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characteristic: geographic location (country and/or sea)

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text: Altromin

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text: healthy

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text: adult

characteristic: host life stage

text: male

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text: host-associated

text: IVC

text: metagenome

text: no medication

text: ZTL Quarantine unit

text: Qiagen AllPrep DNA/RNA

text: Mus musculus

characteristic: organism

text: Variation in C57BL/6J mouse microbiota

text: Mus musculus

text: RNA

text: Illumina Miseq

text: fecal sample

text: 16S rRNA

text: Variation in C57BL/6J mouse microbiota

characteristic: title

text: autoclave


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text: R1-TATGGTAATTGTAGAGTTTGATCCTGGCTCAG;R2-AGTCAGTCAGCCTGCTGCCTCCCGTAGGAGT

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text: The intestinal microbiota is involved in many physiological processes, and it is increasingly recognized that differences in community composition can influence the outcome of a variety of murine models used in biomedical research. In an effort to describe and account for the variation in intestinal microbiota composition across the animal facilities of participating members of the DFG Priority Program 1656 “Intestinal Microbiota”, we performed a survey of C57BL/6J mice from 21 different mouse rooms/facilities located at 13 different institutions across Germany. Fresh feces was sampled from five mice per room/facility using standardized procedures, followed by extraction and 16S rRNA gene profiling (V1-V2 region, Illumina MiSeq) at both the DNA and RNA (reverse transcribed to cDNA) level. In order to determine the variables contributing to bacterial community differences, we collected detailed questionnaires of animal husbandry practices and incorporated this information into our analyses. We identified considerable variation in a number of descriptive aspects including the proportions of major phyla, alpha- and beta diversity, all of which displayed significant associations to specific aspects of husbandry. Salient findings include a reduction in alpha diversity with the use of irradiated chow, an increase in inter-individual variability (beta diversity) with respect to barrier access and open cages and an increase in bacterial community divergence with time since importing from a vendor. We further observe a high degree of facility-level individuality, which is likely due to each facility harboring its own unique combination of multiple varying attributes of animal husbandry. While it is important to account and control for such differences between facilities, the documentation of such diversity may also serve as a valuable future resource for investigating the origins of microbial-driven host phenotypes.

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unit: DD

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text: 98�C-30s, 30 � [98�C-9s, 55�C-60s, 72�C-90s], 72�C-10 min

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characteristic: title

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characteristic: title

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characteristic: environment (material)

text: E

characteristic: facility

text: Germany

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

characteristic: host age

text: colon

characteristic: host body habitat

text: feces

characteristic: host body product

text: house mouse

characteristic: host common name

text: Altromin

characteristic: host diet

text: healthy

characteristic: host disease status

text: adult

characteristic: host life stage

text: male

characteristic: host sex

characteristic: host subject id

characteristic: host taxid

text: host-associated

text: IVC

text: metagenome

text: no medication

text: Charles River

text: Qiagen AllPrep DNA/RNA

text: Mus musculus

characteristic: organism

text: Variation in C57BL/6J mouse microbiota

text: Mus musculus

text: DNA

text: Illumina Miseq

text: fecal sample

text: 16S rRNA

text: Variation in C57BL/6J mouse microbiota

characteristic: title

text: autoclave


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: MPIEVB

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

characteristic: adapters

text: restricted

characteristic: barrier access

text: autoclave

characteristic: bedding treatment

text: Altromin

characteristic: chow provider

text: untreated

characteristic: chow treatment

characteristic: collection date

text: house mouse

characteristic: common name

characteristic: description

text: host associated

characteristic: environment (biome)

text: feces

characteristic: environment (feature)

text: feces

characteristic: environment (material)

text: E

text: Germany

text: colon

text: feces

text: house mouse

text: Altromin

text: healthy

text: adult

text: male

characteristic: host total mass

text: host-associated

characteristic: host-associated environmental package

text: IVC

characteristic: housing condition

text: metagenome

characteristic: investigation type

text: no medication

characteristic: medication

text: Charles River

characteristic: mouse provider

characteristic: multiplex identifiers

text: Qiagen AllPrep DNA/RNA

characteristic: nucleic acid extraction

text: Mus musculus

characteristic: pcr conditions

characteristic: pcr primers

characteristic: presence of other strains

text: Variation in C57BL/6J mouse microbiota

characteristic: project name

text: Mus musculus

text: RNA

characteristic: sequence type

text: Illumina Miseq

characteristic: sequencing method

text: fecal sample

characteristic: source material identifiers

text: 16S rRNA

characteristic: target gene

text: Variation in C57BL/6J mouse microbiota

text: autoclave


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: MPIEVB

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

characteristic: adapters

text: restricted

characteristic: barrier access

text: autoclave

characteristic: bedding treatment

text: Ssniff

characteristic: chow provider

text: autoclave

characteristic: chow treatment

characteristic: collection date

text: house mouse

characteristic: common name

characteristic: description

text: host associated

characteristic: environment (biome)

text: feces

characteristic: environment (feature)

text: feces

characteristic: environment (material)

text: E

characteristic: facility

text: Germany

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

characteristic: host age

text: colon

characteristic: host body habitat

text: feces

characteristic: host body product

text: house mouse

characteristic: host common name

text: Ssniff

characteristic: host diet

text: healthy

characteristic: host disease status

text: adult

characteristic: host life stage

text: male

characteristic: host sex

characteristic: host subject id

characteristic: host taxid

text: host-associated

text: open

text: metagenome

text: no medication

text: Janvier

text: Qiagen AllPrep DNA/RNA

text: Mus musculus

characteristic: organism

text: Variation in C57BL/6J mouse microbiota

text: Mus musculus

text: DNA

text: Illumina Miseq

text: fecal sample

text: 16S rRNA

text: Variation in C57BL/6J mouse microbiota

characteristic: title

text: autoclave


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: MPIEVB

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

characteristic: adapters

text: restricted

characteristic: barrier access

text: autoclave

characteristic: bedding treatment

text: Ssniff

characteristic: chow provider

text: autoclave

characteristic: chow treatment

characteristic: collection date

text: house mouse

characteristic: common name

characteristic: description

text: host associated

characteristic: environment (biome)

text: feces

characteristic: environment (feature)

text: feces

characteristic: environment (material)

