characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: public

tag: Namespace:Institute for Medical Immunology Universite Libre de Bruxelles

text: ArrayExpress

text: RAW 264.7

text: macrophage

text: house mouse

characteristic: common name

text: Protocols: 10e6 RAW 264.7 cells were cultured in medium (DMEM containing 10% of FCS, L-glutamine, pyruvate, non-essential amino acids, and penicillin/streptomycin/gentamycin) in 12 well plates at 37°C with 5% of CO2 overnight. Cells were then stimulated with AS03 (1/30) for 4 or 8 hours in independent triplicates. total RNA was extracted with an RNAeasy Plus Mini Kit (QIAGEN) following manufacturer’s instructions. The RNA concentration and purity were measured with a NanoDrop spectrophotometer. RNA libraries were prepared for sequencing using Illumina Truseq Stranded mRNA library prep kit

characteristic: description

text: adult

characteristic: developmental stage

text: Mus musculus

text: Mus musculus

text: blood

characteristic: organism part

text: Mus musculus

text: male

characteristic: sex

text: BALB/c

characteristic: strain

characteristic: title


status: PUBLIC

tag: attribute

characteristic: ENA-CHECKLIST

characteristic: External Id

text: Institute for Medical Immunology Universite Libre de Bruxelles

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: ArrayExpress

characteristic: broker name

text: RAW 264.7

characteristic: cell line

text: macrophage

characteristic: cell type

text: house mouse

text: adult

text: Mus musculus

characteristic: organism

text: Mus musculus

text: blood

text: Mus musculus

text: male

text: BALB/c


text: gut metagenome

characteristic: ArrayExpress-SPECIES

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: SC

text: public

text: gut metagenome

characteristic: common name

text: gut metagenome

text: gut metagenome

characteristic: subject id


text: Bacteria

text: Whole cell

text: Bifidobacterium pseudocatenulatum

text: Bifidobacterium pseudocatenulatum

characteristic: ENA-CHECKLIST

text: SC

text: public

text: Bifidobacterium pseudocatenulatum

text: Bifidobacterium pseudocatenulatum DSM 20438 = JCM 1200 = LMG 10505

characteristic: title


E-MTAB-5957:Sample 1

characteristic: External Id

text: CSHL

characteristic: INSDC center name

text: public

text: E-MTAB-5957:Sample 1

text: ArrayExpress

characteristic: cultivar

text: Protocols: Maize inbred line B73 and sorghum BTX623 were grown at CSHL Uplands Farm. For maize, root, shoot, leaf, and seedling were collected at 14-day-old stage; ears from stage v8; tassels from stage v7; pollen from stage r1; embryo, endosperm, and pericarp from seeds 20 days after pollination; silk from the R1 stage; and bract from the innermost husk. For sorghum tissues, root, shoot, leaf, and seedling were collected 14 days after germination; embryo, endosperm and pericarp 20 days after pollination; and pollen at the 9-10 weeks’ stage. Inflorescences were collected at the following sizes: 1-5 mm (inflorescence-1), 5-10 mm (inflorescence-2), and 1-2 cm (inflorescence-3). All tissues were immediately frozen in liquid N2. For each tissue, at least 10 plants were pooled in each of three biological replicates. Total RNA was prepared by grinding tissue in TRIzol reagent (Invitrogen 15596026) on dry ice and processing according to the protocol provided by the manufacturer. To remove DNA, an aliquot of total RNA was treated with RQ1 DNase (Promega M6101), followed by phenol/chloroform/isoamyl alcohol extraction, chloroform/isoamyl alcohol extraction using Phase Lock Gel Light tubes (5 PRIME 2302800), and ethanol precipitation. Precipitated RNA was stored at -20°C. PacBio libraries were generated as described (Wang et al. 2016). The 16-mer barcode sequences were shown in Supplementary Table S4. Tissues were barcoded, and SageELF was used for selection of five size-fractionated libraries (<1 kb, 1-2 kb, 2-3 kb, 3-5 kb, > 5kb).

characteristic: description

text: Zea mays

text: Zea mays

text: bract

characteristic: organism part

text: Zea mays

text: Sample 1


E-MTAB-5957:Sample 2

text: CSHL

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-5957:Sample 2

characteristic: Submitter Id

text: ArrayExpress

text: Zea mays

text: Zea mays

text: leaf

text: Zea mays

text: Sample 2


E-MTAB-5957:Sample 3

text: CSHL

text: public

text: E-MTAB-5957:Sample 3

text: ArrayExpress

characteristic: broker name

text: Zea mays

characteristic: organism

text: Zea mays

text: pericarp

text: Zea mays

text: Sample 3


E-MTAB-5957:Sample 4

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: CSHL

text: public

text: E-MTAB-5957:Sample 4

text: ArrayExpress

text: Zea mays

text: Zea mays

text: seedling

text: Zea mays

text: Sample 4


E-MTAB-5957:Sample 5

text: CSHL

text: public

text: E-MTAB-5957:Sample 5

text: ArrayExpress

text: Zea mays

text: Zea mays

text: shoot

text: Zea mays

text: Sample 5


E-MTAB-5957:Sample 6

text: CSHL

text: public

text: E-MTAB-5957:Sample 6

text: ArrayExpress

text: sorghum

characteristic: common name

text: Sorghum bicolor

text: Sorghum bicolor

text: embryo

text: Sorghum bicolor

text: Sample 6


E-MTAB-5957:Sample 7

characteristic: ENA-CHECKLIST

text: CSHL

text: public

text: E-MTAB-5957:Sample 7

text: ArrayExpress

text: sorghum

text: Sorghum bicolor

text: Sorghum bicolor

text: endosperm

text: Sorghum bicolor

text: Sample 7


E-MTAB-5957:Sample 8

text: CSHL

text: public

text: E-MTAB-5957:Sample 8

text: ArrayExpress

text: sorghum

text: Sorghum bicolor

text: Sorghum bicolor

text: Sorghum bicolor

text: Sample 8

characteristic: title


E-MTAB-5957:Sample 9

characteristic: External Id

text: CSHL

text: public

text: E-MTAB-5957:Sample 9

text: ArrayExpress

text: sorghum

text: Sorghum bicolor

text: Sorghum bicolor

text: Sorghum bicolor

text: Sample 9


E-MTAB-5957:Sample 10

text: CSHL

characteristic: INSDC center name

text: public

text: E-MTAB-5957:Sample 10

text: ArrayExpress

text: sorghum

text: Sorghum bicolor

text: Sorghum bicolor

text: Sorghum bicolor

text: Sample 10


E-MTAB-5957:Sample 11

text: CSHL

text: public

text: E-MTAB-5957:Sample 11

text: ArrayExpress

text: sorghum

characteristic: cultivar

text: Sorghum bicolor

text: Sorghum bicolor

text: leaf

text: Sorghum bicolor

text: Sample 11


E-MTAB-5957:Sample 12

text: CSHL

text: public

text: E-MTAB-5957:Sample 12

text: ArrayExpress

text: sorghum

characteristic: description

text: Sorghum bicolor

text: Sorghum bicolor

text: pericarp

text: Sorghum bicolor

text: Sample 12


E-MTAB-5957:Sample 13

text: CSHL

text: public

text: E-MTAB-5957:Sample 13

text: ArrayExpress

text: sorghum

text: Sorghum bicolor

text: Sorghum bicolor

text: pollen

characteristic: organism part

text: Sorghum bicolor

text: Sample 13


E-MTAB-5957:Sample 14

text: CSHL

characteristic: INSDC first public

text: public

text: E-MTAB-5957:Sample 14

text: ArrayExpress

text: sorghum

text: Sorghum bicolor

text: Sorghum bicolor

text: root

text: Sorghum bicolor

text: Sample 14


E-MTAB-5957:Sample 15

text: CSHL

characteristic: INSDC last update

text: public

text: E-MTAB-5957:Sample 15

text: ArrayExpress

text: sorghum

text: Sorghum bicolor

text: Sorghum bicolor

text: seedling

text: Sorghum bicolor

text: Sample 15


E-MTAB-5957:Sample 16

text: CSHL

text: public

characteristic: INSDC status

text: E-MTAB-5957:Sample 16

text: ArrayExpress

text: sorghum

text: Sorghum bicolor

text: Sorghum bicolor

text: shoot

text: Sorghum bicolor

text: Sample 16


text: public

characteristic: SRA accession

tag: Namespace:Centro de Biotecnologia y Genomica de Plantas, Universidad Politecnica de Madrid (UPM) - Instituto Nacional de Investigacion y Tecnologia Agraria y Alimentaria (INIA)

unit: day

characteristic: age

text: ArrayExpress

text: domesticated barley

text: Golden Promise

text: Protocols: Barley plants of Hordeum vulgare cv. Golden Promise were used. Grains were germinated in soil and grown at 22ºC under a 16 h light/8 h darkness photoperiod for 7 days in Sanyo MLR-350-H chambers. Barley transgenic lines overexpressing or silencing the HvPap-1 gene (OE Pap1 and KD Pap1, respectively) were generated using Agrobacterium-mediated gene transfer on immature embryos and homozygous material obtained by double haploid technology. Transgenic barley plants ubiquitously over-expressing the HvPap-1 gene were generated using p6U and p6d35s binary vectors. Silencing of the HvPap-1 gene was performed using the artificial microRNA (amiRNA) technology. Total RNA was extracted from frozen barley leaves by the phenol/chloroform method, followed by precipitation with 8 M LiCl and digested with DNase (Promega). Using poly-T oligo-attached magnetic beads, mRNAs were purified from the total RNA. Then, the mRNAs were fragmented and cDNA was synthesized using random hexamer-primers, DNA polymerase I and RNase H. The double-stranded cDNAs were purified with magnetic beads and ligated to adaptors for Illumina sequencing. The quality and quantity of the library was verified using an Agilent 2100 Bioanalyzer and an ABI StepOnePlus Real-Time PCR system, respectively.

text: Pap1 knockdown

characteristic: genotype

text: Hordeum vulgare subsp. vulgare

text: Hordeum vulgare subsp. vulgare

text: leaf

text: Hordeum vulgare subsp. vulgare

type: has member


text: Centro de Biotecnologia y Genomica de Plantas, Universidad Politecnica de Madrid (UPM) - Instituto Nacional de Investigacion y Tecnologia Agraria y Alimentaria (INIA)

text: public

characteristic: Submitter Id

text: ArrayExpress

characteristic: broker name

text: domesticated barley

text: Golden Promise

text: Pap1 knockdown

text: Hordeum vulgare subsp. vulgare

characteristic: organism

text: Hordeum vulgare subsp. vulgare

text: leaf

text: Hordeum vulgare subsp. vulgare


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: public

text: ArrayExpress

text: domesticated barley

characteristic: common name

text: Golden Promise

text: Pap1 overexpression

text: Hordeum vulgare subsp. vulgare

text: Hordeum vulgare subsp. vulgare

text: leaf

text: Hordeum vulgare subsp. vulgare


characteristic: ENA-CHECKLIST

characteristic: External Id

text: public

text: ArrayExpress

text: domesticated barley

text: Golden Promise

text: wild type genotype

text: Hordeum vulgare subsp. vulgare

text: Hordeum vulgare subsp. vulgare

text: leaf

text: Hordeum vulgare subsp. vulgare

characteristic: title


characteristic: INSDC center name

text: public

tag: Namespace:Natural Resources Institute Finland (Luke)

text: sheep

text: ovary

characteristic: description

text: Ovis aries

text: Ovis aries


text: Natural Resources Institute Finland (Luke)

characteristic: INSDC first public

text: public

text: sheep

text: ovary

text: Ovis aries

text: Ovis aries


E-MTAB-5961:Riboseq CHX pool

characteristic: INSDC last update

text: public

text: E-MTAB-5961:Riboseq CHX pool

tag: Namespace:INGM, National Institute of Molecular Genetics, “Romeo ed Enrica Invernizzi”, Milan, Italy

text: ArrayExpress

text: T-helper 1 cell

characteristic: cell type

text: human

text: Protocols: Naive CD4+ T cells purified from the blood of healthy donors were polarized in vitro to TH1 in RPMI media with 10% FBS, 0.1% Penicillin/Streptomycin 0.1 % nonessential amino acids and 0,1% Sodium Pyruvate at 37°C and 5% CO2. For Riboseq samples, RNA footprints were extracted according to Ingolia et al., 2012 DOI : 10.1038/nprot.2012.086. Libraries for Riboseq were prepared according to Ingolia et al., 2012 DOI :10.1038/nprot.2012.086.

