E-MTAB-6076:Sample 1

text: Stazione Zoologica Anton Dohrn

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-6076:Sample 1

tag: Namespace:Stazione Zoologica Anton Dohrn

characteristic: Submitter Id

text: ArrayExpress

text: Protocols: Females of Calanus finmarchicus were picked from plankton samples collected near Tjärnö Island in the North Sea (Sweden; 58°N51’ - 11°E7’). Skeletonema marinoi strain V32 was cultivated in F2 medium (Guillard, 1975). Photoperiod and irradiance were 12L:12D (16L:8D) and ~80 μmol photos·m-2s-1. At time 0, 10 copepods were added to each of ten 2-litre bottles, leaving another 10 bottles as un-grazed controls. Three grazed and ungrazed bottles were harvested at two time points, after 65 and 89 hours from introducing animals into the bottles (T1 and T2, respectively). 1 l was filtered to isolate RNA. Copepods were excluded from these samples by prefiltering through a sieve (64 μm mesh size). For RNA-seq, three controls and three treated samples were collected. S. marinoi cells for RNA extraction were filtered onto RAWP Millipore cellulose membrane filters (Mf-3Millipore RAWP04700, 1.2 µm porosity) and washed with MilliQ water. Filters were put into 2ml Eppendorf tubes filled with Roche TriPure® isolation reagent (Sigma - Aldrich s.r.l.), snap frozen in liquid nitrogen, and stored at -80°C until use. TriPure®-soaked filters were thawed at room temperature and RNA extraction was conducted as described in Basu et al. (Basu et al., 2017). RNA samples were DNAse-treated (TURBO DNAfree™Kit, Ambion by Life Technologies, cat. n. AM1907) to get rid of genomic DNA contamination and purified with Qiagen RNeasy Mini Kit (Qiagen, Hilden, Germany). Samples were stored at -80°C until use. RNA samples were analysed at an Agilent 2100 Bioanalyzer platform (Agilent Technologies5301 Stevens Creek Blvd. Santa Clara, California 95051 USA) to assess integrity, at a NanoDrop2000 Spectrophotometer (Thermo Fisher Scientific Inc., Waltham, Massachusetts, USA) to assess purity, and quantified at a Qubit fluorometer (Thermo Fisher Scientific Inc.). 500 ng RNA from three controls and three copepod-treated samples per time point were used to produce libraries with the Illumina TruSeq protocol.

text: wild type genotype

text: Skeletonema marinoi

text: Skeletonema marinoi

text: Skeletonema marinoi

text: Sample 1


E-MTAB-6076:Sample 2

status: PUBLIC

tag: attribute

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Stazione Zoologica Anton Dohrn

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: E-MTAB-6076:Sample 2

text: ArrayExpress

characteristic: broker name

characteristic: description

text: wild type genotype

characteristic: genotype

text: Skeletonema marinoi

characteristic: organism

text: Skeletonema marinoi

text: Skeletonema marinoi

characteristic: strain

text: Sample 2

characteristic: title


E-MTAB-6076:Sample 3

text: Stazione Zoologica Anton Dohrn

text: public

text: E-MTAB-6076:Sample 3

text: ArrayExpress

text: wild type genotype

text: Skeletonema marinoi

text: Skeletonema marinoi

text: Skeletonema marinoi

text: Sample 3


E-MTAB-6076:Sample 4

text: Stazione Zoologica Anton Dohrn

text: public

text: E-MTAB-6076:Sample 4

text: ArrayExpress

text: wild type genotype

text: Skeletonema marinoi

text: Skeletonema marinoi

text: Skeletonema marinoi

text: Sample 4


E-MTAB-6076:Sample 5

text: Stazione Zoologica Anton Dohrn

text: public

text: E-MTAB-6076:Sample 5

text: ArrayExpress

text: wild type genotype

text: Skeletonema marinoi

text: Skeletonema marinoi

text: Skeletonema marinoi

text: Sample 5


E-MTAB-6076:Sample 6

text: Stazione Zoologica Anton Dohrn

text: public

text: E-MTAB-6076:Sample 6

text: ArrayExpress

text: wild type genotype

text: Skeletonema marinoi

text: Skeletonema marinoi

text: Skeletonema marinoi

text: Sample 6


E-MTAB-6076:Sample 7

text: Stazione Zoologica Anton Dohrn

text: public

text: E-MTAB-6076:Sample 7

text: ArrayExpress

text: wild type genotype

text: Skeletonema marinoi

text: Skeletonema marinoi

text: Skeletonema marinoi

text: Sample 7


E-MTAB-6076:Sample 8

text: Stazione Zoologica Anton Dohrn

text: public

text: E-MTAB-6076:Sample 8

text: ArrayExpress

text: wild type genotype

text: Skeletonema marinoi

text: Skeletonema marinoi

text: Skeletonema marinoi

text: Sample 8


E-MTAB-6076:Sample 9

text: Stazione Zoologica Anton Dohrn

text: public

text: E-MTAB-6076:Sample 9

text: ArrayExpress

text: wild type genotype

text: Skeletonema marinoi

text: Skeletonema marinoi

text: Skeletonema marinoi

text: Sample 9


E-MTAB-6076:Sample 10

text: Stazione Zoologica Anton Dohrn

text: public

text: E-MTAB-6076:Sample 10

text: ArrayExpress

text: wild type genotype

text: Skeletonema marinoi

text: Skeletonema marinoi

text: Skeletonema marinoi

text: Sample 10


E-MTAB-6076:Sample 11

text: Stazione Zoologica Anton Dohrn

text: public

text: E-MTAB-6076:Sample 11

text: ArrayExpress

text: wild type genotype

text: Skeletonema marinoi

text: Skeletonema marinoi

text: Skeletonema marinoi

text: Sample 11


E-MTAB-6076:Sample 12

text: Stazione Zoologica Anton Dohrn

text: public

text: E-MTAB-6076:Sample 12

text: ArrayExpress

text: wild type genotype

text: Skeletonema marinoi

text: Skeletonema marinoi

text: Skeletonema marinoi

text: Sample 12


text: San Diego State University

text: public

tag: Namespace:San Diego State University

text: MGRAST

characteristic: collection date

text: UTC

text: mgs15548 Taxonomy ID:408172

text: 31 M

text: marine habitat

characteristic: environment (biome)

text: marine habitat

characteristic: environment (feature)

text: marine habitat

characteristic: environment (material)

text: water

characteristic: environmental package

text: USA

characteristic: geographic location (country and/or sea)

unit: m

characteristic: geographic location (depth)

unit: DD

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: Christmas (Kiritimati) Atoll

characteristic: geographic location (region and locality)

text: metagenome

characteristic: investigation type

text: marine

text: marine metagenome

text: Northern Line Islands

characteristic: project name

text: filtering

characteristic: samp mat process

text: The water for the metagenomes was collected from below the boundary layer (in crevices and against the benthos) to avoid confounding problems with the water column. The sampling was conducted at the same time of day to help minimize diurnal effects. The water was collected from over ~20 m2 of reef using a modified bilge pump connected to low density polyethylene (LDPE) collapsible bags (19 l; Cole-Parmer, Vernon Hills, IL; Figure S1). 1) A large fraction containing mostly microbes, some small eukaryotes (such as dinoflagellates and protists), and a few VLPs, and 2) a small fraction containing mostly VLPs and some small microbes. To obtain these fractions the seawater was processed through a series of filters. The large eukaryotes were removed by filtering the entire sample through 100 m Nitex, into a barrel lined with a clean, high-density polyethylene bag. The filtrate was then concentrated to ~500 ml on a 100 kDa tangential flow filter (TFF), which captured the unicellular eukaryotes, microbes and VLPs (i.e., the water was removed). During the filtration, pressures were kept below 0.6 bar (10 psi) to ensure that the viruses were not destroyed. The concentrated sample was then passed through 0.45 m Sterivex filters (Millipore, Inc) using a 50 ml syringe. In this step, the large metagenomic fraction consisting of microbial cells was caught on the filter (microbiomes) and the filtrate was the small metagenomic fraction (viromes). All filtrations were performed on the research vessel, and the samples were stored for further processing in the laboratory at SDSU. The Sterivex filters were frozen at −80C. The 0.45 m filtrates (i.e., the virome) were extracted with chloroform to kill any residual cells (10% vol:vol; most viruses are resistant to chloroform) and stored at 4C.