text: E

text: Germany

text: colon

text: feces

text: house mouse

text: Ssniff

text: healthy

text: adult

text: male

characteristic: host total mass

text: host-associated

characteristic: host-associated environmental package

text: open

characteristic: housing condition

text: metagenome

characteristic: investigation type

text: no medication

characteristic: medication

text: Janvier

characteristic: mouse provider

characteristic: multiplex identifiers

text: Qiagen AllPrep DNA/RNA

characteristic: nucleic acid extraction

text: Mus musculus

characteristic: pcr conditions

characteristic: pcr primers

characteristic: presence of other strains

text: Variation in C57BL/6J mouse microbiota

characteristic: project name

text: Mus musculus

text: RNA

characteristic: sequence type

text: Illumina Miseq

characteristic: sequencing method

text: fecal sample

characteristic: source material identifiers

text: 16S rRNA

characteristic: target gene

text: Variation in C57BL/6J mouse microbiota

text: autoclave


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: MPIEVB

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

characteristic: adapters

text: open

characteristic: barrier access

text: autoclave

characteristic: bedding treatment

text: Ssniff

characteristic: chow provider

text: autoclave

characteristic: chow treatment

characteristic: collection date

text: house mouse

characteristic: common name

characteristic: description

text: host associated

characteristic: environment (biome)

text: feces

characteristic: environment (feature)

text: feces

characteristic: environment (material)

text: E

characteristic: facility

text: Germany

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

characteristic: host age

text: colon

characteristic: host body habitat

text: feces

characteristic: host body product

text: house mouse

characteristic: host common name

text: Ssniff

characteristic: host diet

text: healthy

characteristic: host disease status

text: adult

characteristic: host life stage

text: male

characteristic: host sex

characteristic: host subject id

characteristic: host taxid

text: host-associated

text: IVC

text: metagenome

text: no medication

text: Janvier

text: Qiagen AllPrep DNA/RNA

text: Mus musculus

characteristic: organism

text: Variation in C57BL/6J mouse microbiota

text: Mus musculus

text: DNA

text: Illumina Miseq

text: fecal sample

text: 16S rRNA

text: Variation in C57BL/6J mouse microbiota

characteristic: title

text: autoclave


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: MPIEVB

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

characteristic: adapters

text: open

characteristic: barrier access

text: autoclave

characteristic: bedding treatment

text: Ssniff

characteristic: chow provider

text: autoclave

characteristic: chow treatment

characteristic: collection date

text: house mouse

characteristic: common name

characteristic: description

text: host associated

characteristic: environment (biome)

text: feces

characteristic: environment (feature)

text: feces

characteristic: environment (material)

text: E

text: Germany

text: colon

text: feces

text: house mouse

text: Ssniff

text: healthy

text: adult

text: male

characteristic: host total mass

text: host-associated

characteristic: host-associated environmental package

text: IVC

characteristic: housing condition

text: metagenome

characteristic: investigation type

text: no medication

characteristic: medication

text: Janvier

characteristic: mouse provider

characteristic: multiplex identifiers

text: Qiagen AllPrep DNA/RNA

characteristic: nucleic acid extraction

text: Mus musculus

characteristic: pcr conditions

characteristic: pcr primers

characteristic: presence of other strains

text: Variation in C57BL/6J mouse microbiota

characteristic: project name

text: Mus musculus

text: RNA

characteristic: sequence type

text: Illumina Miseq

characteristic: sequencing method

text: fecal sample

characteristic: source material identifiers

text: 16S rRNA

characteristic: target gene

text: Variation in C57BL/6J mouse microbiota

text: autoclave


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: MPIEVB

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

characteristic: adapters

text: restricted

characteristic: barrier access

text: autoclave

characteristic: bedding treatment

text: Ssniff

characteristic: chow provider

text: autoclave

characteristic: chow treatment

characteristic: collection date

text: house mouse

characteristic: common name

characteristic: description

text: host associated

characteristic: environment (biome)

text: feces

characteristic: environment (feature)

text: feces

characteristic: environment (material)

characteristic: facility

text: Germany

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

characteristic: host age

text: colon

characteristic: host body habitat

text: feces

characteristic: host body product

text: house mouse

characteristic: host common name

text: Ssniff

characteristic: host diet

text: healthy

characteristic: host disease status

text: adult

characteristic: host life stage

text: male

characteristic: host sex

characteristic: host subject id

characteristic: host taxid

text: host-associated

text: open

text: metagenome

text: no medication

text: Charles River

text: Qiagen AllPrep DNA/RNA

text: Mus musculus

characteristic: organism

text: Variation in C57BL/6J mouse microbiota

text: Mus musculus

text: DNA

text: Illumina Miseq

text: fecal sample

text: 16S rRNA

text: Variation in C57BL/6J mouse microbiota

characteristic: title

text: no


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: MPIEVB

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

characteristic: adapters

text: restricted

characteristic: barrier access

text: autoclave

characteristic: bedding treatment

text: Ssniff

characteristic: chow provider

text: autoclave

characteristic: chow treatment

characteristic: collection date

text: house mouse

characteristic: common name

characteristic: description

text: host associated

characteristic: environment (biome)

text: feces

characteristic: environment (feature)

text: feces

characteristic: environment (material)

text: Germany

text: colon

text: feces

text: house mouse

text: Ssniff

text: healthy

text: adult

text: male

characteristic: host total mass

text: host-associated

characteristic: host-associated environmental package

text: open

characteristic: housing condition

text: metagenome

characteristic: investigation type

text: no medication

characteristic: medication

text: Charles River

characteristic: mouse provider

characteristic: multiplex identifiers

text: Qiagen AllPrep DNA/RNA

characteristic: nucleic acid extraction

text: Mus musculus

characteristic: pcr conditions

characteristic: pcr primers

characteristic: presence of other strains

text: Variation in C57BL/6J mouse microbiota

characteristic: project name

text: Mus musculus

text: RNA

characteristic: sequence type

text: Illumina Miseq

characteristic: sequencing method

text: fecal sample

characteristic: source material identifiers

text: 16S rRNA

characteristic: target gene

text: Variation in C57BL/6J mouse microbiota

text: no


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: MPIEVB

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

characteristic: adapters

text: open

characteristic: barrier access

text: autoclave

characteristic: bedding treatment

text: Ssniff

characteristic: chow provider

text: autoclave

characteristic: chow treatment

characteristic: collection date

text: house mouse

characteristic: common name

characteristic: description

text: host associated

characteristic: environment (biome)

text: feces

characteristic: environment (feature)

text: feces

characteristic: environment (material)