text: normal

characteristic: disease

text: Homo sapiens

text: Homo sapiens

text: blood

characteristic: organism part

text: Riboseq

characteristic: protocol

text: Homo sapiens

text: Riboseq CHX pool


E-MTAB-5961:RNA-seq CHX 1

text: INGM, National Institute of Molecular Genetics, “Romeo ed Enrica Invernizzi”, Milan, Italy

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-5961:RNA-seq CHX 1

characteristic: Submitter Id

text: ArrayExpress

text: T-helper 1 cell

text: human

text: Protocols: Naive CD4+ T cells purified from the blood of healthy donors were polarized in vitro to TH1 in RPMI media with 10% FBS, 0.1% Penicillin/Streptomycin 0.1 % nonessential amino acids and 0,1% Sodium Pyruvate at 37°C and 5% CO2. For RNAseq samples, RNA was extracted using the mirVana isolation kit according to manufacturer's instructions (mirVana ThermoFisher #AM 1560) Libraries for RNAseq were prepared using Illumina TruSeq Stranded Total RNA Library Prep Kit

text: normal

text: Homo sapiens

text: Homo sapiens

text: blood

text: RNA-seq

text: Homo sapiens

text: RNA-seq CHX 1


E-MTAB-5961:RNA-seq CHX 2

characteristic: ENA-FIRST-PUBLIC

text: public

text: E-MTAB-5961:RNA-seq CHX 2

text: ArrayExpress

characteristic: broker name

text: T-helper 1 cell

text: human

text: normal

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: blood

text: RNA-seq

text: Homo sapiens

text: RNA-seq CHX 2


E-MTAB-5961:RNA-seq CHX 3

characteristic: ENA-CHECKLIST

characteristic: ENA-LAST-UPDATE

text: public

text: E-MTAB-5961:RNA-seq CHX 3

text: ArrayExpress

text: T-helper 1 cell

text: human

characteristic: common name

text: normal

text: Homo sapiens

text: Homo sapiens

text: blood

text: RNA-seq

text: Homo sapiens

text: RNA-seq CHX 3


characteristic: External Id

text: KAIST

characteristic: INSDC center name

text: public

text: Escherichia coli str. K-12 substr. MG1655

characteristic: title


text: KAIST

characteristic: INSDC first public

characteristic: INSDC last update

text: public


text: public

tag: Namespace:Department of Computer Science and Applied Mathematics, Weizmann Institute of Science

text: ArrayExpress

characteristic: cell line

text: embryonic stem cell

characteristic: cell type

text: human

text: Protocols: Followed by ~2 weeks of growth, a single clone was selected and detached to enable selection and picking of single cells. For the cell picking procedure cells were treated as described in (Biezuner et al. Genome Research. 2016) with the exception that prior to picking to scWGA reactions, cells were detached and dissociated using 550 U/ml StemPro Accutase Cell Dissociation Reagent (Gibco), incubated for 6 minutes, pulled down, re-suspended in iMEFs Conditioned hESC medium (CM) and were spread over a 6cm non-adherent petri dish.At the day of the experiment, before cell treatment, in order to minimize contamination, a clean working environment was established: bench and pipettes were RNase and DNA decontaminated (RNase AWAY, Molecular BioProducts) and consumables (PCR plates, tubes, tips etc.), non-kit reagents (PCR grade water, buffers etc.) and pipettes were UV irradiated. Individual cells were picked and deposited in separated single wells in dedicated 96-well PCR plates (Axigen, each kit in a separate plate), containing the required reagent. All pickings were performed on the same clone and at the same day (besides GPHI-SC, which was performed a few days later due to technical reasons). 1µl of positive (100pg Hela genomic DNA, NEB) and negative (water) controls were added as templates to non-deposited reaction wells. Samples were directly processed by their appropriate scWGA protocol. All reagents were immediately or sequentially (depending on the protocol) added to the original picking well, without material transfer, to avoid material loss. H1 human ES cells (WA01) were obtained from the WiCell Research Institute (Madison, WI). In order to create single cell (SC) clones, SCs were picked and deposited in separated single 96 wells using an automated cell picking device (CellCelector, ALS). Cells were cultured and treated as described in (Biezuner et al. Genome Research. 2016) The following scWGA kits were used (Kit short in manuscript, Kit name, Cat. Number, WGA technique, Manufacturer): Ampli1, Ampli1 WGA Kit, WG 001 050 R02, Linker adapter PCR (LA-PCR), Silicon Biosystems MALBAC, MALBAC Single Cell WGA Kit, YK001B, Multiple Annealing and Looping Based Amplification Cycles (MALBAC), Yikon Genomics GenomePlex, GenomePlex Single Cell Whole Genome Amplification Kit (WGA4), WGA4, Degenerate oligonucleotide-primed PCR (DOP-PCR), Sigma PicoPlex, PicoPLEX WGA Kit, E2620S, displacement DOP-PCR (D-DOP-PCR), New England Biolabs (manufactured by Rubicon) GPHI-SC, illustra Single Cell GenomiPhi DNA Amplification Kit, 29-1081-07, Multiple Displacement amplification (MDA), GE Healthcare RepliG-SC, REPLI-g Single Cell Kit, 150345, MDA, Qiagen TruePrime, TruePrime Single Cell WGA kit, 350025, MDA, SYGNIS Targeted enrichment using Access Array (Fluidigm) using the protocol as described in (Biezuner et al. Genome Research. 2016.) Sequencing primers are described in manuscript Supplementary Table 1.

characteristic: description

text: Homo sapiens

text: Homo sapiens

characteristic: scWGA kit

text: Homo sapiens


text: Department of Computer Science and Applied Mathematics, Weizmann Institute of Science

text: public

characteristic: INSDC status

characteristic: SRA accession

text: ArrayExpress

text: embryonic stem cell

text: human

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens


characteristic: ENA-FIRST-PUBLIC

text: public

characteristic: Submitter Id

text: ArrayExpress

text: embryonic stem cell

text: human

text: Homo sapiens

text: Homo sapiens

text: GenomePlex

text: Homo sapiens


text: public

text: ArrayExpress

characteristic: broker name

text: embryonic stem cell

text: human

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: GPHI-SC

text: Homo sapiens


characteristic: ENA-CHECKLIST

characteristic: ENA-LAST-UPDATE

text: public

text: ArrayExpress

text: embryonic stem cell

text: human

text: Homo sapiens

text: Homo sapiens

text: MALBAC

text: Homo sapiens


characteristic: External Id

text: public

text: ArrayExpress

text: embryonic stem cell

text: human

characteristic: common name

text: Protocols: H1 human ES cells (WA01) were obtained from the WiCell Research Institute (Madison, WI). In order to create single cell (SC) clones, SCs were picked and deposited in separated single 96 wells using an automated cell picking device (CellCelector, ALS). Cells were cultured and treated as described in (Biezuner et al. Genome Research. 2016) DNeasy Blood & Tissue Kit, Qiagen Targeted enrichment using Access Array (Fluidigm) using the protocol as described in (Biezuner et al. Genome Research. 2016.) Sequencing primers are described in manuscript Supplementary Table 1.

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens


characteristic: INSDC center name

text: public

text: ArrayExpress

text: embryonic stem cell

text: human

text: Homo sapiens

text: Homo sapiens

text: PicoPlex

text: Homo sapiens

characteristic: title


characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: ArrayExpress

text: embryonic stem cell

text: human

text: Homo sapiens

text: Homo sapiens

text: RepliG-SC

text: Homo sapiens


text: public

text: ArrayExpress

characteristic: cell line

text: embryonic stem cell

characteristic: cell type

text: human

text: Homo sapiens

text: Homo sapiens

text: TruePrime

text: Homo sapiens


text: public

text: ArrayExpress

text: HeLa

text: epithelial cell

text: human

text: Protocols: No collection. Commercial Hela genomic DNA (NEB) The following scWGA kits were used (Kit short in manuscript, Kit name, Cat. Number, WGA technique, Manufacturer): Ampli1, Ampli1 WGA Kit, WG 001 050 R02, Linker adapter PCR (LA-PCR), Silicon Biosystems MALBAC, MALBAC Single Cell WGA Kit, YK001B, Multiple Annealing and Looping Based Amplification Cycles (MALBAC), Yikon Genomics GenomePlex, GenomePlex Single Cell Whole Genome Amplification Kit (WGA4), WGA4, Degenerate oligonucleotide-primed PCR (DOP-PCR), Sigma PicoPlex, PicoPLEX WGA Kit, E2620S, displacement DOP-PCR (D-DOP-PCR), New England Biolabs (manufactured by Rubicon) GPHI-SC, illustra Single Cell GenomiPhi DNA Amplification Kit, 29-1081-07, Multiple Displacement amplification (MDA), GE Healthcare RepliG-SC, REPLI-g Single Cell Kit, 150345, MDA, Qiagen TruePrime, TruePrime Single Cell WGA kit, 350025, MDA, SYGNIS Targeted enrichment using Access Array (Fluidigm) using the protocol as described in (Biezuner et al. Genome Research. 2016.) Sequencing primers are described in manuscript Supplementary Table 1.

characteristic: description

text: Homo sapiens

text: Homo sapiens

characteristic: scWGA kit

text: Homo sapiens


text: public

characteristic: INSDC status

characteristic: SRA accession

text: ArrayExpress

text: HeLa

text: epithelial cell

text: human

text: Homo sapiens

text: Homo sapiens

text: GenomePlex

text: Homo sapiens


characteristic: ENA-FIRST-PUBLIC

text: public

characteristic: Submitter Id

text: ArrayExpress

text: HeLa

text: epithelial cell

text: human

text: Homo sapiens

text: Homo sapiens

text: GPHI-SC

text: Homo sapiens


text: public

text: ArrayExpress

characteristic: broker name

text: HeLa

text: epithelial cell

text: human

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: MALBAC

text: Homo sapiens


characteristic: ENA-CHECKLIST

characteristic: ENA-LAST-UPDATE

text: public

text: ArrayExpress

text: HeLa

text: epithelial cell

text: human

text: Protocols: No collection. Commercial Hela genomic DNA (NEB) Targeted enrichment using Access Array (Fluidigm) using the protocol as described in (Biezuner et al. Genome Research. 2016.) Sequencing primers are described in manuscript Supplementary Table 1.

text: Homo sapiens

text: Homo sapiens

text: PC - Hela

text: Homo sapiens


characteristic: External Id

text: public

text: ArrayExpress

text: HeLa

text: epithelial cell

text: human

characteristic: common name

text: Homo sapiens

text: Homo sapiens

text: PicoPlex

text: Homo sapiens


characteristic: INSDC center name

text: public

text: ArrayExpress

text: HeLa

text: epithelial cell

text: human

text: Homo sapiens

text: Homo sapiens

text: RepliG-SC

text: Homo sapiens

characteristic: title


characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: ArrayExpress

text: HeLa

text: epithelial cell

text: human

text: Homo sapiens

text: Homo sapiens

text: TruePrime

text: Homo sapiens


text: public

text: ArrayExpress

text: human

text: Protocols: No Collection. Water used as template, either for scWGA reaction or for direct NC for targeted enrichment using Access Array (Fluidigm) The following scWGA kits were used (Kit short in manuscript, Kit name, Cat. Number, WGA technique, Manufacturer): Ampli1, Ampli1 WGA Kit, WG 001 050 R02, Linker adapter PCR (LA-PCR), Silicon Biosystems MALBAC, MALBAC Single Cell WGA Kit, YK001B, Multiple Annealing and Looping Based Amplification Cycles (MALBAC), Yikon Genomics GenomePlex, GenomePlex Single Cell Whole Genome Amplification Kit (WGA4), WGA4, Degenerate oligonucleotide-primed PCR (DOP-PCR), Sigma PicoPlex, PicoPLEX WGA Kit, E2620S, displacement DOP-PCR (D-DOP-PCR), New England Biolabs (manufactured by Rubicon) GPHI-SC, illustra Single Cell GenomiPhi DNA Amplification Kit, 29-1081-07, Multiple Displacement amplification (MDA), GE Healthcare RepliG-SC, REPLI-g Single Cell Kit, 150345, MDA, Qiagen TruePrime, TruePrime Single Cell WGA kit, 350025, MDA, SYGNIS Targeted enrichment using Access Array (Fluidigm) using the protocol as described in (Biezuner et al. Genome Research. 2016.) Sequencing primers are described in manuscript Supplementary Table 1.

