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text: Untreated wastewater was collected in Uppsala at Kungsangsverket over 1 week leading up to 2023-07-17. Daily samples were collected over 24 hours using a flow compensated sampler then combined flow-proportionally into a composite weekly sample.

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characteristic: geographic location (longitude)

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text: Severe acute respiratory syndrome coronavirus 2|NCBITaxon:2697049|http://purl.obolibrary.org/obo/NCBITaxon_2697049

text: 2023-W29 Vasteras Amplified SARS-CoV-2 RNA from wastewater


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text: 2023-W29 Goteborg Amplified SARS-CoV-2 RNA from wastewater


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text: Untreated wastewater was collected in Stockholm-Grodinge at Himmerfjardsverket on 2023-07-17 over 24 hours using a flow compensated sampler

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text: Sweden

text: virus

text: Himmerfjardsverket

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text: 2023-W29 Stockholm-Grodinge Amplified SARS-CoV-2 RNA from wastewater


text: IGBMC

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text: 6 days after hatching

unit: day

characteristic: age

text: ArrayExpress

characteristic: broker name

text: not collected

text: fruit fly

characteristic: common name

text: Protocols: L3 CNS (10 per replicate) were quickly dissected on ice in PBS, put directly in 150µl TRIzol™ (Invitrogen, ref 15596026) once a full sample was collected and stored on ice. CNS were lysed with 10 strokes of microtube pestle (pestle was rinsed with another 150µl TRIzol™), vortex at full speed for 1min and incubate 10 min at RT for full lysis. 1/5 V of Chloroform was added and samples were vortexed 1min at full speed, incubated 5 min at RT and centrifuged at 16000g for 30 min at 4°C. Supernatant was collected, and RNA was extracted with 1V of isopropanol and glycogen (3 µg/mL final concentration), incubate at -20°C for 2h and centrifuge at 16000g for 30 min at 4°C. Pellets were washed twice in ethanol 75%, 15 min at 16000g 4°C, allowed to dry quickly, resuspend in 30µl H2O, treated with 25U DNAse I (Thermo Scientific™ 89836) for 5 min in 50µL total volume at RT. RNA was extracted a second time in 500µL TRIzol™ like previously described. End washing steps were performed 3 times. Total RNA was resuspended in 15µL H20, 2µL were kept for downstream analysis and samples were immediately stored at -80°C till processing. RNA integrity was analyzed on Agilent RNA Chip on bioanalyzer 2100. Library preparation was performed at the GenomEast platform (IGBMC) using using the Illumina® Stranded mRNA Prep.

text: L3 larva

characteristic: developmental stage

characteristic: genotype

text: not collected

characteristic: geographic location (country and/or sea)

text: pool of 10

characteristic: individual

text: not applicable

characteristic: isolate

text: Drosophila melanogaster

text: Drosophila melanogaster

text: central nervous system

characteristic: organism part

text: Drosophila melanogaster

text: female

characteristic: sex

text: rad50∆5.1 null

characteristic: strain

characteristic: title


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text: public

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characteristic: SRA accession

text: 5 days after hatching

text: ArrayExpress

text: not collected

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text: not collected

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text: not applicable

text: Drosophila melanogaster

characteristic: organism

text: Drosophila melanogaster

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text: Drosophila melanogaster

text: female


text: public

tag: Namespace:reNEW, Novo Nordisk Foundation Centre of Stem cell Medicine, University of Copenhagen