text: 150 litres

text: marine metagenome

characteristic: sequencing method

text: 8.410^51.410^5 microbes*ml−1

text: mgs15548 Taxonomy ID:408172

text: water

characteristic: water environmental package


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: San Diego State University

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: MGRAST

characteristic: broker name

text: UTC

text: mgs14993 Taxonomy ID:408172

characteristic: description

text: 56 M

text: marine habitat

text: marine habitat

text: marine habitat

text: water

text: USA

text: Palmyra Atoll

text: metagenome

text: marine

text: marine metagenome

characteristic: organism

text: Northern Line Islands

text: filtering

text: The water for the metagenomes was collected from below the boundary layer (in crevices and against the benthos) to avoid confounding problems with the water column. The sampling was conducted at the same time of day to help minimize diurnal effects. The water was collected from over ~20 m2 of reef using a modified bilge pump connected to low density polyethylene (LDPE) collapsible bags (19 l; Cole-Parmer, Vernon Hills, IL; Figure S1). 1) A large fraction containing mostly microbes, some small eukaryotes (such as dinoflagellates and protists), and a few VLPs, and 2) a small fraction containing mostly VLPs and some small microbes. To obtain these fractions the seawater was processed through a series of filters. The large eukaryotes were removed by filtering the entire sample through 100 m Nitex, into a barrel lined with a clean, high-density polyethylene bag. The filtrate was then concentrated to ~500 ml on a 100 kDa tangential flow filter (TFF), which captured the unicellular eukaryotes, microbes and VLPs (i.e., the water was removed). During the filtration, pressures were kept below 0.6 bar (10 psi) to ensure that the viruses were not destroyed. The concentrated sample was then passed through 0.45 m Sterivex filters (Millipore, Inc) using a 50 ml syringe. In this step, the large metagenomic fraction consisting of microbial cells was caught on the filter (microbiomes) and the filtrate was the small metagenomic fraction (viromes). All filtrations were performed on the research vessel, and the samples were stored for further processing in the laboratory at SDSU. The Sterivex filters were frozen at −80C. The 0.45 m filtrates (i.e., the virome) were extracted with chloroform to kill any residual cells (10% vol:vol; most viruses are resistant to chloroform) and stored at 4C. The DNA for the microbiomes was isolated from the Sterivex filters by removing the filter membranes and performing DNA extractions using a bead-beating protocol (MoBio, Carlsbad CA).

text: 150 litres

text: marine metagenome

text: 2.01051.7104 microbes ml−1

text: mgs14993 Taxonomy ID:408172

text: water


text: San Diego State University

text: public

text: MGRAST

characteristic: collection date

text: UTC

text: mgs15215 Taxonomy ID:408172

text: 41 M

text: marine habitat

characteristic: environment (biome)

text: marine habitat

characteristic: environment (feature)

text: marine habitat

characteristic: environment (material)

text: water

characteristic: environmental package

text: USA

characteristic: geographic location (country and/or sea)

characteristic: geographic location (depth)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: Kingman Atoll

characteristic: geographic location (region and locality)

text: metagenome

characteristic: investigation type

text: marine

text: marine metagenome

text: Northern Line Islands

characteristic: project name

text: filtering

text: 150 litres

text: marine metagenome

text: 5.110^51.510^5 VLPs ml−1

text: mgs15215 Taxonomy ID:408172

characteristic: title

text: water


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: San Diego State University

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: MGRAST

text: UTC

text: mgs15659 Taxonomy ID:408172

text: 42 M

text: marine habitat

text: marine habitat

text: marine habitat

text: water

text: USA

text: Fanning (Tabuaeran) Atoll

text: metagenome

text: marine

text: marine metagenome

text: Northern Line Islands

text: filtering

characteristic: samp mat process

text: 150 litres

text: marine metagenome

characteristic: sequencing method

text: 2.510^61.210^6 VLPs ml−1

text: mgs15659 Taxonomy ID:408172

text: water

characteristic: water environmental package


text: San Diego State University

text: public

text: MGRAST

characteristic: broker name

characteristic: collection date

text: UTC

text: mgs15104 Taxonomy ID:408172

characteristic: description

text: 56 M

text: marine habitat

characteristic: environment (biome)

text: marine habitat

characteristic: environment (feature)

text: marine habitat

characteristic: environment (material)

text: water

characteristic: environmental package

text: USA

characteristic: geographic location (country and/or sea)

characteristic: geographic location (depth)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: Palmyra Atoll

characteristic: geographic location (region and locality)

text: metagenome

text: marine

text: marine metagenome

characteristic: organism

text: Northern Line Islands

text: filtering

text: The water for the metagenomes was collected from below the boundary layer (in crevices and against the benthos) to avoid confounding problems with the water column. The sampling was conducted at the same time of day to help minimize diurnal effects. The water was collected from over ~20 m2 of reef using a modified bilge pump connected to low density polyethylene (LDPE) collapsible bags (19 l; Cole-Parmer, Vernon Hills, IL; Figure S1). 1) A large fraction containing mostly microbes, some small eukaryotes (such as dinoflagellates and protists), and a few VLPs, and 2) a small fraction containing mostly VLPs and some small microbes. To obtain these fractions the seawater was processed through a series of filters. The large eukaryotes were removed by filtering the entire sample through 100 m Nitex, into a barrel lined with a clean, high-density polyethylene bag. The filtrate was then concentrated to ~500 ml on a 100 kDa tangential flow filter (TFF), which captured the unicellular eukaryotes, microbes and VLPs (i.e., the water was removed). During the filtration, pressures were kept below 0.6 bar (10 psi) to ensure that the viruses were not destroyed. The concentrated sample was then passed through 0.45 m Sterivex filters (Millipore, Inc) using a 50 ml syringe. In this step, the large metagenomic fraction consisting of microbial cells was caught on the filter (microbiomes) and the filtrate was the small metagenomic fraction (viromes). All filtrations were performed on the research vessel, and the samples were stored for further processing in the laboratory at SDSU. The Sterivex filters were frozen at −80C. The 0.45 m filtrates (i.e., the virome) were extracted with chloroform to kill any residual cells (10% vol:vol; most viruses are resistant to chloroform) and stored at 4C. The viruses in the small metagenomic fractions (i.e., 0.45 m filtrate treated with chloroform) were purified using cesium chloride (CsCl) step gradients to remove free DNA and any cellular material [29], [30]. Viral DNA was isolated using CTAB/phenol:chloroform extractions and amplified in six to eight 18-hour Genomiphi reactions. These reactions were pooled and purified using silica columns (Qiagen Inc, Valencia, CA). The DNA was then precipitated with ethanol and re-suspended in water at a concentration of approximately 300 ng l−1.

text: 150 litres

text: marine metagenome

text: 1.010^63.710^5 VLPs ml−1

text: mgs15104 Taxonomy ID:408172

text: water


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: San Diego State University

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: MGRAST

text: UTC

text: mgs15326 Taxonomy ID:408172

text: 41 M

text: marine habitat

text: marine habitat

text: marine habitat

text: water

text: USA

text: Kingman Atoll

text: metagenome

characteristic: investigation type

text: marine

text: marine metagenome

text: Northern Line Islands

characteristic: project name

text: filtering

text: 150 litres

text: marine metagenome

text: 7.210^41.710^4 microbes ml−1

text: mgs15326 Taxonomy ID:408172

characteristic: title

text: water


text: San Diego State University

text: public

text: MGRAST

characteristic: broker name

characteristic: collection date

text: UTC

text: mgs15771 Taxonomy ID:408172

characteristic: description

text: 42 M

text: marine habitat

characteristic: environment (biome)

text: marine habitat

characteristic: environment (feature)

text: marine habitat

characteristic: environment (material)

text: water

characteristic: environmental package

text: USA

characteristic: geographic location (country and/or sea)

characteristic: geographic location (depth)

characteristic: geographic location (latitude)

text: Fanning (Tabuaeran) Atoll

text: metagenome

text: marine

text: marine metagenome

text: Northern Line Islands

text: filtering

characteristic: samp mat process

text: 150 litres

text: marine metagenome

characteristic: sequencing method

text: 4.010^52.310^4 microbes ml−1

text: mgs15771 Taxonomy ID:408172

text: water

characteristic: water environmental package


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: San Diego State University