text: S

characteristic: facility

text: Germany

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

characteristic: host age

text: colon

characteristic: host body habitat

text: feces

characteristic: host body product

text: house mouse

characteristic: host common name

text: Ssniff

characteristic: host diet

text: healthy

characteristic: host disease status

text: adult

characteristic: host life stage

text: male

characteristic: host sex

characteristic: host subject id

characteristic: host taxid

text: host-associated

text: IVC

text: metagenome

text: no medication

text: Janvier

text: Qiagen AllPrep DNA/RNA

text: Mus musculus

characteristic: organism

text: Variation in C57BL/6J mouse microbiota

text: Mus musculus

text: DNA

text: Illumina Miseq

text: fecal sample

text: 16S rRNA

text: Variation in C57BL/6J mouse microbiota

characteristic: title

text: autoclave


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: MPIEVB

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

characteristic: adapters

text: open

characteristic: barrier access

text: autoclave

characteristic: bedding treatment

text: Ssniff

characteristic: chow provider

text: autoclave

characteristic: chow treatment

characteristic: collection date

text: house mouse

characteristic: common name

characteristic: description

text: host associated

characteristic: environment (biome)

text: feces

characteristic: environment (feature)

text: feces

characteristic: environment (material)

text: S

text: Germany

text: colon

text: feces

text: house mouse

text: Ssniff

text: healthy

text: adult

text: male

characteristic: host total mass

text: host-associated

characteristic: host-associated environmental package

text: IVC

characteristic: housing condition

text: metagenome

characteristic: investigation type

text: no medication

characteristic: medication

text: Janvier

characteristic: mouse provider

characteristic: multiplex identifiers

text: Qiagen AllPrep DNA/RNA

characteristic: nucleic acid extraction

text: Mus musculus

characteristic: pcr conditions

characteristic: pcr primers

characteristic: presence of other strains

text: Variation in C57BL/6J mouse microbiota

characteristic: project name

text: Mus musculus

text: RNA

characteristic: sequence type

text: Illumina Miseq

characteristic: sequencing method

text: fecal sample

characteristic: source material identifiers

text: 16S rRNA

characteristic: target gene

text: Variation in C57BL/6J mouse microbiota

text: autoclave


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: UNIVERSITY OF DELAWARE

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

tag: Namespace:UNIVERSITY OF DELAWARE

characteristic: Submitter Id

text: 16S rRNA amplicon study of the microbial communities in Glacier Lake

characteristic: description

text: N42.995845 W76.091348

characteristic: lat lon

text: uncultured bacterium

characteristic: organism

text: uncultured bacterium

text: Glacier Lake Microbial Communities

characteristic: title


text: Homo sapiens

characteristic: ArrayExpress-Species

text: SC

text: public

text: human

characteristic: common name

text: Homo sapiens

text: Homo sapiens


text: James Hutton Institute

text: public

tag: Namespace:James Hutton Institute

characteristic: collection date

text: PWN146 Roche 454

text: Portugal

characteristic: geographic location (country and/or sea)

text: Avô, Coimbra, Portugal

characteristic: geographic location (region and locality)

text: Bursaphelenchus xylophilus

characteristic: host

text: Cuticle of of the plant parasitic nematode Bursaphelenchus xylophilus extracted from symptomatic Pinus pinaster in Avô (Coimbra, Portugal)

characteristic: isolation source

text: Serratia marcescens

text: Serratia marcescens

text: PWN146 Roche 454

type: has member


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: James Hutton Institute

characteristic: INSDC center name

text: public

text: PWN146 MiSeq 1

text: Portugal

text: Avô, Coimbra, Portugal

text: Bursaphelenchus xylophilus

text: Serratia marcescens

text: Serratia marcescens

text: PWN146 MiSeq 1


text: James Hutton Institute

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: PWN146 MiSeq 2

text: Portugal

text: Avô, Coimbra, Portugal

text: Bursaphelenchus xylophilus

text: Serratia marcescens

text: Serratia marcescens

text: PWN146 MiSeq 2


text: James Hutton Institute

text: public

text: PWN146 PacBio SMRT cell one

characteristic: description

text: Portugal

text: Avô, Coimbra, Portugal

text: Bursaphelenchus xylophilus

text: Serratia marcescens

characteristic: organism

text: Serratia marcescens

text: PWN146 PacBio 1

characteristic: title


text: DUNDEE

text: public

text: early culminant

characteristic: dev stage

text: Polysphondylium pallidum PN500

text: Polysphondylium pallidum PN500

text: whole organism

characteristic: tissue type

text: Normalised RNA-seq reads from P. pallidum


text: DUNDEE

text: public

text: multiple

text: Dictyostelium lacteum

text: Dictyostelium lacteum

text: whole organism

text: Normalised RNA-seq in D. lacteum


text: DUNDEE

text: public

text: multiple stages

text: Dictyostelium fasciculatum

text: Dictyostelium fasciculatum

text: whole organism

text: Normalised RNA-seq reads from D. fasciculatum


text: public

tag: Namespace:WAGENINGEN UNIVERSITY, LABORATORY OF SYSTEMS AND SYNTHETIC BIOLOGY.

text: Annotation was performed using the Semantic Annotation Platform for Prokaryotes (SAPP)

text: Moorella glycerini

text: Moorella glycerini


text: BANGOR UNIVERSITY

text: public

tag: Namespace:BANGOR UNIVERSITY

characteristic: collection date

text: temperate woodland

characteristic: environment (biome)

text: anthropogenic geographic feature

characteristic: environment (feature)

text: organic material

characteristic: environment (material)

text: United Kingdom

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: metagenome

characteristic: investigation type

text: metagenome

text: plant-associated

characteristic: plant-associated environmental package

characteristic: project name

text: metagenome

text: illumina

characteristic: sequencing method


TBGP

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: irena.maus

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: TBGP

characteristic: Submitter Id

unit: m

characteristic: depth

text: Towards the core microbiome for a thermophilic biogas plant applying metagenome and metatranscriptome analyses complemented by cultivation and characterization if isolates for major functional groups.

text: Thermophilic biogas plant

text: Thermophilic biogas plant

text: Thermophilic biogas plant

text: Germany

characteristic: geographic location (elevation)

text: metagenome

text: metagenome

text: TBGP

text: metagenome

text: Illumina MiSeq

text: soil

characteristic: soil environmental package


text: UNIVERSITY OF ZUERICH

text: public

tag: Namespace:UNIVERSITY OF ZUERICH

text: Sample obtained from a progeny (W302) of a wild type individual (A. halleri subsp. gemmifera (Matsumura) O’Kane & Al-Shehbaz) that was collected from a population located on a contaminated Tada mine site near Tadaginzan, Inagawa, Hyogo, Japan. To obtain W302, five rounds of self-fertilization by bud pollination were conducted in the lab to reduce heterozygosity.

