name: E-MTAB-7114_2:Human_168h Input replicate 2

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: ArrayExpress

text: human

characteristic: common name

text: CEBPA overexpression

text: Homo sapiens

text: Homo sapiens

text: blood

text: Homo sapiens

text: Human_168h Input replicate 2


status: PUBLIC

tag: attribute

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: UCSDMI

characteristic: INSDC center name

characteristic: INSDC first public

text: public

characteristic: SRA accession

text: qiita_sid_13720:13720.mock.community.zymoresearch.gut.2

characteristic: Submitter Id

text: not applicable

characteristic: barcodes

text: not applicable

text: not applicable

text: not provided

text: mock.community

characteristic: description

text: TRUE

text: not collected

characteristic: elevation

text: meters

text: Host-associated

text: Animal

text: Animal surface

text: urban biome

text: human-associated habitat

text: mock.community

text: human-oral

text: Stadt Gottingen

text: Homo sapiens

characteristic: host scientific name

text: years

text: mock.community

text: not collected

text: mock.community

text: mock.community

text: human

text: not collected

text: cm

text: mock.community

text: not collected

text: kg

text: ng

text: not provided

text: not provided

text: not collected

characteristic: latitude

text: Decimal degrees

text: adult

text: not collected

characteristic: longitude

text: Decimal degrees

text: human metagenome

characteristic: organism

characteristic: person

text: UMG

text: FALSE

text: not provided

text: not provided

text: human metagenome

text: not provided

characteristic: sex

text: not provided

characteristic: title

text: mock.community

text: TRUE

text: mock.community


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: University of Bergen, Bergen Norway

characteristic: INSDC last update

text: public

characteristic: INSDC status

tag: Namespace:University of Bergen, Bergen Norway

text: ArrayExpress

characteristic: broker name

text: Protocols: Copepods were collected during sampling cruise in the northern Barents Sea in August 2019 and exposure was performed onboard. The copepod species were captured with a Bongo Net (180 μm mesh size), or a WP-3 net (1000 μm mesh size).The copepods were quickly transferred to a bucket with seawater and kept well diluted at 0−4°C until sorting to species. Calanus hyperboreus copepodite stages CV were hand-picked for exposure. For exposure a sample of 10 individuals was kept in a 0.5 L glass flask filled with 0.4 L filtered seawater and exposure was performed for 72 hours at a temperature of 1.5 ˚C to solvent control (DMSO), 0.1 µM BaP or 0.1 µM Phe in filtered seawater (0.7 µm). For each treatment group, 4-5 replicate flasks (n = 4-5) were used. After 72 hours, the animals were harvested and snap-frozen in liquid nitrogen for storage at -80 °C until RNA-extraction. Total RNA was isolated from frozen slices using TRI Reagent according to the manufacturer’s protocol (Sigma-Aldrich, St. Louis, MO, USA). RNA concentration and quality were assessed using NanoDrop ND-1000 spectrophotometer (NanoDrop Technologies, Wilmington, DE, USA) and Agilent 2100 bioanalyzer (Agilent Technologies, Santa Clara, CA, USA). Performed by Novogene on Illumina NovaSeq 6000 System

characteristic: developmental stage

text: 10 individuals pooled

characteristic: individual

text: Calanus hyperboreus

text: Calanus hyperboreus

text: whole organism

characteristic: organism part

text: Calanus hyperboreus


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: University of Bergen, Bergen Norway

characteristic: INSDC center name

characteristic: INSDC first public

text: public

characteristic: SRA accession

characteristic: Submitter Id

text: ArrayExpress

text: Protocols: Copepods were collected during sampling cruise in the northern Barents Sea in August 2019 and exposure was performed onboard. The copepod species were captured with a Bongo Net (180 μm mesh size), or a WP-3 net (1000 μm mesh size).The copepods were quickly transferred to a bucket with seawater and kept well diluted at 0−4°C until sorting to species. Calanus finmarchicus copepodite stages CV were hand-picked for exposure. For exposure a sample of 20 individuals was kept in a 0.5 L glass flask filled with 0.4 L filtered seawater and exposure was performed for 72 hours at a temperature of 3.5 ˚C to solvent control (DMSO), 0.1 µM BaP or 0.1 µM Phe in filtered seawater (0.7 µm). For each treatment group, 4-5 replicate flasks (n = 5) were used. After 72 hours, the animals were harvested and snap-frozen in liquid nitrogen for storage at -80 °C until RNA-extraction. Total RNA was isolated from frozen slices using TRI Reagent according to the manufacturer’s protocol (Sigma-Aldrich, St. Louis, MO, USA). RNA concentration and quality were assessed using NanoDrop ND-1000 spectrophotometer (NanoDrop Technologies, Wilmington, DE, USA) and Agilent 2100 bioanalyzer (Agilent Technologies, Santa Clara, CA, USA). Performed by Novogene on Illumina NovaSeq 6000 system

characteristic: description

text: 20 individuals pooled

text: Calanus finmarchicus

text: Calanus finmarchicus

text: whole organism

text: Calanus finmarchicus


text: public

tag: Namespace:Institute for Biomedical Aging Research, University of Innsbruck

unit: day

characteristic: age

text: ArrayExpress

text: Protocols: To obtain synchronized populations, gravid adults were treated with hypochlorite and eggs were allowed to hatch in M9 overnight. ~ 700 L1 larvae per strain were plated on 10 cm NG agar plates seeded with concentrated E. coli OP50 and cultured at the required temperatures (GSC(-) and corresponding GSC(+) strains at 25 °C from L1 for 24 h, then shift to 20 °C, to eliminate germ cells [temperature-sensitive glp-1(e2144ts)-mutation]; all other strains 20 °C throughout entire experiment). At the L4-stage, 500 worms per strain were transferred to two E. coli OP50-seeded 6 cm NG agar plates supplemented with 20 µM FUDR to inhibit germ cell proliferation and progeny production. At day 2 of adulthood, worms were harvested by washing them off their plates with M9. After additional washing with M9 and RNAse-free water, worms were suspended in 1 ml Trizol, snap-frozen in liquid nitrogen and stored at -80 °C until RNA-extraction. RNA was extracted using Trizol and cleaned up with the Monarch® Total RNA Miniprep Kit or RNA Cleanup Kit (New England Biolabs) according to the manufacturer’s instructions. RNA library preparation was performed by Eurofins Genomics (Konstanz, Germany) using proprietary protocols and NEBNext Ultra II Directional RNA library preparation kit for Illumina.

text: adult

text: wild type genotype

characteristic: genotype

text: not applicable

characteristic: isolate

text: Caenorhabditis elegans

characteristic: organism

text: Caenorhabditis elegans

text: whole organism

text: Caenorhabditis elegans

text: hermaphrodite

characteristic: sex

characteristic: strain


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: Institute for Biomedical Aging Research, University of Innsbruck

