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characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: house mouse

text: Female

text: Mus musculus

text: Zygote

text: Mus musculus

text: lncRNA Z1 Zygotes Rep1

text: lncRNA Z1 Zygotes Rep1


text: Zygote

text: female

text: Mus musculus

text: SC

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: house mouse

text: Female

text: Mus musculus

text: Zygote

text: Mus musculus

text: lncRNA 2 Zygotes Rep2

text: lncRNA 2 Zygotes Rep2


text: EI

text: public

text: 5e5eceac16aafb00014ce0d9:sample:Nb_gDNA_1_Plant1/2a

characteristic: Submitter Id

unit: week

characteristic: age

text: COPO

characteristic: broker name

unit: hour

characteristic: dark phase of controlled light/dark cycle

text: Before extracting DNA, plants were put in continuous darkness for three days and leaf tissue was harvested, flash frozen in liquid nitrogen, and ground to a fine powder. The tissue for this sample comes from a single plant but it was not recorded if this was individual 1 or individual 2. For high concentration, low integrity DNA (for Illumina sequencing), a modified CTAB-based protocol adapted from Michael et al. Nature communications 9(1),1-8 (2018) was used. Briefly, 5 g of frozen powdered leaf tissue was incubated with 20 mL CTAB lysis buffer (100 mM Tris-HCl, 2% CTAB, 1.4 M NaCl, 20 mM EDTA, pH 8.0) containing 20 _g/mL proteinase K for 20 minutes at 55 ¡C. Aliquots of 2.5 mL were extracted with 0.5 volumes of chloroform, mixed by inversion and centrifuged at 20,000 x g for 30 minutes at room temperature. The upper aqueous phase was mixed with an equal volume volume of 25:24:1 phenol:chloroform:isoamyl alcohol (PCI) and centrifuged at 20,000 x g for 30 minutes at room temperature. DNA was precipitated from the upper aqueous phase with 0.7 volumes (1.4 mL) ice-cold isopropanol. Precipitate was pelleted by centrifugation at 20,000 x g for 30 minutes at 4 ¡C, washed with ice-cold 70% ethanol and air-dried and room temperature, DNA was resuspended in TE buffer (10 mM Tris-HCl pH 7.5, 1 mM EDTA) containing 1.4 mg/mL RNase A at 37 ¡C with vigorous orbital shaking (300 rpm). RNase A was removed by two extractions with PCI with phases separated by centrifugation at 20,000 x g for 20 minutes at 4 ¡C. DNA was precipitated as above and resuspended in 200 µL of TE buffer. To increase the final concentration, all samples were pooled using the Zymo Research Genomic DNA Clean & Concentrator-10 column (Irvine, CA, USA) following the manufacturerÕs instructions and eluted with 50 µL DNA Elution buffer at 70 ¡C to yielding 6.5 µg of DNA (185 ng/µL)

characteristic: extraction

characteristic: light phase of controlled light/dark cycle

text: Nicotiana benthamiana

text: Nicotiana benthamiana

text: leaf tissue

characteristic: source name

unit: Celsius

characteristic: temperature


characteristic: ENA-CHECKLIST

text: EI

text: public

text: 5e5ece6e16aafb00014ce0d6:sample: Nb_gDNA_3_Plant1/2b

text: COPO

text: Before extracting DNA, plants were put in continuous darkness for three days and leaf tissue was harvested, flash frozen in liquid nitrogen, and ground to a fine powder. The tissue for this sample comes from a single plant but it was not recorded if this was individual 1 or individual 2. For high concentration, high integrity DNA (for Oxford Nanopore), a modified CTAB-based protocol adapted from Michael et al. Nature communications 9(1),1-8 (2018) was used. Briefly, 1.0 g of frozen powdered leaf tissue was mixed with 3 mL CTAB lysis buffer containing 20 μg/mL proteinase K and incubated at 55 °C at 500 rpm. After 15 minutes, 20 µL of 100 mg/mL RNaseA was added and incubation continued for 15 minutes before a further 20 µL of 100 mg/mL RNaseA was added. After 15 minutes, the mixture was chilled on ice for five minutes. Extractions with 0.5 volumes of chloroform and equal volumes of PCI were performed as above except that wider-bore pipette tips were used at all stages. DNA was precipitated and resuspended as above in 25 µL TE buffer. Yield (8-21 µg at 350-900 ng/µL) was determined using a Qubit fluorometer (ThermoFisher, Waltham, MA, USA). Fragments of >40 kb were collected for library preparation using BluePippin pulsed-field electrophoresis (Sage Science, Beverly, MA, USA). DNA was not frozen but stored at 4 °C overnight before proceeding directly to library preparation.