characteristic: description

text: Tada mine

characteristic: ecotype

text: Japan

characteristic: geographic location (country and/or sea)

text: Hyogo, Inagawa, Tadaginzan

characteristic: geographic location (region and locality)

characteristic: isolate

text: 34.89 N 135.35 E

characteristic: lat lon

text: Arabidopsis halleri subsp. gemmifera

characteristic: organism

text: Arabidopsis halleri subsp. gemmifera

text: gemmifera

characteristic: sub species

text: leaf

characteristic: tissue type

text: W302 leaf tissue

characteristic: title


E-MTAB-4502:Sample 1

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

text: E-MTAB-4502:Sample 1

tag: Namespace:Laboratory of Molecular Medicine and Genomics

characteristic: biological replicate

text: ArrayExpress

characteristic: broker name

text: exosome

characteristic: cell fraction

text: non tumorigenic hepatocyte cell

characteristic: cell type

text: house mouse

characteristic: common name

text: Protocols: Non tumorigenic hepatocyte cells (3A cells [16]) were grown in RPMI 1640 medium supplemented with 10% FBS (GIBCO® Life Technology, Monza, Italy), 50 ng/ml EGF, 30 ng/ml IGF II (PeproTech Inc., Rocky Hill, NJ, USA), 10 μg/ml insulin (Roche, Mannheim, Germany) and Penicillin/Streptomycin, on collagen I (GIBCO® Life Technology, Monza, Italy) coated dishes. To obtain hepatocyte exosomes, cells were cultured for 48-72h hours in RPMI-1640 supplemented with 10% FBS depleted of bovine exosomes by overnight centrifugation at 100.000xg (Beckman Optima L80; Beckman Coulter, Italy). Hepatocyte exosomes were then prepared from supernatants by sequential centrifugation/ultracentrifugation. Cells conditioned media were centrifuged at 2000xg for 20 minutes and 10.000xg for 30 minutes, to remove cells debris. Cleared supernatants were passed through 0.22 m filter membranes, then ultracentrifuged at 100.000xg for 70 minutes, finally resuspended in PBS. Exosome size was determined by Nanoparticle Tracking Analysis [14] with Nanosight LM-10 (Malvern Instruments, Malverns, UK). Total RNA from cells and exosomes was isolated by Qiazol and miRNeasy Mini Kit (QIAGEN GmbH, Hilden, Germany) following manufacturer’s protocols. RNA purity was assessed by spectrophotometric measure of OD260/OD280 ~2 and OD260/ OD230 >1.8 with Nanodrop 2000c Spectrophotometer (ThermoFisher) and RNA quantitation was performed with QubitTM and Qubit® RNA assay (Life Technologies, Monza, Italy). For miRNAseq experiments the quality of isolated RNA was determined with Bioanalyzer 2100 (Agilent Technologies, Santa Clara, CA). RNA samples to be sequenced were purified from several independent cell cultures and exosome isolation and then pooled together. Indexed libraries were prepared from about 500 ng/ea. purified RNA pool with TruSeq Small RNA Sample Prep Kit (Illumina Inc., San Diego, CA), as described earlier [17]. Then, miRNA expression profiles were analyzed by smallRNA-Seq. Sized indexed miRNA libraries were gel purified and sequenced in triplicates on HiSeq2500 (Illumina Inc., San Diego, CA ) at a concentration of 10pM/lane for 50 plus 7 additional cycles for indices sequencing.