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: ArrayExpress

characteristic: broker name

text: adult

text: wild type genotype

text: not applicable

text: Caenorhabditis elegans

text: Caenorhabditis elegans

text: whole organism

text: Caenorhabditis elegans

text: hermaphrodite

characteristic: title


characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC center name

text: public

text: ArrayExpress

text: adult

characteristic: developmental stage

text: mbk-1(pk1389) X

text: not applicable

text: Caenorhabditis elegans

text: Caenorhabditis elegans

text: whole organism

characteristic: organism part

text: Caenorhabditis elegans

text: hermaphrodite


characteristic: INSDC first public

text: public

characteristic: SRA accession

characteristic: Submitter Id

characteristic: age

text: ArrayExpress

characteristic: description

text: adult

text: daf-2(e1370) III

text: not applicable

text: Caenorhabditis elegans

text: Caenorhabditis elegans

text: whole organism

text: Caenorhabditis elegans

text: hermaphrodite


text: public

text: ArrayExpress

text: adult

text: daf-2(e1370) III; mbk-1(pk1389) X

characteristic: genotype

text: not applicable

characteristic: isolate

text: Caenorhabditis elegans

characteristic: organism

text: Caenorhabditis elegans

text: whole organism

text: Caenorhabditis elegans

text: hermaphrodite

characteristic: sex

characteristic: strain


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: ArrayExpress

characteristic: broker name

text: adult

text: glp-1(e2144ts) III

text: not applicable

text: Caenorhabditis elegans

text: Caenorhabditis elegans

text: whole organism

text: Caenorhabditis elegans

text: hermaphrodite


characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC center name

text: public

text: ArrayExpress

text: adult

characteristic: developmental stage

text: glp-1(e2144ts) III; mbk-1(pk1389) X

text: not applicable

text: Caenorhabditis elegans

text: Caenorhabditis elegans

text: whole organism

text: Caenorhabditis elegans

text: hermaphrodite

characteristic: title


text: UNIVERSITY OF CAMBRIDGE

characteristic: INSDC first public

text: public

characteristic: SRA accession

tag: Namespace:UNIVERSITY OF CAMBRIDGE

characteristic: Submitter Id

text: ArrayExpress

text: epiblast cell

characteristic: cell type

text: rabbit

characteristic: common name

text: Protocols: Rabbit embryos at E6-7 were trypsinized with 0.25% trypsin/EDTA for 5min. Then, single cells were sorted by SH800 into wells of 384 well plates filled with 2.875 ul of lysis buffer (Takara Bio Inc.). We had also included additional samples; cells from posterior epiblast at E7 containing rbPGCs, in vitro rbPSCs, rbPSCs cultured for 2 days with lower concentration (5ng/ml) of FGF (termed as rbPSC_F5), and NT positive d2 rbPGCLCs. To enrich rbPGCs, 3-4 posterior epiblast dissected from E7 (st.3-4) rabbit embryos were dissociated into single cell by TrypLE Express (Thermo Fisher Scientific) at 37℃ for 8 min. After inactivation of the TrypLE Express, dissociated cells were incubated with anti-c-KIT antibody labeled by Biotin Labeling Kit (Dojindo), and subsequently incubated with Alexa Fluor® 647 Streptavidin (Biolegend, San Diego, CA). For rbPSC rbPSC_F5 and rbPGCLC samples, cells dissociated with 0.25% trypsin/EDTA (Thermo Fisher Scientific) were incubated with anti-feeder cell antibody (Miltenyi Biotec) for 15 min at 4℃ to exclude residual MEF by FACS. cells were directly sorted into PCR tubes filled with 10 ul of the lysis buffer by SH800 or MA900 cell sorter. Single-cell transcriptomes of sorted cells were assayed as follows: for E6-7 embryos, reverse transcription and cDNA amplification was performed using the miniaturized version of the SMART-seq HT protocol using the low-volume liquid-handling robot Mosquito HV (SPT Lab Tech). For additional samples, reverse transcription and cDNA amplification was performed according to manufacturer’s protocol of Smart-seq HT kit (Takara Bio Inc.). Libraries were prepared using the Illumina Nextera XT DNA preparation kit.

text: embryonic day 7

text: normal

characteristic: disease

text: wild type genotype

text: PosteriorEnriched

characteristic: individual

text: Oryctolagus cuniculus

text: Oryctolagus cuniculus

text: posterior epiblast

characteristic: sampling site

text: Oryctolagus cuniculus


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: UNIVERSITY OF CAMBRIDGE

text: public

text: ArrayExpress

text: embryonic stem cell

text: rabbit

characteristic: description

text: embryonic day 7

text: normal

text: wild type genotype

characteristic: genotype

text: Oryctolagus cuniculus

characteristic: organism

text: Oryctolagus cuniculus

text: Oryctolagus cuniculus


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: UNIVERSITY OF CAMBRIDGE

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: ArrayExpress

characteristic: broker name

text: embryonic stem cell

text: rabbit

text: embryonic day 6

text: normal

text: wild type genotype

text: Oryctolagus cuniculus

text: Oryctolagus cuniculus

text: Oryctolagus cuniculus


text: UNIVERSITY OF CAMBRIDGE

characteristic: INSDC center name

characteristic: INSDC first public

text: public

characteristic: SRA accession

text: ArrayExpress

text: embryonic stem cell

text: rabbit

text: embryonic day 4

characteristic: developmental stage

text: normal

text: wild type genotype

text: Oryctolagus cuniculus

text: Oryctolagus cuniculus

text: Oryctolagus cuniculus

characteristic: title


text: UNIVERSITY OF CAMBRIDGE

text: public

characteristic: Submitter Id

text: ArrayExpress

text: embryonic stem cell

characteristic: cell type

text: rabbit

characteristic: common name

text: embryonic day 5

text: normal

characteristic: disease

text: wild type genotype

characteristic: individual

text: Oryctolagus cuniculus

text: Oryctolagus cuniculus

text: Oryctolagus cuniculus


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: public

tag: Namespace:Fraunhofer Attract Eco'n'OMICs Fraunhofer Institute for Molecular Biology and Applied Ecology IME

unit: hour

characteristic: age

text: ArrayExpress

text: zebrafish

text: Protocols: For each sample, 10 4-day old zebrafish larvae were randomly picked from the glass well and carefully transferred to a 1.5 ml low binding Eppendorf tube. Once individuals were collected for all samples, they were euthanized at the same time by placing the tubes simultaneously on ice for 10 minutes. Supernatant from the test solutions was then carefully removed without injuring the larvae before adding 350µl of RP1 buffer (NucleoSpin RNA Protein kit; Macherey-Nagel 740933.250) for tissue homogenization. RP1 buffer was freshly prepared with TCEP as reducing agent prior extraction. For detailed information about embryonic incubation conditions and husbandry of adult broodstock please refer to the “Growth protocol”. For detailed information about exposure duration and conditions please refer to the “Treatment protocol”. Adult animal husbandry: Wild-type zebrafish (Danio rerio, Strain AB) broodstocks were maintained under flow-through conditions in 150 L tanks at 26 +/- 2°C on a 12:12 h light/dark cycle. They were fed daily with TetraMin® (Tetra Werke, Melle, Germany) main feed ad libitum and nauplii of Artemia salina. The day before test start, glass spawning-trays with artificial substrate (green glass beads stringed on stainless steel wire) were placed at the bottom of each tank. After mating and spawning in the morning hours eggs were rinsed with clear Cu-reduced water and placed into glass dishes for pre-picking. Fish embryo incubation: For each sample 15 fertilized eggs in the early blastula stage were placed in glass petri dishes (diameter 6 cm) filled with 8 ml of the respective testing solution (Control, Low exposure, High exposure). Embryos were incubated at 27 +/- 1°C on a 14:10 h light/dark cycle. At 24 hours post fertilization (hpf), eggs were inspected visually and single coagulated eggs were recorded and removed. At 48 hpf, overall survival, hatching rates, morphological malformations and physiological changes were recorded and aged solutions were replaced by fresh, aerated test solutions. At 96 hpf again, overall survival, hatching rates, morphological malformations and physiological changes were recorded before RNA and protein extraction. For the test solution preparation, first a high concentrated stock solution was prepared in water. From this stock, respective volumes for each testing concentration were added to a 250 ml DURAN glass bottle. 200 ml of Cu reduced water were added and solutions were stirred in the dark for 3 hours at room temperature. The test solutions were freshly prepared one day prior the start of the experiment and stored at room temperature in the dark. They were constantly aerated and used over the course of the 96 hours exposure experiment. The glass wells for the incubation of the embryos were pre-saturated with the respective test solution overnight and renewed at the beginning of the experiment. Per sample, about 40 - 50 fertilized fish eggs were pre-picked in glass petri dishes (10 cm diameter) filled with 30 ml of the testing solution. Using an optical binokular microscope, 15 embryos of the same early blastula stage were transferred from the pre-picking plate into the test glass wells filled with 8 ml of the test solution. Embryos were then incubated as described in the “growth protocol”. The pooled larvae in RP1 buffer were transferred to a screw-cap eppendorf filled with 0.3 g of Lysing Matrix D (MP Biomedicals, 6913050) ceramic beads. Tissue homogenization was performed at 5 m/s for 45 s with FastPrep-24© (MP Biomedicals, 6004500) at room temperature. From here on total RNA and Protein was extracted from the tissue lysate using the NucleoSpin RNA Protein kit (Macherey-Nagel, 740933.250) according to the manufacturer’s protocol. RNA concentration (>100 ng/µl) was measured using a Nanodrop 2000 spectrophotometer (Thermo Scientific). The sample’s overall RNA quality and corresponding RIN value was fluorometrically determined with a 2100 Bioanalyzer© Instrument system (Agilent, G2939BA) using the Agilent RNA 6000 Nano Kit© (Agilent, 5067-1511) according to the manufacturer’s protocol. Only samples with a RIN > 8 were used for downstream analysis. Samples were stored at -80°C until they were send to the sequencing facility on dry ice. Sequencing libraries were prepared for each sample from 100 ng/µl total RNA at the sequencing facility “NGS-Services for Integrative Genomics” at the University of Göttingen in Germany. According to their standard workflow, cDNA libraries were prepared from protein coding mRNA that were purified through PolyA selection using the TruSeq RNA Library Prep Kit v2 (Illumina). Libraries were validated using a Fragment Analyzer system (Agilent, Santa Clara, USA) before sequencing.