characteristic: Submitter Id

text: ArrayExpress

characteristic: broker name

text: epiblast stem cell

text: not collected

characteristic: collection date

text: house mouse

characteristic: common name

text: CRISPR/Cas9 + Pbx1KO gDNA

characteristic: crispr/cas9 treatment

text: Protocols: For all conditions, two biological replicate samples were collected from independent experiments. EpiSC lines derived from E6.5 mouse embryos (129S6/SvEvTac background) were a kind gift from Dr. M.M. Rothová (The Novo Nordisk Foundation Center for Stem Cell Biology, University of Copenhagen, Copenhagen, Denmark). The lines were derived in EpiSC medium as previously described [1]. EpiSC lines were maintained in 6-well cell-culture plates (Corning, 3506) pre-coated with 15 µg/ml human Fibronectin (Merck Millipore, FC01015) in N2B27 medium (prepared as described in Ying and Smith, 2003) supplemented with 20 ng/ml Activin A, 10 ng/ml bFGF and 1 µM XAV939 (EpiSC medium). Both mESC lines were cultured in 0.1% gelatin-coated plates 6-well Corning cell-culture plates. mESCs were cultured in standard conditions in either serum/LIF or 2i/LIF conditions with CHIR-99021, PD03 and LIF (made in house). All lines used in this study were karyotyped and routinely tested for mycoplasma. [1] Guo, G. et al. Klf4 reverts developmentally programmed restriction of ground state pluripotency. Development 136, 1063-9 (2009). Generation of Pbx1 ESC/EpiSC lines using the CRISPR/Cas9 system. The strategy to inactivate Pbx1 in ESCs and EpiSCs was the same. Pbx1-KO lines were generated by inserting a floxed CMV-hygromycin-Poly (A) cassette between Exon 2 and Intron 2 of Pbx1 to disrupt Pbx1 gene expression, employing the CRISPR Nickase system. Guide RNAs (gRNAs) were designed using the CRISPR/Cas9 design tool (crispr.mit.edu) and cloned into pX335 (a gift from Prof. F. Zhang; Addgene, 42335). Cells were co-transfected with a pair of gRNA-pX335 plasmids (gRNA 1: GTCCAGGCTCTGGTCCGTGA; gRNA 2: CCAAGTGAGTGCCCCCACCC; 100 ng each vector) and 1 µg linearized targeting vector using Lipofectamine 2000 (Thermo Fisher Scientific, 11668030), seeded at low density and selected for hygromycin resistance for 8-10 days. Single colonies were screened by diagnostic PCR, Southern blot and Western blot analyses. Pbx1 gRNA used (GGCCATCCCGACCCCAGCGT) EpiSC differentiation to germ-layer lineages. All differentiation was conducted in serum-free, feeder-free and monolayer conditions in chemically-defined N2B27-based media. EpiSCs were seeded at ~10.5 x 103 cells/cm2 in 6-well cell-culture plates pre-coated with 15 µg/ml human Fibronectin, and cultured in EpiSC medium for 24h. EpiSCs were differentiated towards either APSD using 30 ng/ml Activin A, 4 µM CHIR-99021, 20 ng/ml bFGF and 100 nM PIK-90 (APS medium) for 24 For NMP/PSM differentiation, EpiSCs were first differentiated towards APSD, and then to NMP/PSM using 1 µM A-83-01, 3 µM CHIR-99021, 250 nM LDN193189 and 20 ng/ml bFGF for 48-72h (PSM media). For DE differentiation, EpiSCs were first differentiated towards APSD in N2B27-basal media over 24 h, and then to DE using 30 ng/ml Activin A, 4 µM CHIR-99021 and 100 nM PIK-90 in RPMI(Glutamax) + B27 (Without insulin) basal media (DE medium) for 48 h. EpiSCs were differentiated towards neuroectoderm based on known media requirements [1]. Differentiation of EpiSCs towards PPS and ExM were done as previously described [2]. [1] Greber, B. et al. Conserved and divergent roles of FGF signaling in mouse epiblast stem cells and human embryonic stem cells. Cell Stem Cell 6, 215-26 (2010). [2] Drozd, A.M. et al. Progesterone Receptor Modulates Extraembryonic Mesoderm and Cardiac Progenitor Specification during Mouse Gastrulation. Int J Mol Sci 23(2022). Nuclear extracts (NE) for EMSA were prepared from in vitro-differentiated paraxial mesoderm cells. Cells were resuspended in 200 μl lysis buffer (10 mM HEPES pH 7.9, 30 mM KCl, 1.5 mM MgCl2, 1 mM DTT, supplemented with 1x Protease inhibitor cocktail (Roche, 11836170001)), kept on ice for 10 min and supplemented with addition of Triton X-100 to a final concentration of 0.1%. The nuclei were collected by centrifugation at 4 °C. Nuclear extracts were prepared by resuspending the nuclear pellet in 50 μl nuclear buffer (20 mM HEPES pH 7.9, 25% (v/v) glycerol, 0.42 M NaCl, 1.5 mM MgCl2, 1 mM DTT, supplemented with 1x Protease inhibitor cocktail). NE preparations were incubated at 4 °C with rotation for 30 min and cleared by centrifugation. Finally, the extracts were quantified by NanoDrop, aliquoted and stored at −80 °C. ATAC-seq was performed on 50,000 cells per replicate as described in Buenrostro et al.64 (with modifications based on Corces et al.65), on EpiSCs and PSM-differentiated cell populations at desired time-points. Libraries were generated using the Ad1_noMX and Ad2.1–2.16 barcoded primers64 and amplified for 10 total PCR cycles. Libraries were purified with AMPure XP beads to remove contaminating primer dimers and fragments >1,000 bp. Library quality was assessed using the Fragment analyzer and quantitated by Qubit assay. The libraries were sequenced with 50 bp paired-end reads on a Next-Seq 500 Sequencer (Illumina) at the DanStem Genomics Platform (University of Copenhagen, Copenhagen, Denmark).

characteristic: description

text: embryo

characteristic: developmental stage

text: Unsorted

characteristic: flow cytometry processing

text: CRISPR/Cas9 mediated Pbx1 homozygous knockout

characteristic: genotype

text: not collected

characteristic: geographic location (country and/or sea)

text: EpiSCs (Post-implantation)

characteristic: growth condition

characteristic: illumina sequencing machine

text: Post-implantation

characteristic: implantation stage at sampling

text: not applicable

text: Mus musculus

text: Mus musculus

characteristic: replicate

text: Mus musculus

characteristic: sequencing date

characteristic: sequencing kit barcode


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: reNEW, Novo Nordisk Foundation Centre of Stem cell Medicine, University of Copenhagen

