characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: Department of New Biology, DGIST

text: public

text: ArrayExpress

text: house mouse

text: 2-cell embryo

text: Stella maternal / zygotic knockout

text: Mus musculus

text: Mus musculus

text: whole organism

text: Mus musculus

characteristic: strain


status: PUBLIC

tag: attribute

characteristic: External Id

text: Department of New Biology, DGIST

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

tag: Namespace:Department of New Biology, DGIST

characteristic: Submitter Id

text: ArrayExpress

characteristic: broker name

text: house mouse

characteristic: common name

text: Protocols: Ovulated oocytes were collected from female mice crossed with vasectomised male at 9am, E0.5, where mating is assumed have occurred at E0.0. 1-cell and 2-cell embryos were collected at 4pm on E0.5 and 9am-3pm on E1.5 respectively. All oocytes and embryos were morphologically assessed to ensure only viable samples are collected. Oocytes were incubated with 0.3 mg/ml hyaluronidase (Sigma, St. Louis, MO) to remove the cumulus cells. Zona pellucida was removed from oocytes and embryos prior to lysis. RNA were extracted from single oocytes, 1-cell embryos or whole 2-cell embryos; and cDNA were amplified as described previously with modifications (Tang et al., 2010). Between 1:10,000 - 1:60,000 dilution of ERCC RNA Spike-In mix (ThermoFisher Scientific, Hemel Hempstead, UK) was added to lysis buffer to estimate efficiency of amplification. Tang, F., Barbacioru, C., Nordman, E., Li, B., Xu, N., Bashkirov, V.I., Lao, K., and Surani, M.A. (2010). RNA-Seq analysis to capture the transcriptome landscape of a single cell. Nat Protoc 5, 516-535. For RNA-seq, cDNA were fragmented to ~ 200bp with Focused-ultrasonicator (Covaris, Woburn, MA) and adaptor ligated libraries were generated using NEBNext® UltraTM DNA library Prep Kit for illumina® (New England Labs, Ipswich, MA).

characteristic: description

text: oocyte

characteristic: developmental stage

text: Stella knockout

characteristic: genotype

text: Mus musculus

characteristic: organism

text: Mus musculus

text: germ cell

characteristic: organism part

text: Mus musculus

characteristic: title

type: has member


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: Department of New Biology, DGIST