characteristic: description

text: larval day 4

text: wild type genotype

characteristic: genotype

text: Danio rerio

text: Danio rerio

text: whole organism

characteristic: organism part

text: Danio rerio

text: mixed

characteristic: sex

text: AB

characteristic: strain


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Fraunhofer Attract Eco'n'OMICs Fraunhofer Institute for Molecular Biology and Applied Ecology IME

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: ArrayExpress

characteristic: broker name

text: zebrafish

text: larval day 4

text: wild type genotype

text: Danio rerio

characteristic: organism

text: Danio rerio

text: whole organism

text: Danio rerio

text: mixed

text: AB


text: Human Embryo and Stem Cell Laboratory

text: public

characteristic: SRA accession

tag: Namespace:Human Embryo and Stem Cell Laboratory

characteristic: Submitter Id

text: ArrayExpress

characteristic: cell line

text: embryonic stem cell

characteristic: cell type

text: human

characteristic: common name

text: Protocols: RNA was isolated using TRI reagent (Sigma) by applying 1 ml reagent in-plate to one 6-well of cells and scraping to collect all material. All naïve hESCs were cultured at 5% O2 and 5% CO2, according to recently published protocols (Guo et al., 2017; Bredenkamp et al., 2019) on mitotically inactivated DR4 MEFs (prepared in-house) plated at a density of 1x106 per well of a 6-well plate 12-16hrs prior to hESC seeding. Naïve hESCs were passaged as single cells by 4 minutes treatment with Accutase (Thermo Fisher) at 37°C, at split ratios between 1:3 and 1:6, every 3 to 6 days. For culture in (t)t2iL+Gö, 10 μM ROCK inhibitor (Y-27632, Tocris Bioscience) was added overnight before and after passaging, to aid survival. In-house generated, chemically reset, naïve H9 cells were maintained in tt2iL+Gö, with 0.3 μM CHIR99021 (Guo et al., 2017), and XAV supplementation until naïve passage 5 (p5). Chemical resetting media and naive maintenance media (Guo et al., 2017) consist of the following: cRM-1 = NDiff227 (Takara) supplemented with 1% Pen/Strep, 1 μM PD0325901 (Cambridge Bioscience), 10 ng/ml hLIF (PeproTech) and 1 mM valproic acid (VPA, Cayman Chemical Company). cRM-2 = NDiff277 (Takara) supplemented with 1% Pen/Strep, 1 μM PD032590 (Cambridge Bioscience), 2 μM Gö6983 (Bio-Techne), 10 ng/ml hLIF (PeproTech) and 2 μM XAV939 (Cambridge Bioscience). tt2iL+Go (+XAV) = 500 ml NDiff227 (Takara) basal medium was supplemented with 5 ml (1%) Pen/Strep, 1 μM PD0325901 (Cambridge Bioscience), 0.3 μM CHIR99021 (Cambridge Bioscience), 2 μM Gö6983 (Bio-Techne) and 10 ng/ml hLIF (PeproTech), with optional addition of 2 μM XAV939 (Cambridge Bioscience). To generate KLF17-null and WT control hESCs, H9 hESCs were nucleofected with 4 μg pSpCas9(BB)-2A-Puro (PX459) V2.0 containing the gRNA KLF17(3_1), which targets the third exon of the human KLF17 gene. Nucleofection was carried out on an Amaxa 4D-Nucleofector (Lonza). 24 hours prior to nucleofection, H9 hESCs were treated with 10 μM Y-27632 (Tocris Bioscience). hESCs were harvested as single cells by Accutase treatment (5min, 37°C) and counted with an automatic cell counter (Nucleocounter NC-200, ChemoMetec). 2x106 cells were resuspended in 100 μl P3 Primary Cell 4D-Nucleofector X Solution and transferred to nucleocuvettes with 4 μg plasmid. Nucleofection was performed with the pre-set H9 hESC programme (CB-150), then cells resuspended in antibiotic-free mTeSR1 medium supplemented with 10 μM Y-27632 and plated onto wells coated with DR4 MEFs to aid attachment and survival. After 24hrs, medium was changed to mTeSR1 supplemented with puromycin at 0.5 μg/ml for 48hrs. Cells were allowed to recover for 8 days, then manually passaged as single cells following treatment with Accutase (5 minutes, 37°C) or Accumax (10 minutes, 37°C; Sigma Aldrich) at clonal density into Matrigel-coated 24-well tissue culture plates (Corning). Cells were sub-cloned once more by manual picking and single-cell dissociation into 12-well plates and then expanded for genotyping and subsequent experiments. WT control hESCs went through the above process, but were confirmed wild-type at the KLF17 on-target locus by MiSeq high-throughput sequencing. The two KLF17-null (KO) clones each harbour one allele with a 1 bp insertion and one allele with an 8 bp deletion, leading to premature termination. TRI reagent samples were subjected to phenol/chloroform-based extraction, and DNase I-treated (Ambion). DNase-treated RNA was supplied to the in-house sequencing facility and subjected to library construction via the KAPA mRNA (polyA) HyperPrep protocol.