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: ArrayExpress

text: epiblast stem cell

text: not collected

text: house mouse

text: CRISPR/Cas9 + Pbx1KO gDNA

text: embryo

text: Unsorted

text: not collected

text: EpiSCs (Post-implantation)

text: Post-implantation

text: not applicable

characteristic: isolate

text: Mus musculus

characteristic: organism

text: Mus musculus

text: Mus musculus

characteristic: strain

characteristic: title


text: public

characteristic: Submitter Id

text: ArrayExpress

characteristic: broker name

text: ExM

text: not collected

characteristic: collection date

text: house mouse

characteristic: common name

text: CRISPR/Cas9 + Pbx1KO gDNA

characteristic: crispr/cas9 treatment

characteristic: description

text: embryo

characteristic: developmental stage

text: Unsorted

characteristic: flow cytometry processing

characteristic: genotype

text: not collected

characteristic: geographic location (country and/or sea)

text: EpiSCs + 24h towards PPS + 24h towards ExM

characteristic: growth condition

characteristic: illumina sequencing machine

text: Extracted from post-implantation embryo and differentiated

characteristic: implantation stage at sampling

text: not applicable

text: Mus musculus

text: Mus musculus

text: Mus musculus

text: AHCHVMBGXC


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

text: ArrayExpress

text: embryonic stem cell

text: not collected

text: house mouse

text: CRISPR/Cas9 + Pbx1KO gDNA

text: embryo

text: Unsorted

text: not collected

text: (2i/LIF) (Pre-implantation)

text: Pre-implantation

text: not applicable

characteristic: isolate

text: Mus musculus

text: Mus musculus

characteristic: replicate

text: Mus musculus

characteristic: sequencing date

text: AHCHVMBGXC

characteristic: sequencing kit barcode


text: public

characteristic: Submitter Id

text: ArrayExpress

characteristic: broker name

text: APSD

text: not collected

characteristic: collection date

text: house mouse

characteristic: common name

characteristic: crispr/cas9 treatment

characteristic: description

text: embryo

characteristic: developmental stage

text: CLDN6High (Sorted)

characteristic: flow cytometry processing

text: wild type genotype

characteristic: genotype

text: not collected

characteristic: geographic location (country and/or sea)

text: EpiSCs + 24h towards APSD

text: not applicable

text: Mus musculus

characteristic: organism

text: Mus musculus

text: Mus musculus

characteristic: strain

characteristic: title


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

text: ArrayExpress

text: APSD

text: not collected

text: house mouse

text: embryo

text: CLDN6Low (Sorted)

text: wild type genotype

text: not collected

text: EpiSCs + 24h towards APSD

characteristic: growth condition

characteristic: illumina sequencing machine

characteristic: implantation stage at sampling

text: not applicable

characteristic: isolate

text: Mus musculus

text: Mus musculus

text: Mus musculus


text: public

characteristic: Submitter Id

text: ArrayExpress

characteristic: broker name

text: epiblast stem cell

text: not collected

characteristic: collection date

text: house mouse

characteristic: common name

characteristic: crispr/cas9 treatment

characteristic: description

text: embryo

characteristic: developmental stage

text: CLDN6High (Sorted)

characteristic: flow cytometry processing

text: wild type genotype

characteristic: genotype

text: not collected

characteristic: geographic location (country and/or sea)

text: EpiSCs (Post-implantation)

text: Post-implantation

text: not applicable

text: Mus musculus

text: Mus musculus

characteristic: replicate

text: Mus musculus

characteristic: sequencing date

characteristic: sequencing kit barcode


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

text: ArrayExpress

text: epiblast stem cell

text: not collected

text: house mouse

text: embryo

text: CLDN6Low (Sorted)

text: wild type genotype

text: not collected

text: EpiSCs (Post-implantation)

characteristic: growth condition

text: Post-implantation

text: not applicable

text: Mus musculus

characteristic: organism

text: Mus musculus

text: Mus musculus

characteristic: strain

characteristic: title


text: public

characteristic: Submitter Id

text: ArrayExpress

characteristic: broker name

text: ExM

text: not collected

characteristic: collection date

text: house mouse

characteristic: common name

characteristic: crispr/cas9 treatment

characteristic: description

text: embryo

characteristic: developmental stage

text: Unsorted

characteristic: flow cytometry processing

text: Pbx1 -/-

characteristic: genotype

text: not collected

characteristic: geographic location (country and/or sea)

characteristic: illumina sequencing machine

characteristic: implantation stage at sampling

text: not applicable

characteristic: isolate

text: Mus musculus

text: Mus musculus

text: Mus musculus


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

text: ArrayExpress

text: PPS

text: not collected

text: house mouse

text: embryo

text: Unsorted

text: Pbx1 -/-

text: not collected

text: EpiSCs + 24h towards PPS

characteristic: growth condition

text: not applicable

text: Mus musculus

text: Mus musculus

characteristic: replicate

text: Mus musculus

characteristic: sequencing date

characteristic: sequencing kit barcode


text: public

characteristic: Submitter Id

text: ArrayExpress

characteristic: broker name

text: epiblast stem cell

text: not collected

characteristic: collection date

text: house mouse

characteristic: common name

characteristic: crispr/cas9 treatment

characteristic: description

text: embryo

characteristic: developmental stage

text: Unsorted

characteristic: flow cytometry processing

text: wild type genotype

characteristic: genotype

text: not collected

characteristic: geographic location (country and/or sea)