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: MGRAST

text: UTC

text: mgs15437 Taxonomy ID:408172

text: 31 M

text: marine habitat

text: marine habitat

text: marine habitat

text: water

text: USA

characteristic: geographic location (longitude)

text: Christmas (Kiritimati) Atoll

characteristic: geographic location (region and locality)

text: metagenome

text: marine

text: marine metagenome

characteristic: organism

text: Northern Line Islands

text: filtering

text: 150 litres

text: marine metagenome

text: 4.910^61.110^6 VLPs ml−1

text: mgs15437 Taxonomy ID:408172

text: water


text: Elizabethkingia meningoseptica

characteristic: ArrayExpress-SPECIES

text: SC

text: public

text: Elizabethkingia meningoseptica

characteristic: common name

text: Elizabethkingia meningoseptica

text: Elizabethkingia meningoseptica

characteristic: subject id

characteristic: title


text: Elizabethkingia miricola

characteristic: ENA-CHECKLIST

text: SC

text: public

text: Elizabethkingia miricola

text: Elizabethkingia miricola

text: Elizabethkingia miricola


text: male

characteristic: ArrayExpress-SEX

text: Schistosoma bovis

text: Villar de la Yegua- Salamanca, (Spain)

characteristic: ENA-FIRST-PUBLIC

text: SC

text: public

text: Schistosoma bovis

text: Male

characteristic: gender

text: Schistosoma bovis

text: Schistosoma bovis

text: Schistosoma bovis


text: Dracunculus medinensis

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: SC

characteristic: INSDC center name

text: public

text: Guinea worm

text: Dracunculus medinensis

text: Dracunculus medinensis

text: Dracunculus medinensis


text: ISTANBUL UNIVERSITY

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

tag: Namespace:ISTANBUL UNIVERSITY

text: metagenome

text: metagenome


text: Anopheles gambiae

text: SC

text: public

characteristic: SRA accession

characteristic: Submitter Id

text: African malaria mosquito

text: Anopheles gambiae

text: Anopheles gambiae


text: gut metagenome

text: SC

text: public

text: gut metagenome

text: gut metagenome

characteristic: organism

text: gut metagenome


HDIA

text: JLU

text: public

text: HDIA

text: Hartmannibacter diazotrophicus strain E19T

characteristic: description

text: Hartmannibacter diazotrophicus

text: Hartmannibacter diazotrophicus

characteristic: strain


text: DTU-GE

text: public

text: DTU Bioinformatics

characteristic: broker name

text: Frank Aarestrup

characteristic: collected by

characteristic: collection date

text: No

characteristic: environmental sample

text: Denmark

characteristic: geo loc name

text: Denmark

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: healthy

characteristic: host health state

text: Odobenus rosmarus

characteristic: host scientific name

text: Yes

characteristic: is the sequenced pathogen host associated?

characteristic: isolate

text: Animal

characteristic: isolation source host associated

text: Staphylococcus pseudintermedius

text: Staphylococcus pseudintermedius

type: has member


text: Mus musculus

characteristic: ArrayExpress-SPECIES

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: SC

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: house mouse

characteristic: common name

text: Mus musculus

text: Mus musculus

characteristic: subject id

characteristic: title


text: Vibrio cholerae

text: SC

text: public

text: Vibrio cholerae

text: Vibrio cholerae

characteristic: organism

text: Vibrio cholerae


text: UNIVERSITY OF FLORENCE

text: public

tag: Namespace:UNIVERSITY OF FLORENCE

text: house mouse

text: Nod2+/+ mice at weaning (4 weeks of age

characteristic: description

text: mouse

characteristic: host scientific name

text: Mus musculus

text: Mus musculus

text: fecal microbiota


text: UNIVERSITY OF FLORENCE

text: public

text: house mouse

text: Nod2+/+ mice at weaning (4 weeks of age)

text: mouse

text: Mus musculus

text: Mus musculus

text: fecal microbiota


text: UNIVERSITY OF FLORENCE

text: public

text: house mouse

text: Nod2+/+ mice 8 weeks of age; cohousing

text: mouse

text: Mus musculus

text: Mus musculus

text: fecal microbiota


text: UNIVERSITY OF FLORENCE

text: public

text: house mouse

text: Nod2+/+ mice cohousing; after TNBS induced-colitis

text: mouse

text: Mus musculus

text: Mus musculus

text: fecal microbiota


text: UNIVERSITY OF FLORENCE

text: public

text: house mouse

text: Nod2-/- mice at weaning (4 weeks of age)

text: mouse

text: Mus musculus

text: Mus musculus

text: fecal microbiota


text: UNIVERSITY OF FLORENCE

text: public

text: house mouse

text: Nod2-/- mice 8 weeks of age; cohousing

text: mouse

text: Mus musculus

text: Mus musculus

text: fecal microbiota


text: UNIVERSITY OF FLORENCE

text: public

text: house mouse

text: Nod2-/- mice cohousing; after TNBS induced-colitis

text: mouse

text: Mus musculus

text: Mus musculus

text: fecal microbiota


text: UNIVERSITY OF FLORENCE

text: public

text: house mouse

text: Nod2+/+ mice 8 weeks of age; reared separately

text: mouse

text: Mus musculus

text: Mus musculus

text: fecal microbiota


text: UNIVERSITY OF FLORENCE

text: public

text: house mouse

text: Nod2+/+ mice reared separately; after TNBS induced-colitis

text: mouse

text: Mus musculus

text: Mus musculus

text: fecal microbiota


text: UNIVERSITY OF FLORENCE

text: public

text: house mouse

text: Nod2-/- mice 8 weeks of age; reared separately

text: mouse

text: Mus musculus

text: Mus musculus

text: fecal microbiota


text: UNIVERSITY OF FLORENCE

text: public

text: house mouse

text: Nod2-/- mice reared separately; after TNBS induced-colitis

text: mouse

text: Mus musculus

text: Mus musculus

text: fecal microbiota


text: Doherty Institute

text: public

text: AUS

tag: Namespace:Doherty Institute

characteristic: collection date

text: N. gonorrhoeae transmission between MSM partners study

text: Neisseria

characteristic: genus

text: Australia

characteristic: geographic location (country and/or sea)

text: Homo sapiens

characteristic: host

text: diseased

characteristic: host health state

text: Homo sapiens

text: male

text: Pharyngeal

characteristic: isolation source

text: respiratory tract

text: Neisseria gonorrhoeae

text: Neisseria gonorrhoeae

characteristic: strain

text: Clinical sample

type: AMR curated data - CABBAGE

value: ciprofloxacin

value: agar dilution

value: mg/L

value: susceptible

value: Neisseria gonorrhoeae

value: penicillin

value: ceftriaxone

value: azithromycin

value: spectinomycin


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Doherty Institute

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: AUS

text: Neisseria

text: Australia

text: Homo sapiens

text: diseased

text: Homo sapiens

text: male

text: Urethra

text: urinary tract

text: Neisseria gonorrhoeae

text: Neisseria gonorrhoeae

text: Clinical sample


text: Doherty Institute

text: public

characteristic: INSDC status

text: AUS

characteristic: SRA accession

characteristic: Submitter Id

text: Neisseria

text: Australia

text: Homo sapiens

text: diseased

text: Homo sapiens

text: male

text: Rectal

text: gastrointestinal system

text: Neisseria gonorrhoeae

characteristic: organism

text: Neisseria gonorrhoeae

text: Clinical sample

characteristic: title

value: intermediate

value: resistant


text: Doherty Institute

text: public

text: AUS

characteristic: collection date

characteristic: description

text: Neisseria

characteristic: genus

text: Australia

characteristic: geographic location (country and/or sea)

