExpress

text: human

characteristic: common name

text: embryo

text: normal

characteristic: disease

text: wild type genotype

text: Homo sapiens

text: Homo sapiens

text: kidney

text: Homo sapiens


characteristic: INSDC last update

text: public

characteristic: INSDC status

text: E-MTAB-115061667384789:ChIP_HEK_WT_PHF3-GFP_br2

text: ArrayExpress

text: human

text: embryo

text: normal

text: wild type genotype

characteristic: genotype

text: Homo sapiens

text: Homo sapiens

text: kidney

text: Homo sapiens


text: public

characteristic: SRA accession

text: E-MTAB-115061667384789:ChIP_HEK_WT_PHF3-GFP_br3

characteristic: Submitter Id

text: ArrayExpress

text: human

text: embryo

text: normal

text: wild type genotype

text: Homo sapiens

text: Homo sapiens

text: kidney

text: Homo sapiens

characteristic: title


text: public

text: E-MTAB-115061667384789:ChIP_HEK_WT_PHF3_br1

text: ArrayExpress

characteristic: broker name

text: human

characteristic: description

text: embryo

characteristic: developmental stage

text: normal

text: wild type genotype

text: Homo sapiens

text: Homo sapiens

text: kidney

text: Homo sapiens


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: public

text: E-MTAB-115061667384789:ChIP_HEK_WT_PHF3_br2

text: ArrayExpress

text: human

text: embryo

text: normal

text: wild type genotype

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: kidney

text: Homo sapiens


characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC center name

text: public

text: E-MTAB-115061667384789:ChIP_HEK_WT_PHF3_br3

text: ArrayExpress

text: human

text: embryo

text: normal

text: wild type genotype

text: Homo sapiens

text: Homo sapiens

text: kidney

text: Homo sapiens


characteristic: INSDC first public

text: public

text: E-MTAB-115061667384789:ChIP_HEK_WT_SHARP-GFP_br1

text: ArrayExpress

text: human

characteristic: common name

text: embryo

text: normal

text: wild type genotype

text: Homo sapiens

text: Homo sapiens

text: kidney

characteristic: organism part

text: Homo sapiens


characteristic: INSDC last update

text: public

characteristic: INSDC status

text: E-MTAB-115061667384789:ChIP_HEK_WT_SHARP-GFP_br2

text: ArrayExpress

text: human

text: embryo

text: normal

characteristic: disease

text: wild type genotype

text: Homo sapiens

text: Homo sapiens

text: kidney

text: Homo sapiens


text: public

characteristic: SRA accession

text: E-MTAB-115061667384789:ChIP_mES_WT_PHF3-GFP_br1

characteristic: Submitter Id

text: ArrayExpress

text: human

text: embryo

text: normal

text: wild type genotype

characteristic: genotype

text: Homo sapiens

text: Homo sapiens

text: kidney

text: Homo sapiens


text: public

text: E-MTAB-115061667384789:ChIP_mES_WT_PHF3-GFP_br2

text: ArrayExpress

characteristic: broker name

text: human

characteristic: description

text: embryo

text: normal

text: wild type genotype

text: Homo sapiens

text: Homo sapiens

text: kidney

text: Homo sapiens

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: public

text: E-MTAB-115061667384789:ChIP_mES_WT_PHF3_br1

text: ArrayExpress

text: human

text: embryo

characteristic: developmental stage

text: normal

text: wild type genotype

text: Homo sapiens

text: Homo sapiens

text: kidney

text: Homo sapiens


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: public

text: E-MTAB-115061667384789:ChIP_mES_WT_PHF3_br2

text: ArrayExpress

text: human