text: public

text: ArrayExpress

text: house mouse

text: 1-cell embryo

text: wild type genotype

text: Mus musculus

text: Mus musculus

text: whole organism

text: Mus musculus


characteristic: External Id

text: Department of New Biology, DGIST

characteristic: INSDC center name

text: public

text: ArrayExpress

text: house mouse

text: 2-cell embryo

text: wild type genotype

text: Mus musculus

text: Mus musculus

text: whole organism

text: Mus musculus

characteristic: strain


text: Department of New Biology, DGIST

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: ArrayExpress

text: house mouse

text: oocyte

text: wild type genotype

text: Mus musculus

text: Mus musculus

text: germ cell

text: Mus musculus


text: Klebsiella pneumoniae

characteristic: ArrayExpress-Species

characteristic: ArrayExpress-StrainOrLine

text: SC

text: public

characteristic: SRA accession

characteristic: Submitter Id

text: Klebsiella pneumoniae

text: Klebsiella pneumoniae

text: Klebsiella pneumoniae


text: 29553330; 30687793; 32375989; 34662348

text: PUBLIC HEALTH ENGLAND

text: public

text: GBR

tag: Namespace:PUBLIC HEALTH ENGLAND

characteristic: broker name

characteristic: description

text: Neisseria

characteristic: genus

characteristic: isolate

text: Neisseria meningitidis

text: Neisseria meningitidis

type: AMR curated data - CABBAGE

value: chloramphenicol

value: susceptible

value: Neisseria meningitidis

value: cefotaxime

value: penicillin

value: rifampin

value: ciprofloxacin


text: 29553330; 30687793; 32375989

characteristic: ENA-CHECKLIST

text: PUBLIC HEALTH ENGLAND

text: public

text: GBR

text: Neisseria

text: Neisseria meningitidis

characteristic: organism

text: Neisseria meningitidis

characteristic: title


text: 29553330; 30687793; 32375989; 34662348

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: PUBLIC HEALTH ENGLAND

text: public

text: GBR

text: Neisseria

text: Neisseria meningitidis

text: Neisseria meningitidis


text: 29553330; 30687793; 32375989

text: PUBLIC HEALTH ENGLAND

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: GBR

text: Neisseria

text: Neisseria meningitidis

text: Neisseria meningitidis


text: 29553330; 30687793; 32375989; 34662348

text: PUBLIC HEALTH ENGLAND

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: GBR

text: Neisseria

text: Neisseria meningitidis

text: Neisseria meningitidis


text: PUBLIC HEALTH ENGLAND

text: public

text: Neisseria meningitidis

text: Neisseria meningitidis


text: PUBLIC HEALTH ENGLAND

text: public

text: Neisseria cinerea

text: Neisseria cinerea


text: EBI

text: public

text: ENA

text: SL21 FAP RJ Passage B8S2 vaccine culture

text: Mycobacterium bovis BCG str. Moreau RDJ

text: Mycobacterium bovis BCG str. Moreau RDJ

text: Moreau RDJ

characteristic: strain

text: BioSample for Mycobacterium bovis BCG str. Moreau RDJ genome


Oleispira antarctica RB-8 genome

text: EBI

text: public

characteristic: SRA accession

text: Oleispira antarctica RB-8 genome

text: ENA

text: Oleispira antarctica RB-8

text: Oleispira antarctica RB-8

text: BioSample for Oleispira antarctica RB-8 genome


Vibrio nigripulchritudo SFn1 genome

text: EBI

text: public

text: Vibrio nigripulchritudo SFn1 genome

characteristic: Submitter Id

text: ENA

text: Vibrio nigripulchritudo

text: Vibrio nigripulchritudo

text: BioSample for Vibrio nigripulchritudo SFn1 genome


text: EBI

text: public

text: ENA

characteristic: broker name

text: Candidatus Phytoplasma solani

text: Candidatus Phytoplasma solani

text: BioSample for Candidatus Phytoplasma solani 284/09 genome


text: EBI

text: public

text: ENA

text: Candidatus Phytoplasma solani

text: Candidatus Phytoplasma solani

text: BioSample for Candidatus Phytoplasma solani 231/09 genome


Acholeplasma palmae J233 genome

text: EBI

text: public

text: Acholeplasma palmae J233 genome

text: ENA

text: Acholeplasma palmae

text: Acholeplasma palmae

text: BioSample for Acholeplasma palmae J233 genome


Acholeplasma brassicae O502 genome

text: EBI

text: public

text: Acholeplasma brassicae O502 genome

text: ENA

text: Acholeplasma brassicae

text: Acholeplasma brassicae

text: BioSample for Acholeplasma brassicae O502 genome


Chlamydia trachomatis E/C599 genome

text: EBI

text: public

text: Chlamydia trachomatis E/C599 genome

text: ENA

text: Chlamydia trachomatis E/C599

text: Chlamydia trachomatis E/C599

text: BioSample for Chlamydia trachomatis E/C599 genome


text: EBI

text: public

text: ENA

text: Chlamydia trachomatis F/SWFPminus

text: Chlamydia trachomatis F/SWFPminus

text: F/SWFPminus

text: BioSample for Chlamydia trachomatis F/SWFPminus genome


text: EBI

text: public

text: ENA

text: Felis catus

characteristic: host

text: infected host blood

characteristic: isolation source

text: Birmingham 1

text: BioSample for Candidatus Mycoplasma haemominutum 'Birmingham 1' genome


Taylorella equigenitalis 14/56 genome

text: EBI

text: public

text: Taylorella equigenitalis 14/56 genome

text: ENA

characteristic: collection date

text: United Arab Emirates

characteristic: country

text: Equus caballus

text: stallion, pre-export checks

text: Taylorella equigenitalis 14/56

text: Taylorella equigenitalis 14/56

text: BioSample for Taylorella equigenitalis 14/56 genome


Taylorella asinigenitalis 14/45 genome

characteristic: ENA-CHECKLIST

text: EBI

text: public

text: Taylorella asinigenitalis 14/45 genome

text: ENA

text: Sweden

text: Equus caballus

text: 3 year old Ardennes stallion, pre-breeding tests

text: Taylorella asinigenitalis 14/45

characteristic: organism

text: Taylorella asinigenitalis 14/45

text: BioSample for Taylorella asinigenitalis 14/45 genome


characteristic: ENA-FIRST-PUBLIC

text: EBI

text: public

text: ENA

text: Homo sapiens

text: host faecal sample

characteristic: isolate

characteristic: serotype

text: BioSample for Yersinia enterocolitica (type O:5) str. YE53/03 genome

characteristic: title


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: EBI

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: ENA

text: Pseudomonas pseudoalcaligenes CECT 5344

text: Pseudomonas pseudoalcaligenes CECT 5344

text: BioSample for Pseudomonas pseudoalcaligenes CECT 5344 genome


Rickettsia monacensis IrR/Munich genome

text: EBI

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: Rickettsia monacensis IrR/Munich genome

text: ENA

text: Rickettsia monacensis

text: Rickettsia monacensis

text: IrR/Munich

characteristic: strain

text: BioSample for Rickettsia monacensis IrR/Munich genome


text: CNRS Universite Grenoble - Alpes

text: public

tag: Namespace:CNRS Universite Grenoble - Alpes

characteristic: Submitter Id

text: yellow fever mosquito

characteristic: common name

text: Laboratory (French Polynesia)