text: Homo sapiens

text: diseased

text: Homo sapiens

characteristic: host scientific name

text: male

text: Urethra

text: urinary tract

text: Neisseria gonorrhoeae

text: Neisseria gonorrhoeae

text: Clinical sample


characteristic: ENA-CHECKLIST

text: Doherty Institute

text: public

text: AUS

text: Neisseria

text: Australia

text: Homo sapiens

characteristic: host

text: diseased

characteristic: host health state

text: Homo sapiens

text: male

text: Urethra

characteristic: isolation source

text: urinary tract

text: Neisseria gonorrhoeae

text: Neisseria gonorrhoeae

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text: Doherty Institute

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: AUS

characteristic: SRA accession

text: Neisseria

text: Australia

text: Homo sapiens

text: diseased

text: Homo sapiens

text: male

text: Rectal

text: gastrointestinal system

text: Neisseria gonorrhoeae

text: Neisseria gonorrhoeae

text: Clinical sample

characteristic: title


text: Doherty Institute

text: public

text: AUS

characteristic: Submitter Id

characteristic: collection date

characteristic: description

text: Neisseria

characteristic: genus

text: Australia

text: Homo sapiens

text: diseased

text: Homo sapiens

text: male

text: Urethra

characteristic: isolation source

text: urinary tract

text: Neisseria gonorrhoeae

text: Neisseria gonorrhoeae

text: Clinical sample


characteristic: ENA-CHECKLIST

text: Doherty Institute

text: public

text: AUS

text: Neisseria

text: Australia

characteristic: geographic location (country and/or sea)

text: Homo sapiens

characteristic: host

text: diseased

characteristic: host health state

text: Homo sapiens

text: male

text: Pharyngeal

text: respiratory tract

text: Neisseria gonorrhoeae

text: Neisseria gonorrhoeae

characteristic: strain

text: Clinical sample


text: 29247013; 33785063

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Doherty Institute

characteristic: INSDC center name

text: public

text: AUS

text: Neisseria

text: Australia

text: Homo sapiens

text: diseased

text: Homo sapiens

characteristic: host scientific name

text: male

text: Urethra

text: urinary tract

text: Neisseria gonorrhoeae

text: Neisseria gonorrhoeae

text: Clinical sample


text: 29247013; 33785063

text: Doherty Institute

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: AUS

characteristic: SRA accession

text: Neisseria

text: Australia

text: Homo sapiens

text: diseased

text: Homo sapiens

text: male

text: Rectal

text: gastrointestinal system

text: Neisseria gonorrhoeae

characteristic: organism

text: Neisseria gonorrhoeae

text: Clinical sample


text: 29247013; 33785063

text: Doherty Institute

text: public

text: AUS

characteristic: Submitter Id

characteristic: collection date

characteristic: description

text: Neisseria

characteristic: genus

text: Australia

text: Homo sapiens

text: diseased

text: Homo sapiens

text: male

text: Pharyngeal

text: respiratory tract

text: Neisseria gonorrhoeae

text: Neisseria gonorrhoeae

text: Clinical sample

characteristic: title


text: 29247013; 33785063

characteristic: ENA-CHECKLIST

text: Doherty Institute

text: public

text: AUS

text: Neisseria

text: Australia

characteristic: geographic location (country and/or sea)

text: Homo sapiens

characteristic: host

text: diseased

characteristic: host health state

text: Homo sapiens

text: male

text: Urethra

characteristic: isolation source

text: urinary tract

text: Neisseria gonorrhoeae

text: Neisseria gonorrhoeae

text: Clinical sample


text: 29247013; 33785063

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Doherty Institute

characteristic: INSDC center name

text: public

text: AUS

text: Neisseria

text: Australia

text: Homo sapiens

text: diseased

text: Homo sapiens

text: male

text: Pharyngeal

text: respiratory tract

text: Neisseria gonorrhoeae

text: Neisseria gonorrhoeae

characteristic: strain

text: Clinical sample


text: 29247013; 33785063

text: Doherty Institute

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: AUS

characteristic: SRA accession

text: Neisseria

text: Australia

text: Homo sapiens

text: diseased

text: Homo sapiens

characteristic: host scientific name

text: male

text: Rectal

text: gastrointestinal system

text: Neisseria gonorrhoeae

text: Neisseria gonorrhoeae

text: Clinical sample


text: Doherty Institute

text: public

text: AUS

characteristic: Submitter Id

characteristic: collection date

characteristic: description

text: Neisseria

characteristic: genus

text: Australia

text: Homo sapiens

text: diseased

text: Homo sapiens

text: male

text: Urethra

text: urinary tract

text: Neisseria gonorrhoeae

characteristic: organism

text: Neisseria gonorrhoeae

text: Clinical sample


characteristic: ENA-CHECKLIST

text: Doherty Institute

text: public

text: AUS

text: Neisseria

text: Australia

characteristic: geographic location (country and/or sea)

text: Homo sapiens

characteristic: host

text: diseased

characteristic: host health state

text: Homo sapiens

text: male

text: Rectal

text: gastrointestinal system

text: Neisseria gonorrhoeae

text: Neisseria gonorrhoeae

text: Clinical sample

characteristic: title


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Doherty Institute

characteristic: INSDC center name

text: public

text: AUS

text: Neisseria

text: Australia

text: Homo sapiens

text: diseased

text: Homo sapiens

text: male

text: Pharyngeal

characteristic: isolation source

text: respiratory tract

text: Neisseria gonorrhoeae

text: Neisseria gonorrhoeae

text: Clinical sample


text: Doherty Institute

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: AUS

characteristic: SRA accession

text: Neisseria

text: Australia

text: Homo sapiens

text: diseased

text: Homo sapiens

text: male

text: Pharyngeal

text: respiratory tract

text: Neisseria gonorrhoeae

text: Neisseria gonorrhoeae

characteristic: strain

text: Clinical sample


text: Doherty Institute

text: public

text: AUS

characteristic: Submitter Id

characteristic: collection date

characteristic: description

text: Neisseria

characteristic: genus

text: Australia

text: Homo sapiens

text: diseased

text: Homo sapiens

characteristic: host scientific name

text: male

text: Rectal

text: gastrointestinal system

text: Neisseria gonorrhoeae

text: Neisseria gonorrhoeae

text: Clinical sample


characteristic: ENA-CHECKLIST

text: Doherty Institute

text: public

text: AUS

text: Neisseria

text: Australia

characteristic: geographic location (country and/or sea)

text: Homo sapiens

characteristic: host

text: diseased

characteristic: host health state

text: Homo sapiens

text: male

text: Rectal

text: gastrointestinal system

text: Neisseria gonorrhoeae

characteristic: organism

text: Neisseria gonorrhoeae

text: Clinical sample


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Doherty Institute

characteristic: INSDC center name

text: public

text: AUS

text: Neisseria

text: Australia

text: Homo sapiens

text: diseased

text: Homo sapiens

text: male

text: Urethra

text: urinary tract

text: Neisseria gonorrhoeae

text: Neisseria gonorrhoeae

text: Clinical sample

characteristic: title


text: Doherty Institute

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: AUS

characteristic: SRA accession

text: Neisseria

text: Australia

text: Homo sapiens

text: diseased

text: Homo sapiens

text: male

text: Urethra

characteristic: isolation source

text: urinary tract

text: Neisseria gonorrhoeae

text: Neisseria gonorrhoeae

text: Clinical sample


text: Doherty Institute

text: public

text: AUS

characteristic: Submitter Id

characteristic: collection date

characteristic: description

text: Neisseria

characteristic: genus

text: Australia

text: Homo sapiens

text: diseased

text: Homo sapiens

text: male

text: Rectal

text: gastrointestinal system

text: Neisseria gonorrhoeae

text: Neisseria gonorrhoeae

characteristic: strain

text: Clinical sample


characteristic: ENA-CHECKLIST

text: Doherty Institute

text: public

text: AUS

text: Neisseria

text: Australia

characteristic: geographic location (country and/or sea)