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens


text: public

text: ArrayExpress

text: human

text: Homo sapiens

text: Homo sapiens

text: GenomePlex

text: Homo sapiens


text: public

text: ArrayExpress

text: human

text: Homo sapiens

text: Homo sapiens

text: GPHI-SC

text: Homo sapiens


text: public

text: ArrayExpress

text: human

text: Homo sapiens

text: Homo sapiens

text: MALBAC

text: Homo sapiens


text: public

text: ArrayExpress

text: human

text: Protocols: No Collection. Water used as template, either for scWGA reaction or for direct NC for targeted enrichment using Access Array (Fluidigm) Targeted enrichment using Access Array (Fluidigm) using the protocol as described in (Biezuner et al. Genome Research. 2016.) Sequencing primers are described in manuscript Supplementary Table 1.

text: Homo sapiens

text: Homo sapiens

text: NC - DDW

text: Homo sapiens


text: public

text: ArrayExpress

text: human

text: Homo sapiens

text: Homo sapiens

text: PicoPlex

text: Homo sapiens


text: public

text: ArrayExpress

text: human

text: Homo sapiens

text: Homo sapiens

text: RepliG-SC

text: Homo sapiens


text: public

text: ArrayExpress

text: human

text: Homo sapiens

text: Homo sapiens

text: TruePrime

text: Homo sapiens


text: wangjianhua

text: public

characteristic: collection date

text: water samples from conventional and recirculating aquaculture systems

text: seawater from aquaculture system

characteristic: environment (biome)

text: seawater

characteristic: environment (feature)

text: water

characteristic: environment (material)

text: China

characteristic: geographic location (country and/or sea)

unit: m

characteristic: geographic location (depth)

unit: DD

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: metagenome

characteristic: investigation type

text: metagenome

text: Metagenomic profiles of samples from conventional and recirculating aquaculture systems

characteristic: project name

text: metagenome

text: pyrosequencing

characteristic: sequencing method

text: DF&ZZ

text: water

characteristic: water environmental package


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: sheep

characteristic: common name

characteristic: description

text: Ovis aries

characteristic: organism

text: Ovis aries

text: Female

characteristic: sex

text: ovary

characteristic: tissue type


text: Plasmodium falciparum

characteristic: ArrayExpress-SPECIES

text: SC

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: malaria parasite P. falciparum

text: Plasmodium falciparum

text: Plasmodium falciparum

characteristic: subject id

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: IPK-Gatersleben

text: public

text: domesticated barley

text: Genomic DNA isolated from leaf tissue

text: Hordeum vulgare subsp. vulgare

text: Hordeum vulgare subsp. vulgare

text: Genotype 'Barke'


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: IPK-Gatersleben

text: public

text: domesticated barley

text: Genomic DNA isolated from leaf tissue

text: Hordeum vulgare subsp. vulgare

text: Hordeum vulgare subsp. vulgare

text: Genotype 'HOR 10350'


text: IPK-Gatersleben

text: public

characteristic: INSDC status

characteristic: SRA accession

text: wild barley

text: Genomic DNA isolated from leaf tissue

text: Hordeum vulgare subsp. spontaneum

text: Hordeum vulgare subsp. spontaneum

text: Genotype 'B1K-04-12'


text: Skin

characteristic: ArrayExpress-PHENOTYPE

text: male

characteristic: ArrayExpress-SEX

text: Mus musculus

text: SC

text: public

characteristic: Submitter Id

text: house mouse

characteristic: common name

text: Male

characteristic: gender

text: Mus musculus

text: Skin

characteristic: phenotype

text: Mus musculus


text: Skin

text: female

text: Mus musculus

characteristic: ArrayExpress-SPECIES

text: SC

characteristic: INSDC center name

text: public

text: house mouse

text: Female

text: Mus musculus

characteristic: organism

text: Skin

text: Mus musculus


text: Liver

text: male

text: Mus musculus

text: SC

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: house mouse

text: Male

text: Mus musculus

text: Liver

text: Mus musculus

characteristic: subject id


text: Liver

text: female

text: Mus musculus

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: SC

text: public

text: house mouse

text: Female

text: Mus musculus

text: Liver

text: Mus musculus

characteristic: title


E-MTAB-5967:Prep ChIP 3.5hpf rep1

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: UOM

text: public

characteristic: INSDC status

text: E-MTAB-5967:Prep ChIP 3.5hpf rep1

unit: hour

characteristic: age

text: ArrayExpress

characteristic: broker name

text: zebrafish

text: Protocols: Groups of 500 zebrafish embryos (total of 10,000 at 3.5hpf and 5,000 at 12hpf per biological replicate) were dissociated in 1XPBS by pipetting and fixed for 10 minutes in 1% formaldehyde. Fixation was stopped by the addition of glycin to a final concentration of 125mM and cells were pelleted and frozen in liquid nitrogen. DNA fragments were recovered in 10μl nuclease free water using a PCR purification mini-elute kit (Qiagen). Cell pellets were processed following a ChIP protocol described previously (Amin et al., 2015). Nuclei were extracted by the addition of 500μl L1 buffer (50mM Tris-HCl pH8.0, 2mM EDTA, 0.1% NP-40, 10% glycerol, 1mM PMSF) followed by incubation for 5 minutes on ice and pelleted by centrifugation (3000rpm, 5 minutes at 8°C). Nuclei were lysed in 300μl SDS lysis buffer (50mM Tris-HCl pH8.0, 10mM EDTA, 1% SDS) and chromatin sheared into smaller fragments (300bp on average) by 3 rounds of sonication with a Palmer sonicator (10 seconds ON - 2 seconds OFF for a total of 1 minute per round, amplitude 40%). Samples were diluted 10 times in dilution buffer (50mM Tris-HCl pH8.0, 5mM EDTA, 200mM NaCl, 0.5% NP-40, 1mM PMSF) and pre-cleared by the addition of 50μl protein-A dynabeads (ThermoFisher Scientific) and incubation for 3 hours at 4°C. After removal of the beads, 10ul of anti-Prep or pre-bleed antiserum was added (see Key Resources Table for a full list of antibodies used in this study). Immune complexes were precipitated by the addition of 50μl of protein-A dynabeads (ThermoFisher Scientific) and incubated for 3 hours at 4°C. Beads were washed 5 times in wash buffer (20mM Tris-HCl pH8.0, 2mM EDTA, 500mM NaCl, 1% NP-40, 0.1% SDS, 1mM PMSF), 3 times in LiCl buffer (20mM Tris-HCl pH8.0, 2mM EDTA, 500mM LiCl, 1% NP-40, 0.1% SDS, 1mM PMSF) and 3 times in TE buffer (10mM Tris-HCl pH8.0, 1mM EDTA, 1mM PMSF). Chromatin fragments were eluted by the addition of 50μl of freshly made elution buffer (10mM Tris-HCl pH8.0, 1mM EDTA, 2% SDS) and incubation at 25°C for 15 minutes followed by an incubation at 65°C for another 15 minutes. Then, DNA fragments were reverse cross-linked by adding 2.5μl of 5M NaCl and incubating at 65°C O/N. Finally, DNA fragments were recovered in 10μl nuclease free water using a PCR purification mini-elute kit (Qiagen). ChIP DNA fragments and their corresponding Input were quantified on a Qubit with the dsDNA HS assay kit (ThermoFisher Scientific). 10ng of DNA was used for library preparation using the Tru-seq ChIP Sample Preparation Guide (Illumina Inc). For samples containing less than 10ng of DNA the entire eluted DNA was used. Briefly, sample DNA was blunt-ended and phosphorylated, and a single 'A' nucleotide added to the 3' ends of the fragments in preparation for ligation to an adapter with a single-base 'T' overhang. Omitting the size selection step, the ligation products were then PCR-amplified to enrich for fragments with adapters on both ends. Libraries were sequenced on an Illumina HiSeq2500 Sequencer. Amin, S., Donaldson, I.J., Zannino, D.A., Hensman, J., Rattray, M., Losa, M., Spitz, F., Ladam, F., Sagerstrom, C., Bobola, N., 2015. Hoxa2 selectively enhances Meis binding to change a branchial arch ground state. Dev. Cell 32, 265-277. doi:10.1016/j.devcel.2014.12.024

characteristic: description

text: embryo

characteristic: developmental stage

text: Danio rerio

text: Danio rerio

text: whole organism

characteristic: organism part

text: Danio rerio

text: Prep ChIP 3.5hpf rep1


E-MTAB-5967:Prep ChIP 3.5hpf rep2

text: UOM

text: public

characteristic: SRA accession

text: E-MTAB-5967:Prep ChIP 3.5hpf rep2

characteristic: Submitter Id

text: ArrayExpress

text: zebrafish

characteristic: common name

text: embryo

text: Danio rerio

text: Danio rerio

text: whole organism

text: Danio rerio

text: Prep ChIP 3.5hpf rep2


E-MTAB-5967:Prep Input 3.5hpf rep1

text: UOM

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: E-MTAB-5967:Prep Input 3.5hpf rep1