text: 2-4 days old adult, non blood fed

characteristic: dev stage

text: Aedes aegypti

text: susceptible

characteristic: resistance phenotype

text: Aedes aegypti

text: females

characteristic: sex

text: Bora Bora

text: Bora Bora strain


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: CNRS Universite Grenoble - Alpes

text: public

text: yellow fever mosquito

text: Laboratory (Benin)

characteristic: country

text: 2-4 days old adult, non blood fed

text: Aedes aegypti

characteristic: organism

text: susceptible

text: Aedes aegypti

text: females

text: Liverpool

text: Liverpool strain


characteristic: ENA-LAST-UPDATE

text: CNRS Universite Grenoble - Alpes

text: public

text: yellow fever mosquito

text: Laboratory (Benin)

text: 2-4 days old adult, non blood fed

text: Aedes aegypti

text: susceptible

text: Aedes aegypti

text: females

text: Liverspool

text: Liverpool strain

characteristic: title


characteristic: External Id

text: CNRS Universite Grenoble - Alpes

characteristic: INSDC center name

text: public

text: yellow fever mosquito

text: Laboratory USA

text: 2-4 days old adult, non blood fed

text: Aedes aegypti

text: suceptible

text: Aedes aegypti

text: females

text: New Orleans

text: New Orleans strain


text: CNRS Universite Grenoble - Alpes

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: yellow fever mosquito

text: Laboratory (USA)

text: 2-4 days old adult, non blood fed

text: Aedes aegypti

text: suceptible

text: Aedes aegypti

text: females

text: New Orleans

text: New Orleans strain


text: CNRS Universite Grenoble - Alpes

text: public

characteristic: INSDC status

characteristic: SRA accession

text: yellow fever mosquito

text: Laboratory

text: 2-4 days old adult, non blood fed

text: Aedes aegypti

text: resistant

text: Aedes aegypti

text: females

text: DeltaR

text: DeltaR strain


text: CNRS Universite Grenoble - Alpes

text: public

characteristic: Submitter Id

text: yellow fever mosquito

text: French Guiana

text: 2-4 days old adult, non blood fed

text: Aedes aegypti

text: resistant

text: Aedes aegypti

text: females

text: Cayenne

characteristic: strain

text: Cayenne strain


text: CNRS Universite Grenoble - Alpes

text: public

text: yellow fever mosquito

characteristic: common name

text: French Guiana

text: 2-4 days old adult, non blood fed

characteristic: dev stage

text: Aedes aegypti

text: resistant

text: Aedes aegypti

text: females

text: Saint-Georges

text: Saint-Georges strain


text: CNRS Universite Grenoble - Alpes

text: public

text: yellow fever mosquito

text: Thailand

text: 2-4 days old adult, non blood fed

text: Aedes aegypti

text: resistant

characteristic: resistance phenotype

text: Aedes aegypti

text: females

characteristic: sex

text: Nakhonsawan

text: Nakhonsawan strain


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: CNRS Universite Grenoble - Alpes

text: public

text: yellow fever mosquito

text: Thailand

text: 2-4 days old adult, non blood fed

text: Aedes aegypti

text: resistant

text: Aedes aegypti

text: females

text: Phetchaburi

text: Phetchaburi strain


text: OX

text: public

characteristic: broker name

characteristic: description

text: Shigella flexneri

characteristic: organism

text: Shigella flexneri


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: OX

text: public

text: unidentified

text: unidentified

characteristic: title


text: 29553330; 30687793; 32375989; 33770146

text: PUBLIC HEALTH ENGLAND

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: GBR

text: Neisseria

characteristic: genus

characteristic: isolate

text: Neisseria meningitidis

text: Neisseria meningitidis


text: 29553330; 30687793; 32375989; 33770146

text: PUBLIC HEALTH ENGLAND

text: public

characteristic: INSDC status

text: GBR

characteristic: SRA accession

characteristic: Submitter Id

text: Neisseria

text: Neisseria meningitidis

text: Neisseria meningitidis


text: 29553330; 30687793; 32375989; 33770146

text: PUBLIC HEALTH ENGLAND

text: public

text: GBR

text: Neisseria

text: Neisseria meningitidis

text: Neisseria meningitidis


text: 29553330; 30687793; 32375989; 33770146

text: PUBLIC HEALTH ENGLAND

text: public

text: GBR

text: Neisseria

text: Neisseria meningitidis

text: Neisseria meningitidis


text: PUBLIC HEALTH ENGLAND

text: public

text: Neisseria meningitidis

text: Neisseria meningitidis


text: Oesophagus

characteristic: ArrayExpress-Phenotype

text: Mus musculus

characteristic: ArrayExpress-Species

text: SC

text: public

text: house mouse

characteristic: common name

text: Mus musculus

text: Mus musculus


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: OX

text: public

characteristic: broker name

text: Escherichia coli

text: Escherichia coli


characteristic: ENA-LAST-UPDATE

text: COPENHAGEN UNIVERSITY

text: public

tag: Namespace:COPENHAGEN UNIVERSITY

text: unidentified phage

characteristic: organism

text: unidentified phage

text: Induced Bacteriophage Metaviromes


AS-1 assembly

characteristic: External Id

text: COPENHAGEN UNIVERSITY

text: public

text: AS-1 assembly

text: Contigs assembled from metaviromes prepared from spontaneously induced undefined mixed-strain mesophilic LD-starter culture A