text: Homo sapiens

characteristic: host

text: diseased

characteristic: host health state

text: Homo sapiens

characteristic: host scientific name

text: male

text: Rectal

text: gastrointestinal system

text: Neisseria gonorrhoeae

text: Neisseria gonorrhoeae

text: Clinical sample


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Doherty Institute

characteristic: INSDC center name

text: public

text: AUS

text: Neisseria

text: Australia

text: Homo sapiens

text: diseased

text: Homo sapiens

text: male

text: Pharyngeal

text: respiratory tract

text: Neisseria gonorrhoeae

characteristic: organism

text: Neisseria gonorrhoeae

text: Clinical sample


text: Doherty Institute

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: AUS

characteristic: SRA accession

text: Neisseria

text: Australia

text: Homo sapiens

text: diseased

text: Homo sapiens

text: male

text: Rectal

text: gastrointestinal system

text: Neisseria gonorrhoeae

text: Neisseria gonorrhoeae

text: Clinical sample

characteristic: title


text: Doherty Institute

text: public

text: AUS

characteristic: Submitter Id

characteristic: collection date

characteristic: description

text: Neisseria

characteristic: genus

text: Australia

text: Homo sapiens

text: diseased

text: Homo sapiens

text: male

text: Urethra

characteristic: isolation source

text: urinary tract

text: Neisseria gonorrhoeae

text: Neisseria gonorrhoeae

text: Clinical sample


characteristic: ENA-CHECKLIST

text: Doherty Institute

text: public

text: AUS

text: Neisseria

text: Australia

characteristic: geographic location (country and/or sea)

text: Homo sapiens

characteristic: host

text: diseased

characteristic: host health state

text: Homo sapiens

text: male

text: Rectal

text: gastrointestinal system

text: Neisseria gonorrhoeae

text: Neisseria gonorrhoeae

characteristic: strain

text: Clinical sample


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Doherty Institute

characteristic: INSDC center name

text: public

text: AUS

text: Neisseria

text: Australia

text: Homo sapiens

text: diseased

text: Homo sapiens

characteristic: host scientific name

text: male

text: Pharyngeal

text: respiratory tract

text: Neisseria gonorrhoeae

text: Neisseria gonorrhoeae

text: Clinical sample


text: Doherty Institute

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: AUS

characteristic: SRA accession

text: Neisseria

text: Australia

text: Homo sapiens

text: diseased

text: Homo sapiens

text: male

text: Urethra

text: urinary tract

text: Neisseria gonorrhoeae

characteristic: organism

text: Neisseria gonorrhoeae

text: Clinical sample


text: Doherty Institute

text: public

text: AUS

characteristic: Submitter Id

characteristic: collection date

characteristic: description

text: Neisseria

characteristic: genus

text: Australia

text: Homo sapiens

text: diseased

text: Homo sapiens

text: male

text: Urethra

text: urinary tract

text: Neisseria gonorrhoeae

text: Neisseria gonorrhoeae

text: Clinical sample

characteristic: title


characteristic: ENA-CHECKLIST

text: Doherty Institute

text: public

text: AUS

text: Neisseria

text: Australia

characteristic: geographic location (country and/or sea)

text: Homo sapiens

characteristic: host

text: diseased

characteristic: host health state

text: Homo sapiens

text: male

text: Rectal

characteristic: isolation source

text: gastrointestinal system

text: Neisseria gonorrhoeae

text: Neisseria gonorrhoeae

text: Clinical sample


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Doherty Institute

characteristic: INSDC center name

text: public

text: AUS

text: Neisseria

text: Australia

text: Homo sapiens

text: diseased

text: Homo sapiens

text: male

text: Pharyngeal

text: respiratory tract

text: Neisseria gonorrhoeae

text: Neisseria gonorrhoeae

characteristic: strain

text: Clinical sample


text: Doherty Institute

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: AUS

characteristic: SRA accession

text: Neisseria

text: Australia

text: Homo sapiens

text: diseased

text: Homo sapiens

characteristic: host scientific name

text: male

text: Rectal

text: gastrointestinal system

text: Neisseria gonorrhoeae

text: Neisseria gonorrhoeae

text: Clinical sample


text: 29247013; 33785063

text: Doherty Institute

text: public

text: AUS

characteristic: Submitter Id

characteristic: collection date

characteristic: description

text: Neisseria

characteristic: genus

text: Australia

text: Homo sapiens

text: diseased

text: Homo sapiens

text: male

text: Urethra

text: urinary tract

text: Neisseria gonorrhoeae

characteristic: organism

text: Neisseria gonorrhoeae

text: Clinical sample


text: 29247013; 33785063

characteristic: ENA-CHECKLIST

text: Doherty Institute

text: public

text: AUS

text: Neisseria

text: Australia

characteristic: geographic location (country and/or sea)

text: Homo sapiens

characteristic: host

text: diseased

characteristic: host health state

text: Homo sapiens

text: male

text: Rectal

text: gastrointestinal system

text: Neisseria gonorrhoeae

text: Neisseria gonorrhoeae

text: Clinical sample

characteristic: title


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC center name

text: public

tag: Namespace:NSERM UMR1163, Laboratory of Normal and Pathological Homeostasis of the Immune System, Paris, France

text: ArrayExpress

characteristic: broker name

text: B cell

characteristic: cell type

text: human

characteristic: common name

text: Protocols: Original B-lymphobast cells come from peripheral blood mononuclear cells (PBMC). These cells are obtained from blood samples after ficoll separation. PBMC from controls and patients were transduced with the Epstein Barr Virus (EBV) to generate the B-lymphobast cells lines. Cells were expanded and frozen. The B-lymphobast are cultured in medium composed of RPMI, Glutamine, Fetal bovin serum and penicillin-streptomycin. B-lymphoblastoid cell lines transformed with EBV of 3 controls (C1 to C3) and 3 TTC7A deficient patients (P3_E71K, P4_E71K, P*/L478P) were cultured in RPMI medium 1640+Glutamax (Gibco, ref 61870-010) supplemented with 10% (vol/vol) Fetal Bovine Serum (Gibco), sodium pyruvate (1 mM, LifeTechnologies) and penicillin and streptomycin (100U/ml each, LifeTechnologies). Cells with blocked in early G1/S phase with thymidine double blockage (2mM, 18 h first treatment, 9 h release and 15 h second treatment). The antibodies used for ChIP were: H3K27ac (catalogue number: 39685, active motif), H3K27me3 (catalogue number: 39155, active motif) Immunoprecipitated DNA (ChIP) and whole cell extracts DNA (input) were treated with RNaseA and proteinase K then purified by using Qiaquick PCR purification kit (Qiagen, 28106). TruSeq ChIP kit from Illumina was used to perform library preparation according to the manufacturer's recommendations. Briefly, IP and input DNA were first size selected using SPRIselect beads (Agencourt) in order to have fragments between 100 and 500bp after BioAnalyzer profiling. 1 to 10ng of DNA were used in a first step of end-repair followed by the adenylation of 3’-end allowing further ligation of specific Illumina adaptors required for sequencing. These adaptors contain specific indexes (barcodes) different for each sample so that library from different samples can be mixed together before sequencing. After PCR amplification (12-15 cycles), quality assessment of DNA libraries was achieved using BioAnalyzer profiling and Qubit quantification. After equimolar pooling of libraries, the final dilution was accurately quantified using Kapa library quantification kit.

text: wild type genotype

characteristic: genotype

characteristic: individual

text: Homo sapiens

text: Homo sapiens

text: blood

characteristic: organism part

text: normal

characteristic: phenotype

text: Homo sapiens


text: NSERM UMR1163, Laboratory of Normal and Pathological Homeostasis of the Immune System, Paris, France