text: EpiSCs (Post-implantation)

text: Post-implantation

text: not applicable

text: Mus musculus

characteristic: organism

text: Mus musculus

text: Mus musculus

characteristic: strain

characteristic: title


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

text: ArrayExpress

text: ExM

text: not collected

text: house mouse

text: embryo

text: Unsorted

text: wild type genotype

text: not collected

characteristic: growth condition

characteristic: illumina sequencing machine

characteristic: implantation stage at sampling

text: not applicable

characteristic: isolate

text: Mus musculus

text: Mus musculus

text: Mus musculus

text: AHCHVMBGXC


text: public

characteristic: Submitter Id

text: ArrayExpress

characteristic: broker name

text: ExM

text: not collected

characteristic: collection date

text: house mouse

characteristic: common name

characteristic: crispr/cas9 treatment

characteristic: description

text: embryo

characteristic: developmental stage

text: Unsorted

characteristic: flow cytometry processing

text: wild type genotype

characteristic: genotype

text: not collected

characteristic: geographic location (country and/or sea)

text: not applicable

text: Mus musculus

text: Mus musculus

characteristic: replicate

text: Mus musculus

characteristic: sequencing date

characteristic: sequencing kit barcode


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

text: ArrayExpress

text: embryonic stem cell

text: not collected

text: house mouse

text: embryo

text: Unsorted

text: wild type genotype

text: not collected

text: (2i/LIF) (Pre-implantation)

characteristic: growth condition

text: Pre-implantation

text: not applicable

text: Mus musculus

characteristic: organism

text: Mus musculus

text: Mus musculus

text: AHCHVMBGXC

characteristic: strain

characteristic: title


text: public

characteristic: Submitter Id

text: ArrayExpress

characteristic: broker name

text: PPS

text: not collected

characteristic: collection date

text: house mouse

characteristic: common name

characteristic: crispr/cas9 treatment

characteristic: description

text: embryo

characteristic: developmental stage

text: Unsorted

characteristic: flow cytometry processing

text: wild type genotype

characteristic: genotype

text: not collected

characteristic: geographic location (country and/or sea)

text: EpiSCs + 24h towards PPS

characteristic: illumina sequencing machine

characteristic: implantation stage at sampling

text: not applicable

characteristic: isolate

text: Mus musculus

text: Mus musculus

text: Mus musculus


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: IGBMC

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: age

text: ArrayExpress

text: not collected

text: fruit fly

text: Protocols: Brains : 70 brains dissected in PBS 250µL, pellet 3' at 4°C 600g, resuspent in 200µL 1mg/mL collagenase D 1h at 700rpm 37°C. Isolated cells washed once in PBS at 600g 10' 4°C and resuspend in 300µL PBS and pass through FACS filter for sorting. 10 oregon brains were used as negative control for FACS. E16 embryos are collected, washed, dechorionated 1min in bleach, washed extensively and crushed using a dounce tissue grinder, first using the loose pestle than the tight one. Cells are FACSed using 100µm nozzle. Strain used : elav-nRFP Nuclei isolation : Add 200µL ice cold nuclear extraction buffer (HEPES-KOH pH 7.9 20mM, KCl 10mM, Spermidine 0.5mM, triton X-100 0,1%, glycerol 20%, PIC 1X), mix well and incubate on balancelle 10'. Pellet isolated nuclei at 1400rcf 15' 4°C, wash once in 250mL PBS, 1400g, 10' 4°C Tagmentation: Resuspend isolated nuclei in 50µL tagmentation buffer (33mM tris-acetate pH 7.8, 66mM potassium acetate, 10mM Mg-acetate, 16% dimethylformamide, 0.01% digitonin) + 0.5µL pre-loaded Tn5, mix well. Incubate 60' at 37°C 300rpm. DNA isolation add 50µL STOP buffer (EDTA 20mM, tris-HCl pH 7.5 10mM) add 200µL H20, mix well, add 300µL basic Phenol-chloroforme-isoamyl alcool, vortex 10s, incubate RT 10', centrifuge 15' 160000g 4°C Collect supernatent, add 1V chloroforme, vortex 10s, centrifuge 15' 4°C 160000g Collect supernatent, add 2V Et-OH 100%, 1/10V NaAc 3M, incubate at -20°C ON Centrifuge 16000g 15' 4°, remove supernatent, add 500µL 75% Et-OH, centrifuge 15' 4°C 16000g, repeat twice Air-dry 10', 65°C 5', resuspend in 25µL H20. Amplify purified library : 1. 72°C 5' 2. 98°C 30\" 3. 98°C 10\" 4. 63°C 30\" 5. 72°C 1' 6. Hold 4°C repeat Step 3-4 14 times

text: embryonic stage 16

text: elav-nRFP

text: not collected

text: not applicable

text: Drosophila melanogaster

text: Drosophila melanogaster

text: embryonic central brain neuron

characteristic: organism part

characteristic: replicate

text: Drosophila melanogaster

text: mixed

characteristic: sex

text: WT


text: IGBMC

text: public

characteristic: Submitter Id

text: ArrayExpress

characteristic: broker name

text: not collected

characteristic: collection date

text: fruit fly

characteristic: common name

characteristic: description

text: L3 larva

characteristic: developmental stage

text: elav-nRFP

characteristic: genotype

text: not collected

characteristic: geographic location (country and/or sea)

text: not applicable

text: Drosophila melanogaster

characteristic: organism

text: Drosophila melanogaster

text: brain

text: Drosophila melanogaster

text: mixed

text: WT

characteristic: strain

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: IGBMC, Illkirch-Graffenstaden, France