text: Mus musculus

text: Mus musculus

text: control

characteristic: rna interference

text: Mus musculus

text: Sample 1


E-MTAB-4502:Sample 10

text: Laboratory of Molecular Medicine and Genomics

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-4502:Sample 10

characteristic: Submitter Id

text: ArrayExpress

text: cell

text: non tumorigenic hepatocyte cell

text: house mouse

characteristic: description

text: Mus musculus

characteristic: organism

text: Mus musculus

text: control

text: Mus musculus

text: Sample 10


E-MTAB-4502:Sample 11

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: public

text: E-MTAB-4502:Sample 11

text: ArrayExpress

text: cell

text: non tumorigenic hepatocyte cell

text: house mouse

text: Mus musculus

text: Mus musculus

text: control

text: Mus musculus

text: Sample 11

characteristic: title


E-MTAB-4502:Sample 12

characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC center name

text: public

text: E-MTAB-4502:Sample 12

text: ArrayExpress

text: cell

text: non tumorigenic hepatocyte cell

text: house mouse

text: Mus musculus

text: Mus musculus

text: control

text: Mus musculus

text: Sample 12


E-MTAB-4502:Sample 13

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: E-MTAB-4502:Sample 13

characteristic: biological replicate

text: ArrayExpress

text: cell

text: non tumorigenic hepatocyte cell

text: house mouse

text: Mus musculus

text: Mus musculus

text: control

text: Mus musculus

text: Sample 13


E-MTAB-4502:Sample 14

text: public

text: E-MTAB-4502:Sample 14

text: ArrayExpress

characteristic: broker name

text: cell

characteristic: cell fraction

text: non tumorigenic hepatocyte cell

characteristic: cell type

text: house mouse

text: Mus musculus

text: Mus musculus

text: control

text: Mus musculus

text: Sample 14


E-MTAB-4502:Sample 15

text: public

characteristic: INSDC status

text: E-MTAB-4502:Sample 15

text: ArrayExpress

text: cell

text: non tumorigenic hepatocyte cell

text: house mouse

characteristic: common name

text: Mus musculus

text: Mus musculus

text: control

characteristic: rna interference

text: Mus musculus

text: Sample 15


E-MTAB-4502:Sample 16

text: public

characteristic: SRA accession

text: E-MTAB-4502:Sample 16

characteristic: Submitter Id

text: ArrayExpress

text: cell

text: non tumorigenic hepatocyte cell

text: house mouse

characteristic: description

text: Mus musculus

text: Mus musculus

text: control

text: Mus musculus

text: Sample 16


E-MTAB-4502:Sample 17

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: public

text: E-MTAB-4502:Sample 17

text: ArrayExpress

text: cell

text: non tumorigenic hepatocyte cell

text: house mouse

text: Mus musculus

characteristic: organism

text: Mus musculus

text: control

text: Mus musculus

text: Sample 17


E-MTAB-4502:Sample 18

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: public

text: E-MTAB-4502:Sample 18

text: ArrayExpress

text: cell

text: non tumorigenic hepatocyte cell

text: house mouse

text: Mus musculus

text: Mus musculus

text: control

text: Mus musculus

text: Sample 18

characteristic: title


E-MTAB-4502:Sample 19

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: E-MTAB-4502:Sample 19

text: ArrayExpress

text: exosome

text: non tumorigenic hepatocyte cell

text: house mouse

text: Mus musculus

text: Mus musculus

text: shSyn

text: Mus musculus

text: Sample 19


E-MTAB-4502:Sample 2

text: public

text: E-MTAB-4502:Sample 2

characteristic: biological replicate

text: ArrayExpress

characteristic: broker name

text: exosome

characteristic: cell fraction

text: non tumorigenic hepatocyte cell

text: house mouse

text: Mus musculus

text: Mus musculus

text: control

text: Mus musculus

text: Sample 2


E-MTAB-4502:Sample 20

text: public

characteristic: INSDC status

text: E-MTAB-4502:Sample 20

text: ArrayExpress

text: exosome

text: non tumorigenic hepatocyte cell

characteristic: cell type

text: house mouse

characteristic: common name

text: Mus musculus

text: Mus musculus

text: shSyn

text: Mus musculus

text: Sample 20


E-MTAB-4502:Sample 21

text: public

characteristic: SRA accession

text: E-MTAB-4502:Sample 21

characteristic: Submitter Id

text: ArrayExpress

text: exosome

text: non tumorigenic hepatocyte cell

text: house mouse

text: Mus musculus

text: Mus musculus

text: shSyn

characteristic: rna interference

text: Mus musculus

text: Sample 21


E-MTAB-4502:Sample 22

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: public

text: E-MTAB-4502:Sample 22

text: ArrayExpress

text: exosome

text: non tumorigenic hepatocyte cell

text: house mouse

characteristic: description

text: Mus musculus

text: Mus musculus

text: shSyn

text: Mus musculus

text: Sample 22


E-MTAB-4502:Sample 23

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: public

text: E-MTAB-4502:Sample 23

text: ArrayExpress

text: exosome

text: non tumorigenic hepatocyte cell

text: house mouse

text: Mus musculus

characteristic: organism

text: Mus musculus

text: shSyn

text: Mus musculus

text: Sample 23


E-MTAB-4502:Sample 24

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: E-MTAB-4502:Sample 24

text: ArrayExpress

text: exosome

text: non tumorigenic hepatocyte cell

text: house mouse

text: Mus musculus

text: Mus musculus

text: shSyn

text: Mus musculus

text: Sample 24

characteristic: title


E-MTAB-4502:Sample 25

characteristic: INSDC last update

text: public

text: E-MTAB-4502:Sample 25

characteristic: biological replicate

text: ArrayExpress

characteristic: broker name

text: cell

text: non tumorigenic hepatocyte cell

text: house mouse

text: Mus musculus

text: Mus musculus

text: shSyn

text: Mus musculus

text: Sample 25


E-MTAB-4502:Sample 26

text: public

characteristic: INSDC status

text: E-MTAB-4502:Sample 26

text: ArrayExpress

text: cell

characteristic: cell fraction

text: non tumorigenic hepatocyte cell

characteristic: cell type

text: house mouse

text: Mus musculus

text: Mus musculus

text: shSyn

text: Mus musculus

text: Sample 26


E-MTAB-4502:Sample 27

text: public

characteristic: SRA accession

text: E-MTAB-4502:Sample 27

characteristic: Submitter Id

text: ArrayExpress

text: cell

text: non tumorigenic hepatocyte cell

text: house mouse

characteristic: common name

text: Mus musculus

text: Mus musculus

text: shSyn

text: Mus musculus

text: Sample 27


E-MTAB-4502:Sample 28

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: public

text: E-MTAB-4502:Sample 28

text: ArrayExpress

text: cell

text: non tumorigenic hepatocyte cell

text: house mouse

text: Mus musculus

text: Mus musculus

text: shSyn

characteristic: rna interference

text: Mus musculus

text: Sample 28


E-MTAB-4502:Sample 29

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: public

text: E-MTAB-4502:Sample 29

text: ArrayExpress

text: cell

text: non tumorigenic hepatocyte cell

text: house mouse

characteristic: description

text: Mus musculus

text: Mus musculus

text: shSyn

text: Mus musculus

text: Sample 29


E-MTAB-4502:Sample 3

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: E-MTAB-4502:Sample 3

text: ArrayExpress

text: exosome

text: non tumorigenic hepatocyte cell

text: house mouse

text: Mus musculus

characteristic: organism

text: Mus musculus

text: control

text: Mus musculus

text: Sample 3


E-MTAB-4502:Sample 30

characteristic: INSDC last update

text: public

text: E-MTAB-4502:Sample 30

characteristic: biological replicate

text: ArrayExpress

text: cell

text: non tumorigenic hepatocyte cell

text: house mouse

text: Mus musculus

text: Mus musculus

text: shSyn

text: Mus musculus

text: Sample 30

characteristic: title


E-MTAB-4502:Sample 4

text: public

characteristic: INSDC status

text: E-MTAB-4502:Sample 4

text: ArrayExpress

characteristic: broker name

text: exosome

characteristic: cell fraction

text: non tumorigenic hepatocyte cell

text: house mouse

text: Mus musculus

text: Mus musculus

text: control

text: Mus musculus

text: Sample 4


E-MTAB-4502:Sample 5

text: public

characteristic: SRA accession

text: E-MTAB-4502:Sample 5

characteristic: Submitter Id

text: ArrayExpress

text: exosome

text: non tumorigenic hepatocyte cell

characteristic: cell type

text: house mouse

text: Mus musculus

text: Mus musculus

text: control

text: Mus musculus

text: Sample 5


E-MTAB-4502:Sample 6

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: public

text: E-MTAB-4502:Sample 6

text: ArrayExpress

text: exosome

text: non tumorigenic hepatocyte cell

text: house mouse

characteristic: common name

text: Mus musculus

text: Mus musculus

text: control

text: Mus musculus

text: Sample 6


E-MTAB-4502:Sample 7

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: public

text: E-MTAB-4502:Sample 7

text: ArrayExpress

text: exosome

text: non tumorigenic hepatocyte cell

text: house mouse

text: Mus musculus

text: Mus musculus

text: control

characteristic: rna interference

text: Mus musculus

text: Sample 7


E-MTAB-4502:Sample 8

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: E-MTAB-4502:Sample 8

text: ArrayExpress

text: exosome

text: non tumorigenic hepatocyte cell

text: house mouse

characteristic: description

text: Mus musculus

text: Mus musculus

text: control

text: Mus musculus

text: Sample 8


E-MTAB-4502:Sample 9

characteristic: INSDC last update

text: public

text: E-MTAB-4502:Sample 9

characteristic: biological replicate

text: ArrayExpress

text: exosome

text: non tumorigenic hepatocyte cell

text: house mouse

text: Mus musculus

characteristic: organism

text: Mus musculus

text: control

text: Mus musculus

text: Sample 9


text: VALE INSTITUTE OF TECHNOLOGY

text: public

characteristic: INSDC status

tag: Namespace:VALE INSTITUTE OF TECHNOLOGY

characteristic: collection date

characteristic: depth

text: Metagenomics lakes

text: lake

characteristic: environment (biome)