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: ArrayExpress

text: B cell

text: human

characteristic: description

text: wild type genotype

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: blood

text: normal

text: Homo sapiens


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: public

text: ArrayExpress

text: B cell

text: human

text: homozygous loss of function mutation in TTC7A

text: Homo sapiens

text: Homo sapiens

text: blood

text: immune deficiency and intestinal disorder

text: Homo sapiens

characteristic: title


characteristic: External Id

characteristic: INSDC center name

text: public

tag: Namespace:INSERM UMR1163, Laboratory of Normal and Pathological Homeostasis of the Immune System, Paris, France

text: ArrayExpress

characteristic: broker name

text: B cell

characteristic: cell type

text: human

text: Protocols: Original B-lymphobast cells come from peripheral blood mononuclear cells (PBMC). These cells are obtained from blood samples after ficoll separation. PBMC from controls and patients were transduced with the Epstein Barr Virus (EBV) to generate the B-lymphobast cells lines. Cells were expanded and frozen. The B-lymphobast are cultured in medium composed of RPMI, Glutamine, Fetal bovin serum and penicillin-streptomycin. 2 control B-lymphoblastoid cell lines were established to stably express TTC7A_WT-3*Flag-HA-ires-EGFP. ChIP was performed using two distinct Flag antibodies: IP-1, sigma F1804 with 100*10e6 cells and IP-2, sigma F3165 with 30*10e6 cells. Cells were cultured in RPMI medium 1640+Glutamax (Gibco, ref 61870-010) supplemented with 10% (vol/vol) Fetal Bovine Serum (Gibco), sodium pyruvate (1 mM, LifeTechnologies) and penicillin and streptomycin (100U/ml each, LifeTechnologies). Cells with blocked in early G1/S phase with thymidine double blockage (2mM, 18 h first treatment, 9 h release and 15 h second treatment). Immunoprecipitated DNA (ChIP) and whole cell extracts DNA (input) were treated with RNaseA and proteinase K then purified by using Qiaquick PCR purification kit (Qiagen, 28106). TruSeq ChIP kit from Illumina was used to perform library preparation according to the manufacturer's recommendations. Briefly, IP and input DNA were first size selected using SPRIselect beads (Agencourt) in order to have fragments between 100 and 500bp after BioAnalyzer profiling. 1 to 10ng of DNA were used in a first step of end-repair followed by the adenylation of 3’-end allowing further ligation of specific Illumina adaptors required for sequencing. These adaptors contain specific indexes (barcodes) different for each sample so that library from different samples can be mixed together before sequencing. After PCR amplification (12-15 cycles), quality assessment of DNA libraries was achieved using BioAnalyzer profiling and Qubit quantification. After equimolar pooling of libraries, the final dilution was accurately quantified using Kapa library quantification kit.

text: normal

characteristic: disease

text: wild type genotype

text: Homo sapiens

text: Homo sapiens

text: blood

text: Homo sapiens

text: input


text: INSERM UMR1163, Laboratory of Normal and Pathological Homeostasis of the Immune System, Paris, France

text: public

text: ArrayExpress

text: B cell

text: human

characteristic: common name

text: normal

characteristic: genotype

text: Homo sapiens

text: Homo sapiens

text: blood

characteristic: organism part

text: Homo sapiens


text: ESTONIAN BIOCENTRE, ESTONIA

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

tag: Namespace:ESTONIAN BIOCENTRE, ESTONIA

text: human

text: Homo sapiens

text: Homo sapiens

text: human Y chromosome


text: Not supplied

characteristic: ArrayExpress-PHENOTYPE

text: unidentified influenza virus

characteristic: ArrayExpress-SPECIES

text: SC

text: public

characteristic: SRA accession

characteristic: Submitter Id

text: unidentified influenza virus

text: unidentified influenza virus

text: Not supplied

characteristic: phenotype

text: unidentified influenza virus

characteristic: subject id


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: public

tag: Namespace:Cell Signal Unit, Okinawa Institute of Science and Technology Graduate University

unit: week

characteristic: age

text: ArrayExpress

text: house mouse

text: Protocols: Mice were maintained on a 12 hr light / dark cycle in a temperature-controlled (22ºC) barrier facility with free access to water and a normal diet (NCD, CA-1, CLEA Japan, Inc.). Control (Cnot1fl/fl) and Cnot1 LKO mice placed on tamoxifen-containing food at 6 weeks of age for 2 weeks. Lysate from liver was subjected to ChIP assay with Histone H3 (tri methyl K4) (H3K4me3) antibody (ab8580; abcam) using SimpleChIP Enzyatic Chromatin IP Kit (#9003; Cell Signaling Technology) with modification. Briefly, after micrococcal nuclease treatment, cross-linked chromatin was incubated with anti-H3K4me3 antibody at 4ºC for 24 hr. The immune complex was washed, and DNA was eluted and de-cross-linked. Libraries for DNA sequence were prepared from DNA isolated by ChIP assays with a KAPA Hyper Prep Kit (Illumina), according to the manufacturer’s protocol.

characteristic: description

text: Cnot1 flox/flox

text: Mus musculus

characteristic: organism

text: Mus musculus

text: liver

text: wild type phenotype

text: Mus musculus

text: male

characteristic: sex

characteristic: strain

characteristic: title


text: Cell Signal Unit, Okinawa Institute of Science and Technology Graduate University

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: ArrayExpress

characteristic: broker name

text: house mouse

characteristic: common name

text: Cnot1 flox/flox

characteristic: genotype

text: Mus musculus

text: Mus musculus

text: liver

characteristic: organism part

text: wild type phenotype

text: Mus musculus

text: male


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: public

characteristic: SRA accession

characteristic: Submitter Id

text: ArrayExpress

text: house mouse

text: Alb-Cre-ERT2 / Cnot1 flox/flox

text: Mus musculus

text: Mus musculus

text: liver

text: liver-specific Cnot1 knockout

characteristic: phenotype

text: Mus musculus

text: male


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: public

characteristic: age

text: ArrayExpress

text: house mouse

text: Protocols: Mice were maintained on a 12 hr light / dark cycle in a temperature-controlled (22ºC) barrier facility with free access to water and a normal diet (NCD, CA-1, CLEA Japan, Inc.). For comprehensive mRNA half-life profiling, we injected control (Cnot1 fl/fl) and Cnot1 LKO mice, which were placed on a tamoxifen-containing diet at 6 weeks of age for 2 weeks, intraperitoneally with 2 mg actinomycin D per g body weight for 4 and 8 hr, and then liver samples were collected. Total RNA was isolated from liver using Isogen II (Nippongene), according to the manufacturer’s protocol 1 µg of total RNA was used for RNA-seq library preparation with TruSeq Stranded mRNA LT Sample Prep Kit (Illumina), according to the manufacturer’s protocol.

characteristic: description

text: normal

characteristic: disease

text: Mus musculus

characteristic: organism

text: Mus musculus

text: liver

text: wild type phenotype

text: Mus musculus

text: male


characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: ArrayExpress

text: house mouse

text: normal

text: Cnot1 flox/flox

text: Mus musculus

text: Mus musculus

text: liver

text: wild type phenotype

text: Mus musculus

text: male

characteristic: sex

characteristic: strain

characteristic: title


characteristic: ENA-CHECKLIST

text: public

characteristic: INSDC status

text: E-MTAB-5901:Cnot1_control_liver_ActD_4h_1

text: ArrayExpress

characteristic: broker name

text: house mouse

characteristic: common name

text: normal

text: Cnot1 flox/flox

characteristic: genotype

text: Mus musculus

text: Mus musculus

text: liver

characteristic: organism part

text: wild type phenotype

text: Mus musculus

text: male


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: public

characteristic: SRA accession

text: E-MTAB-5901:Cnot1_control_liver_ActD_4h_2

characteristic: Submitter Id

text: ArrayExpress

text: house mouse

text: normal

text: Cnot1 flox/flox

text: Mus musculus

text: Mus musculus

text: liver

text: wild type phenotype

characteristic: phenotype

text: Mus musculus

text: male


characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: E-MTAB-5901:Cnot1_control_liver_ActD_4h_3

characteristic: age

text: ArrayExpress

text: house mouse

characteristic: description

text: normal

characteristic: disease

text: Cnot1 flox/flox

text: Mus musculus

characteristic: organism

text: Mus musculus

text: liver

text: wild type phenotype

text: Mus musculus

text: male


characteristic: ENA-CHECKLIST

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: E-MTAB-5901:Cnot1_control_liver_ActD_8h_2