characteristic: description

text: unidentified phage

text: unidentified phage

text: Induced Bacteriophage Metavirome Assemblies

characteristic: title


AS-2 assembly

text: COPENHAGEN UNIVERSITY

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: AS-2 assembly

text: unidentified phage

text: unidentified phage


AS-4 assembly

text: COPENHAGEN UNIVERSITY

text: public

characteristic: INSDC status

text: AS-4 assembly

text: unidentified phage

text: unidentified phage


AM-1 assembly

text: COPENHAGEN UNIVERSITY

text: public

characteristic: SRA accession

text: AM-1 assembly

text: Contigs assembled from metaviromes prepared from mitomycin-C-induced undefined mixed-strain mesophilic LD-starter culture A

text: unidentified phage

text: unidentified phage


AM-2 assembly

text: COPENHAGEN UNIVERSITY

text: public

text: AM-2 assembly

characteristic: Submitter Id

text: unidentified phage

text: unidentified phage


AM-4 assembly

text: COPENHAGEN UNIVERSITY

text: public

text: AM-4 assembly

text: unidentified phage

text: unidentified phage


BS-1 assembly

text: COPENHAGEN UNIVERSITY

text: public

text: BS-1 assembly

text: Contigs assembled from metaviromes prepared from spontaneously induced undefined mixed-strain mesophilic LD-starter culture B

text: unidentified phage

text: unidentified phage


BS-2 assembly

text: COPENHAGEN UNIVERSITY

text: public

text: BS-2 assembly

text: unidentified phage

text: unidentified phage


BS-4 assembly

text: COPENHAGEN UNIVERSITY

text: public

text: BS-4 assembly

text: unidentified phage

text: unidentified phage


BM-1 assembly

text: COPENHAGEN UNIVERSITY

text: public

text: BM-1 assembly

text: Contigs assembled from metaviromes prepared from mitomycin-C-induced undefined mixed-strain mesophilic LD-starter culture B

text: unidentified phage

text: unidentified phage


BM-2 assembly

text: COPENHAGEN UNIVERSITY

text: public

text: BM-2 assembly

text: unidentified phage

text: unidentified phage


BM-4 assembly

text: COPENHAGEN UNIVERSITY

text: public

text: BM-4 assembly

text: unidentified phage

text: unidentified phage


CS-2 assembly

text: COPENHAGEN UNIVERSITY

text: public

text: CS-2 assembly

text: Contigs assembled from metaviromes prepared from spontaneously induced undefined mixed-strain mesophilic LD-starter culture C

text: unidentified phage

text: unidentified phage


CS-4 assembly

text: COPENHAGEN UNIVERSITY

text: public

text: CS-4 assembly

text: unidentified phage

text: unidentified phage


CS-7 assembly

text: COPENHAGEN UNIVERSITY

text: public

text: CS-7 assembly

text: unidentified phage

text: unidentified phage


CM-2 assembly

text: COPENHAGEN UNIVERSITY

text: public

text: CM-2 assembly

text: Contigs assembled from metaviromes prepared from mitomycin-C-induced undefined mixed-strain mesophilic LD-starter culture C

text: unidentified phage

text: unidentified phage


CM-3 assembly

text: COPENHAGEN UNIVERSITY

text: public

text: CM-3 assembly

text: unidentified phage

text: unidentified phage


CM-4 assembly

text: COPENHAGEN UNIVERSITY

text: public

text: CM-4 assembly

text: unidentified phage

text: unidentified phage


Clostridium ultunense strain Esp

text: SLU

text: public

text: Clostridium ultunense strain Esp

text: Clostridium ultunense strain Esp belongs to the functional group of syntrophic acetate-oxidizing bacteria (SAOB), which have been identified as key organisms for efficient biogas production from protein-rich materials. Genome analysis and comparative genomics might aid us to define physiological features that are essential for maintaining this particular syntrophic lifestyle.