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: ArrayExpress

text: not collected

text: fruit fly

text: Protocols: Embryonic cells were isolated as follows. Staged egg laying was carried out to produce E16 embryos. elav-nRFP and Oregon-R strains were amplified, staged lays were done on yeast apple juice agar at 25°C. After a pre-lay period of 30 min, the agar plates and yeast were replaced with fresh plates and flies were left to lay for 3 hours at 25°C. Agar plates were removed and kept at 25°C, embryos were collected 11 hours and 40 min AEL, when they had reached stage 16. Embryos were then isolated from the medium and washed on a 100 µm mesh. The collected embryos were transferred into a cold solution of phosphate-buffered saline (PBS) in a Dounce homogenizer on ice. The embryos were dissociated using the large clearance pestle then the small clearance pestle, then filtered (70 µm filter). L3 neurons were purified from elav-nRFP larvae. Larval brains were dissected in cold PBS on ice and transferred to tubes containing 0.5μg of collagenase IV (Gibco, Invitrogen) in 220µL of PBS. Brains were incubated at 37°C on a Thermomixer with shaking at 500 rpm for 20 min. Then the brains were dissociated by pipetting up and down with 10-gauge needles and syringes and filtered through a 70 µm filter. Cells were sorted using FACS Aria II (BD Biosciences) at 4°C in three independent biological replicates for each genotype. Live cells were first selected based on the forward scatter and side scatter and only single cells were sorted according to the RFP signal. Oregon-R cells were used as a negative control to set the gate and sort the RFP positive cells After sorting cells were washed in PBS (600 g 5 min, 4°C) and nuclei were extracted in triton buffer (20 mM HEPES-KOH pH 7.9, KCl 10 mM, spermidine 0.5 mM, triton-X-100 0.1%, glycerol 20%, protease inhibitor (Sigma Aldrich #5056489001)) for 10 min at 4°C on a rotating platform. Extracted nuclei were washed once in 1V PBS (1300 g, 5 min, 4°C) and fixed in paraformaldehyde (PFA) (1% final) 2 min at RT. PFA was quenched by the addition of 2.5 M glycine (5 min at RT). Nuclei were washed 3 times in 1 mL binding buffer (HEPES-KOH pH 7.9 20 mM, KCl 10 mM, CaCl2 1 mM, MnCl2 1 mM, protease inhibitor) and incubated for 10 min on a rotating platform at 4°C with 1 mL binding buffer containing 10µl magnetic concanavalin A-coated beads (Bangs Laboratories #BP531) per sample. Bead-bound nuclei were then handled on a magnet stand. Nuclei were washed once in EDTA buffer (wash buffer supplemented with 0.2 mM EDTA) and 3 times in wash buffer (HEPES-KOH pH 79 20 mM, NaCl 150 mM, Spermidine tetrahydrochloride 0.5 mM, BSA 0.1%, protease inhibitor). Nuclei were resuspended in 50µl wash buffer per sample, split in 6 samples, supplemented with 1µl primary antibody (H3K27me3: cell signaling 9733, H3K4me3: abcam ab8580, rabbit anti-mouse IgG abcam ab46540) and incubated overnight on a rotating platform at 4°C. The next day, nuclei were washed 3 times in wash buffer, incubated 1h at RT with a secondary antibody (Guinea-pig anti-Rabbit IgG ABIN101961), washed again 3 times in wash buffer, resuspend in 100µl wash buffer supplemented with pA-MNase at 0.7 ng/mL final concentration) and incubated 1h at 4°C. Nuclei were than washed 3 times in wash buffer, resuspend in 300µl wash buffer containing 1mM CaCl2 to induce the digestion and incubated 30 min on ice cold water. Reaction was stop by adding 150µl EDTA buffer for 20 min at 37°C. Crosslink and MNase were digested for 10 min at 70°C by addition of SDS (0.05% final concentration) and Proteinase K (0.6 mg/mL final concentration). DNA was extracted using phenol/chloroform/isoamyl alcohol extraction. Precipitation of DNA was performed with addition of glycogen (3 µg/mL final concentration). Library preparation was performed using NEBNext®Ultra II DNA Library Prep Kit for Illumina® using following protocol with 14 amplification cycles: (dx.doi.org/10.17504/protocols.io.wvgfe3w).