text: Protocols: Cells were resuspended in 50 mL PBS/108 cells and fixed by adding 1% formaldehyde for 10 min. Formaldehyde was quenched by addition of 0.6 M glycine pH 3 for 15 min. Cells were washed twice in cold PBS. Nuclei were isolated by resuspending the cells in 5 mL cold lysis buffer 1 (50 mM HEPES/KOH pH 7.5, 140 mM NaCl, 1 mM EDTA, 10% glycerol, 0.5% Nonidet P-40, 0.25% Triton X-100, 1x Complete protease inhibitors (Roche)) per 108 cells and rotating at 4°C for 10 min. After centrifugation nuclei were resuspended in 5mL/108 cells cold lysis buffer 2 (10 mM Tris-Cl pH 8, 200 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 1x Complete protease inhibitors (Roche)) and rotated for 10 min at room temperature. The pellet after centrifugation was resuspended in 3 mL lysis buffer 3 (10 mM Tris-Cl pH 8, 100 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 0.1% Na-deoxycholate, 0.5% N-lauroylsarcosine, 1x Complete protease inhibitors (Roche)) and chromatin was sheared to an average size of 200-600 bp by sonication for 20 cycles 30 sec on/30 sec off using Bioruptor Pico (Diagenode). 1% Triton X-100 was added after sonication. 5-10% of chromatin was kept as an input control for qPCR. For ChIP-seq 1.5% spike-in chromatin from a mouse cell line expressing endogenously tagged PHF3-GFP was added. Anti-GFP antiserum (Abcam ab290) was added to sheared chromatin and rotated ON at 4°C. Protein A Dynabeads (Invitrogen) were washed in cold block solution (0.5% BSA in PBS) three times, mixed with antibody-bound chromatin and rotated for 4-6 h at 4°C. Beads were washed in RIPA washing buffer (50 mM Hepes/KOH pH 7.5, 500 mM LiCl, 1 mM EDTA, 1% NP-40, 0.7% Na-deoxycholate) five times and in 50 mM NaCl in TE once. Immunoprecipitated protein-DNA complexes were eluted in 200 µL elution buffer (50 mM Tris-Cl pH 8, 10 mM EDTA, 1% SDS) for 15 min at 65°C. Eluates were incubated ON at 65°C to reverse crosslinks, treated with 0.2 mg/mL RNase A for 2 h at 37°C and 0.2 mg/mL proteinase K and 5.25 mM CaCl2 for 30 min at 55°C. DNA was purified by phenol-chloroform extraction followed by ethanol precipitation and resuspended in 50 µL nuclease free water. ChIP-seq libraries were prepared using NEBNext Ultra II DNA library prep kit for Illumina (New England Biolabs) and NEBNext Multiplex Oligos for Illumina (New England Biolabs) according to the manufacturer’s instructions.

text: embryo

text: normal

text: wild type genotype

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: kidney

text: Homo sapiens


text: Bioinformatics and Omics Data Science Group, BIMSB, Berlin

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: E-MTAB-115061667384789:ChIP_mES_WT_PHF3_br3

text: ArrayExpress

text: human

characteristic: common name

text: embryo

text: normal

text: wild type genotype

text: Homo sapiens

text: Homo sapiens

text: kidney

text: Homo sapiens


text: ISTANBUL UNIVERSITY

characteristic: INSDC last update

text: public

characteristic: INSDC status

tag: Namespace:ISTANBUL UNIVERSITY

text: Yenikapi

text: uncultured eukaryote

text: uncultured eukaryote


text: ISTANBUL UNIVERSITY

text: public

characteristic: SRA accession

text: Agregate

text: uncultured eukaryote

text: uncultured eukaryote


text: ISTANBUL UNIVERSITY

text: public

characteristic: Submitter Id

text: Cinarcik

text: uncultured eukaryote

text: uncultured eukaryote


text: ISTANBUL UNIVERSITY

text: public

text: Armutlu

text: uncultured eukaryote

text: uncultured eukaryote


text: ISTANBUL UNIVERSITY

text: public

text: Incesu

text: uncultured eukaryote

text: uncultured eukaryote


text: National Veterinary Institute

text: public

tag: Namespace:National Veterinary Institute

text: Tick salivary glands metagenome. 16S V3-V4 region.