text: [Clostridium] ultunense Esp

text: [Clostridium] ultunense Esp

text: Genome sequence of Clostridium ultunense strain Esp


text: public

tag: Namespace:Department of Plant Biotechnology and Bioinformatics, Ghent University, Gent, Belgium Department of Plant Systems Biology,VIB, Gent, Belgium

text: ArrayExpress

text: Scots pine

text: Protocols: Immature cones were harvested periodically during July of 2012 from an open-pollinated seed orchard clone (W4009) of Scots pine (Pinus sylvestris L.) located in Hade, central Sweden. Zygotic embryos were excised from the megagametophytes under a stereomicroscope and collected in Eppendorf tubes, placed on ice. Both the embryos (E) and the megagametophytes (M) were sorted separately and classified into four developmental stages. Stage 1, the ovules contained a single embryo at the stage before cleavage (E1, M1); Stage 2, the ovules contained an embryo at the stage of cleavage (E2, M2); Stage 3, the ovules contained a dominant embryo, DO, and subordinate embryos, SUs (the dominant and the subordinate embryos were sampled separately, E3DO, E3SU, M3); Stage 4, the ovule contained a dominant embryo just before cotyledon differentiation (E4, M4). After a maximum of 10 minutes on ice, the Eppendorf tubes with collected embryos or megagametophytes were frozen in liquid nitrogen. Each sample included from 27 to 50 embryos, depending on the developmental stage. Total RNA from zygotic embryo and megagametophyte samples was extracted using the RNAqueous-Micro RNA Isolation Kit (Ambion) and Spectrum Plant Total RNA kit (Sigma-Aldrich), respectively, followed by a DNase I treatment to remove any residual genomic DNA, according to manufacturer’s instructions. The concentration of the isolated RNA was determined fluorimetrically using a Qubit fluorometer (Invitrogen). The integrity of RNA was verified by an Agilent BioAnalyzer using the RNA 6000 Nano chip (Agilent Tecnologies). Samples with an RNA integrity number (RIN) higher than 7 were used for double strand cDNA synthesis and amplification with the Mint-2 cDNA synthesis kit (Evrogen). First-strand synthesis was initiated from 1 μg of total RNA, according to manufacturer’s instructions followed by the second strand synthesis and PCR amplification. The number of cycles (18 or 21) for double-strand cDNA amplification was estimated individually for each sample. Amplified cDNA was then purified with the NucleoSpin Gel and PCR Clean-up kit (Macheray-Nagel). Finally, a re-amplification step was performed with specific primers for 454 pyrosequencing. In total, nine different dsDNA enriched libraries were constructed, five from zygotic embryos at stage E1, E2, E3DO, E3SU and E4, and four from megagametophytes at stage M1, M2, M3 and M4. The quantity of the cDNA libraries for the RNA sequencing was determined fluorometrically using the Quant-iTTM PicoGreen® dsDNA Kit (Invitrogen) and the quality was estimated by using the Agilent High Sensitivity DNA Kit in a 2100 Bioanalyzer (Agilent).

text: Stage 1

characteristic: developmental stage

text: Pinus sylvestris

text: Pinus sylvestris

text: embryo

characteristic: organism part

text: Pinus sylvestris


text: Department of Plant Biotechnology and Bioinformatics, Ghent University, Gent, Belgium Department of Plant Systems Biology,VIB, Gent, Belgium