text: lake

characteristic: environment (feature)

text: sed

characteristic: environment (material)

text: Brazil

characteristic: geographic location (country and/or sea)

characteristic: geographic location (elevation)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: metagenome

characteristic: investigation type

text: sediment metagenome

text: metagenomics

characteristic: project name

text: sediment metagenome

text: sediment

characteristic: sediment environmental package

text: illumina

characteristic: sequencing method

text: Metagenomics

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: University of Dundee

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: SRA accession

tag: Namespace:University of Dundee

characteristic: Submitter Id

text: HeLa

characteristic: cell line

text: human

characteristic: common name

text: Homo sapiens

text: Homo sapiens

text: The chromatin remodelling enzymes SNF2H and SNF2L position nucleosomes adjacent to CTCF and other transcription factors.


TBGPM

text: irena.maus

text: public

characteristic: INSDC status

text: TBGPM

characteristic: collection date

characteristic: depth

text: Towards the core microbiome for a thermophilic biogas plant applying metagenome and metatranscriptome analyses complemented by cultivation and characterization of isolates for major functional groups.

characteristic: description

text: Thermophilic biogas plant

characteristic: environment (biome)

text: Thermophilic biogas plant

characteristic: environment (feature)

text: Thermophilic biogas plant

characteristic: environment (material)

text: Germany

characteristic: geographic location (country and/or sea)

characteristic: geographic location (elevation)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: metatranscriptome

text: metagenome

characteristic: organism

text: TBGPM

text: metagenome

text: Illumina MiSeq

text: soil

characteristic: soil environmental package


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: UNIVERISTY OF OXFORD

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: SRA accession

tag: Namespace:UNIVERISTY OF OXFORD

text: Staphylococcus aureus

text: Staphylococcus aureus

characteristic: title


text: UNIVERSITY OF TARTU

text: public

characteristic: INSDC status

tag: Namespace:UNIVERSITY OF TARTU

characteristic: Submitter Id

characteristic: collection date

characteristic: depth

text: forest

characteristic: environment (biome)

text: birch stand

characteristic: environment (feature)

text: soil

text: Russia

text: metagenome

characteristic: investigation type

text: metagenome

characteristic: project name

text: metagenome

text: Illumina 2000

characteristic: sequencing method

text: soil

text: Birch


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: UNIVERSITY OF TARTU

text: public

text: Rhizosphere sample

characteristic: description

text: forest

text: birch stand

text: soil

characteristic: environment (material)

text: Russia

characteristic: geographic location (country and/or sea)

characteristic: geographic location (elevation)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: metagenome

text: metagenome

characteristic: organism

text: metagenome

text: Illumina 2000

text: soil

characteristic: soil environmental package

text: Birch


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: UNIVERSITY OF TARTU

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

characteristic: collection date

text: forest

text: birch stand

text: soil

text: Finland

text: metagenome

text: metagenome

text: metagenome

text: Illumina 2000

text: soil

text: Birch

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: UNIVERSITY OF TARTU

text: public

characteristic: depth

text: Rhizosphere sample

characteristic: description

text: forest

characteristic: environment (biome)

text: birch stand

characteristic: environment (feature)

text: soil

characteristic: environment (material)

text: Finland

text: metagenome

characteristic: investigation type

text: metagenome

characteristic: project name

text: metagenome

text: Illumina 2000

characteristic: sequencing method

text: soil

text: Birch


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: UNIVERSITY OF TARTU

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: forest

text: birch stand

text: soil

text: Estonia

characteristic: geographic location (country and/or sea)

characteristic: geographic location (elevation)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: metagenome

text: metagenome

characteristic: organism

text: metagenome

text: Illumina 2000

text: soil

characteristic: soil environmental package

text: Birch


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: UNIVERSITY OF TARTU

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

characteristic: collection date

characteristic: depth

text: Rhizosphere sample

characteristic: description

text: forest

text: birch stand

text: soil

text: Estonia

text: metagenome

text: metagenome

text: metagenome

text: Illumina 2000

text: soil

text: Birch

characteristic: title


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: UNIVERSITY OF TARTU

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: forest

characteristic: environment (biome)

text: birch stand

characteristic: environment (feature)

text: soil

characteristic: environment (material)

text: United Kingdom

text: metagenome

characteristic: investigation type

text: metagenome

characteristic: project name

text: metagenome

text: Illumina 2000

characteristic: sequencing method

text: soil

text: Birch


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: UNIVERSITY OF TARTU

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: Rhizosphere sample

text: forest

text: birch stand

text: soil

text: United Kingdom

characteristic: geographic location (country and/or sea)

characteristic: geographic location (elevation)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: metagenome

text: metagenome

characteristic: organism

text: metagenome

text: Illumina 2000

text: soil

characteristic: soil environmental package

text: Birch


characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC first public

text: public

characteristic: SRA accession

tag: Namespace:CNRS - CENTRE NATIONAL DE LA RECHERCHE SCIENTIFIQU

characteristic: Submitter Id

characteristic: collection date

characteristic: depth

text: terrestrial biome

text: contaminated soil

text: contaminated soil

text: Bare soil

characteristic: experimental factor

text: France

text: metagenome

text: soil metagenome

text: soil metagenome

text: MiSeq PE250

text: soil

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: CNRS - CENTRE NATIONAL DE LA RECHERCHE SCIENTIFIQU

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: terrestrial biome

characteristic: environment (biome)

text: contaminated soil

characteristic: environment (feature)

text: contaminated soil

characteristic: environment (material)