text: embryonic stage 16

text: elav-nRFP

text: not collected

text: not applicable

characteristic: isolate

text: Drosophila melanogaster

text: Drosophila melanogaster

text: neurons

text: Drosophila melanogaster

text: mixed

text: WT


text: IGBMC, Illkirch-Graffenstaden, France

text: public

characteristic: SRA accession

characteristic: Submitter Id

characteristic: age

text: ArrayExpress

characteristic: broker name

text: not collected

characteristic: collection date

text: fruit fly

characteristic: common name

text: L3 larva

text: elav-nRFP

text: not collected

text: not applicable

text: Drosophila melanogaster

text: Drosophila melanogaster

text: neurons

characteristic: organism part

characteristic: replicate

text: Drosophila melanogaster

text: mixed

characteristic: sex

text: WT


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: GHENT UNIVERSITY

text: public

tag: Namespace:GHENT UNIVERSITY

text: Digestive tract environment

characteristic: broad-scale environmental context

text: Sample number 0; Donor 1; Faecal sample; Faecal sample; Day 0; forward

characteristic: description

text: SHIME environment

characteristic: environmental medium

text: Belgium

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: human-gut

characteristic: human gut environmental package

characteristic: investigation type

text: City

characteristic: local environmental context

text: human gut metagenome

characteristic: organism

text: EOS-MiQuant

characteristic: project name

text: human gut metagenome

text: Illumina Miseq

characteristic: sequencing method

text: 0; Donor 1; FS; FS; Day 0; forward

characteristic: title


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: GHENT 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: Digestive tract environment

characteristic: collection date

text: Sample number 102; Donor 2; Short SHIME transit; Proximal colon; Day 4; forward

text: SHIME environment

text: Belgium

text: human-gut

text: City

text: human gut metagenome

text: EOS-MiQuant

text: human gut metagenome

text: Illumina Miseq

text: 102; Donor 2; ST; P; Day 4; forward


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: GHENT UNIVERSITY

text: public

text: Digestive tract environment

characteristic: broad-scale environmental context

text: Sample number 103; Donor 2; Short SHIME transit; Distal colon; Day 4; forward

characteristic: description

text: SHIME environment

characteristic: environmental medium

text: Belgium

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: human-gut

text: City

text: human gut metagenome

text: EOS-MiQuant

text: human gut metagenome

text: Illumina Miseq

text: 103; Donor 2; ST; D; Day 4; forward


characteristic: ENA-LAST-UPDATE

text: GHENT UNIVERSITY

text: public

text: Digestive tract environment

text: Sample number 169; Donor 2; Long SHIME transit; Distal colon; Day 18; forward

text: SHIME environment

text: Belgium

text: human-gut

characteristic: human gut environmental package

characteristic: investigation type

text: City

characteristic: local environmental context

text: human gut metagenome

characteristic: organism

text: EOS-MiQuant

characteristic: project name

text: human gut metagenome

text: Illumina Miseq

characteristic: sequencing method

text: 169; Donor 2; LT; D; Day 18; forward

characteristic: title


characteristic: External Id

text: GENOME INSTITUTE OF SINGAPORE

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: SGNex_HEYA8_directcDNA_replicate1_run3_fast5

tag: Namespace:GENOME INSTITUTE OF SINGAPORE

characteristic: Submitter Id

characteristic: collection date

text: human

characteristic: common name

text: Singapore

text: Homo sapiens

text: Homo sapiens


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: GENOME INSTITUTE OF SINGAPORE

text: public

text: SGNex_HEYA8_directcDNA_replicate2_run3_fast5

text: human

characteristic: description

text: Singapore

characteristic: geographic location (country and/or sea)

text: Homo sapiens

text: Homo sapiens


text: GENOME INSTITUTE OF SINGAPORE

text: public

text: SGNex_HEYA8_directcDNA_replicate3_run2_fast5

text: human

text: Singapore

text: Homo sapiens

characteristic: organism

text: Homo sapiens


text: GENOME INSTITUTE OF SINGAPORE

text: public

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characteristic: description

text: Spain

characteristic: geographic location (country and/or sea)

text: Human

text: not provided

text: Homo sapiens

text: female

characteristic: organism


characteristic: ENA-CHECKLIST

characteristic: ENA-LAST-UPDATE

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: ena-upload-cli

tag: Namespace:Hospital General Universitario Santa Lucía

text: C. Minarete, s/n

text: Iglesias-Caballero, M. Sandonís, V. Vázquez-Morón, S. Camarero, S. Pozo, F. Casas, I. Jiménez, P. Zaballos, A. Monzón, S. Varona, S. Cuesta, I.BLAZQUEZ ABELLAN, ANA

text: RELECOV

text: Not Provided

text: Human--Nasopharynx--Aspiration

text: Spain

text: Human

characteristic: host common name

text: not provided

characteristic: host health state

text: Homo sapiens

characteristic: host scientific name

text: female

characteristic: host sex

characteristic: host subject id

characteristic: isolate


characteristic: ENA-FIRST-PUBLIC

characteristic: External Id

text: Hospital General Universitario Santa Lucía

characteristic: INSDC center name

characteristic: INSDC first public

text: public

characteristic: SRA accession

text: ena-upload-cli

characteristic: Submitter Id

text: C. Minarete, s/n

characteristic: address

characteristic: authors

text: RELECOV

characteristic: collection date

text: Not Provided

text: Human--Nasopharynx--Aspiration

text: Spain

text: Human

text: not provided

text: Homo sapiens

text: female

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-LAST-UPDATE

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: ena-upload-cli

text: C. Minarete, s/n

text: RELECOV

characteristic: broker name

characteristic: collecting institution

text: Not Provided

characteristic: collector name

text: Human--Nasopharynx--Aspiration

characteristic: description

text: Spain

characteristic: geographic location (country and/or sea)