text: Sweden

characteristic: geographic location (country and/or sea)

text: Forsmark (Uppsala County)

characteristic: geographic location (region and locality)

text: salivary glands

characteristic: host body site

text: Ixodes ricinus

characteristic: host scientific name

text: Tick salivary glands

text: tick metagenome

text: tick metagenome

characteristic: target gene

characteristic: target subfragment


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: National Veterinary Institute

text: public

text: Tick ovary metagenome. 16S V3-V4 region.

characteristic: description

text: Sweden

text: Forsmark (Uppsala County)

text: ovary

text: Ixodes ricinus

text: Tick ovary

text: tick metagenome

text: tick metagenome

characteristic: title


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: National Veterinary Institute

characteristic: INSDC center name

text: public

text: Tick gut metagenome. 16S V3-V4 region.

text: Sweden

text: Forsmark (Uppsala County)

text: gut

text: Ixodes ricinus

text: Tick gut

text: tick metagenome

characteristic: organism

text: tick metagenome


text: National Veterinary Institute

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: Tick malpighian tubules metagenome. 16S V3-V4 region.

text: Sweden

text: Forsmark (Uppsala County)

text: malpighian tubules

text: Ixodes ricinus

text: Tick malpighian tubules

text: tick metagenome

text: tick metagenome


text: National Veterinary Institute

text: public

characteristic: SRA accession

characteristic: Submitter Id

text: Sweden

characteristic: geographic location (country and/or sea)

text: Kyrkby (Uppsala County)

text: salivary glands

text: Ixodes ricinus

text: Tick salivary glands

text: tick metagenome

text: tick metagenome


text: National Veterinary Institute

text: public

text: Sweden

text: Kyrkby (Uppsala County)

characteristic: geographic location (region and locality)

text: ovary

characteristic: host body site

text: Ixodes ricinus

characteristic: host scientific name

text: Tick ovary

text: tick metagenome

text: tick metagenome


characteristic: ENA-CHECKLIST

text: National Veterinary Institute

text: public

text: Tick gut metagenome. 16S V3-V4 region.

text: Sweden

text: Kyrkby (Uppsala County)

text: gut

text: Ixodes ricinus

text: Tick gut

text: tick metagenome

text: tick metagenome

characteristic: target gene

characteristic: target subfragment


characteristic: ENA-FIRST-PUBLIC

text: National Veterinary Institute

text: public

characteristic: description

text: Sweden

text: Kyrkby (Uppsala County)

text: malpighian tubules

text: Ixodes ricinus

text: Tick malpighian tubules

text: tick metagenome

text: tick metagenome

characteristic: title


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: National Veterinary Institute

characteristic: INSDC center name

text: public

text: Whole tick metagenome. 16S V3-V4 region.

text: Sweden

text: Ockelbo

text: whole tick

text: Ixodes ricinus

text: Whole tick

text: tick metagenome

text: tick metagenome


text: National Veterinary Institute

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: Sweden

text: Ånge

text: whole tick

text: Ixodes ricinus

text: Whole tick

text: tick metagenome

characteristic: organism

text: tick metagenome


text: National Veterinary Institute

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: Sweden

text: Timrå

text: whole tick

text: Ixodes ricinus

text: Whole tick

text: tick metagenome

text: tick metagenome


text: National Veterinary Institute

text: public

text: Sweden

characteristic: geographic location (country and/or sea)

text: Hudiksvall

characteristic: geographic location (region and locality)

text: whole tick

characteristic: host body site

text: Ixodes ricinus

text: Whole tick

text: tick metagenome

text: tick metagenome


characteristic: ENA-CHECKLIST

text: National Veterinary Institute

text: public

text: Sweden

text: Härnösand

text: whole tick

text: Ixodes ricinus

characteristic: host scientific name

text: Whole tick

text: tick metagenome

text: tick metagenome

characteristic: target gene


characteristic: ENA-FIRST-PUBLIC

text: National Veterinary Institute

text: public

characteristic: description

text: Sweden

text: Malung-Sälen

text: whole tick

text: Ixodes ricinus

text: Whole tick

text: tick metagenome

text: tick metagenome

characteristic: target subfragment


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: National Veterinary Institute