text: Nicotiana benthamiana

characteristic: organism

text: Nicotiana benthamiana

text: leaf tissue

characteristic: title


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: EI

text: public

text: 5e5ece6e16aafb00014ce0d6:sample:Nb_gDNA_12_Plant9

text: COPO

text: Before extracting DNA, plants were put in continuous darkness for three days and leaf tissue was harvested from a single unique plant, flash frozen in liquid nitrogen, and ground to a fine powder. For high concentration, high integrity DNA (for Oxford Nanopore), a modified CTAB-based protocol adapted from Michael et al. Nature communications 9(1),1-8 (2018) was used. Briefly, 1.0 g of frozen powdered leaf tissue was mixed with 3 mL CTAB lysis buffer containing 20 μg/mL proteinase K and incubated at 55 °C at 500 rpm. After 15 minutes, 20 µL of 100 mg/mL RNaseA was added and incubation continued for 15 minutes before a further 20 µL of 100 mg/mL RNaseA was added. After 15 minutes, the mixture was chilled on ice for five minutes. Extractions with 0.5 volumes of chloroform and equal volumes of PCI were performed as above except that wider-bore pipette tips were used at all stages. DNA was precipitated and resuspended as above in 25 µL TE buffer. Yield (8-21 µg at 350-900 ng/µL) was determined using a Qubit fluorometer (ThermoFisher, Waltham, MA, USA). Fragments of >40 kb were collected for library preparation using BluePippin pulsed-field electrophoresis (Sage Science, Beverly, MA, USA). DNA was not frozen but stored at 4 °C overnight before proceeding directly to library preparation.

text: Nicotiana benthamiana

text: Nicotiana benthamiana

text: leaf tissue


text: EI

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: 5e5ece6e16aafb00014ce0d6:sample:Nb_gDNA_13_Plant8

text: COPO

text: Nicotiana benthamiana

text: Nicotiana benthamiana

text: leaf tissue


text: EI

text: public

characteristic: INSDC status

characteristic: SRA accession

text: 5e5e2957f2ab270001af18fd:sample: Nb_gDNA_3_Plant1/2b

characteristic: Submitter Id

text: COPO

text: Nicotiana benthamiana

text: Nicotiana benthamiana

text: leaf tissue


text: ZOOLOGICAL INSTITUTE KIEL

text: public

tag: Namespace:ZOOLOGICAL INSTITUTE KIEL

characteristic: collection date

text: investigation of cembio bacteria frequencies in their host

characteristic: description

text: whole host

characteristic: environment (biome)

text: microbial feature

characteristic: environment (feature)

text: nematodes

characteristic: environment (material)

text: worms

characteristic: experiment type

text: cembio

text: 72 h

text: Germany

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: roundworm

characteristic: host common name

text: Caenorhabditis elegans

characteristic: host scientific name

characteristic: host taxid

text: host-associated

characteristic: host-associated environmental package

text: metagenome

characteristic: investigation type

text: PCR

characteristic: library construction method

text: gel purification

characteristic: library screening strategy

text: ATCGTACG

characteristic: multiplex identifiers-fwd

text: AACTCTCG

characteristic: multiplex identifiers-rev

characteristic: nucleic acid amplification

text: metagenome

text: 314 F

characteristic: pcr primers fwd

text: 806 R

characteristic: pcr primers rev

text: CeMbio - The C. elegans microbiome resource: Experiment 3

characteristic: project name

text: metagenome

text: Illumina MiSeq

characteristic: sequencing method

text: 16S rRNA

characteristic: target gene

characteristic: target subfragment

text: cembio frequency screen


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: ZOOLOGICAL INSTITUTE KIEL

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

characteristic: description

text: whole host

characteristic: environment (biome)