text: ArrayExpress

text: house mouse

text: normal

text: Cnot1 flox/flox

text: Mus musculus

text: Mus musculus

text: liver

text: wild type phenotype

text: Mus musculus

text: male

characteristic: sex

characteristic: strain

characteristic: title


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: public

text: E-MTAB-5901:Cnot1_control_liver_ActD_8h_3

text: ArrayExpress

characteristic: broker name

text: house mouse

characteristic: common name

text: normal

text: Cnot1 flox/flox

characteristic: genotype

text: Mus musculus

text: Mus musculus

text: liver

characteristic: organism part

text: wild type phenotype

text: Mus musculus

text: male


characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC first public

text: public

characteristic: SRA accession

text: E-MTAB-5901:Cnot1_control_liver_ActD_8h_4

characteristic: Submitter Id

text: ArrayExpress

text: house mouse

text: normal

text: Cnot1 flox/flox

text: Mus musculus

text: Mus musculus

text: liver

text: wild type phenotype

characteristic: phenotype

text: Mus musculus

text: male


characteristic: ENA-CHECKLIST

characteristic: INSDC last update

text: public

characteristic: age

text: ArrayExpress

text: house mouse

characteristic: description

text: hepatitis

characteristic: disease

text: Alb-Cre-ERT2 / Cnot1 flox/flox

text: Mus musculus

characteristic: organism

text: Mus musculus

text: liver

text: liver-specific Cnot1 knockout

text: Mus musculus

text: male


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: Wallenberg laboratory

text: public

characteristic: INSDC status

tag: Namespace:Wallenberg laboratory

text: house mouse

text: microbial metatranscriptomics (10 human strains) from SIM mice-SW male-HFD

text: Mus musculus

text: Mus musculus

text: SIM

characteristic: title


text: Wallenberg laboratory

text: public

text: house mouse

characteristic: common name

text: microbial metatranscriptomics (10 human strains) from SIM mice-SW male-ZFD

text: Mus musculus

text: Mus musculus

text: SIM


characteristic: External Id

text: Wallenberg laboratory

text: public

text: house mouse

text: microbial metatranscriptomics (10 human strains) from SIM mice-SW male-CHO

text: Mus musculus

text: Mus musculus

text: SIM


text: Friedrich-Loeffler-Institute

characteristic: INSDC center name

text: public

text: Institute of Molecular Virology and Cell Biology, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Greifswald - Insel Riems, Germany

characteristic: collecting institution

characteristic: collection date

text: Thomas Mueller

characteristic: collector name

text: Defining objective clusters for rabies virus sequences using affinity propagation clustering

text: Sudan

characteristic: geographic location (country and/or sea)

text: dog

characteristic: host common name

text: dead

characteristic: host disease outcome

text: diseased

characteristic: host health state

text: Canis lupus familiaris

characteristic: host scientific name

text: not collected

characteristic: host sex

characteristic: host subject id

characteristic: isolate

text: brain

characteristic: isolation source host associated

text: Rabies lyssavirus

text: Rabies lyssavirus

text: Rabies lyssavirus strain 13177


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: Friedrich-Loeffler-Institute

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: Thomas Mueller

characteristic: description

text: Mexico

text: dog

text: dead

text: diseased

text: Canis lupus familiaris

text: not collected

text: brain

text: Rabies lyssavirus

characteristic: organism

text: Rabies lyssavirus

text: Rabies lyssavirus strain 13212


characteristic: External Id

text: Friedrich-Loeffler-Institute

characteristic: INSDC center name

text: public

characteristic: collecting institution

characteristic: collection date

text: Thomas Mueller

characteristic: collector name

text: Chile

characteristic: geographic location (country and/or sea)

text: human

characteristic: host common name

text: dead

characteristic: host disease outcome

text: diseased

text: Homo sapiens

text: not collected

text: brain

text: Rabies lyssavirus

text: Rabies lyssavirus

text: Rabies lyssavirus strain 13249

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: Friedrich-Loeffler-Institute

text: public

text: Thomas Mueller

text: Pakistan

text: dog

text: dead

text: diseased

characteristic: host health state

text: Canis lupus familiaris

characteristic: host scientific name

text: not collected

characteristic: host sex

characteristic: host subject id

characteristic: isolate

text: brain

characteristic: isolation source host associated

text: Rabies lyssavirus

text: Rabies lyssavirus

text: Rabies lyssavirus strain 13086


characteristic: External Id

text: Friedrich-Loeffler-Institute

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: Thomas Mueller

characteristic: description

text: Afghanistan

text: dog

text: dead

text: diseased

text: Canis lupus familiaris

text: not collected

text: brain

text: Rabies lyssavirus

characteristic: organism

text: Rabies lyssavirus

text: Rabies lyssavirus strain 20282


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: Friedrich-Loeffler-Institute

text: public

characteristic: collecting institution

characteristic: collection date

text: Thomas Mueller

characteristic: collector name

text: Algeria

characteristic: geographic location (country and/or sea)

text: dog

characteristic: host common name

text: dead

characteristic: host disease outcome

text: diseased

text: Canis lupus familiaris

text: not collected

text: brain

text: Rabies lyssavirus

text: Rabies lyssavirus

text: Rabies lyssavirus strain 13125

characteristic: title


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Friedrich-Loeffler-Institute

characteristic: INSDC center name

text: public

text: Thomas Mueller

text: Saudi Arabia

text: fox

text: dead

text: diseased

characteristic: host health state

text: Vulpes vulpes

characteristic: host scientific name

text: not collected

characteristic: host sex

characteristic: host subject id

characteristic: isolate

text: brain

characteristic: isolation source host associated

text: Rabies lyssavirus

text: Rabies lyssavirus

text: Rabies lyssavirus strain 13043


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: Friedrich-Loeffler-Institute

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: Thomas Mueller

characteristic: description

text: Iran

text: fox

text: dead

text: diseased

text: Vulpes vulpes

text: not collected

text: brain

text: Rabies lyssavirus

characteristic: organism

text: Rabies lyssavirus

text: Rabies lyssavirus strain 13162


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Friedrich-Loeffler-Institute

text: public

characteristic: collecting institution

characteristic: collection date

text: Thomas Mueller

characteristic: collector name

text: Indonesia

characteristic: geographic location (country and/or sea)

text: dog

characteristic: host common name

text: dead

characteristic: host disease outcome

text: diseased

text: Canis lupus familiaris

text: not collected

text: brain

text: Rabies lyssavirus

text: Rabies lyssavirus

text: Rabies lyssavirus strain 13102

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: Friedrich-Loeffler-Institute

characteristic: INSDC center name

text: public

text: Thomas Mueller

text: India

text: dog

text: dead

text: diseased

characteristic: host health state

text: Canis lupus familiaris

characteristic: host scientific name

text: not collected

characteristic: host sex

characteristic: host subject id

characteristic: isolate

text: brain

characteristic: isolation source host associated

text: Rabies lyssavirus

text: Rabies lyssavirus

text: Rabies lyssavirus strain 13182


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Friedrich-Loeffler-Institute

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: Thomas Mueller

characteristic: description

text: Tanzania

text: fox

text: dead

text: diseased

text: Vulpes vulpes

text: not collected

text: brain

text: Rabies lyssavirus

characteristic: organism

text: Rabies lyssavirus

text: Rabies lyssavirus strain 20520


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: Friedrich-Loeffler-Institute

text: public

characteristic: collecting institution

characteristic: collection date

text: Thomas Mueller

characteristic: collector name

text: Algeria

characteristic: geographic location (country and/or sea)

text: dog

characteristic: host common name

text: dead

characteristic: host disease outcome

text: diseased

text: Canis lupus familiaris

text: not collected

text: brain

text: Rabies lyssavirus

text: Rabies lyssavirus

text: Rabies lyssavirus strain 13123

characteristic: title


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Friedrich-Loeffler-Institute

characteristic: INSDC center name

text: public

text: Thomas Mueller

text: Algeria

text: dog

text: dead

text: diseased

characteristic: host health state

text: Canis lupus familiaris

characteristic: host scientific name

text: not collected

characteristic: host sex

characteristic: host subject id

characteristic: isolate

text: brain

characteristic: isolation source host associated

text: Rabies lyssavirus

text: Rabies lyssavirus

text: Rabies lyssavirus strain 13122


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: Friedrich-Loeffler-Institute