text: Bare soil

text: France

text: metagenome

characteristic: investigation type

text: soil metagenome

characteristic: project name

text: soil metagenome

text: MiSeq PE250

characteristic: sequencing method

text: soil


characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: terrestrial biome

text: contaminated soil

text: contaminated soil

text: Ryegrass-vegetated soil

text: France

characteristic: geographic location (country and/or sea)

characteristic: geographic location (elevation)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: metagenome

text: soil metagenome

characteristic: organism

text: soil metagenome

text: MiSeq PE250

text: soil

characteristic: soil environmental package


E-MTAB-4511:Non transfected #1

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-4511:Non transfected #1

tag: Namespace:Institute for Molecular Bioscience, University of Queenland, Brisbane, QLD 4072, Australia

characteristic: Submitter Id

text: ArrayExpress

characteristic: broker name

text: HUVEC

characteristic: cell line

text: human

characteristic: common name

text: Protocols: HUVECs were obtained from LONZA and grown according to suppliers recommendations. Cells were cultured in EBM2 media, supplemented with EGM2. Transfection (7 hours) was performed using Roche X-tremegene DNA transfection reagent in 0.4% FBS media. Directly following transfection, cells were stimulated (14 hours) with small molecule (or DMSO), in 0.4% FBS media. RNA was extracted using RNeasy mini kit (Qiagen). Samples (>100 ng RNA) were processed for whole transcriptome sequencing using TruSeq stranded total RNA library prep kit (Ribo‐Zero GOLD, Illumina).

characteristic: description

text: transfected with cMyc

characteristic: genotype

text: EGM2 supplemented media + vascular endothelial growth factor A

characteristic: growth condition

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens

text: Non transfected #1

characteristic: title


E-MTAB-4511:Non transfected #2

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Institute for Molecular Bioscience, University of Queenland, Brisbane, QLD 4072, Australia

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: E-MTAB-4511:Non transfected #2

text: ArrayExpress

text: HUVEC

text: human

text: transfected with cMyc

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens

text: Non transfected #2


E-MTAB-4511:Non transfected #3

characteristic: ENA-CHECKLIST

text: public

text: E-MTAB-4511:Non transfected #3

text: ArrayExpress

text: HUVEC

text: human

text: transfected with cMyc

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: Homo sapiens

text: Non transfected #3


E-MTAB-4511:Non transfected #4

characteristic: ENA-FIRST-PUBLIC

characteristic: INSDC last update

text: public

text: E-MTAB-4511:Non transfected #4

text: ArrayExpress

text: HUVEC

text: human

text: transfected with cMyc

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens

text: Non transfected #4


E-MTAB-4511:Sox18 o.e. #1

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-4511:Sox18 o.e. #1

text: ArrayExpress

text: HUVEC

text: human

text: transfected with Sox18-cMyc

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens

text: Sox18 o.e. #1


E-MTAB-4511:Sox18 o.e. #2

text: public

text: E-MTAB-4511:Sox18 o.e. #2

characteristic: Submitter Id

text: ArrayExpress

characteristic: broker name

text: HUVEC

text: human

text: transfected with Sox18-cMyc

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens

text: Sox18 o.e. #2


E-MTAB-4511:Sox18 o.e. #3

text: public

text: E-MTAB-4511:Sox18 o.e. #3

text: ArrayExpress

text: HUVEC

characteristic: cell line

text: human

characteristic: common name

text: transfected with Sox18-cMyc

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens

text: Sox18 o.e. #3


E-MTAB-4511:Sox18 o.e. #4

text: public

text: E-MTAB-4511:Sox18 o.e. #4

text: ArrayExpress

text: HUVEC

text: human

characteristic: description

text: transfected with Sox18-cMyc

characteristic: genotype

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens

text: Sox18 o.e. #4


E-MTAB-4511:Sox18 o.e. + Sm4 #1

text: public

text: E-MTAB-4511:Sox18 o.e. + Sm4 #1

text: ArrayExpress

text: HUVEC

text: human

text: transfected with Sox18-cMyc

characteristic: growth condition

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens

text: Sox18 o.e. + Sm4 #1

characteristic: title


E-MTAB-4511:Sox18 o.e. + Sm4 #2

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: public

text: E-MTAB-4511:Sox18 o.e. + Sm4 #2

text: ArrayExpress

text: HUVEC

text: human

text: transfected with Sox18-cMyc

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens

text: Sox18 o.e. + Sm4 #2


E-MTAB-4511:Sox18 o.e. + Sm4 #3

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: E-MTAB-4511:Sox18 o.e. + Sm4 #3

text: ArrayExpress

text: HUVEC

text: human

text: transfected with Sox18-cMyc

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens

text: Sox18 o.e. + Sm4 #3


E-MTAB-4511:Sox18 o.e. + Sm4 #4

characteristic: ENA-CHECKLIST

text: public

text: E-MTAB-4511:Sox18 o.e. + Sm4 #4

text: ArrayExpress

text: HUVEC

text: human

text: transfected with Sox18-cMyc

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: Homo sapiens

text: Sox18 o.e. + Sm4 #4


characteristic: ENA-FIRST-PUBLIC

text: Brighton and Sussex Medical School

characteristic: INSDC last update

text: public

tag: Namespace:Brighton and Sussex Medical School

text: ArrayExpress

text: fruit fly

text: Protocols: For pcm[14] rescue males the UAS-pcm[WT] construct was first crossed into the pcm[14] stock to generate y[1] pcm[14]/FM7i-GFP; UAS-pcm[WT]/CyO-GFP stock. Virgin females from this stock were then crossed to males of arm-GAL4 driver. For wild-type E1-E3 is clean excision of the P element (Bloomington stock 11456) used to create pcm[14]. For wild-type G1-G3 is arm-Gal4 parent. For wild-type U1-U3 is UAS parent. 60 testes were dissected per biological replicate for wild-type samples. 120 testes were dissected per replicate for pcm[14] rescue sample. RNA was extracted using a Qiagen miRNeasy micro kit (217084) with on-column DNase treatment (79254) Sequencing libraries were created using an Illumina TruSeq RNA Sample Prep Kit v2

text: 2-3 days old males

characteristic: developmental stage

text: wild-type

characteristic: genetic modification

text: w[1118], 50E

text: Drosophila melanogaster

text: Drosophila melanogaster

text: testis

characteristic: organism part

text: Drosophila melanogaster


text: Brighton and Sussex Medical School

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: ArrayExpress

characteristic: broker name

text: fruit fly

text: 2-3 days old males

text: wild-type

text: w[*];; P{w[+mW.hs]=GAL4-arm.S}4a P{w[+mW.hs]=GAL4-arm.S}4b/TM3, Sb[1] Ser[1]