text: public

text: Sweden

text: Nordanstig

text: whole tick

text: Ixodes ricinus

text: Whole tick

text: tick metagenome

text: tick metagenome

characteristic: title


text: National Veterinary Institute

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: Sweden

text: Ånge

text: whole tick

text: Ixodes trianguliceps

text: Whole tick

text: tick metagenome

text: tick metagenome


text: National Veterinary Institute

text: public

characteristic: INSDC status

characteristic: SRA accession

text: Sweden

text: Ovanåker

text: whole tick

text: Ixodes ricinus

text: Whole tick

text: tick metagenome

characteristic: organism

text: tick metagenome


text: National Veterinary Institute

text: public

characteristic: Submitter Id

text: Sweden

characteristic: geographic location (country and/or sea)

text: Leksand

characteristic: geographic location (region and locality)

text: whole tick

text: Ixodes ricinus

text: Whole tick

text: tick metagenome

text: tick metagenome


characteristic: ENA-CHECKLIST

text: National Veterinary Institute

text: public

text: Sweden

text: Mora

text: whole tick

characteristic: host body site

text: Ixodes ricinus

characteristic: host scientific name

text: Whole tick

text: tick metagenome

text: tick metagenome


characteristic: ENA-FIRST-PUBLIC

text: National Veterinary Institute

text: public

characteristic: description

text: Sweden

text: Gagnef

text: whole tick

text: Ixodes ricinus

text: Whole tick

text: tick metagenome

text: tick metagenome

characteristic: target gene


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: National Veterinary Institute

text: public

text: Sweden

text: Bollnäs

text: whole tick

text: Ixodes ricinus

text: Whole tick

text: tick metagenome

text: tick metagenome

characteristic: target subfragment


text: National Veterinary Institute

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: Sweden

text: Rättvik

text: whole tick

text: Ixodes ricinus

text: Whole tick

text: tick metagenome

text: tick metagenome

characteristic: title


text: National Veterinary Institute

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: Sweden

text: Falun

text: whole tick

text: Ixodes ricinus

text: Whole tick

text: tick metagenome

text: tick metagenome


text: National Veterinary Institute

text: public

characteristic: Submitter Id

text: Sweden

characteristic: geographic location (country and/or sea)

text: Söderhamn

text: whole tick

text: Ixodes ricinus

text: Whole tick

text: tick metagenome

characteristic: organism

text: tick metagenome


characteristic: ENA-CHECKLIST

text: National Veterinary Institute

text: public

text: Sweden

text: Orsa

characteristic: geographic location (region and locality)

text: whole tick

characteristic: host body site

text: Ixodes ricinus

text: Whole tick

text: tick metagenome

text: tick metagenome


characteristic: ENA-FIRST-PUBLIC

text: National Veterinary Institute

text: public

characteristic: description

text: Sweden

text: Kramfors

text: whole tick

text: Ixodes ricinus

characteristic: host scientific name

text: Whole tick

text: tick metagenome

text: tick metagenome


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: National Veterinary Institute

text: public

text: Sweden

text: Avesta

text: whole tick

text: Ixodes ricinus

text: Whole tick

text: tick metagenome

text: tick metagenome

characteristic: target gene


text: National Veterinary Institute

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: Sweden

text: Ljusdal

text: whole tick

text: Ixodes ricinus

text: Whole tick

text: tick metagenome

text: tick metagenome

characteristic: target subfragment


text: National Veterinary Institute

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: Sweden

text: Haparanda

text: whole tick

text: Ixodes persulcatus/Ixodes ricinus

text: Whole tick

text: tick metagenome

text: tick metagenome

characteristic: title


text: National Veterinary Institute

text: public

characteristic: SRA accession

characteristic: Submitter Id

text: Sweden

characteristic: geographic location (country and/or sea)

text: Kalix

text: whole tick

text: Ixodes persulcatus

text: Whole tick

text: tick metagenome

text: tick metagenome


characteristic: ENA-CHECKLIST

text: National Veterinary Institute

text: public

text: Sweden

text: Kalix

characteristic: geographic location (region and locality)