text: microbial feature

characteristic: environment (feature)

text: nematodes

characteristic: environment (material)

text: worms

characteristic: experiment type

text: cembio

text: 72 h

text: Germany

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: roundworm

text: Caenorhabditis elegans

text: host-associated

text: metagenome

text: PCR

text: gel purification

text: ATCGTACG

text: ACTATGTC

text: metagenome

characteristic: organism

text: 314 F

text: 806 R

text: metagenome

text: Illumina MiSeq

text: 16S rRNA

text: cembio frequency screen

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: ZOOLOGICAL INSTITUTE KIEL

characteristic: INSDC center name

text: public

text: whole host

text: microbial feature

text: nematodes

text: worms

text: cembio

text: 96 h

text: Germany

text: roundworm

characteristic: host common name

text: Caenorhabditis elegans

characteristic: host scientific name

characteristic: host taxid

text: host-associated

characteristic: host-associated environmental package

text: metagenome

characteristic: investigation type

text: PCR

characteristic: library construction method

text: gel purification

characteristic: library screening strategy

text: ATCGTACG

characteristic: multiplex identifiers-fwd

text: AGTAGCGT

characteristic: multiplex identifiers-rev

characteristic: nucleic acid amplification

text: metagenome

text: 314 F

characteristic: pcr primers fwd

text: 806 R

characteristic: pcr primers rev

characteristic: project name

text: metagenome

text: Illumina MiSeq

characteristic: sequencing method

text: 16S rRNA

characteristic: target gene

characteristic: target subfragment

text: cembio frequency screen


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: ZOOLOGICAL INSTITUTE KIEL

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

characteristic: description

text: whole host

characteristic: environment (biome)

text: microbial feature

characteristic: environment (feature)

text: nematodes

characteristic: environment (material)

text: worms

characteristic: experiment type

text: cembio

text: 96 h

text: Germany

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: roundworm

text: Caenorhabditis elegans

text: host-associated

text: metagenome

text: PCR

text: gel purification

text: ATCGTACG

text: CAGTGAGT

text: metagenome

characteristic: organism

text: 314 F

text: 806 R

text: metagenome

text: Illumina MiSeq

text: 16S rRNA

text: cembio frequency screen

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: ZOOLOGICAL INSTITUTE KIEL

characteristic: INSDC center name

text: public

text: whole host

text: microbial feature

text: nematodes

text: worms

text: cembio

text: 48 h

text: Germany

text: roundworm

characteristic: host common name

text: Caenorhabditis elegans

characteristic: host scientific name

characteristic: host taxid

text: host-associated

characteristic: host-associated environmental package

text: metagenome

characteristic: investigation type

text: PCR

characteristic: library construction method

text: gel purification

characteristic: library screening strategy

text: ATCGTACG

characteristic: multiplex identifiers-fwd

text: CGTACTCA

characteristic: multiplex identifiers-rev

characteristic: nucleic acid amplification

text: metagenome

text: 314 F

characteristic: pcr primers fwd

text: 806 R

characteristic: pcr primers rev

characteristic: project name

text: metagenome

text: Illumina MiSeq

characteristic: sequencing method

text: 16S rRNA

characteristic: target gene

characteristic: target subfragment

text: cembio frequency screen


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: ZOOLOGICAL INSTITUTE KIEL

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

characteristic: description

text: whole host

characteristic: environment (biome)

text: microbial feature

characteristic: environment (feature)

text: nematodes

characteristic: environment (material)

text: worms

characteristic: experiment type

text: cembio

text: 48 h

text: Germany

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: roundworm

text: Caenorhabditis elegans

text: host-associated

text: metagenome

text: PCR

text: gel purification

text: ATCGTACG

text: CTACGCAG

text: metagenome

characteristic: organism

text: 314 F

text: 806 R

text: metagenome

text: Illumina MiSeq

text: 16S rRNA

text: cembio frequency screen

characteristic: title