text: ArrayExpress

text: zebrafish

text: embryo

text: Danio rerio

characteristic: organism

text: Danio rerio

text: whole organism

text: Danio rerio

text: Prep Input 3.5hpf rep1


E-MTAB-5967:Prep Input 3.5hpf rep2

characteristic: ENA-CHECKLIST

text: UOM

characteristic: INSDC last update

text: public

text: E-MTAB-5967:Prep Input 3.5hpf rep2

text: ArrayExpress

text: zebrafish

text: embryo

text: Danio rerio

text: Danio rerio

text: whole organism

text: Danio rerio

text: Prep Input 3.5hpf rep2


E-MTAB-5967:Prep ChIP 12hpf rep1

characteristic: ENA-FIRST-PUBLIC

text: UOM

text: public

text: E-MTAB-5967:Prep ChIP 12hpf rep1

text: ArrayExpress

text: zebrafish

text: embryo

text: Danio rerio

text: Danio rerio

text: whole organism

text: Danio rerio

text: Prep ChIP 12hpf rep1

characteristic: title


E-MTAB-5967:Prep ChIP 12hpf rep2

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: UOM

text: public

text: E-MTAB-5967:Prep ChIP 12hpf rep2

text: ArrayExpress

text: zebrafish

text: embryo

text: Danio rerio

text: Danio rerio

text: whole organism

text: Danio rerio

text: Prep ChIP 12hpf rep2


E-MTAB-5967:Prep Input 12hpf rep1

text: UOM

text: public

characteristic: INSDC status

text: E-MTAB-5967:Prep Input 12hpf rep1

characteristic: age

text: ArrayExpress

text: zebrafish

text: embryo

text: Danio rerio

text: Danio rerio

text: whole organism

text: Danio rerio

text: Prep Input 12hpf rep1


E-MTAB-5967:Prep Input 12hpf rep2

text: UOM

text: public

text: E-MTAB-5967:Prep Input 12hpf rep2

text: ArrayExpress

characteristic: broker name

text: zebrafish

characteristic: description

text: embryo

text: Danio rerio

text: Danio rerio

text: whole organism

text: Danio rerio

text: Prep Input 12hpf rep2


RRBS_IL-10eGFP- day 1 R1

text: Universitaet des Saarlandes

text: public

text: RRBS_IL-10eGFP- day 1 R1

tag: Namespace:Universitaet des Saarlandes

text: todo

text: house mouse

text: Mus musculus

text: Mus musculus

text: female

characteristic: sex

characteristic: strain

text: Spleen

characteristic: tissue type

text: RRBS_IL-10eGFP- day 1 R1


RRBS_IL-10eGFP- day 1 R2

text: Universitaet des Saarlandes

text: public

characteristic: SRA accession

text: RRBS_IL-10eGFP- day 1 R2

characteristic: Submitter Id

text: todo

text: house mouse

characteristic: common name

text: Mus musculus

text: Mus musculus

text: female

text: Spleen

text: RRBS_IL-10eGFP- day 1 R2


RRBS_IL-10eGFP- day 1 R3

text: Universitaet des Saarlandes

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: RRBS_IL-10eGFP- day 1 R3

text: todo

text: house mouse

text: Mus musculus

characteristic: organism

text: Mus musculus

text: female

text: Spleen

text: RRBS_IL-10eGFP- day 1 R3


RRBS_LAG-3- day 1 R1

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: Universitaet des Saarlandes