text: whole tick

text: Ixodes persulcatus/Ixodes ricinus

text: Whole tick

text: tick metagenome

characteristic: organism

text: tick metagenome


characteristic: ENA-FIRST-PUBLIC

text: National Veterinary Institute

text: public

characteristic: description

text: Sweden

text: Kiruna

text: whole tick

characteristic: host body site

text: Ixodes persulcatus

text: Whole tick

text: tick metagenome

text: tick metagenome


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: National Veterinary Institute

text: public

text: Sweden

text: Skellefteå

text: whole tick

text: Ixodes persulcatus/Ixodes ricinus

characteristic: host scientific name

text: Whole tick

text: tick metagenome

text: tick metagenome


text: National Veterinary Institute

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: Sweden

text: Kiruna

text: whole tick

text: Ixodes ricinus

text: Whole tick

text: tick metagenome

text: tick metagenome

characteristic: target gene


text: National Veterinary Institute

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: Sweden

text: Haparanda

text: whole tick

text: Ixodes persulcatus

text: Whole tick

text: tick metagenome

text: tick metagenome

characteristic: target subfragment


text: National Veterinary Institute

text: public

characteristic: SRA accession

characteristic: Submitter Id

text: Sweden

text: Jokkmokk

text: whole tick

text: Ixodes ricinus

text: Whole tick

text: tick metagenome

text: tick metagenome

characteristic: title


characteristic: ENA-CHECKLIST

text: National Veterinary Institute

text: public

text: Sweden

characteristic: geographic location (country and/or sea)

text: Sorsele

characteristic: geographic location (region and locality)

text: whole tick

text: Ixodes ricinus

text: Whole tick

text: tick metagenome

text: tick metagenome


characteristic: ENA-FIRST-PUBLIC

text: National Veterinary Institute

text: public

characteristic: description

text: Sweden

text: Älvsbyn

text: whole tick

text: Ixodes ricinus

text: Whole tick

text: tick metagenome

characteristic: organism

text: tick metagenome


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: National Veterinary Institute

text: public

text: Sweden

text: Kalix

text: whole tick

characteristic: host body site

text: Ixodes ricinus

text: Whole tick

text: tick metagenome

text: tick metagenome


text: National Veterinary Institute

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: Sweden

text: Lycksele

text: whole tick

text: Ixodes ricinus

characteristic: host scientific name

text: Whole tick

text: tick metagenome

text: tick metagenome


text: National Veterinary Institute

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: Sweden

text: Norsjö

text: whole tick

text: Ixodes ricinus

text: Whole tick

text: tick metagenome

text: tick metagenome

characteristic: target gene


text: National Veterinary Institute

text: public

characteristic: SRA accession

characteristic: Submitter Id

text: Sweden

text: Skellefteå

text: whole tick

text: Ixodes ricinus

text: Whole tick

text: tick metagenome

text: tick metagenome

characteristic: target subfragment


characteristic: ENA-CHECKLIST

text: National Veterinary Institute

text: public

text: Sweden

characteristic: geographic location (country and/or sea)

text: Vindeln

text: whole tick

text: Ixodes ricinus

text: Whole tick

text: tick metagenome

text: tick metagenome

characteristic: title


characteristic: ENA-FIRST-PUBLIC

text: National Veterinary Institute

text: public

characteristic: description

text: Sweden

text: Nordmaling

characteristic: geographic location (region and locality)

text: whole tick

text: Ixodes ricinus

text: Whole tick

text: tick metagenome

text: tick metagenome


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: National Veterinary Institute

text: public

text: Sweden

text: Piteå

text: whole tick

text: Ixodes ricinus

text: Whole tick

text: tick metagenome

characteristic: organism

text: tick metagenome


text: National Veterinary Institute

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: Sweden

text: Luleå

text: whole tick

characteristic: host body site

text: Ixodes ricinus

text: Whole tick

text: tick metagenome

text: tick metagenome


text: National Veterinary Institute

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: Sweden

text: Dorotea

text: whole tick

text: Ixodes ricinus

characteristic: host scientific name

text: Whole tick

text: tick metagenome

text: tick metagenome