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: Thomas Mueller

characteristic: description

text: Estonia

text: fox

text: dead

text: diseased

text: Vulpes vulpes

text: not collected

text: brain

text: Rabies lyssavirus

characteristic: organism

text: Rabies lyssavirus

text: Rabies lyssavirus strain 12951


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Friedrich-Loeffler-Institute

text: public

characteristic: collecting institution

characteristic: collection date

text: Thomas Mueller

characteristic: collector name

text: Nigeria

characteristic: geographic location (country and/or sea)

text: cat

characteristic: host common name

text: dead

characteristic: host disease outcome

text: diseased

text: Felis catus

text: not collected

text: brain

text: Rabies lyssavirus

text: Rabies lyssavirus

text: Rabies lyssavirus strain 13135

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: Friedrich-Loeffler-Institute

characteristic: INSDC center name

text: public

text: Thomas Mueller

text: Chile

text: human

text: dead

text: diseased

characteristic: host health state

text: Homo sapiens

characteristic: host scientific name

text: not collected

characteristic: host sex

characteristic: host subject id

characteristic: isolate

text: brain

characteristic: isolation source host associated

text: Rabies lyssavirus

text: Rabies lyssavirus

text: Rabies lyssavirus strain 13251


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Friedrich-Loeffler-Institute

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: Thomas Mueller

characteristic: description

text: Poland

text: fox

text: dead

text: diseased

text: Vulpes vulpes

text: not collected

text: brain

text: Rabies lyssavirus

characteristic: organism

text: Rabies lyssavirus

text: Rabies lyssavirus strain 12929


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: Friedrich-Loeffler-Institute

text: public

characteristic: collecting institution

characteristic: collection date

text: Thomas Mueller

characteristic: collector name

text: Kenya

characteristic: geographic location (country and/or sea)

text: fox

characteristic: host common name

text: dead

characteristic: host disease outcome

text: diseased

text: Vulpes vulpes

text: not collected

text: brain

text: Rabies lyssavirus

text: Rabies lyssavirus

text: Rabies lyssavirus strain 13465

characteristic: title


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Friedrich-Loeffler-Institute

characteristic: INSDC center name

text: public

text: Thomas Mueller

text: Kenya

text: dog

text: dead

text: diseased

characteristic: host health state

text: Canis lupus familiaris

characteristic: host scientific name

text: not collected

characteristic: host sex

characteristic: host subject id

characteristic: isolate

text: brain

characteristic: isolation source host associated

text: Rabies lyssavirus

text: Rabies lyssavirus

text: Rabies lyssavirus strain 13471


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: Friedrich-Loeffler-Institute

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: Thomas Mueller

characteristic: description

text: Nigeria

text: dog

text: dead

text: diseased

text: Canis lupus familiaris

text: not collected

text: brain

text: Rabies lyssavirus

characteristic: organism

text: Rabies lyssavirus

text: Rabies lyssavirus strain 13138


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Friedrich-Loeffler-Institute

text: public

characteristic: collecting institution

characteristic: collection date

text: Thomas Mueller

characteristic: collector name

text: Thailand

characteristic: geographic location (country and/or sea)

text: not provided

characteristic: host common name

text: not provided

text: not provided

text: not collected

text: not provided

text: Rabies lyssavirus

text: Rabies lyssavirus

text: Rabies lyssavirus strain 34873

characteristic: title


characteristic: ENA-CHECKLIST

text: Friedrich-Loeffler-Institute

characteristic: INSDC center name

text: public

text: Thomas Mueller

text: Germany

text: fox

text: dead

characteristic: host disease outcome

text: diseased

characteristic: host health state

text: Vulpes vulpes

characteristic: host scientific name

text: not collected

characteristic: host sex

characteristic: host subject id

characteristic: isolate

text: brain

characteristic: isolation source host associated

text: Rabies lyssavirus

text: Rabies lyssavirus

text: Rabies lyssavirus strain 13284


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: Friedrich-Loeffler-Institute

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: Thomas Mueller

characteristic: description

text: Saudi Arabia

text: fox

text: dead

text: diseased

text: Vulpes vulpes

text: not collected

text: brain

text: Rabies lyssavirus

characteristic: organism

text: Rabies lyssavirus

text: Rabies lyssavirus strain 13044


characteristic: ENA-CHECKLIST

characteristic: External Id

text: Friedrich-Loeffler-Institute

characteristic: INSDC center name

text: public

characteristic: collecting institution

characteristic: collection date

text: Thomas Mueller

characteristic: collector name

text: Ethiopia

characteristic: geographic location (country and/or sea)

text: dog

characteristic: host common name

text: dead

text: diseased

text: Canis lupus familiaris

text: not collected

text: brain

text: Rabies lyssavirus

text: Rabies lyssavirus

text: Rabies lyssavirus strain 13473

characteristic: title


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: Friedrich-Loeffler-Institute

text: public

text: Thomas Mueller

text: Norway

text: fox

text: dead

characteristic: host disease outcome

text: diseased

characteristic: host health state

text: Vulpes vulpes

characteristic: host scientific name

text: not collected

characteristic: host sex

characteristic: host subject id

characteristic: isolate

text: brain

characteristic: isolation source host associated

text: Rabies lyssavirus

text: Rabies lyssavirus

text: Rabies lyssavirus strain 13020


characteristic: ENA-CHECKLIST

characteristic: External Id

text: Friedrich-Loeffler-Institute

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: Thomas Mueller

characteristic: description

text: Finland

text: fox

text: dead

text: diseased

text: Vulpes vulpes

text: not collected

text: brain

text: Rabies lyssavirus

characteristic: organism

text: Rabies lyssavirus

text: Rabies lyssavirus strain 12989


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: UMCG

characteristic: INSDC center name

text: public

text: human

characteristic: common name

text: TRUE

characteristic: germline

text: Homo sapiens

text: Homo sapiens

text: Blood

characteristic: tissue type

text: Patient ALK_14 Normal

characteristic: title


text: UMCG

text: public

text: human

text: FALSE

text: Homo sapiens

text: Homo sapiens

text: Lung adenocarcinoma

text: Patient ALK_14 Tumor Resistant


text: UMCG

text: public

text: human

text: TRUE

text: Homo sapiens

text: Homo sapiens

text: Blood

text: Patient ALK_16 Normal


text: UMCG

text: public

text: human

text: FALSE

text: Homo sapiens

text: Homo sapiens

text: Lung adenocarcinoma

text: Patient ALK_16 Tumor Primary


text: UMCG

text: public

text: human

text: FALSE

text: Homo sapiens

text: Homo sapiens

text: Lung adenocarcinoma

text: Patient ALK_16 Tumor Resistant


text: UMCG

text: public

text: human

text: TRUE

text: Homo sapiens

text: Homo sapiens

text: Blood

text: Patient ALK_4 Normal


text: UMCG

text: public

text: human

text: FALSE

text: Homo sapiens

text: Homo sapiens

text: Lung adenocarcinoma

text: Patient ALK_4 Tumor Primary


text: UMCG

text: public

text: human

text: FALSE

text: Homo sapiens

text: Homo sapiens

text: Lung adenocarcinoma

text: Patient ALK_4 Tumor Resistant


text: UMCG

text: public

text: human

text: TRUE

text: Homo sapiens

text: Homo sapiens

text: Blood

text: Patient ALK_6 Normal


text: UMCG

text: public

text: human

text: FALSE

text: Homo sapiens

text: Homo sapiens

text: Lung adenocarcinoma

text: Patient ALK_6 Tumor Primary


text: UMCG

text: public

text: human

text: FALSE

text: Homo sapiens

text: Homo sapiens

text: Lung adenocarcinoma

text: Patient ALK_6 Tumor Resistant


text: UMCG

text: public

text: human

text: TRUE

text: Homo sapiens

text: Homo sapiens

text: Blood

text: Patient ALK_8 Normal


text: UMCG

text: public

text: human

text: FALSE

text: Homo sapiens

text: Homo sapiens

text: Lung adenocarcinoma

text: Patient ALK_8 Tumor Resistant


text: EMBL

text: public

characteristic: collection date

text: human stool

characteristic: environment (biome)

text: human stool

characteristic: environment (feature)

text: human stool

characteristic: environment (material)

text: Germany

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: human-gut

characteristic: human gut environmental package

text: metagenome

characteristic: investigation type

text: gut metagenome

text: SALT

characteristic: project name

text: gut metagenome

text: Illumina

characteristic: sequencing method

text: HSD intervention pilot study sample.