text: Drosophila melanogaster

text: Drosophila melanogaster

text: testis

text: Drosophila melanogaster


text: Brighton and Sussex Medical School

text: public

text: ArrayExpress

text: fruit fly

characteristic: common name

characteristic: description

text: 2-3 days old males

text: pcm null

text: w[1118], pcm[14]/+; UAS-pcm[WT]/+; arm-Gal4/+

characteristic: genotype

text: Drosophila melanogaster

text: Drosophila melanogaster

text: testis

text: Drosophila melanogaster


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Brighton and Sussex Medical School

text: public

text: ArrayExpress

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text: 2-3 days old males

text: wild-type

text: w[*]; UAS-pcm[WT]

text: Drosophila melanogaster

text: Drosophila melanogaster

text: testis

text: Drosophila melanogaster

characteristic: title


text: Klebsiella pneumoniae

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characteristic: ArrayExpress-StrainOrLine

characteristic: ENA-CHECKLIST

text: SC

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text: public

text: Klebsiella pneumoniae

text: Klebsiella pneumoniae

text: Klebsiella pneumoniae

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text: Enterobacter cloacae

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text: SC

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text: public

text: Enterobacter cloacae

text: Enterobacter cloacae

characteristic: organism

text: Enterobacter cloacae


text: public

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tag: Namespace:Microbial Genomics and Biotechnology Center for Biotechnology - CeBiTec Bielefeld University

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text: ArrayExpress

text: Protocols: For stress experiments Mycobacterium smegmatis mc2155 wild type strain was grown in modified Hartmans-de Bont minimal medium (HdB) (finally per liter: EDTA [0.01 g], MgCl2x6H2O [0.1 g], CaCl2x2H2O [1 mg], NaMoO4x2H2O [0.2 mg], CoCl2x6H2O [0.4 mg] , MnCl2x2H2O [1 mg] , ZnSO4x7H2O [2 mg] , FeSO4x7H2O [5 mg] , CuSO4x5H2O [0.2 mg]; complemented with 15 mM (NH4)2SO4, 0.05% Tween80, 27.4 mM glycerol, 50 mM MOPS; 8.90 mM K2HPO4 and 7.08 mM NaH2PO4; pH 7.0) at 37°C and vigorous agitation. 15% sodium hypochlorite (NaOCl) was purchased from Sigma Aldrich. After harvesting control samples cultures were exposed to 1 mM NaOCl at an optical density at 500 nm (OD500) of 0.4 - 0.45 in the early log phase. Briefly, M. smegmatis mc2155 cells of 3 replicate experiments were harvested before and 30 min after exposure to 1 mM NaOCl and disrupted in 3 mM EDTA/ 200 mM NaCl lysis buffer with a Precellys24 Ribolyzer. RNA isolation was performed using phenol-chloroform-isoamylalcohol approach. After precipitation with 3 M sodium acetate and isopropanol, the total RNA was washed with cold ethanol and the pellet was solved in sterile water. Initially RNA quality was checked by Trinean Xpose (Gentbrugge,Belgium) and Agilent RNA Nano 6000 kit on Agilent 2100 Bioanalyzer (Agilent Technologies, Boblingen, Germany). Samples contaminated with DNA were treated with DNase (Qiagen), cleaned as described above and rechecked by Xpose and Agilent Bioanalyzer. Ribo-Zero rRNA Removal Kit (Bacteria) from Illumina (San Diego, CA, USA) was used to remove the ribosomal RNA molecules from the isolated total RNA. Removal of rRNA was checked by Agilent RNA Pico 6000 kit on Agilent 2100 Bioanalyzer (Agilent Technologies, Boblingen, Germany).

text: Mycobacterium smegmatis str. MC2 155

text: Mycobacterium smegmatis str. MC2 155

text: Mycobacterium smegmatis str. MC2 155


text: Microbial Genomics and Biotechnology Center for Biotechnology - CeBiTec Bielefeld University

text: public

text: ArrayExpress

characteristic: broker name

characteristic: description

text: Mycobacterium smegmatis str. MC2 155

text: Mycobacterium smegmatis str. MC2 155

text: Mycobacterium smegmatis str. MC2 155


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: public

text: ArrayExpress

text: Mycobacterium smegmatis str. MC2 155

text: Mycobacterium smegmatis str. MC2 155

text: Mycobacterium smegmatis str. MC2 155

text: 30 min 1mM NaOCl treatment in early log phase

characteristic: stimulus


text: public

tag: Namespace:IBET - INSTITUTO DE BIOLOGIA EXPERIMENTAL E TECNOLOGICA

text: Developing xylem samples from tension wood after 3 & 4 week of gravitropic stimulus. Genotype MB43.

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text: Eucalyptus globulus subsp. globulus

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text: IBET - INSTITUTO DE BIOLOGIA EXPERIMENTAL E TECNOLOGICA

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text: public

text: Developing xylem samples from tension wood after 3 & 4 week of gravitropic stimulus. Genotype GM58.

text: Eucalyptus globulus subsp. globulus

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text: developing xylem


characteristic: ENA-FIRST-PUBLIC

characteristic: INSDC last update

text: public

text: Developing xylem sample from opposite wood after 1 week of gravitropic stimulus. Genotype GB3.

text: Eucalyptus globulus subsp. globulus

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text: public

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text: developing xylem


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text: developing xylem


text: public

text: Developing xylem sample from tension wood after 1 week of gravitropic stimulus. Genotype GB3.

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text: Developing xylem sample from tension wood after 1 week of gravitropic stimulus. Genotype GM58.

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text: Developing xylem sample from tension wood after 1 week of gravitropic stimulus. Genotype MB43.

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text: Developing xylem samples from opposite wood after 3 & 4 week of gravitropic stimulus. Genotype GB3.

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text: developing xylem


text: public

text: Developing xylem samples from opposite wood after 3 & 4 week of gravitropic stimulus. Genotype GM58.

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text: developing xylem


text: public

text: Developing xylem samples from opposite wood after 3 & 4 week of gravitropic stimulus. Genotype MB43.

text: Eucalyptus globulus subsp. globulus

text: Eucalyptus globulus subsp. globulus

text: developing xylem


text: public

text: Developing xylem samples from tension wood after 3 & 4 week of gravitropic stimulus. Genotype GB3.

text: Eucalyptus globulus subsp. globulus

text: Eucalyptus globulus subsp. globulus

text: developing xylem


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