text: embryo stage

characteristic: developmental stage

text: normal

characteristic: disease

text: KLF17 knockout

characteristic: growth condition

text: Homo sapiens

text: Homo sapiens

text: blastocyst

characteristic: passage

text: Homo sapiens

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Human Embryo and Stem Cell Laboratory

text: public

text: ArrayExpress

text: embryonic stem cell

text: human

characteristic: description

text: embryo stage

text: normal

text: KLF17 knockout

characteristic: genotype

text: Primed (mTeSR1)

text: Homo sapiens

text: Homo sapiens

text: blastocyst

characteristic: organism part

text: Homo sapiens


text: Human Embryo and Stem Cell Laboratory

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: ArrayExpress

characteristic: broker name

text: embryonic stem cell

text: human

text: embryo stage

text: normal

text: wild type genotype

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: blastocyst

text: Homo sapiens


text: Human Embryo and Stem Cell Laboratory

text: public

characteristic: Submitter Id

text: ArrayExpress

characteristic: cell line

text: embryonic stem cell

characteristic: cell type

text: human

characteristic: common name

text: embryo stage

characteristic: developmental stage

text: normal

characteristic: disease

text: wild type genotype

text: Primed (mTeSR1)

characteristic: growth condition

text: Homo sapiens

text: Homo sapiens

text: blastocyst

text: Homo sapiens


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Human embryo and stem cell laboratory

text: public

tag: Namespace:Human embryo and stem cell laboratory

text: ArrayExpress

text: embryonic stem cell

text: human

text: Protocols: RNA was isolated using TRI reagent (Sigma) by applying 1 ml reagent in-plate to one 6-well of cells and scraping to collect all material. H9 KLF17-HA inducible hESCs were pre-treated overnight with 10 μM ROCKi, then harvested from standard culture (mTeSR1 on Matrigel) by 5 minutes incubation at 37°C with Accutase, resuspended in culture medium supplemented with 10 μM ROCKi and counted. 2x105 hESCs were plated per 6-well pre-coated in DR4 MEFs and the cells placed at 5% O2 and 5% CO2 for ~24hrs. The following day (day 0), medium was changed to PXGL supplemented with 1 μg/ml Dox. From day 2, medium was replenished each day with PXGL freshly supplemented with 1 μg/ml Dox. On day 5, cells were passaged by 4min incubation in Accutase and plated in PXGL with 10 μM ROCKi at a split ratio between 1:5 and 1:20, dependent upon density. Within 24hrs, the cells adopted a domed morphology with highly-refractile colony edges. Cells were passaged again on day 7 or 8 and could subsequently be maintained similarly to chemically reset cells (Guo et al., 2017), with passaging every 3-4 days at split ratios of between 1:3 and 1:6. Doxycycline-inducible overexpression of HA-tagged proteins was achieved using the Lenti-X Tet-On 3G Inducible Expression System (Clontech) following the manufacturer’s protocol, and as outlined previously (Wamaitha et al., 2015). Lentiviral packaging was achieved using 7 μg of transgene-containing plasmid and the Lenti-X Packaging Single Shot reagents. Lentiviral supernatant was harvested after 48hrs and concentrated by ultracentrifugation. To produce stably transduced cells, hESCs were plated under standard conditions and changed into fresh medium the following morning. 24hrs post-plating, 10 μl concentrated virus was added to hESCs for transduction overnight (~16hrs). hESCs were dual selected with 150 μg/ml G418 and 0.5 μg/ml puromycin 48hrs post-transduction. For initiation of resetting, cells were switched from mTeSR to naive-permissive PXGL medium ~30 hours after plating. For induction of transgene expression in +Dox cells, doxycycline was added to the growth medium at 1 μg/ml, while uninduced cells were left untreated. TRI reagent samples were subjected to phenol/chloroform-based extraction, and DNase I-treated (Ambion). DNase-treated RNA was supplied to the in-house sequencing facility and subjected to library construction via the KAPA mRNA (polyA) HyperPrep protocol.

characteristic: description

text: embryo stage

text: KLF17-HA tet-on

text: naive pluripotency-supportive PXGL medium

text: Homo sapiens

text: Homo sapiens

text: blastocyst

characteristic: passage number

text: KLF17 overexpression

characteristic: phenotype

text: Homo sapiens

text: doxycycline

characteristic: stimulus

characteristic: title


text: Human embryo and stem cell laboratory

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: ArrayExpress

characteristic: broker name

text: embryonic stem cell

text: human

text: embryo stage

text: KLF17-HA tet-on

characteristic: genotype

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: blastocyst

characteristic: organism part

text: wild type

text: Homo sapiens


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: NMBU

text: public

characteristic: Submitter Id

text: Atlantic salmon

characteristic: common name

text: Whole Genome Sequencing

text: Salmo salar

text: Salmo salar

text: Male

characteristic: sex

text: fin clip


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: NMBU

text: public

text: Atlantic salmon

text: Whole Genome Sequencing

characteristic: description

text: Salmo salar

text: Salmo salar

text: Female

text: fin clip


text: PGIMER, Chandigarh, India

characteristic: INSDC center name

text: public

tag: Namespace:PGIMER, Chandigarh, India

text: Jaspreet Mahindroo

characteristic: collected by

characteristic: collection date

text: India

characteristic: geographic location (country and/or sea)

text: Human

characteristic: host scientific name

characteristic: isolate

text: Human stool

characteristic: isolation source host associated

text: Salmonella enterica subsp. enterica

text: Salmonella enterica subsp. enterica

text: Non-typhoidal Salmonella in Northern India

characteristic: title


text: PGIMER, Chandigarh, India

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: Jaspreet Mahindroo

text: India

text: Chicken

text: Chicken stool

text: Salmonella enterica subsp. enterica

characteristic: organism

text: Salmonella enterica subsp. enterica


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: PGIMER, Chandigarh, India

text: public

characteristic: Submitter Id

text: Jaspreet Mahindroo

text: India

text: Chicken

text: Chicken meat

text: Salmonella enterica subsp. enterica

text: Salmonella enterica subsp. enterica


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: PGIMER, Chandigarh, India

text: public

text: Jaspreet Mahindroo

text: India

text: Goat

text: Goat stool

text: Salmonella enterica subsp. enterica

text: Salmonella enterica subsp. enterica


text: PGIMER, Chandigarh, India

characteristic: INSDC center name

text: public

text: Jaspreet Mahindroo

characteristic: collected by

text: India

text: Goat

text: Goat meat

text: Salmonella enterica subsp. enterica

text: Salmonella enterica subsp. enterica


text: PGIMER, Chandigarh, India

text: public

text: Jaspreet Mahindroo

characteristic: collection date

text: India

characteristic: geographic location (country and/or sea)

text: Pig

text: Pig stool

text: Salmonella enterica subsp. enterica

text: Salmonella enterica subsp. enterica


text: PGIMER, Chandigarh, India

text: public

text: Jaspreet Mahindroo

text: India

text: Pig

characteristic: host scientific name

characteristic: isolate

text: Pig meat

text: Salmonella enterica subsp. enterica

text: Salmonella enterica subsp. enterica


text: public

tag: Namespace:Hospital General Universitario Gregorio Maranon

text: Mycobacterium tuberculosis

text: Mycobacterium tuberculosis

characteristic: title


text: Hospital General Universitario Gregorio Maranon

characteristic: INSDC first public

text: public

text: Mycobacterium tuberculosis

text: Mycobacterium tuberculosis


text: FREIE UNIVERSITAET BERLIN

characteristic: INSDC last update

text: public

tag: Namespace:FREIE UNIVERSITAET BERLIN

text: desert hamster

characteristic: common name

text: Phodopus roborovskii

text: Phodopus roborovskii

text: Phodopus roborovskii


text: CICESE

text: public

characteristic: INSDC status

characteristic: SRA accession

text: Metagenome from deep sea sediments in the Gulf of Mexico

characteristic: description

text: marine sediments

characteristic: environment (biome)

text: marine sediments

characteristic: environment (feature)

text: marine sediments

characteristic: environment (material)

text: Mexico

unit: m

characteristic: geographic location (depth)

characteristic: geographic location (elevation)

unit: DD

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: metagenome

characteristic: investigation type

text: metagenome

characteristic: project name

text: metagenome

text: sediment

characteristic: sediment environmental package

text: Illumina

characteristic: sequencing method


Infectious diabetic foot 03

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: SIR RUN RUN SHAW HOSPITAL

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: Yes

characteristic: Is the sequenced pathogen host associated?