text: public

text: ArrayExpress

text: Scots pine

characteristic: common name

text: Stage 1

text: Pinus sylvestris

text: Pinus sylvestris

text: megagametophyte

text: Pinus sylvestris


characteristic: ENA-CHECKLIST

text: public

text: ArrayExpress

text: Scots pine

text: Stage 2

text: Pinus sylvestris

text: Pinus sylvestris

text: embryo

text: Pinus sylvestris


characteristic: ENA-FIRST-PUBLIC

text: public

text: ArrayExpress

text: Scots pine

text: Stage 4

text: Pinus sylvestris

text: Pinus sylvestris

text: megagametophyte

text: Pinus sylvestris


text: public

text: ArrayExpress

characteristic: broker name

text: Scots pine

text: Stage 3

text: Pinus sylvestris

text: Pinus sylvestris

text: embryo

text: Pinus sylvestris


characteristic: ENA-LAST-UPDATE

text: public

text: ArrayExpress

text: Scots pine

text: Stage 4

text: Pinus sylvestris

text: Pinus sylvestris

text: embryo

text: Pinus sylvestris


E-MTAB-5206:Sample 1

text: public

text: E-MTAB-5206:Sample 1

tag: Namespace:Department of Pathology, University of Cambridge

text: ArrayExpress

characteristic: cell line

text: fibroblast

characteristic: cell type

text: house mouse

text: Protocols: L929 cells in 60-mm dishes were infected at an MOI of 10 in an initial volume of 1.5 ml DMEM with 1% FBS. After 1 h adsorption at 37 °C an additional 3.5 ml was added and incubation continued. At the appropriate time points, cells were treated with cycloheximide (Sigma-Aldrich; to 100 μg/ml; 2 min). Cells were rinsed with 5 ml of ice-cold PBS, the dishes submerged in a reservoir of liquid nitrogen for 10 s, transferred to dry ice and 400 μl of lysis buffer [20 mM Tris-HCl pH 7.5, 150 mM NaCl, 5 mM MgCl2, 1 mM DTT, 1% Triton X-100, 100 μg/ml cycloheximide and 25 U/ml TURBO DNase (Life Technologies)] dripped onto the cells. The cells were scraped extensively to ensure lysis, collected and triturated with a 26-G needle ten times. Lysates were clarified by centrifugation for 20 min at 13,000 g at 4 °C, the supernatants recovered and stored in liquid nitrogen. Cell lysates were subjected to Ribo-Seq and RNA-Seq. The methodologies employed were based on the original protocols of Ingolia and colleagues (Ingolia et al., 2009; Ingolia et al., 2012), except library amplicons were constructed using a small RNA cloning strategy (Guo et al., 2010) adapted to Illumina smallRNA v2 to allow multiplexing, as described previously (Chung et al., 2015).