text: Human

text: not provided

text: Homo sapiens

text: male

characteristic: organism


characteristic: ENA-FIRST-PUBLIC

characteristic: External Id

text: Consejería de Sanidad

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: ena-upload-cli

tag: Namespace:Consejería de Sanidad

text: Avda. de Francia, 4.

text: RELECOV

text: Consejería de Sanidad

text: Not Provided

text: Human--Nasopharynx--Aspiration

text: Spain

text: Human

characteristic: host common name

text: not provided

characteristic: host health state

text: Homo sapiens

characteristic: host scientific name

text: female

characteristic: host sex

characteristic: host subject id

characteristic: isolate


characteristic: ENA-CHECKLIST

characteristic: ENA-LAST-UPDATE

text: Hospital General Universitario de Ciudad Real

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: ena-upload-cli

characteristic: Submitter Id

text: C. Obispo Rafael Torija, s/n

characteristic: address

text: Iglesias-Caballero, M. Sandonís, V. Vázquez-Morón, S. Camarero, S. Pozo, F. Casas, I. Jiménez, P. Zaballos, A. Monzón, S. Varona, S. Cuesta, I.ILLESCAS FERNANDEZ-BERMEJO, M. SOLEDAD

characteristic: authors

text: RELECOV

characteristic: collection date

text: Not Provided

text: Human--Nasopharynx--Aspiration

text: Spain

text: Human

text: not provided

text: Homo sapiens

text: female

characteristic: title


characteristic: ENA-FIRST-PUBLIC

characteristic: External Id

text: Consejería de Sanidad

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: ena-upload-cli

text: Avda. de Francia, 4.

text: Iglesias-Caballero, M. Sandonís, V. Vázquez-Morón, S. Camarero, S. Pozo, F. Casas, I. Jiménez, P. Zaballos, A. Monzón, S. Varona, S. Cuesta, I.Gutiérrez, G

text: RELECOV

characteristic: broker name

text: Consejería de Sanidad

characteristic: collecting institution

text: Not Provided

characteristic: collector name

text: Human--Nasopharynx--Aspiration

characteristic: description

text: Spain

characteristic: geographic location (country and/or sea)

text: Human

text: not provided

text: Homo sapiens

text: female

characteristic: organism


characteristic: ENA-CHECKLIST

characteristic: ENA-LAST-UPDATE

text: Hospital Comarcal de Melilla

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: ena-upload-cli

tag: Namespace:Hospital Comarcal de Melilla

text: Remonta, 2

text: Iglesias-Caballero, M. Sandonís, V. Vázquez-Morón, S. Camarero, S. Pozo, F. Casas, I. Jiménez, P. Zaballos, A. Monzón, S. Varona, S. Cuesta, I.Roman. S.

text: RELECOV

text: Hospital Comarcal de Melilla

text: Not Provided

text: Human--Nasopharynx--Aspiration

text: Spain

text: Human

characteristic: host common name

text: not provided

characteristic: host health state

text: Homo sapiens

characteristic: host scientific name

text: male

characteristic: host sex

characteristic: host subject id

characteristic: isolate


characteristic: ENA-FIRST-PUBLIC

characteristic: External Id

text: Hospital Comarcal de Melilla

characteristic: INSDC center name

characteristic: INSDC first public

text: public

characteristic: SRA accession

text: ena-upload-cli

characteristic: Submitter Id

text: Remonta, 2

characteristic: address

characteristic: authors

text: RELECOV

text: Hospital Comarcal de Melilla

characteristic: collection date

text: Not Provided

text: Human--Nasopharynx--Aspiration

text: Spain

text: Human

text: not provided

text: Homo sapiens

text: female

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-LAST-UPDATE

text: no

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: raw milk cheese

characteristic: Sample

text: food

characteristic: Source

text: Dairy

tag: Namespace:NATIONAL INSTITUTE OF HEALTH DR. RICARDO JORGE

characteristic: description

text: Portugal

characteristic: geographic location (country and/or sea)