text: Infectious diabetic foot 03

tag: Namespace:SIR RUN RUN SHAW HOSPITAL

characteristic: Submitter Id

text: researchers

characteristic: collection date

text: No

text: China

characteristic: geographic location (country and/or sea)

text: diseased

characteristic: host health state

text: patient

characteristic: host scientific name

text: human body

characteristic: isolate

text: bacterium

characteristic: organism

text: bacterium

text: Sample 03

characteristic: title


Infectious diabetic foot 05

text: SIR RUN RUN SHAW HOSPITAL

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: Yes

characteristic: SRA accession

text: Infectious diabetic foot 05

text: researchers

text: No

text: China

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: diseased

text: patient

text: human body

text: bacterium

text: bacterium

text: Sample 05


Infectious diabetic foot 08

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: SIR RUN RUN SHAW HOSPITAL

text: public

text: Yes

text: Infectious diabetic foot 08

text: researchers

text: No

text: China

text: diseased

text: patient

text: human body

text: bacterium

text: bacterium

text: Sample 08


Infectious diabetic foot 09

text: SIR RUN RUN SHAW HOSPITAL

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: Yes

characteristic: Is the sequenced pathogen host associated?

text: Infectious diabetic foot 09

characteristic: Submitter Id

text: researchers

text: No

text: China

text: diseased

text: patient

text: human body

text: bacterium

text: bacterium

text: Sample 09


Infectious diabetic foot 11

text: SIR RUN RUN SHAW HOSPITAL

text: public

text: Yes

text: Infectious diabetic foot 11

text: researchers

characteristic: collection date

text: No

text: China

characteristic: geographic location (country and/or sea)

text: diseased

characteristic: host health state

text: patient

characteristic: host scientific name

text: human body

text: bacterium

text: bacterium

text: Sample 11


Infectious diabetic foot 13

text: SIR RUN RUN SHAW HOSPITAL

characteristic: INSDC last update

text: public

text: Yes

text: Infectious diabetic foot 13

text: researchers

text: No

text: China

text: diseased

text: patient

text: human body

characteristic: isolate

text: bacterium

characteristic: organism

text: bacterium

text: Sample 13

characteristic: title


Infectious diabetic foot 15

text: SIR RUN RUN SHAW HOSPITAL

text: public

characteristic: INSDC status

text: Yes

characteristic: SRA accession

text: Infectious diabetic foot 15

text: researchers

text: No

text: China

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: diseased

text: patient

text: human body

text: bacterium

text: bacterium

text: Sample 15


Infectious diabetic foot 16

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: SIR RUN RUN SHAW HOSPITAL

text: public

text: Yes

text: Infectious diabetic foot 16

text: researchers

text: No

text: China

text: diseased

text: patient

text: human body

text: bacterium

text: bacterium

text: Sample 16


text: CENTER FOR AGRICULTURAL BIOTECHNOLOGY

characteristic: INSDC center name

characteristic: INSDC first public

text: public

tag: Namespace:CENTER FOR AGRICULTURAL BIOTECHNOLOGY

characteristic: Submitter Id

text: Hugo Volkaert

characteristic: collected by

text: dwarf banana

characteristic: common name

text: DNA extracted from cigar leaf of Musa acuminata growing along road connecting Ban Tak with Mae Ramat in Thailand

characteristic: description

text: 500 Mb

characteristic: estimated size

characteristic: extrachromosomal elements

text: Thailand

characteristic: geographic location (elevation)

text: Mae Ramat district, Tak province

characteristic: geographic location (region and locality)

text: field

characteristic: growth facility

text: Hugo Volkaert

characteristic: identified by

text: Natural environment

characteristic: isolation and growth condition

characteristic: number of replicons

text: Musa acuminata

text: Wild banana

characteristic: organism common name

text: mature

characteristic: plant developmental stage

text: soil

characteristic: plant growth medium

text: unfolding leaf

characteristic: plant structure

characteristic: ploidy

text: vegetative propagation (sucker)

characteristic: propagation

text: Musa acuminata

characteristic: source material identifiers

text: Wild banana from Ban Tak, Thailand


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: CENTER FOR AGRICULTURAL BIOTECHNOLOGY

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: Hugo Volkaert

characteristic: collected by

characteristic: collection date

text: DNA extracted from cigar leaf of Musa yunnanensis from Huay-nahm-dang National Park area in Thailand

text: 500 Mb

text: Thailand

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: Pai district, Maehongson province

text: field

text: Hugo Volkaert

text: Natural environment

text: Musa yunnanensis

characteristic: organism

text: Wild banana

text: mature

text: soil

text: unfolding leaf

text: vegetative propagation (sucker)

text: Musa yunnanensis

text: Wild banana (Musa yunnanensis) from Huay-nahm-dang national park, Thailand

characteristic: title


characteristic: ENA-CHECKLIST

text: CENTER FOR AGRICULTURAL BIOTECHNOLOGY

text: public

text: Hugo Volkaert

text: DNA extracted from cigar leaf of Musa sp terminiflora growing along road connecting Phrao to Wiang Papao in Thailand

characteristic: description

text: 500 Mb

characteristic: estimated size

characteristic: extrachromosomal elements

text: Thailand

characteristic: geographic location (elevation)

text: Wiang Papao district, Chiangrai province

characteristic: geographic location (region and locality)

text: field

characteristic: growth facility

text: Hugo Volkaert

characteristic: identified by

text: Natural environment

characteristic: isolation and growth condition

characteristic: number of replicons

text: Musa sp. 1 HV-2019

text: Wild banana

characteristic: organism common name

text: mature

characteristic: plant developmental stage

text: soil

characteristic: plant growth medium

text: unfolding leaf

characteristic: plant structure

characteristic: ploidy

text: vegetative propagation (sucker)

characteristic: propagation

text: Musa sp. 1 HV-2019

characteristic: source material identifiers

text: Wild banana from Phrao district, Thailand


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: CENTER FOR AGRICULTURAL BIOTECHNOLOGY

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: Hugo Volkaert

characteristic: collected by

characteristic: collection date

text: DNA extracted from cigar leaf of Musa sp terminiflora growing along the road between Phop Phra and Umphang districts in Thailand

text: 500 Mb

text: Thailand

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: Phop Phra district, Tak province

text: field

text: Hugo Volkaert

text: Natural environment

text: Musa sp. 1 HV-2019

characteristic: organism

text: Wild banana

text: mature

text: soil

text: unfolding leaf

text: vegetative propagation (sucker)

text: Musa sp. 1 HV-2019

text: Wild banana from Phop Phra district, Thailand

characteristic: title


characteristic: ENA-CHECKLIST

text: CENTER FOR AGRICULTURAL BIOTECHNOLOGY

text: public

text: Hugo Volkaert

text: DNA extracted from cigar leaf of Musa sp terminiflora from Huay-nahm-dang National Park area in Thailand

characteristic: description

text: 500 Mb

characteristic: estimated size

characteristic: extrachromosomal elements

text: Thailand

characteristic: geographic location (elevation)

text: Pai district, Maehongson province

characteristic: geographic location (region and locality)

text: field

characteristic: growth facility

text: Hugo Volkaert

characteristic: identified by

text: Natural environment

characteristic: isolation and growth condition

characteristic: number of replicons

text: Musa sp. 1 HV-2019

text: Wild banana

characteristic: organism common name

text: mature

characteristic: plant developmental stage

text: soil

characteristic: plant growth medium

text: unfolding leaf

characteristic: plant structure

characteristic: ploidy

text: vegetative propagation (sucker)