text: cycloheximide

characteristic: growth condition

text: Mus musculus

characteristic: organism

text: Mus musculus

text: Ribo-Seq

characteristic: protocol

text: Mus musculus

text: Sample 1


E-MTAB-5206:Sample 10

characteristic: External Id

text: Department of Pathology, University of Cambridge

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: E-MTAB-5206:Sample 10

text: ArrayExpress

text: fibroblast

text: house mouse

characteristic: description

text: cycloheximide

text: Mus musculus

text: Mus musculus

text: Ribo-Seq

text: Mus musculus

text: Sample 10

characteristic: title


E-MTAB-5206:Sample 11

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-5206:Sample 11

characteristic: Submitter Id

text: ArrayExpress

text: fibroblast

text: house mouse

text: cycloheximide

text: Mus musculus

text: Mus musculus

text: Ribo-Seq

text: Mus musculus

text: Sample 11


E-MTAB-5206:Sample 12

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: public

text: E-MTAB-5206:Sample 12

text: ArrayExpress

text: fibroblast

text: house mouse

characteristic: common name

text: cycloheximide

text: Mus musculus

text: Mus musculus

text: Ribo-Seq

text: Mus musculus

text: Sample 12


E-MTAB-5206:Sample 13

characteristic: ENA-LAST-UPDATE

text: public

text: E-MTAB-5206:Sample 13

text: ArrayExpress

characteristic: broker name

characteristic: cell line

text: fibroblast

text: house mouse

text: cycloheximide

text: Mus musculus

text: Mus musculus

text: Ribo-Seq

text: Mus musculus

text: Sample 13


E-MTAB-5206:Sample 14

text: public

text: E-MTAB-5206:Sample 14

text: ArrayExpress

text: fibroblast

characteristic: cell type

text: house mouse

text: cycloheximide

characteristic: growth condition

text: Mus musculus

characteristic: organism

text: Mus musculus

text: Ribo-Seq

text: Mus musculus

text: Sample 14


E-MTAB-5206:Sample 15

characteristic: External Id

characteristic: INSDC center name

text: public

text: E-MTAB-5206:Sample 15

text: ArrayExpress

text: fibroblast

text: house mouse

text: cycloheximide

text: Mus musculus

text: Mus musculus

text: RNA-Seq

characteristic: protocol

text: Mus musculus

text: Sample 15


E-MTAB-5206:Sample 16

characteristic: INSDC first public

text: public

text: E-MTAB-5206:Sample 16

text: ArrayExpress

text: fibroblast

text: house mouse

characteristic: description

text: cycloheximide

text: Mus musculus

text: Mus musculus

text: RNA-Seq

text: Mus musculus

text: Sample 16

characteristic: title


E-MTAB-5206:Sample 17

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-5206:Sample 17

text: ArrayExpress

text: fibroblast

text: house mouse

text: cycloheximide

text: Mus musculus

text: Mus musculus

text: RNA-Seq

text: Mus musculus

text: Sample 17


E-MTAB-5206:Sample 18

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: public

text: E-MTAB-5206:Sample 18

characteristic: Submitter Id

text: ArrayExpress

text: fibroblast

text: house mouse

text: cycloheximide

text: Mus musculus

text: Mus musculus

text: RNA-Seq

text: Mus musculus

text: Sample 18


E-MTAB-5206:Sample 19

characteristic: ENA-LAST-UPDATE

text: public

text: E-MTAB-5206:Sample 19

text: ArrayExpress

characteristic: broker name

text: fibroblast

text: house mouse

characteristic: common name

text: cycloheximide

text: Mus musculus

text: Mus musculus

text: RNA-Seq

text: Mus musculus

text: Sample 19


E-MTAB-5206:Sample 2

text: public

text: E-MTAB-5206:Sample 2

text: ArrayExpress

characteristic: cell line

text: fibroblast

characteristic: cell type

text: house mouse

text: cycloheximide

characteristic: growth condition

text: Mus musculus

text: Mus musculus

text: Ribo-Seq

text: Mus musculus

text: Sample 2


E-MTAB-5206:Sample 20

characteristic: External Id

characteristic: INSDC center name

text: public

text: E-MTAB-5206:Sample 20

text: ArrayExpress

text: fibroblast

text: house mouse

text: cycloheximide

text: Mus musculus

characteristic: organism

text: Mus musculus

text: RNA-Seq

text: Mus musculus

text: Sample 20


E-MTAB-5206:Sample 3

characteristic: INSDC first public

text: public

text: E-MTAB-5206:Sample 3

text: ArrayExpress

text: fibroblast

text: house mouse

characteristic: description

text: cycloheximide

text: Mus musculus

text: Mus musculus

text: Ribo-Seq

characteristic: protocol

text: Mus musculus

text: Sample 3


E-MTAB-5206:Sample 4

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: E-MTAB-5206:Sample 4

text: ArrayExpress

text: fibroblast

text: house mouse

text: cycloheximide

text: Mus musculus

text: Mus musculus

text: Ribo-Seq

text: Mus musculus

text: Sample 4

characteristic: title


E-MTAB-5206:Sample 5

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: public

characteristic: SRA accession

text: E-MTAB-5206:Sample 5

text: ArrayExpress

text: fibroblast

text: house mouse

text: cycloheximide

text: Mus musculus

text: Mus musculus

text: Ribo-Seq

text: Mus musculus

text: Sample 5


E-MTAB-5206:Sample 6

characteristic: ENA-LAST-UPDATE

text: public

text: E-MTAB-5206:Sample 6

characteristic: Submitter Id

text: ArrayExpress

characteristic: broker name

text: fibroblast

text: house mouse

text: cycloheximide

text: Mus musculus

text: Mus musculus

text: Ribo-Seq

text: Mus musculus

text: Sample 6


E-MTAB-5206:Sample 7

text: public

text: E-MTAB-5206:Sample 7

text: ArrayExpress

characteristic: cell line

text: fibroblast

characteristic: cell type

text: house mouse

characteristic: common name

text: cycloheximide

text: Mus musculus

text: Mus musculus

text: Ribo-Seq

text: Mus musculus

text: Sample 7


E-MTAB-5206:Sample 8

characteristic: External Id

characteristic: INSDC center name

text: public

text: E-MTAB-5206:Sample 8

text: ArrayExpress

text: fibroblast

text: house mouse

text: cycloheximide

characteristic: growth condition

text: Mus musculus

text: Mus musculus

text: Ribo-Seq

text: Mus musculus

text: Sample 8


E-MTAB-5206:Sample 9

characteristic: INSDC first public

text: public

text: E-MTAB-5206:Sample 9

text: ArrayExpress

text: fibroblast

text: house mouse

characteristic: description

text: cycloheximide

text: Mus musculus

characteristic: organism

text: Mus musculus

text: Ribo-Seq

text: Mus musculus

text: Sample 9


characteristic: INSDC last update

text: public

characteristic: INSDC status

tag: Namespace:AP-HP and Paris Cite Sorbonne University

characteristic: collection date

text: human

text: plasma sample

text: Homo sapiens

text: Homo sapiens

text: circulating DNA

characteristic: tissue type

text: circulating tumor DNA NSCLC


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: AP-HP and Paris Cite Sorbonne University

text: public

characteristic: SRA accession

text: human

text: plasma sample

text: Homo sapiens

text: Homo sapiens

text: circulating DNA

text: circulating tumor DNA NSCLC

characteristic: title


characteristic: ENA-LAST-UPDATE

text: public

characteristic: Submitter Id

text: Boshi Yu

characteristic: collected by

text: The shotgun genome of Lyngbya hieronymusii CHAB3367

text: China

characteristic: geographic location (country and/or sea)

text: Erhai Lake

characteristic: geographic location (region and locality)

text: Gongliang Yu

characteristic: identified by

text: lake

characteristic: isolation source

text: Limnoraphis hieronymusii

text: Limnoraphis hieronymusii

text: The genome of Lyngbya hieronymusii CHAB3367


text: D

characteristic: DNA extraction batch

characteristic: External Id

text: UH/IB

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: terrestrial biome

characteristic: environment (biome)

text: human-associated habitat

characteristic: environment (feature)

text: bile

characteristic: environment (material)

text: human-associated

characteristic: environmental package

text: Finland

unit: DD

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

unit: year

characteristic: host age

characteristic: host body mass index

text: bile

characteristic: host body product

unit: cm

characteristic: host height

text: male

characteristic: host sex

unit: kg

characteristic: host total mass

text: human-associated

characteristic: human associated environmental package

text: yes

characteristic: ibd

text: metagenome

characteristic: investigation type

text: human bile metagenome

text: Hemochromatosis

text: forward: AGAGTTTGATCMTGGCTCAG, reverse: GTATTACCGCGGCTGCTG

characteristic: pcr primers

text: Bile microbiota in PSC

characteristic: project name

characteristic: psc

text: progressed

text: human bile metagenome

text: Illumina MiSeq

characteristic: sequencing method

text: A

characteristic: target gene

characteristic: target subfragment

text: Bile microbiome PSC


text: D

characteristic: DNA extraction batch

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: UH/IB

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: terrestrial biome

characteristic: environment (biome)