characteristic: INSDC last update

text: public

text: RRBS_LAG-3- day 1 R1

text: todo

text: house mouse

text: Mus musculus

text: Mus musculus

text: female

text: Spleen

text: RRBS_LAG-3- day 1 R1


RRBS_LAG-3- day 1 R3

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Universitaet des Saarlandes

text: public

text: RRBS_LAG-3- day 1 R3

text: todo

text: house mouse

text: Mus musculus

text: Mus musculus

text: female

text: Spleen

text: RRBS_LAG-3- day 1 R3

characteristic: title


RRBS_LAG-3- day 1 R2

text: Universitaet des Saarlandes

text: public

characteristic: INSDC status

text: RRBS_LAG-3- day 1 R2

text: todo

characteristic: age

text: house mouse

text: Mus musculus

text: Mus musculus

text: female

text: Spleen

text: RRBS_LAG-3- day 1 R2


RRBS_LAG-3+ day 1 R1

text: Universitaet des Saarlandes

text: public

text: RRBS_LAG-3+ day 1 R1

text: todo

text: house mouse

text: Mus musculus

text: Mus musculus

text: female

characteristic: sex

text: Spleen

text: RRBS_LAG-3+ day 1 R1


RRBS_LAG-3+ day 1 R2

text: Universitaet des Saarlandes

text: public

text: RRBS_LAG-3+ day 1 R2

text: todo

text: house mouse

text: Mus musculus

text: Mus musculus

text: female

characteristic: strain

text: Spleen

text: RRBS_LAG-3+ day 1 R2


RRBS_LAG-3+ day 1 R3

text: Universitaet des Saarlandes

text: public

text: RRBS_LAG-3+ day 1 R3

text: todo

text: house mouse

text: Mus musculus

text: Mus musculus

text: female

text: Spleen

characteristic: tissue type

text: RRBS_LAG-3+ day 1 R3


RRBS_IL-10eGFP+ day 1 R1

text: Universitaet des Saarlandes

text: public

characteristic: SRA accession

text: RRBS_IL-10eGFP+ day 1 R1

text: todo

text: house mouse

text: Mus musculus

text: Mus musculus

text: female

text: Spleen

text: RRBS_IL-10eGFP+ day 1 R1


RRBS_IL-10eGFP+ day 1 R2

text: Universitaet des Saarlandes

text: public

text: RRBS_IL-10eGFP+ day 1 R2

characteristic: Submitter Id

text: todo

text: house mouse

text: Mus musculus

text: Mus musculus

text: female

text: Spleen

text: RRBS_IL-10eGFP+ day 1 R2


RRBS_IL-10eGFP+ day 1 R3

text: Universitaet des Saarlandes

text: public

text: RRBS_IL-10eGFP+ day 1 R3

text: todo

text: house mouse

characteristic: common name

text: Mus musculus

text: Mus musculus

text: female

text: Spleen

text: RRBS_IL-10eGFP+ day 1 R3


RRBS_LAG-3+ R1

text: Universitaet des Saarlandes

characteristic: INSDC center name

text: public

text: RRBS_LAG-3+ R1

text: todo

text: house mouse

text: Mus musculus

text: Mus musculus

text: female

text: Spleen

text: RRBS_LAG-3+ R1


RRBS_LAG-3+ R2

text: Universitaet des Saarlandes

characteristic: INSDC first public

text: public

text: RRBS_LAG-3+ R2

text: todo

text: house mouse

text: Mus musculus

text: Mus musculus

text: female

text: Spleen

text: RRBS_LAG-3+ R2


RRBS_LAG-3+ R3

text: Universitaet des Saarlandes

text: public

text: RRBS_LAG-3+ R3

text: todo

text: house mouse

text: Mus musculus

characteristic: organism

text: Mus musculus

text: female

text: Spleen

text: RRBS_LAG-3+ R3


RRBS_LAG-3- R1

characteristic: ENA-CHECKLIST

text: Universitaet des Saarlandes

text: public

text: RRBS_LAG-3- R1

text: todo

text: house mouse

text: Mus musculus

text: Mus musculus

text: female

text: Spleen

text: RRBS_LAG-3- R1


RRBS_LAG-3- R2

characteristic: ENA-FIRST-PUBLIC

text: Universitaet des Saarlandes

text: public

text: RRBS_LAG-3- R2

text: todo

text: house mouse

text: Mus musculus

text: Mus musculus

text: female

text: Spleen

text: RRBS_LAG-3- R2


RRBS_LAG-3- R3

text: Universitaet des Saarlandes

characteristic: INSDC last update

text: public

text: RRBS_LAG-3- R3

text: todo

text: house mouse

text: Mus musculus

text: Mus musculus

text: female

text: Spleen

text: RRBS_LAG-3- R3


RRBS_B1a R1

characteristic: ENA-LAST-UPDATE

text: Universitaet des Saarlandes

text: public

text: RRBS_B1a R1

text: todo

text: house mouse

text: Mus musculus

text: Mus musculus

text: female

text: Peritoneal cavity

text: RRBS_B1a R1


RRBS_B1a R2

characteristic: External Id

text: Universitaet des Saarlandes

text: public

text: RRBS_B1a R2

text: todo

text: house mouse

text: Mus musculus

text: Mus musculus

text: female

text: Peritoneal cavity

text: RRBS_B1a R2


RRBS_B1a R3

text: Universitaet des Saarlandes

text: public

text: RRBS_B1a R3

text: todo

text: house mouse

text: Mus musculus

text: Mus musculus

text: female

text: Peritoneal cavity

text: RRBS_B1a R3

characteristic: title


RRBS_B1b R1

text: Universitaet des Saarlandes

text: public

characteristic: INSDC status

text: RRBS_B1b R1

text: todo

text: house mouse

text: Mus musculus

text: Mus musculus

text: female

text: Peritoneal cavity

text: RRBS_B1b R1


RRBS_B1b R2

text: Universitaet des Saarlandes

text: public

text: RRBS_B1b R2

text: todo

characteristic: age

text: house mouse

text: Mus musculus

text: Mus musculus

text: female

text: Peritoneal cavity

text: RRBS_B1b R2


RRBS_B1b R3

text: Universitaet des Saarlandes

text: public

text: RRBS_B1b R3

text: todo

text: house mouse

text: Mus musculus

text: Mus musculus

text: female

characteristic: sex

text: Peritoneal cavity

text: RRBS_B1b R3


RRBS_B2 R1

text: Universitaet des Saarlandes

text: public

text: RRBS_B2 R1

text: todo

text: house mouse

text: Mus musculus

text: Mus musculus

text: female

characteristic: strain

text: Peritoneal cavity

text: RRBS_B2 R1


RRBS_B2 R3

text: Universitaet des Saarlandes

text: public

text: RRBS_B2 R3

text: todo

text: house mouse

text: Mus musculus

text: Mus musculus

text: female

text: Peritoneal cavity

characteristic: tissue type

text: RRBS_B2 R3


RRBS_B2 R2

text: Universitaet des Saarlandes

text: public

characteristic: SRA accession

text: RRBS_B2 R2

text: todo

text: house mouse

text: Mus musculus

text: Mus musculus

text: female

text: Peritoneal cavity

text: RRBS_B2 R2


RRBS_T1 R1

text: Universitaet des Saarlandes

text: public

text: RRBS_T1 R1

characteristic: Submitter Id

text: todo

text: house mouse

text: Mus musculus

text: Mus musculus

text: female

text: Spleen

text: RRBS_T1 R1


RRBS_T1 R2

text: Universitaet des Saarlandes

text: public

text: RRBS_T1 R2

text: todo

text: house mouse

characteristic: common name

text: Mus musculus

text: Mus musculus

text: female

text: Spleen

text: RRBS_T1 R2


RRBS_T1 R3

text: Universitaet des Saarlandes

characteristic: INSDC center name

text: public

text: RRBS_T1 R3

text: todo

text: house mouse

text: Mus musculus

text: Mus musculus

text: female

text: Spleen

text: RRBS_T1 R3


RRBS_T2 R1

text: Universitaet des Saarlandes

characteristic: INSDC first public

text: public

text: RRBS_T2 R1

text: todo

text: house mouse

text: Mus musculus

text: Mus musculus

text: female

text: Spleen

text: RRBS_T2 R1


RRBS_T2 R2

text: Universitaet des Saarlandes

text: public

text: RRBS_T2 R2

text: todo

text: house mouse

text: Mus musculus

characteristic: organism

text: Mus musculus

text: female

text: Spleen

text: RRBS_T2 R2


RRBS_T2 R3

characteristic: ENA-CHECKLIST

text: Universitaet des Saarlandes

text: public

text: RRBS_T2 R3

text: todo

text: house mouse

text: Mus musculus

text: Mus musculus

text: female

text: Spleen

text: RRBS_T2 R3


RRBS_MZ R1

characteristic: ENA-FIRST-PUBLIC

text: Universitaet des Saarlandes

text: public

text: RRBS_MZ R1

text: todo

text: house mouse

text: Mus musculus

text: Mus musculus

text: female

text: Spleen

text: RRBS_MZ R1


RRBS_MZ R2

text: Universitaet des Saarlandes

characteristic: INSDC last update

text: public

text: RRBS_MZ R2

text: todo

text: house mouse

text: Mus musculus

text: Mus musculus

text: female

text: Spleen

text: RRBS_MZ R2


RRBS_MZ R3

characteristic: ENA-LAST-UPDATE

text: Universitaet des Saarlandes

text: public

text: RRBS_MZ R3

text: todo

text: house mouse

text: Mus musculus

text: Mus musculus

text: female

text: Spleen

text: RRBS_MZ R3


RRBS_FO R1

characteristic: External Id

text: Universitaet des Saarlandes

text: public

text: RRBS_FO R1

text: todo

text: house mouse

text: Mus musculus

text: Mus musculus

text: female

text: Spleen

text: RRBS_FO R1


RRBS_FO R2

text: Universitaet des Saarlandes

text: public

text: RRBS_FO R2

text: todo

text: house mouse

text: Mus musculus

text: Mus musculus

text: female

text: Spleen

text: RRBS_FO R2

characteristic: title


RRBS_FO R3

text: Universitaet des Saarlandes

text: public

characteristic: INSDC status

text: RRBS_FO R3

text: todo

text: house mouse

text: Mus musculus

text: Mus musculus

text: female

text: Spleen

text: RRBS_FO R3


mRNA_LAG-3- day 1 R1

text: Universitaet des Saarlandes

text: public

text: mRNA_LAG-3- day 1 R1

text: todo

characteristic: age

text: house mouse

text: Mus musculus

text: Mus musculus

text: female

text: Spleen

text: mRNA_LAG-3- day 1 R1


mRNA_LAG-3- day 1 R2

text: Universitaet des Saarlandes

text: public

text: mRNA_LAG-3- day 1 R2

text: todo

text: house mouse

text: Mus musculus

text: Mus musculus

text: female

characteristic: sex

text: Spleen

text: mRNA_LAG-3- day 1 R2


mRNA_LAG-3- day 1 R3

text: Universitaet des Saarlandes

text: public

text: mRNA_LAG-3- day 1 R3

text: todo

text: house mouse

text: Mus musculus

text: Mus musculus

text: female

characteristic: strain

text: Spleen

text: mRNA_LAG-3- day 1 R3


mRNA_LAG-3- R1

text: Universitaet des Saarlandes

text: public

text: mRNA_LAG-3- R1

text: todo

text: house mouse

text: Mus musculus

text: Mus musculus

text: female

text: Spleen

characteristic: tissue type

text: mRNA_LAG-3- R1


mRNA_LAG-3- R2

text: Universitaet des Saarlandes

text: public

characteristic: SRA accession

text: mRNA_LAG-3- R2

text: todo

text: house mouse

text: Mus musculus

text: Mus musculus

text: female

text: Spleen

text: mRNA_LAG-3- R2


mRNA_LAG-3+ R1

text: Universitaet des Saarlandes

text: public

text: mRNA_LAG-3+ R1

characteristic: Submitter Id

text: todo

text: house mouse

text: Mus musculus

text: Mus musculus

text: female

text: Spleen

text: mRNA_LAG-3+ R1


mRNA_LAG-3+ R2

text: Universitaet des Saarlandes

text: public

text: mRNA_LAG-3+ R2

text: todo

text: house mouse

characteristic: common name

text: Mus musculus

text: Mus musculus

text: female

text: Spleen

text: mRNA_LAG-3+ R2


mRNA_LAG-3+ day 1 R1

text: Universitaet des Saarlandes

characteristic: INSDC center name

text: public

text: mRNA_LAG-3+ day 1 R1

text: todo

text: house mouse

text: Mus musculus

text: Mus musculus

text: female

text: Spleen

text: mRNA_LAG-3+ day 1 R1


mRNA_LAG-3+ day 1 R2

text: Universitaet des Saarlandes

characteristic: INSDC first public

text: public

text: mRNA_LAG-3+ day 1 R2

text: todo

text: house mouse

text: Mus musculus

text: Mus musculus

text: female

text: Spleen

text: mRNA_LAG-3+ day 1 R2


text: Bifidobacterium

characteristic: ArrayExpress-Phenotype

text: Bifidobacterium choerinum

characteristic: ArrayExpress-Species

text: SC

text: public

text: Bifidobacterium choerinum

text: Bifidobacterium choerinum

characteristic: organism

text: Bacterial DNA

characteristic: sample description

text: Bifidobacterium choerinum


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: NATIONAL CENTRE FOR BIOLOGICAL SCIENCES

characteristic: INSDC last update

text: public

tag: Namespace:NATIONAL CENTRE FOR BIOLOGICAL SCIENCES

characteristic: collection date

text: EnvO

characteristic: environment (biome)

text: EnvO

characteristic: environment (feature)

text: EnvO

characteristic: environment (material)

text: India

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: host-associated

characteristic: host-associated environmental package

text: metagenome

characteristic: investigation type

text: insect gut metagenome

text: Bacterial communities associated with butterflies

characteristic: project name

text: insect gut metagenome

text: Illumina

characteristic: sequencing method

text: Elymnias caudata (Larva1)


characteristic: External Id

text: NATIONAL CENTRE FOR BIOLOGICAL SCIENCES

characteristic: INSDC center name

characteristic: INSDC first public

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: EnvO

text: EnvO

text: EnvO

text: India

text: host-associated

text: metagenome

text: insect gut metagenome

characteristic: organism

text: insect gut metagenome

text: Illumina

text: Elymnias caudata (Larva2)

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: NATIONAL CENTRE FOR BIOLOGICAL SCIENCES

characteristic: INSDC last update

text: public

characteristic: collection date

text: EnvO

characteristic: environment (biome)

text: EnvO

characteristic: environment (feature)

text: EnvO

text: India

text: host-associated

text: metagenome

text: insect gut metagenome

text: insect gut metagenome

text: Illumina

text: Elymnias caudata (Pupa1)


text: NATIONAL CENTRE FOR BIOLOGICAL SCIENCES

text: public

text: EnvO

text: EnvO

text: EnvO

characteristic: environment (material)

text: India

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: host-associated

characteristic: host-associated environmental package

text: metagenome

characteristic: investigation type

text: insect gut metagenome

characteristic: project name

text: insect gut metagenome

text: Illumina

text: Elymnias caudata (Pupa2)


characteristic: External Id

text: NATIONAL CENTRE FOR BIOLOGICAL SCIENCES

characteristic: INSDC center name

characteristic: INSDC first public

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: EnvO

text: EnvO

text: EnvO

text: India

text: host-associated

text: metagenome

text: insect gut metagenome

text: insect gut metagenome

text: Illumina

characteristic: sequencing method

text: Elymnias caudata (Pupa3)


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: NATIONAL CENTRE FOR BIOLOGICAL SCIENCES

characteristic: INSDC last update

text: public

characteristic: collection date

text: EnvO

text: EnvO

text: EnvO

text: India

text: host-associated

text: metagenome

text: insect gut metagenome

characteristic: organism

text: insect gut metagenome

text: Illumina

text: Elymnias caudata (Adult1)

characteristic: title


text: NATIONAL CENTRE FOR BIOLOGICAL SCIENCES

text: public

text: EnvO

characteristic: environment (biome)

text: EnvO

characteristic: environment (feature)

text: EnvO

characteristic: environment (material)

text: India

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: host-associated

characteristic: host-associated environmental package

text: metagenome

text: insect gut metagenome

text: insect gut metagenome

text: Illumina

text: Elymnias caudata (Adult2)


characteristic: External Id

text: NATIONAL CENTRE FOR BIOLOGICAL SCIENCES

characteristic: INSDC center name

characteristic: INSDC first public

text: public

characteristic: INSDC status

characteristic: SRA accession

text: EnvO

text: EnvO

text: EnvO

text: India

text: host-associated

text: metagenome

characteristic: investigation type

text: insect gut metagenome

characteristic: project name

text: insect gut metagenome

text: Illumina

text: Elymnias caudata (Adult3)


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: UNIV-WUE

characteristic: INSDC last update

text: public

characteristic: Submitter Id

characteristic: collection date

text: Koompassia malaccensis

characteristic: common name

text: peat swamp forest

text: peat swamp

text: peat

text: Malaysia

characteristic: geographic location (depth)

characteristic: geographic location (elevation)

text: mimarks-survey

text: Koompassia malaccensis

text: Peat Swamp Microbiota

text: Koompassia malaccensis

text: MiSeq Amplicons

characteristic: sequencing method

text: soil

characteristic: soil environmental package

text: Peat Sample


characteristic: External Id

text: UNIV-WUE

characteristic: INSDC center name

text: public

text: Shorea uliginosa

text: peat swamp forest

characteristic: environment (biome)

text: peat swamp

characteristic: environment (feature)

text: peat

characteristic: environment (material)

text: Malaysia

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: mimarks-survey

text: Shorea uliginosa

characteristic: organism

text: Peat Swamp Microbiota

text: Shorea uliginosa

text: MiSeq Amplicons

text: soil

text: Peat Sample

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: UNIV-WUE

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: Eleiodoxa conferta

text: peat swamp forest

text: peat swamp

text: peat

text: Malaysia

text: mimarks-survey

characteristic: investigation type

text: Eleiodoxa conferta

text: Peat Swamp Microbiota

characteristic: project name

text: Eleiodoxa conferta

text: MiSeq Amplicons

text: soil

text: Peat Sample


characteristic: External Id

text: UNIV-WUE

characteristic: INSDC center name

text: public

characteristic: collection date

text: mimarks-survey

characteristic: description

text: peat swamp forest

characteristic: environment (biome)

text: peat swamp

characteristic: environment (feature)

text: peat

text: Malaysia

characteristic: geographic location (depth)

characteristic: geographic location (elevation)

text: mimarks-survey

text: unidentified

text: Peat Swamp Microbiota

text: unidentified

text: MiSeq Amplicons

characteristic: sequencing method

text: soil

characteristic: soil environmental package

text: Control Sample


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: St Andrews Bioinformatics Unit

characteristic: INSDC first public

text: public

tag: Namespace:St Andrews Bioinformatics Unit

text: Right antecubital fossa,lateral border, 18 hour enriched colony 1

text: United Kingdom

characteristic: geographic location (country and/or sea)