characteristic: propagation

text: Musa sp. 1 HV-2019

characteristic: source material identifiers

text: Wild banana from Huay-nahm-dang national park, Thailand


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

tag: Namespace:EGE UNIVERSITY DEPARTMENT OF BIOENGINEERING

characteristic: Submitter Id

text: Wild type

characteristic: biological status

characteristic: collection date

text: Complete chloroplast genome of Cicer echinospermum

text: Turkey

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: field

text: X

text: Cicer echinospermum

characteristic: organism

text: Cicer echinospermum

text: X

text: Soil

text: X

text: Cicer echinospermum

text: Cicer echinospermum

characteristic: title


characteristic: ENA-CHECKLIST

text: EGE UNIVERSITY DEPARTMENT OF BIOENGINEERING

text: public

text: Wild type

text: Complete chloroplast genome of Cicer reticulatum

characteristic: description

characteristic: estimated size

text: Turkey

text: field

characteristic: growth facility

text: X

characteristic: isolation and growth condition

text: Cicer reticulatum

text: Cicer reticulatum

characteristic: organism common name

text: X

characteristic: plant developmental stage

text: Soil

characteristic: plant growth medium

text: X

characteristic: plant structure

text: Cicer reticulatum

text: Cicer reticulatum


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

text: Wild type

text: Complete chloroplast genome of Cicer bijugum

text: Turkey

text: field

text: X

text: Cicer bijugum

text: Cicer bijugum

text: X

text: Soil

text: X

text: Cicer bijugum

text: Cicer bijugum


characteristic: ENA-CHECKLIST

text: public

text: Wild type

characteristic: biological status

characteristic: collection date

text: Complete chloroplast genome of Cicer pinnatifidum

characteristic: description

text: Turkey

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: field

text: X

text: Cicer pinnatifidum

characteristic: organism

text: Cicer pinnatifidum

text: X

text: Soil

text: X

text: Cicer pinnatifidum

text: Cicer pinnatifidum

characteristic: title


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: public

text: Wild type

text: Complete chloroplast genome of Lens lamottei

characteristic: estimated size

text: Turkey

text: field

characteristic: growth facility

text: X

characteristic: isolation and growth condition

text: Lens lamottei

text: Lens lamottei

characteristic: organism common name

text: X

characteristic: plant developmental stage

text: Soil

characteristic: plant growth medium

text: X

characteristic: plant structure

text: Lens lamottei

text: Lens lamottei


characteristic: ENA-CHECKLIST

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

text: Wild type

characteristic: biological status

text: Complete chloroplast genome of Lens tomentosus

text: Turkey

text: field

text: X

text: Lens culinaris subsp. tomentosus

text: Lens culinaris subsp. tomentosus

text: X

text: Soil

text: X

text: Lens culinaris subsp. tomentosus

text: Lens tomentosus


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: public

text: Wild type

characteristic: collection date

text: Complete chloroplast genome of Lens ervoides

characteristic: description

text: Turkey

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: field

text: X

text: Lens ervoides

characteristic: organism

text: Lens ervoides

text: X

text: Soil

text: X

text: Lens ervoides

text: Lens ervoides

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: External Id

text: LAVAL UNIVERSITY

text: public

tag: Namespace:LAVAL UNIVERSITY

text: SADI HF_week_0

text: rat

characteristic: environment (biome)

text: gut

characteristic: environment (feature)

text: feces

characteristic: environment (material)

text: Canada

text: host-associated

characteristic: host-associated environmental package

text: metagenome

characteristic: investigation type

text: rat gut metagenome

characteristic: project name

text: rat gut metagenome

text: Illumina MiSeq

characteristic: sequencing method

text: Consistent gut bacterial and short-chain fatty acid signatures in hypoabsorptive bariatric surgeries correlate with metabolic benefits in rats


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: LAVAL UNIVERSITY

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: SADI HF_week_2

text: rat

text: gut

text: feces

text: Canada

text: host-associated

text: metagenome

text: rat gut metagenome

text: rat gut metagenome

text: Illumina MiSeq


characteristic: ENA-CHECKLIST

text: LAVAL UNIVERSITY

text: public

characteristic: collection date

text: SADI HF_week_8

characteristic: description

text: rat

text: gut

text: feces

text: Canada

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: host-associated

text: metagenome

text: rat gut metagenome

characteristic: organism

text: rat gut metagenome

text: Illumina MiSeq

characteristic: title


characteristic: External Id

text: LAVAL UNIVERSITY

text: public

text: RYGB HF_week_0

text: rat

characteristic: environment (biome)

text: gut

characteristic: environment (feature)

text: feces

characteristic: environment (material)

text: Canada

text: host-associated

characteristic: host-associated environmental package

text: metagenome

characteristic: investigation type

text: rat gut metagenome

characteristic: project name

text: rat gut metagenome

text: Illumina MiSeq

characteristic: sequencing method


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: LAVAL UNIVERSITY

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: RYGB HF_week_2

text: rat

text: gut

text: feces

text: Canada

text: host-associated

text: metagenome

text: rat gut metagenome

text: rat gut metagenome

text: Illumina MiSeq


characteristic: ENA-CHECKLIST

text: LAVAL UNIVERSITY

text: public

characteristic: collection date

text: RYGB HF_week_8

characteristic: description

text: rat

text: gut

text: feces

text: Canada

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: host-associated

text: metagenome

text: rat gut metagenome

characteristic: organism

text: rat gut metagenome

text: Illumina MiSeq

characteristic: title


characteristic: External Id

text: LAVAL UNIVERSITY

text: public

text: SHAM HF-PW_week_0

text: rat

characteristic: environment (biome)

text: gut

characteristic: environment (feature)

text: feces

characteristic: environment (material)

text: Canada

text: host-associated

characteristic: host-associated environmental package

text: metagenome

characteristic: investigation type

text: rat gut metagenome

characteristic: project name

text: rat gut metagenome

text: Illumina MiSeq

characteristic: sequencing method


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: LAVAL UNIVERSITY

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: SHAM HF-PW_week_2

text: rat

text: gut

text: feces

text: Canada

text: host-associated

text: metagenome

text: rat gut metagenome

text: rat gut metagenome

text: Illumina MiSeq


characteristic: ENA-CHECKLIST

text: LAVAL UNIVERSITY

text: public

characteristic: collection date

text: SHAM HF-PW_week_8

characteristic: description

text: rat

text: gut

text: feces

text: Canada

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: host-associated

text: metagenome

text: rat gut metagenome

characteristic: organism

text: rat gut metagenome

text: Illumina MiSeq

characteristic: title


characteristic: External Id

text: LAVAL UNIVERSITY

text: public

text: SHAM LF_week_0

text: rat

characteristic: environment (biome)

text: gut

characteristic: environment (feature)

text: feces

characteristic: environment (material)

text: Canada

text: host-associated

characteristic: host-associated environmental package

text: metagenome

characteristic: investigation type

text: rat gut metagenome

characteristic: project name

text: rat gut metagenome

text: Illumina MiSeq

characteristic: sequencing method


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: LAVAL UNIVERSITY

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: SHAM LF_week_2

text: rat

text: gut

text: feces

text: Canada

text: host-associated

text: metagenome

text: rat gut metagenome

text: rat gut metagenome

text: Illumina MiSeq


characteristic: ENA-CHECKLIST

text: LAVAL UNIVERSITY

text: public

characteristic: collection date

text: SHAM LF_week_8

characteristic: description

text: rat

text: gut

text: feces

text: Canada

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: host-associated

text: metagenome

text: rat gut metagenome

characteristic: organism

text: rat gut metagenome

text: Illumina MiSeq

characteristic: title


characteristic: External Id

text: LAVAL UNIVERSITY

text: public

text: SG HF_week_0

text: rat

characteristic: environment (biome)

text: gut

characteristic: environment (feature)

text: feces

characteristic: environment (material)