text: human-associated habitat

characteristic: environment (feature)

text: bile

characteristic: environment (material)

text: human-associated

characteristic: environmental package

text: Finland

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

text: bile

text: male

text: human-associated

text: yes

text: metagenome

text: human bile metagenome

characteristic: organism

text: Nodular prurigo

text: Bile microbiota in PSC

text: early

text: human bile metagenome

text: Illumina MiSeq

text: A

text: Bile microbiome PSC

characteristic: title


text: H

characteristic: DNA extraction batch

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: UH/IB

text: public

text: terrestrial biome

text: human-associated habitat

text: bile

text: human-associated

text: Finland

characteristic: geographic location (longitude)

characteristic: host age

characteristic: host body mass index

text: bile

characteristic: host body product

characteristic: host height

text: male

characteristic: host sex

characteristic: host total mass

text: human-associated

characteristic: human associated environmental package

text: no

characteristic: ibd

text: metagenome

characteristic: investigation type

text: human bile metagenome

text: Sacroileitis, Arthritis, Fatty liver, asthma

characteristic: pcr primers

text: Bile microbiota in PSC

characteristic: project name

characteristic: psc

text: progressed

text: human bile metagenome

text: Illumina MiSeq

characteristic: sequencing method

text: B

characteristic: target gene

characteristic: target subfragment

text: Bile microbiome PSC


text: I

characteristic: DNA extraction batch

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: UH/IB

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: terrestrial biome

characteristic: environment (biome)

text: human-associated habitat

characteristic: environment (feature)

text: bile

characteristic: environment (material)

text: human-associated

characteristic: environmental package

text: Finland

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

text: bile

text: male

text: human-associated

text: no

text: metagenome

text: human bile metagenome

characteristic: organism

text: DMtype1, Hypertension, hypercholesterolemia, asthma

text: Bile microbiota in PSC

text: progressed

text: human bile metagenome

text: Illumina MiSeq

text: A

text: Bile microbiome PSC

characteristic: title


text: D

characteristic: DNA extraction batch

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: UH/IB

text: public

text: terrestrial biome

text: human-associated habitat

text: bile

text: human-associated

text: Finland

characteristic: geographic location (longitude)

characteristic: host age

characteristic: host body mass index

text: bile

characteristic: host body product

characteristic: host height

text: male

characteristic: host sex

characteristic: host total mass

text: human-associated

characteristic: human associated environmental package

text: yes

characteristic: ibd

text: metagenome

characteristic: investigation type

text: human bile metagenome

characteristic: pcr primers

text: Bile microbiota in PSC

characteristic: project name

characteristic: psc

text: dysplasia/carcinoma

text: human bile metagenome

text: Illumina MiSeq

characteristic: sequencing method

text: B

characteristic: target gene

characteristic: target subfragment

text: Bile microbiome PSC


text: K

characteristic: DNA extraction batch

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: UH/IB

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: terrestrial biome

characteristic: environment (biome)

text: human-associated habitat

characteristic: environment (feature)

text: bile

characteristic: environment (material)

text: human-associated

characteristic: environmental package

text: Finland

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

text: bile

text: female

text: human-associated

text: no

text: metagenome

text: human bile metagenome

characteristic: organism

text: Cholecystolithiasis

text: Bile microbiota in PSC

text: human bile metagenome

text: Illumina MiSeq

text: B

text: Bile microbiome PSC

characteristic: title


text: K

characteristic: DNA extraction batch

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: UH/IB

text: public

text: terrestrial biome

text: human-associated habitat

text: bile

text: human-associated

text: Finland

characteristic: geographic location (longitude)

characteristic: host age

characteristic: host body mass index

text: bile

characteristic: host body product

characteristic: host height

text: female

characteristic: host sex

characteristic: host total mass

text: human-associated

characteristic: human associated environmental package

text: no

characteristic: ibd

text: metagenome

characteristic: investigation type

text: human bile metagenome

characteristic: pcr primers

text: Bile microbiota in PSC

characteristic: project name

characteristic: psc

text: human bile metagenome

text: Illumina MiSeq

characteristic: sequencing method

text: A

characteristic: target gene

characteristic: target subfragment

text: Bile microbiome PSC


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: Clostridium difficile

characteristic: common name

text: UK

characteristic: country

text: United Kingdom

characteristic: geographic location (country and/or sea)

text: Diseased

text: Faeces

text: Peptoclostridium difficile

characteristic: organism

text: Peptoclostridium difficile

characteristic: serovar

text: Homo Sapien

characteristic: strain

characteristic: title