text: diseased

characteristic: host health state

text: Homo sapiens

characteristic: host scientific name

characteristic: isolate

text: Skin

characteristic: isolation source

text: 56.46/ -2.99

characteristic: lat lon

text: Staphylococcus aureus

characteristic: organism

text: Staphylococcus aureus

text: Right nostril, 18 hour enriched colony 4

characteristic: title


characteristic: External Id

text: St Andrews Bioinformatics Unit

characteristic: INSDC center name

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

characteristic: collection date

text: Right antecubital fossa,lateral border, 18 hour enriched colony 3

characteristic: description

text: United Kingdom

text: diseased

text: Homo sapiens

text: Skin

text: 56.46/ -2.99

text: Staphylococcus aureus

text: Staphylococcus aureus

text: Left popliteal fossa medial border, colony 8


text: Corynebacterium renale

characteristic: ArrayExpress-SPECIES

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: SC

characteristic: INSDC first public

text: public

text: Corynebacterium renale

characteristic: common name

text: Corynebacterium renale

text: Corynebacterium renale

characteristic: subject id


text: Suttonella indologenes

text: SC

text: public

text: Suttonella indologenes

text: Suttonella indologenes

characteristic: organism

text: Suttonella indologenes


text: Streptobacillus moniliformis

text: SC

text: public

text: Streptobacillus moniliformis

text: Streptobacillus moniliformis

text: Streptobacillus moniliformis

characteristic: title


text: Fusobacterium naviforme

characteristic: External Id

text: SC

text: public

text: Fusobacterium naviforme

text: Fusobacterium naviforme

text: Fusobacterium naviforme


text: Shigella dysenteriae

text: SC

characteristic: INSDC center name

text: public

text: Shigella dysenteriae

text: Shigella dysenteriae

text: Shigella dysenteriae


text: Neisseria meningitidis

text: SC

characteristic: INSDC last update

text: public

text: Neisseria meningitidis

text: Neisseria meningitidis

text: Neisseria meningitidis


text: Burkholderia pseudomallei

text: SC

text: public

characteristic: INSDC status

text: Burkholderia pseudomallei

text: Burkholderia pseudomallei

text: Burkholderia pseudomallei


text: Actinomadura pelletieri

text: SC

text: public

characteristic: SRA accession

text: Actinomadura pelletieri

text: Actinomadura pelletieri

text: Actinomadura pelletieri


text: Corynebacterium jeikeium

text: SC

text: public

characteristic: Submitter Id

text: Corynebacterium jeikeium

text: Corynebacterium jeikeium

text: Corynebacterium jeikeium


text: Bergeyella zoohelcum

text: SC

text: public

text: Bergeyella zoohelcum

text: Bergeyella zoohelcum

text: Bergeyella zoohelcum


text: Tatlockia micdadei

text: SC

text: public

text: Tatlockia micdadei

text: Tatlockia micdadei

text: Tatlockia micdadei


text: Mycoplasma sualvi

text: SC

text: public

text: Mycoplasma sualvi

text: Mycoplasma sualvi

text: Mycoplasma sualvi


text: Mycoplasma lipofaciens

text: SC

text: public

text: Mycoplasma lipofaciens

text: Mycoplasma lipofaciens

text: Mycoplasma lipofaciens


text: Streptococcus agalactiae

text: SC

text: public

text: Streptococcus agalactiae

text: Streptococcus agalactiae

text: Streptococcus agalactiae


text: Helicobacter mustelae

text: SC

text: public

text: Helicobacter mustelae

text: Helicobacter mustelae

text: Helicobacter mustelae


text: Campylobacter fetus subsp. venerealis

text: SC

text: public

text: Campylobacter fetus subsp. venerealis

text: Campylobacter fetus subsp. venerealis

text: Campylobacter fetus subsp. venerealis


text: Acinetobacter baumannii

text: SC

text: public

text: Acinetobacter baumannii

text: Acinetobacter baumannii

text: Acinetobacter baumannii


text: Haemophilus pittmaniae

text: SC

text: public

text: Haemophilus pittmaniae

text: Haemophilus pittmaniae

text: Haemophilus pittmaniae


text: Mycoplasma phocarhinis

text: SC

text: public

text: Mycoplasma phocarhinis

text: Mycoplasma phocirhinis

text: Mycoplasma phocirhinis


text: INSTITUT PASTEUR DE PARIS

text: public

tag: Namespace:INSTITUT PASTEUR DE PARIS

characteristic: collection date

text: Bacterial culture

text: France

characteristic: geographic location (country and/or sea)

text: diseased

characteristic: host health state

text: Homo sapiens

characteristic: host scientific name

characteristic: isolate

text: nasopharynx

characteristic: isolation source

text: Whooping cough Nat. Ref. Center, Institut Pasteur, Paris

characteristic: lab host

text: Bordetella pertussis

text: Bordetella pertussis

text: Bordetella pertussis strain


Tohama

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: INSTITUT PASTEUR DE PARIS

characteristic: INSDC first public

text: public

text: Tohama

text: Bacterial culture

characteristic: description

text: Japan

text: diseased

text: Homo sapiens

text: Tohama

text: nasopharynx

text: Bordetella pertussis

text: Bordetella pertussis

text: Bordetella pertussis strain


characteristic: External Id

text: UNIVERSITY OF SOUTHERN CALIFORNIA

characteristic: INSDC center name

text: public

tag: Namespace:UNIVERSITY OF SOUTHERN CALIFORNIA

text: seawater metagenome

characteristic: common name

characteristic: depth

characteristic: environment (biome)

characteristic: environment (feature)

characteristic: environment (material)

text: water

characteristic: environmental package

text: Pacific Ocean

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: metagenome

characteristic: investigation type

text: seawater metagenome

characteristic: organism

characteristic: project name

text: seawater metagenome

text: PE Illumina Hiseq 2500 2x250

characteristic: sequencing method

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: UNIVERSITY OF SOUTHERN CALIFORNIA

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

characteristic: collection date

text: seawater metagenome

text: water

text: Pacific Ocean

characteristic: geographic location (country and/or sea)

text: metagenome

text: seawater metagenome

text: seawater metagenome

text: PE Illumina Hiseq 2500 2x251


characteristic: External Id

text: UNIVERSITY OF SOUTHERN CALIFORNIA

characteristic: INSDC center name

text: public

text: seawater metagenome

characteristic: common name

characteristic: depth

characteristic: environment (biome)

characteristic: environment (feature)

characteristic: environment (material)

text: water

characteristic: environmental package

text: Pacific Ocean

characteristic: geographic location (latitude)

text: metagenome

text: seawater metagenome

text: seawater metagenome

text: PE Illumina Hiseq 2500 2x252


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: UNIVERSITY OF SOUTHERN CALIFORNIA

text: public

text: seawater metagenome

text: water

text: Pacific Ocean

characteristic: geographic location (longitude)

text: metagenome

characteristic: investigation type

text: seawater metagenome

characteristic: organism

characteristic: project name

text: seawater metagenome

text: PE Illumina Hiseq 2500 2x253

characteristic: sequencing method

characteristic: title


characteristic: External Id

text: UNIVERSITY OF SOUTHERN CALIFORNIA

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: seawater metagenome

text: water

text: Pacific Ocean

characteristic: geographic location (country and/or sea)

text: metagenome

text: seawater metagenome

text: seawater metagenome

text: PE Illumina Hiseq 2500 2x254


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: UNIVERSITY OF SOUTHERN CALIFORNIA

text: public

text: seawater metagenome

characteristic: common name

characteristic: depth

characteristic: environment (biome)

characteristic: environment (feature)

characteristic: environment (material)

text: water

characteristic: environmental package

text: Pacific Ocean

characteristic: geographic location (latitude)

text: metagenome

text: seawater metagenome

text: seawater metagenome

text: PE Illumina Hiseq 2500 2x255


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: UNIVERSITY OF SOUTHERN CALIFORNIA

characteristic: INSDC center name

text: public

text: seawater metagenome

text: water

text: Pacific Ocean

characteristic: geographic location (longitude)

text: metagenome

characteristic: investigation type

text: seawater metagenome

characteristic: organism

characteristic: project name

text: seawater metagenome

text: PE Illumina Hiseq 2500 2x256

characteristic: sequencing method

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: UNIVERSITY OF SOUTHERN CALIFORNIA

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

characteristic: collection date

text: seawater metagenome

text: water

text: Pacific Ocean

characteristic: geographic location (country and/or sea)

text: metagenome

text: seawater metagenome

text: seawater metagenome

text: PE Illumina Hiseq 2500 2x257


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: UNIVERSITY OF SOUTHERN CALIFORNIA

text: public

text: seawater metagenome

characteristic: common name

characteristic: depth

characteristic: environment (biome)

characteristic: environment (feature)

characteristic: environment (material)

text: water

characteristic: environmental package

text: Pacific Ocean

characteristic: geographic location (latitude)

text: metagenome

text: seawater metagenome

text: seawater metagenome

text: PE Illumina Hiseq 2500 2x258


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: UNIVERSITY OF SOUTHERN CALIFORNIA

characteristic: INSDC center name

text: public

text: seawater metagenome

text: water

text: Pacific Ocean

characteristic: geographic location (longitude)

text: metagenome

characteristic: investigation type

text: seawater metagenome

characteristic: organism

characteristic: project name

text: seawater metagenome

text: PE Illumina Hiseq 2500 2x259

characteristic: sequencing method

characteristic: title


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: UNIVERSITY OF SOUTHERN CALIFORNIA

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

characteristic: collection date

text: seawater metagenome

text: water

text: Pacific Ocean

characteristic: geographic location (country and/or sea)

text: metagenome

text: seawater metagenome

text: seawater metagenome

text: PE Illumina Hiseq 2500 2x260


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: UNIVERSITY OF SOUTHERN CALIFORNIA

text: public

text: seawater metagenome

characteristic: common name

characteristic: depth

characteristic: environment (biome)

characteristic: environment (feature)

characteristic: environment (material)

text: water

characteristic: environmental package

text: Pacific Ocean

characteristic: geographic location (latitude)

text: metagenome

text: seawater metagenome

text: seawater metagenome

text: PE Illumina Hiseq 2500 2x261


Sample 1

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Anisa

characteristic: INSDC center name

text: public

text: Sample 1

text: metagenomes

characteristic: organism

text: metagenomes

text: Entomological signatures in honey: an environmental DNA metabarcoding approach can disclose information on plant-sucking insects in agricultural and forest landscapes

characteristic: title


Sample 2

text: Anisa

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: Sample 2

characteristic: Submitter Id

text: metagenomes

text: metagenomes


Sample 3

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: Anisa

text: public

text: Sample 3

text: metagenomes

text: metagenomes


Sample 4

text: Anisa

text: public

text: Sample 4

text: metagenomes

text: metagenomes


Sample 5

text: Anisa

text: public

text: Sample 5

text: metagenomes

text: metagenomes


Sample 6

text: Anisa

text: public

text: Sample 6

text: metagenomes

text: metagenomes


Sample 7

text: Anisa

text: public

text: Sample 7

text: metagenomes

text: metagenomes


Library 1

text: Anisa

text: public

text: Library 1

text: metagenomes

text: metagenomes

text: Application of next generation semiconductor based sequencing of a plant DNA barcoding region to detect the botanical composition and geographic origin of monofloral, polyfloral and honeydew honey


Library 2

text: Anisa

text: public

text: Library 2

text: metagenomes

text: metagenomes


Library 3

text: Anisa

text: public

text: Library 3

text: metagenomes

text: metagenomes


Library 4

text: Anisa

text: public

text: Library 4

text: metagenomes

text: metagenomes


Library 5

text: Anisa

text: public

text: Library 5

text: metagenomes

text: metagenomes


Library 6

text: Anisa

text: public

text: Library 6

text: metagenomes

text: metagenomes


Library 7

text: Anisa

text: public

text: Library 7

text: metagenomes

text: metagenomes


Library 8

text: Anisa

text: public

text: Library 8

text: metagenomes

text: metagenomes


Library 9

text: Anisa

text: public

text: Library 9

text: metagenomes

text: metagenomes


text: Federal University of Minas Gerais

text: public

tag: Namespace:Federal University of Minas Gerais

text: house mouse

characteristic: common name

text: Mus musculus

text: Mus musculus

text: DNA from feaces of WT and STING KO.


text: public

tag: Namespace:BIODIVERSITY AND CLIMATE RESEARCH CENTRE

text: Martin Jansen

characteristic: collected by

characteristic: collection date

text: water eDNA 16S amplicons

characteristic: description

text: Bolivia

characteristic: geographic location (country and/or sea)

text: Chiquitano

characteristic: geographic location (region and locality)

text: filter paper

characteristic: isolation source

text: S16.3622, W62.00225

characteristic: lat lon

text: amphibian environmental sample

text: amphibian environmental sample


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: BIODIVERSITY AND CLIMATE RESEARCH CENTRE

characteristic: INSDC center name

text: public

text: Martin Jansen

text: water eDNA 16S amplicons

text: Bolivia

text: Chiquitano

text: filter paper

text: S16.3622, W62.00225

text: amphibian environmental sample

characteristic: organism

text: amphibian environmental sample


text: WELLCOME TRUST SANGER INSTITUTE

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

tag: Namespace:WELLCOME TRUST SANGER INSTITUTE

text: dog

text: CTVT tumour

text: Gambia

characteristic: host

text: Kombo

text: Canis lupus familiaris

text: Canis lupus familiaris

text: CTVT tumour

characteristic: strain

text: CTVT tumour

characteristic: tissue type

text: Canis lupus familiaris; 608T-Dog

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: WELLCOME TRUST SANGER INSTITUTE

text: public

characteristic: SRA accession

characteristic: Submitter Id

text: dog

characteristic: common name

text: CTVT host dog

text: Gambia

text: Kombo

text: Canis lupus familiaris

text: Canis lupus familiaris

text: Male

characteristic: sex

text: Gambian mixed dog

text: Testis

text: Canis lupus familiaris; 608H-Dog


characteristic: ENA-LAST-UPDATE

text: WELLCOME TRUST SANGER INSTITUTE

text: public

text: dog

text: CTVT tumour

characteristic: description

text: Gambia

characteristic: geographic location (country and/or sea)