text: Canada

text: host-associated

characteristic: host-associated environmental package

text: metagenome

characteristic: investigation type

text: rat gut metagenome

characteristic: project name

text: rat gut metagenome

text: Illumina MiSeq

characteristic: sequencing method


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: LAVAL UNIVERSITY

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: SG HF_week_2

text: rat

text: gut

text: feces

text: Canada

text: host-associated

text: metagenome

text: rat gut metagenome

text: rat gut metagenome

text: Illumina MiSeq


characteristic: ENA-CHECKLIST

text: LAVAL UNIVERSITY

text: public

characteristic: collection date

text: SG HF_week_8

characteristic: description

text: rat

text: gut

text: feces

text: Canada

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: host-associated

text: metagenome

text: rat gut metagenome

characteristic: organism

text: rat gut metagenome

text: Illumina MiSeq

characteristic: title


characteristic: External Id

text: LAVAL UNIVERSITY

text: public

text: BPD/DS HF_week_0

text: rat

characteristic: environment (biome)

text: gut

characteristic: environment (feature)

text: feces

characteristic: environment (material)

text: Canada

text: host-associated

characteristic: host-associated environmental package

text: metagenome

characteristic: investigation type

text: rat gut metagenome

characteristic: project name

text: rat gut metagenome

text: Illumina MiSeq

characteristic: sequencing method


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: LAVAL UNIVERSITY

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: BPD/DS HF_week_2

text: rat

text: gut

text: feces

text: Canada

text: host-associated

text: metagenome

text: rat gut metagenome

text: rat gut metagenome

text: Illumina MiSeq


characteristic: ENA-CHECKLIST

text: LAVAL UNIVERSITY

text: public

characteristic: collection date

text: BPD/DS HF_week_8

characteristic: description

text: rat

text: gut

text: feces

text: Canada

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: host-associated

text: metagenome

text: rat gut metagenome

characteristic: organism

text: rat gut metagenome

text: Illumina MiSeq

characteristic: title


characteristic: External Id

text: LAVAL UNIVERSITY

text: public

text: SADI HF_week_0

text: rat

characteristic: environment (biome)

text: gut

characteristic: environment (feature)

text: feces

characteristic: environment (material)

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text: 171; 448

characteristic: investigation type

text: microbial mat/biofilm

text: metagenome

text: Biofilm formation deep biosphere

characteristic: project name

text: metagenome

characteristic: sequencing method


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: LINNAEUS UNIVERSITY

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: Planktonic 0.2 micron filter borehole KA3385A-1 after biofilm formation 16S rRNA gene amplicon sequences

text: aquifer terrestrial deep biosphere

characteristic: environment (biome)

text: groundwater underneath Baltic Sea

characteristic: environment (feature)

text: water

characteristic: environment (material)

text: Sweden

characteristic: geographic location (country and/or sea)

text: 171; 448

text: 171; 448

text: microbial mat/biofilm

text: metagenome

characteristic: organism

text: Biofilm formation deep biosphere

text: metagenome

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: External Id

text: LINNAEUS UNIVERSITY

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: Planktonic 0.1 micron filter borehole KA3385A-1 before biofilm formation 16S rRNA gene amplicon sequences

text: aquifer terrestrial deep biosphere

text: groundwater underneath Baltic Sea

text: water

text: Sweden

text: 171; 448

characteristic: geographic location (depth)

text: 171; 448

characteristic: geographic location (elevation)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: microbial mat/biofilm

characteristic: microbial mat/biofilm environmental package

text: metagenome

text: Biofilm formation deep biosphere

text: metagenome


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: LINNAEUS UNIVERSITY

characteristic: INSDC center name

characteristic: INSDC first public

text: public

characteristic: Submitter Id

characteristic: collection date

text: Planktonic 0.2 micron filter borehole KA3385A-1 before biofilm formation 16S rRNA gene amplicon sequences

characteristic: description

text: aquifer terrestrial deep biosphere

text: groundwater underneath Baltic Sea

text: water

text: Sweden

text: 171; 448

text: 171; 448

characteristic: investigation type

text: microbial mat/biofilm

text: metagenome

text: Biofilm formation deep biosphere

characteristic: project name

text: metagenome

characteristic: sequencing method


characteristic: ENA-CHECKLIST

characteristic: External Id

text: LINNAEUS UNIVERSITY

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: Biofilm community borehole KA3385A-1 20 days formation 16S rRNA gene amplicon sequences

text: aquifer terrestrial deep biosphere

characteristic: environment (biome)

text: groundwater underneath Baltic Sea

characteristic: environment (feature)

text: water

characteristic: environment (material)

text: Sweden

characteristic: geographic location (country and/or sea)

text: 171; 448

text: 171; 448

text: microbial mat/biofilm

text: metagenome

characteristic: organism

text: Biofilm formation deep biosphere

text: metagenome

characteristic: title


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: LINNAEUS UNIVERSITY

characteristic: INSDC center name

characteristic: INSDC first public

text: public

characteristic: SRA accession

text: Biofilm community borehole KA3385A-1 40 days formation 16S rRNA gene amplicon sequences

text: aquifer terrestrial deep biosphere

text: groundwater underneath Baltic Sea

text: water

text: Sweden

text: 171; 448

characteristic: geographic location (depth)

text: 171; 448

characteristic: geographic location (elevation)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: microbial mat/biofilm

characteristic: microbial mat/biofilm environmental package

text: metagenome

text: Biofilm formation deep biosphere

text: metagenome


characteristic: ENA-CHECKLIST

characteristic: External Id

text: LINNAEUS UNIVERSITY

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: Submitter Id

characteristic: collection date

text: Biofilm community borehole KA3385A-1 75 days formation 16S rRNA gene amplicon sequences

characteristic: description

text: aquifer terrestrial deep biosphere

text: groundwater underneath Baltic Sea

text: water

text: Sweden

text: 171; 448

text: 171; 448

characteristic: investigation type

text: microbial mat/biofilm

text: metagenome

text: Biofilm formation deep biosphere

characteristic: project name

text: metagenome

characteristic: sequencing method


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: LINNAEUS UNIVERSITY

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: Biofilm community borehole SA1229A-1 20 days formation 16S rRNA gene amplicon sequences

text: aquifer terrestrial deep biosphere

characteristic: environment (biome)

text: groundwater underneath Baltic Sea

characteristic: environment (feature)

text: water

characteristic: environment (material)

text: Sweden

characteristic: geographic location (country and/or sea)

text: 171; 448

text: 171; 448

text: microbial mat/biofilm

text: metagenome

characteristic: organism

text: Biofilm formation deep biosphere

text: metagenome

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: External Id

text: LINNAEUS UNIVERSITY

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: Biofilm community borehole SA1229A-1 40 days formation 16S rRNA gene amplicon sequences

text: aquifer terrestrial deep biosphere

text: groundwater underneath Baltic Sea

text: water

text: Sweden

text: 171; 448

characteristic: geographic location (depth)

text: 171; 448

characteristic: geographic location (elevation)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: microbial mat/biofilm

characteristic: microbial mat/biofilm environmental package

text: metagenome

text: Biofilm formation deep biosphere

text: metagenome


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: LINNAEUS UNIVERSITY

characteristic: INSDC center name

characteristic: INSDC first public

text: public

characteristic: Submitter Id

characteristic: collection date

text: Biofilm community borehole SA1229A-1 75 days formation 16S rRNA gene amplicon sequences

characteristic: description

text: aquifer terrestrial deep biosphere

text: groundwater underneath Baltic Sea

text: water

text: Sweden

text: 171; 448

text: 171; 448

characteristic: investigation type

text: microbial mat/biofilm

text: metagenome

text: Biofilm formation deep biosphere

characteristic: project name

text: metagenome

characteristic: sequencing method


characteristic: ENA-CHECKLIST

characteristic: External Id

text: LINNAEUS UNIVERSITY

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: Planktonic 0.1 micron filter borehole SA1229A-1 before biofilm formation 16S rRNA gene amplicon sequences

text: aquifer terrestrial deep biosphere

characteristic: environment (biome)

text: groundwater underneath Baltic Sea

characteristic: environment (feature)

text: water

characteristic: environment (material)

text: Sweden

characteristic: geographic location (country and/or sea)

text: 171; 448

text: 171; 448

text: microbial mat/biofilm

text: metagenome

characteristic: organism

text: Biofilm formation deep biosphere

text: metagenome

characteristic: title


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: LINNAEUS UNIVERSITY

characteristic: INSDC center name

characteristic: INSDC first public

text: public

characteristic: SRA accession

text: Planktonic 0.2 micron filter borehole SA1229A-1 before biofilm formation 16S rRNA gene amplicon sequences

text: aquifer terrestrial deep biosphere

text: groundwater underneath Baltic Sea

text: water

text: Sweden

text: 171; 448

characteristic: geographic location (depth)

text: 171; 448

characteristic: geographic location (elevation)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: microbial mat/biofilm

characteristic: microbial mat/biofilm environmental package

text: metagenome

text: Biofilm formation deep biosphere

text: metagenome


characteristic: ENA-CHECKLIST

characteristic: External Id

text: UNSW Australia

characteristic: INSDC last update

text: public

characteristic: INSDC status

tag: Namespace:UNSW Australia

characteristic: Submitter Id

text: human

characteristic: common name

text: Homo sapiens

text: Homo sapiens

text: Vagina


tag: attribute

text: Aquatic Breeding

text: public

tag: Namespace:Aquatic Breeding

text: spot-fin porcupinefish

text: muscle

characteristic: description

text: Diodon hystrix

characteristic: organism

text: Diodon hystrix

text: Transcriptome data of Diodon hystrix

characteristic: title


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: QIB

characteristic: INSDC center name

text: public

text: Quadram Institute Bioscience

characteristic: broker name

characteristic: collection date

text: Comparison of PCR versus PCR-free DNA library preparation for characterising the human fecal virome

text: Faeces

characteristic: environment (biome)

text: Faeces

characteristic: environment (feature)

text: Faeces

characteristic: environment (material)

text: United Kingdom

characteristic: geographic location (country and/or sea)

text: host-associated

characteristic: host-associated environmental package

text: metagenome

characteristic: investigation type

text: Homo sapiens environmental sample

text: Human faecal virome

characteristic: project name

text: Homo sapiens environmental sample

text: Illumina

characteristic: sequencing method

text: faecal virome


characteristic: ENA-CHECKLIST

characteristic: External Id

text: IHU - Mediterranee Infection

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

tag: Namespace:IHU - Mediterranee Infection

characteristic: Submitter Id

text: Blood culture

characteristic: isolation source

text: Staphylococcus sp. Marseille-Q1834

text: Staphylococcus sp. Marseille-Q1834

characteristic: strain

text: New species in clinical microbiology


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: UNIVERSITY OF HELSINKI

characteristic: INSDC center name

text: public

tag: Namespace:UNIVERSITY OF HELSINKI

characteristic: collection date

text: human

characteristic: common name

text: vagina

characteristic: environment (biome)

text: mid-vaginal wall

text: vaginal swab

text: Finland

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: human-vaginal

characteristic: human vaginal environmental package

text: Homo sapiens

characteristic: organism

text: EMV

text: Homo sapiens

text: illumina Miseq

text: Vaginal microbiome of pregnant women

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: External Id

text: AARHUS UNIVERSITY, DENMARK

characteristic: INSDC first public

characteristic: INSDC last update

text: public

tag: Namespace:AARHUS UNIVERSITY, DENMARK

text: Agriculture

text: Drainage water

characteristic: environment (feature)

text: Woodchip + water

characteristic: environment (material)

text: Yes

text: Denmark

characteristic: geographic location (country and/or sea)

text: Pseudomonas proteolytica

text: F1 - R13

characteristic: pcr primers

text: Pseudomonas proteolytica

text: 16s rRNA

characteristic: target gene

text: V3 V4

characteristic: target subfragment


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: AARHUS UNIVERSITY, DENMARK

characteristic: INSDC center name

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

characteristic: collection date

text: Agriculture

text: Drainage water

text: Woodchip + water

text: Yes

text: Denmark

text: Pseudomonas brenneri

text: F1 - R13

text: Pseudomonas brenneri

text: 16s rRNA

text: V3 V4


characteristic: ENA-CHECKLIST

text: AARHUS UNIVERSITY, DENMARK

text: public

text: Agriculture

characteristic: environment (biome)

text: Drainage water

text: Woodchip + water

text: Yes

text: Denmark

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: Pseudomonas veronii

characteristic: organism

text: F1 - R13

text: Pseudomonas veronii

text: 16s rRNA

text: V3 V4

characteristic: title


characteristic: External Id

text: AARHUS UNIVERSITY, DENMARK

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: Agriculture

text: Drainage water

characteristic: environment (feature)

text: Woodchip + water

characteristic: environment (material)

text: Yes

text: Denmark

characteristic: geographic location (country and/or sea)

text: Janthinobacterium lividum

text: F1 - R13

text: Janthinobacterium lividum

text: 16s rRNA

text: V3 V4


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: AARHUS UNIVERSITY, DENMARK

characteristic: INSDC center name

text: public

text: Agriculture

text: Drainage water

text: Woodchip + water

text: Yes

text: Denmark

text: Kluyvera intermedia

text: F1 - R13

characteristic: pcr primers

text: Kluyvera intermedia

text: 16s rRNA

characteristic: target gene

text: V3 V4

characteristic: target subfragment


characteristic: ENA-CHECKLIST

text: AARHUS UNIVERSITY, DENMARK

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

characteristic: collection date

text: Agriculture

characteristic: environment (biome)

text: Drainage water

text: Woodchip + water

text: Yes

text: Denmark

text: Pseudomonas chlororaphis subsp. aurantiaca

text: F1 - R13

text: 16s rRNA

text: V3 V4


characteristic: External Id

text: AARHUS UNIVERSITY, DENMARK

characteristic: INSDC first public

text: public

text: Agriculture

text: Enrichment from woodchip bioreactor

text: Woodchip + drainage water

text: Yes

text: Denmark

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: wetland metagenome

characteristic: organism

text: 341.2FDI and 805.2RDI

text: wetland metagenome

text: 16s rRNA

text: V3 V4

characteristic: title


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: KAROLINSKA INSTITUTE

characteristic: INSDC last update

text: public

tag: Namespace:KAROLINSKA INSTITUTE

text: house mouse

characteristic: common name

text: RNA-seq of mouse heart, single cell

characteristic: description

characteristic: dev stage

text: Mus musculus

text: Mus musculus

text: postnatal heart

characteristic: tissue type

text: scRNA-seq of mouse heart: A1


characteristic: ENA-CHECKLIST

text: KAROLINSKA INSTITUTE

characteristic: INSDC center name

text: public

characteristic: INSDC status

characteristic: SRA accession

text: house mouse

text: RNA-seq of mouse heart, single cell

text: Mus musculus

text: Mus musculus

text: postnatal heart

text: scRNA-seq of mouse heart: A2


characteristic: External Id

text: KAROLINSKA INSTITUTE

text: public

characteristic: Submitter Id

text: house mouse

text: RNA-seq of mouse heart, single cell

text: Mus musculus

text: Mus musculus

text: postnatal heart

text: scRNA-seq of mouse heart: A3


text: KAROLINSKA INSTITUTE

characteristic: INSDC first public

text: public

text: house mouse

text: RNA-seq of mouse heart, single cell

text: Mus musculus

text: Mus musculus

text: postnatal heart

text: scRNA-seq of mouse heart: A4


text: KAROLINSKA INSTITUTE

text: public

text: house mouse

text: RNA-seq of mouse heart, single cell

text: Mus musculus

text: Mus musculus

text: postnatal heart

text: scRNA-seq of mouse heart: A5