text: Kombo

characteristic: isolation source

text: Canis lupus familiaris

text: Canis lupus familiaris

text: CTVT tumour

text: CTVT tumour

text: Canis lupus familiaris; 609T-Dog


characteristic: External Id

text: WELLCOME TRUST SANGER INSTITUTE

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: dog

text: CTVT host dog

text: Gambia

text: Kombo

text: Canis lupus familiaris

characteristic: organism

text: Canis lupus familiaris

text: Female

text: Gambian mixed dog

text: Ovary

text: Canis lupus familiaris; 609H-Dog


text: MASSEY UNIVERSITY

characteristic: INSDC last update

text: public

characteristic: INSDC status

tag: Namespace:MASSEY UNIVERSITY

characteristic: collection date

text: New Zealand

characteristic: isolate

text: Human

text: Salmonella enterica

text: Salmonella enterica

text: Typhimurium

characteristic: serovar

text: DT56 variant

characteristic: strain

text: DT56 variant


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: MASSEY UNIVERSITY

text: public

characteristic: SRA accession

characteristic: Submitter Id

text: New Zealand

text: Human

text: Salmonella enterica

text: Salmonella enterica

text: Typhimurium

text: DT56 variant

text: DT56 variant 100

characteristic: title


characteristic: ENA-LAST-UPDATE

text: MASSEY UNIVERSITY

text: public

text: New Zealand

characteristic: geographic location (country and/or sea)

text: Bovine

text: Salmonella enterica

text: Salmonella enterica

text: Typhimurium

text: DT56 variant

text: DT56 variant 107


characteristic: External Id

text: MASSEY UNIVERSITY

text: public

text: New Zealand

text: Avian

characteristic: isolation source

text: Salmonella enterica

text: Salmonella enterica

text: Typhimurium

text: DT56 variant

text: DT56 variant SA145


text: MASSEY UNIVERSITY

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: New Zealand

text: Feline

text: Salmonella enterica

text: Salmonella enterica

text: Typhimurium

text: DT56 variant

text: DT56 variant SM1


text: MASSEY UNIVERSITY

characteristic: INSDC last update

text: public

text: New Zealand

text: Bovine

text: Salmonella enterica

characteristic: organism

text: Salmonella enterica

text: Typhimurium

text: DT56 variant

text: DT56 variant V1


text: MASSEY UNIVERSITY

text: public

characteristic: INSDC status

characteristic: collection date

text: New Zealand

text: Human

text: Salmonella enterica

text: Salmonella enterica

text: Typhimurium

text: DT56 variant

text: DT56 variant V2


text: MASSEY UNIVERSITY

text: public

text: New Zealand

characteristic: isolate

text: Human

text: Salmonella enterica

text: Salmonella enterica

text: Typhimurium

characteristic: serovar

text: DT56 variant

text: DT56 variant V3


E-MTAB-5974:Sample 1

characteristic: ENA-CHECKLIST

text: CHALMERS

text: public

text: E-MTAB-5974:Sample 1

text: 24 to 26

unit: week

characteristic: age

text: ArrayExpress

characteristic: broker name

text: house mouse

characteristic: common name

text: Protocols: Each mouse received 250.000 Lewis lung carcinoma cells suspended in 100 ul PBS, injected subcutaneously at the left flank. RNA was extracted using the Trizol-Chloroform-Isopropanol method. Tissue, a metal bullet and 1 ml Trizol was added to cool 2 ml eppendorf tubes, and tissue was homogenized in a Qiagen Tissuelyser at 25 Hz for 2-3 x 1,5 min, and incubated 5 min at RT. 200 ul Chloroform was added to all samples and shaken. Samples were incubated for 3-5 min at RT to ensure dissociation of nucleic acids from protein complexes, and spun at 12,000 g for 15 min, 4 ºC. The upper clear aqueous phases (approx. 450 ul) were transferred to new PCR clean tubes. This is the RNA. RNA was precipitated with 0.45 ml isopropyl alcohol (1:1 reaction) at RT, and samples were vortexed for 5-10 sec and incubated 10 min at RT. Samples were spun at 12000 g, 15 min, 4 ºC, and placed in -20C cold blocks. The aqueous phases were poured out, and pellets were washed with 900uL (-20C chilled) 75% ethanol and spun at 8000 g, 5 min, 4ºC. This step was repeated once. Pellets were dried by placing tubes horizontally on a rack so that the tops “hung off” the edge of the rack and the air flow from the hood moved past the open tops of the tubes in a perpendicular manner. Tubes were left for 3-5 minutes until pellets had “just” dried and had NO remaining liquid. Pellets were dissolved in 15-30µl of Ultrapure RNase/DNase free water. Sequencing libraries were prepared from 1μg total RNA using the TruSeq stranded mRNA library preparation kit (Cat# RS- 122-2101/2102, Illumina Inc.) including polyA selection. The library preparation was performed according to the manufacturers’ protocol (#15031047). Library preparation using TruSeq stranded mRNA sample preparation kit is an accredited method.

characteristic: description

text: Lewis lung carcinoma

characteristic: disease

text: no access to running wheel

characteristic: environmental history

text: wild type genotype

characteristic: genotype

text: Mus musculus

text: Mus musculus

text: muscle tissue

characteristic: organism part

text: Mus musculus

text: female

characteristic: sex

characteristic: strain

text: Sample 1


E-MTAB-5974:Sample 2

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: CHALMERS

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: SRA accession

text: E-MTAB-5974:Sample 2

characteristic: Submitter Id

text: 24 to 26

text: ArrayExpress

text: house mouse

text: Lewis lung carcinoma

text: no access to running wheel

text: wild type genotype

text: Mus musculus

text: Mus musculus

text: muscle tissue

text: Mus musculus

text: female

text: Sample 2

characteristic: title


E-MTAB-5974:Sample 3

characteristic: ENA-CHECKLIST

text: CHALMERS

text: public

characteristic: INSDC status

text: E-MTAB-5974:Sample 3

text: 24 to 26

characteristic: age

text: ArrayExpress

characteristic: broker name

text: house mouse

characteristic: common name

text: Lewis lung carcinoma

text: no access to running wheel

text: wild type genotype

text: Mus musculus

characteristic: organism

text: Mus musculus

text: muscle tissue

text: Mus musculus

text: female

text: Sample 3


E-MTAB-5974:Sample 4

text: CHALMERS

text: public

text: E-MTAB-5974:Sample 4

text: 24 to 26

text: ArrayExpress

text: house mouse

characteristic: description

text: Lewis lung carcinoma

characteristic: disease

text: no access to running wheel

characteristic: environmental history

text: wild type genotype

characteristic: genotype

text: Mus musculus

text: Mus musculus

text: muscle tissue

characteristic: organism part

text: Mus musculus

text: female

characteristic: sex

text: Sample 4


E-MTAB-5974:Sample 5

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: CHALMERS

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: E-MTAB-5974:Sample 5

text: 24 to 26

text: ArrayExpress

text: house mouse

text: Lewis lung carcinoma

text: no access to running wheel

text: wild type genotype

text: Mus musculus

text: Mus musculus

text: muscle tissue

text: Mus musculus

text: female

characteristic: strain

text: Sample 5


E-MTAB-5974:Sample 6

characteristic: ENA-CHECKLIST

text: CHALMERS

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-5974:Sample 6

characteristic: Submitter Id

text: 24 to 26

text: ArrayExpress

text: house mouse

text: Lewis lung carcinoma

text: no access to running wheel

text: wild type genotype

text: Mus musculus

text: Mus musculus

text: muscle tissue

text: Mus musculus

text: female

text: Sample 6

characteristic: title


E-MTAB-5974:Sample 7

text: CHALMERS

text: public

text: E-MTAB-5974:Sample 7

text: 24 to 26

characteristic: age

text: ArrayExpress

characteristic: broker name

text: house mouse

characteristic: common name

characteristic: description

text: Lewis lung carcinoma

characteristic: disease

text: no access to running wheel

text: wild type genotype

text: Mus musculus

characteristic: organism

text: Mus musculus

text: muscle tissue

text: Mus musculus

text: female

text: Sample 7


E-MTAB-5974:Sample 8

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: CHALMERS

text: public

text: E-MTAB-5974:Sample 8

text: 24 to 26

text: ArrayExpress

text: house mouse

text: Lewis lung carcinoma

text: no access to running wheel

characteristic: environmental history

text: wild type genotype

characteristic: genotype

text: Mus musculus

text: Mus musculus

text: muscle tissue

characteristic: organism part

text: Mus musculus

text: female

characteristic: sex

text: Sample 8


E-MTAB-5974:Sample 9

characteristic: ENA-CHECKLIST

characteristic: External Id

text: CHALMERS

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: E-MTAB-5974:Sample 9

text: 24 to 26

text: ArrayExpress

text: house mouse

text: Lewis lung carcinoma

text: no access to running wheel

text: wild type genotype

text: Mus musculus

text: Mus musculus

text: muscle tissue

text: Mus musculus

text: female

characteristic: strain

text: Sample 9


E-MTAB-5974:Sample 10

text: CHALMERS

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-5974:Sample 10

characteristic: Submitter Id

text: 24 to 26

characteristic: age

text: ArrayExpress

characteristic: broker name

text: house mouse

text: Lewis lung carcinoma

text: no access to running wheel

text: wild type genotype

text: Mus musculus

text: Mus musculus

text: muscle tissue

text: Mus musculus

text: female

text: Sample 10

characteristic: title


E-MTAB-5974:Sample 11

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: CHALMERS

text: public

text: E-MTAB-5974:Sample 11

text: 24 to 26

text: ArrayExpress

text: house mouse

characteristic: common name

characteristic: description

text: Lewis lung carcinoma

characteristic: disease

text: access to running wheel

text: wild type genotype

text: Mus musculus

characteristic: organism

text: Mus musculus

text: muscle tissue

text: Mus musculus

text: female

text: Sample 11


E-MTAB-5974:Sample 12

characteristic: ENA-CHECKLIST

characteristic: External Id

text: CHALMERS

text: public

text: E-MTAB-5974:Sample 12

text: 24 to 26

text: ArrayExpress

text: house mouse

text: Lewis lung carcinoma

text: access to running wheel

characteristic: environmental history

text: wild type genotype

characteristic: genotype

text: Mus musculus

text: Mus musculus

text: muscle tissue

characteristic: organism part

text: Mus musculus

text: female

characteristic: sex

text: Sample 12


E-MTAB-5974:Sample 13

text: CHALMERS

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-5974:Sample 13

text: 24 to 26

text: ArrayExpress

text: house mouse

text: Lewis lung carcinoma

text: access to running wheel

text: wild type genotype

text: Mus musculus

text: Mus musculus

text: muscle tissue

text: Mus musculus

text: female

characteristic: strain

text: Sample 13


E-MTAB-5974:Sample 14

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: CHALMERS

text: public

text: E-MTAB-5974:Sample 14

characteristic: Submitter Id

text: 24 to 26

characteristic: age

text: ArrayExpress

characteristic: broker name

text: house mouse

text: Lewis lung carcinoma

text: access to running wheel

text: wild type genotype

text: Mus musculus

text: Mus musculus

text: muscle tissue

text: Mus musculus

text: female

text: Sample 14

characteristic: title


E-MTAB-5974:Sample 15

characteristic: ENA-CHECKLIST

characteristic: External Id

text: CHALMERS

text: public

text: E-MTAB-5974:Sample 15

text: 24 to 26

text: ArrayExpress

text: house mouse

characteristic: common name

characteristic: description

text: Lewis lung carcinoma

characteristic: disease

text: access to running wheel

text: wild type genotype

text: Mus musculus

characteristic: organism

text: Mus musculus

text: muscle tissue

text: Mus musculus

text: female

text: Sample 15


E-MTAB-5974:Sample 16

text: CHALMERS

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: E-MTAB-5974:Sample 16

text: 24 to 26

text: ArrayExpress

text: house mouse

text: Lewis lung carcinoma

text: access to running wheel

characteristic: environmental history

text: wild type genotype

characteristic: genotype

text: Mus musculus

text: Mus musculus

text: muscle tissue

characteristic: organism part

text: Mus musculus

text: female

characteristic: sex

text: Sample 16


E-MTAB-5974:Sample 17

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: CHALMERS

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-5974:Sample 17

text: 24 to 26

text: ArrayExpress

text: house mouse

text: Lewis lung carcinoma

text: access to running wheel

text: wild type genotype

text: Mus musculus

text: Mus musculus

text: muscle tissue

text: Mus musculus

text: female

characteristic: strain

text: Sample 17


E-MTAB-5974:Sample 18

characteristic: ENA-CHECKLIST

characteristic: External Id

text: CHALMERS

text: public

text: E-MTAB-5974:Sample 18

characteristic: Submitter Id

text: 24 to 26

characteristic: age

text: ArrayExpress

characteristic: broker name

text: house mouse

text: Lewis lung carcinoma

text: access to running wheel

text: wild type genotype

text: Mus musculus

text: Mus musculus

text: muscle tissue

text: Mus musculus

text: female

text: Sample 18

characteristic: title


E-MTAB-5974:Sample 19

text: CHALMERS

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: E-MTAB-5974:Sample 19

text: 24 to 26

text: ArrayExpress

text: house mouse

characteristic: common name

characteristic: description

text: Lewis lung carcinoma

characteristic: disease

text: access to running wheel

text: wild type genotype

text: Mus musculus

characteristic: organism

text: Mus musculus

text: muscle tissue

text: Mus musculus

text: female

text: Sample 19


E-MTAB-5974:Sample 20

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: CHALMERS

text: public

text: E-MTAB-5974:Sample 20

text: 24 to 26

text: ArrayExpress

text: house mouse

text: Lewis lung carcinoma

text: access to running wheel

characteristic: environmental history

text: wild type genotype

characteristic: genotype

text: Mus musculus

text: Mus musculus

text: muscle tissue

characteristic: organism part

text: Mus musculus

text: female

characteristic: sex

text: Sample 20


E-MTAB-5974:Sample 21

characteristic: ENA-CHECKLIST

characteristic: External Id

text: CHALMERS

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-5974:Sample 21

text: 24 to 26

text: ArrayExpress

text: house mouse

text: Lewis lung carcinoma

text: access to running wheel

text: wild type genotype

text: Mus musculus

text: Mus musculus

text: muscle tissue

text: Mus musculus

text: female

characteristic: strain

text: Sample 21


E-MTAB-5974:Sample 22

text: CHALMERS

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: E-MTAB-5974:Sample 22

characteristic: Submitter Id

text: 24 to 26

characteristic: age

text: ArrayExpress

characteristic: broker name

text: house mouse

text: Lewis lung carcinoma

text: access to running wheel

text: wild type genotype

text: Mus musculus

text: Mus musculus

text: muscle tissue

text: Mus musculus

text: female

text: Sample 22

characteristic: title


E-MTAB-5974:Sample 23

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: CHALMERS

text: public

text: E-MTAB-5974:Sample 23

text: 24 to 26

text: ArrayExpress

text: house mouse

characteristic: common name

characteristic: description

text: Lewis lung carcinoma

characteristic: disease

text: access to running wheel

text: wild type genotype

text: Mus musculus

characteristic: organism

text: Mus musculus

text: muscle tissue

text: Mus musculus

text: female

text: Sample 23


E-MTAB-5974:Sample 24

characteristic: ENA-CHECKLIST

characteristic: External Id

text: CHALMERS

text: public

text: E-MTAB-5974:Sample 24

text: 24 to 26

text: ArrayExpress

text: house mouse

text: Lewis lung carcinoma

text: access to running wheel

characteristic: environmental history

text: wild type genotype

characteristic: genotype

text: Mus musculus

text: Mus musculus

text: muscle tissue

characteristic: organism part

text: Mus musculus

text: female

characteristic: sex

text: Sample 24


text: Plasmodium falciparum

characteristic: ArrayExpress-SPECIES

text: SC

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: malaria parasite P. falciparum

text: Plasmodium falciparum

text: Plasmodium falciparum

characteristic: subject id


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: UPSC

text: public

characteristic: Submitter Id

text: Norway spruce

characteristic: common name

text: Apical sample replicate number 1 strand specific sequencing

text: Picea abies

text: Picea abies

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: External Id

text: UPSC

text: public

text: Norway spruce

text: Apical sample replicate number 2 aRNA strand specific sequencing

characteristic: description

text: Picea abies

characteristic: organism

text: Picea abies


text: UPSC

text: public

text: Norway spruce

text: Suspensor sample replicate number 1 strand specific sequencing

text: Picea abies

text: Picea abies


text: UPSC

text: public

text: Norway spruce

text: Suspensor sample replicate number 2 aRNA strand specific sequencing

text: Picea abies

text: Picea abies


text: public

tag: Namespace:NATIONAL HEART AND LUNG INSTITUTE, IMPERIAL COLLEGE LONDON

text: AATGATACGGCGACCACCGAGATCTACAC, CAAGCAGAAGACGGCATACGAGAT

characteristic: adapters

characteristic: collection date

text: human lung metagenome

text: Spontaneously expectorated sputum from subject 81

text: Human

characteristic: environment (biome)

text: Lung

characteristic: environment (feature)

text: Sputum

characteristic: environment (material)

characteristic: fvc

text: United Kingdom

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

unit: year

characteristic: host age

text: Case

characteristic: host disease status

characteristic: host subject id

text: human-associated

characteristic: human associated environmental package

text: metagenome

characteristic: investigation type

text: Cowman et al. 2017

characteristic: library construction method

text: Idiopathic bronchiectasis

characteristic: lung/pulmonary disorder

text: TCGCCTTATAGATCGC

characteristic: multiplex identifiers

text: FALSE

text: M. avium complex

text: TRUE

text: Cowman et al. 2017

characteristic: nucleic acid amplification

text: Cowman et al. 2017

characteristic: nucleic acid extraction

text: FALSE

text: No

text: human lung metagenome

text: TB11, TB12

characteristic: pcr primers

text: Profiling mycobacterial communities in pulmonary nontuberculous mycobacterial disease

characteristic: project name

unit: g

characteristic: sample volume or weight for DNA extraction

text: human lung metagenome

text: Illumina Miseq

characteristic: sequencing method

text: No growth

characteristic: target gene


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: NATIONAL HEART AND LUNG INSTITUTE, IMPERIAL COLLEGE LONDON

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

characteristic: adapters

characteristic: collection date

text: human lung metagenome

characteristic: common name

text: Spontaneously expectorated sputum from subject 39

characteristic: description

text: Human

characteristic: environment (biome)

text: Lung

characteristic: environment (feature)

text: Sputum

characteristic: environment (material)

characteristic: fvc

text: United Kingdom

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

text: Case

text: human-associated

text: metagenome

text: Cowman et al. 2017

text: Secondary bronchiectasis

text: TTCTGCCTTAGATCGC

text: FALSE

text: M. kansasii

text: FALSE

text: Cowman et al. 2017

text: Cowman et al. 2017

text: FALSE

text: No

text: human lung metagenome

characteristic: organism

text: TB11, TB12

text: human lung metagenome

text: Illumina Miseq

text: M. kansasii

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: human lung metagenome

text: Spontaneously expectorated sputum from subject 161

text: Human

text: Lung

text: Sputum

text: United Kingdom

characteristic: geographic location (longitude)

characteristic: host age

text: Control

characteristic: host disease status

characteristic: host subject id

text: human-associated

characteristic: human associated environmental package

text: metagenome

characteristic: investigation type

text: Cowman et al. 2017

characteristic: library construction method

text: Secondary bronchiectasis

characteristic: lung/pulmonary disorder

text: GCTCAGGATAGATCGC

characteristic: multiplex identifiers

text: TRUE

text: FALSE

text: Cowman et al. 2017

characteristic: nucleic acid amplification

text: Cowman et al. 2017

characteristic: nucleic acid extraction

text: TRUE

text: No

text: human lung metagenome

text: TB11, TB12

characteristic: pcr primers

characteristic: project name

characteristic: sample volume or weight for DNA extraction

text: human lung metagenome

text: Illumina Miseq

characteristic: sequencing method

text: No growth

characteristic: target gene


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

characteristic: adapters

characteristic: collection date

text: human lung metagenome

characteristic: common name

text: Spontaneously expectorated sputum from subject 19

characteristic: description

text: Human

characteristic: environment (biome)

text: Lung

characteristic: environment (feature)

text: Sputum

characteristic: environment (material)

characteristic: fvc

text: United Kingdom

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

text: Case

text: human-associated

text: metagenome

text: Cowman et al. 2017

text: COPD

text: CATGCCTATAGATCGC

text: FALSE

text: M. kansasii

text: FALSE

text: Cowman et al. 2017

text: Cowman et al. 2017

text: FALSE

text: No

text: human lung metagenome

characteristic: organism

text: TB11, TB12

text: human lung metagenome

text: Illumina Miseq

text: M. kansasii

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: human lung metagenome

text: Spontaneously expectorated sputum from subject 26

text: Human

text: Lung

text: Sputum

text: United Kingdom

characteristic: geographic location (longitude)

characteristic: host age

text: Control

characteristic: host disease status

characteristic: host subject id

text: human-associated

characteristic: human associated environmental package

text: metagenome

characteristic: investigation type

text: Cowman et al. 2017

characteristic: library construction method

text: Secondary bronchiectasis

characteristic: lung/pulmonary disorder

text: TCCTCTACTAGATCGC

characteristic: multiplex identifiers

text: FALSE

text: FALSE

text: Cowman et al. 2017

characteristic: nucleic acid amplification

text: Cowman et al. 2017

characteristic: nucleic acid extraction

text: FALSE

text: No

text: human lung metagenome

text: TB11, TB12

characteristic: pcr primers

characteristic: project name

characteristic: sample volume or weight for DNA extraction

text: human lung metagenome

text: Illumina Miseq

characteristic: sequencing method

text: No growth

characteristic: target gene


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

characteristic: adapters

characteristic: collection date

text: human lung metagenome

characteristic: common name

text: Spontaneously expectorated sputum from subject 84

characteristic: description

text: Human

characteristic: environment (biome)

text: Lung

characteristic: environment (feature)

text: Sputum

characteristic: environment (material)

characteristic: fvc

text: United Kingdom

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

text: Case

text: human-associated

text: metagenome

text: Cowman et al. 2017

text: CTAGTACGCTCTCTAT

text: FALSE

text: M. avium complex

text: FALSE

text: Cowman et al. 2017

text: Cowman et al. 2017

text: TRUE

text: No

text: human lung metagenome

characteristic: organism

text: TB11, TB12

text: human lung metagenome

text: Illumina Miseq

text: M. xenopi

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: human lung metagenome

text: Spontaneously expectorated sputum from subject 14

text: Human

text: Lung

text: Sputum

text: United Kingdom

characteristic: geographic location (longitude)

characteristic: host age

text: Case

characteristic: host disease status

characteristic: host subject id

text: human-associated

characteristic: human associated environmental package

text: metagenome

characteristic: investigation type

text: Cowman et al. 2017

characteristic: library construction method

text: Secondary bronchiectasis

characteristic: lung/pulmonary disorder

text: TTCTGCCTCTCTCTAT

characteristic: multiplex identifiers

text: FALSE

text: M. avium complex

text: FALSE

text: Cowman et al. 2017

characteristic: nucleic acid amplification

text: Cowman et al. 2017

characteristic: nucleic acid extraction

text: FALSE

text: No

text: human lung metagenome

text: TB11, TB12

characteristic: pcr primers

characteristic: project name

characteristic: sample volume or weight for DNA extraction

text: human lung metagenome

text: Illumina Miseq

characteristic: sequencing method

text: M. abscessus

characteristic: target gene