text: Listeria monocytogenes

characteristic: organism

text: Listeria monocytogenes


characteristic: ENA-FIRST-PUBLIC

characteristic: External Id

text: no

text: NATIONAL INSTITUTE OF HEALTH DR. RICARDO JORGE

characteristic: INSDC center name

text: public

text: raw milk cheese

text: food

text: Dairy

text: Portugal

characteristic: host scientific name

text: Listeria monocytogenes

text: Listeria monocytogenes


text: no

characteristic: INSDC first public

text: public

characteristic: SRA accession

text: raw milk cheese

text: food

text: Dairy

characteristic: Submitter Id

text: Portugal

text: Listeria innocua

text: Listeria innocua


text: GHENT UNIVERSITY

text: public

tag: Namespace:GHENT UNIVERSITY

text: Digestive tract environment

characteristic: broad-scale environmental context

characteristic: collection date

text: Sample number 0; Donor 1; Faecal sample; Faecal sample; Day 0; reverse

text: SHIME environment

characteristic: environmental medium

text: Belgium

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: human-gut

characteristic: human gut environmental package

characteristic: investigation type

text: City

characteristic: local environmental context

text: human gut metagenome

text: EOS-MiQuant

characteristic: project name

text: human gut metagenome

text: Illumina Miseq

characteristic: sequencing method

text: 0; Donor 1; FS; FS; Day 0; reverse

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: GHENT UNIVERSITY

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: Digestive tract environment

text: Sample number 1; Donor 1; Short SHIME transit; Proximal colon; Day 1; reverse

characteristic: description

text: SHIME environment

text: Belgium

characteristic: geographic location (country and/or sea)

text: human-gut

text: City

text: human gut metagenome

characteristic: organism

text: EOS-MiQuant

text: human gut metagenome

text: Illumina Miseq

text: 1; Donor 1; ST; P; Day 1; reverse


text: GHENT UNIVERSITY

characteristic: INSDC center name

characteristic: INSDC first public

text: public

characteristic: SRA accession

characteristic: Submitter Id

text: Digestive tract environment

characteristic: broad-scale environmental context

characteristic: collection date

text: Sample number 102; Donor 2; Short SHIME transit; Proximal colon; Day 4; reverse

text: SHIME environment

characteristic: environmental medium

text: Belgium

characteristic: geographic location (latitude)

text: human-gut

text: City

text: human gut metagenome

text: EOS-MiQuant

text: human gut metagenome

text: Illumina Miseq

text: 102; Donor 2; ST; P; Day 4; reverse


characteristic: ENA-CHECKLIST

text: GHENT UNIVERSITY

text: public

text: Digestive tract environment

text: Sample number 103; Donor 2; Short SHIME transit; Distal colon; Day 4; reverse

text: SHIME environment

text: Belgium

characteristic: geographic location (longitude)

text: human-gut

characteristic: human gut environmental package

characteristic: investigation type

text: City

characteristic: local environmental context

text: human gut metagenome

text: EOS-MiQuant

characteristic: project name

text: human gut metagenome

text: Illumina Miseq

characteristic: sequencing method

text: 103; Donor 2; ST; D; Day 4; reverse

characteristic: title


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: GHENT UNIVERSITY

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: Digestive tract environment

text: Sample number 104; Donor 2; Medium SHIME transit; Proximal colon; Day 4; reverse

characteristic: description

text: SHIME environment

text: Belgium

characteristic: geographic location (country and/or sea)

text: human-gut

text: City

text: human gut metagenome

characteristic: organism

text: EOS-MiQuant

text: human gut metagenome

text: Illumina Miseq

text: 104; Donor 2; MT; P; Day 4; reverse


text: GHENT UNIVERSITY

characteristic: INSDC center name

characteristic: INSDC first public

text: public

characteristic: SRA accession

characteristic: Submitter Id

text: Digestive tract environment

characteristic: broad-scale environmental context

characteristic: collection date

text: Sample number 114; Donor 2; Short SHIME transit; Proximal colon; Day 6; reverse

text: SHIME environment

characteristic: environmental medium

text: Belgium

characteristic: geographic location (latitude)

text: human-gut

text: City

text: human gut metagenome

text: EOS-MiQuant

text: human gut metagenome

text: Illumina Miseq

text: 114; Donor 2; ST; P; Day 6; reverse


characteristic: ENA-CHECKLIST

text: GHENT UNIVERSITY

text: public

text: Digestive tract environment

text: Sample number 115; Donor 2; Short SHIME transit; Distal colon; Day 6; reverse

text: SHIME environment

text: Belgium

characteristic: geographic location (longitude)

text: human-gut

characteristic: human gut environmental package

characteristic: investigation type

text: City

characteristic: local environmental context

text: human gut metagenome

text: EOS-MiQuant

characteristic: project name

text: human gut metagenome

text: Illumina Miseq

characteristic: sequencing method

text: 115; Donor 2; ST; D; Day 6; reverse

characteristic: title


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: GHENT UNIVERSITY

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: Digestive tract environment

text: Sample number 117; Donor 2; Medium SHIME transit; Distal colon; Day 6; reverse

characteristic: description

text: SHIME environment

text: Belgium

characteristic: geographic location (country and/or sea)

text: human-gut

text: City

text: human gut metagenome

characteristic: organism

text: EOS-MiQuant

text: human gut metagenome

text: Illumina Miseq

text: 117; Donor 2; MT; D; Day 6; reverse


text: GHENT UNIVERSITY

characteristic: INSDC center name

characteristic: INSDC first public

text: public

characteristic: SRA accession

characteristic: Submitter Id

text: Digestive tract environment

characteristic: broad-scale environmental context

characteristic: collection date

text: Sample number 118; Donor 2; Long SHIME transit; Proximal colon; Day 6; reverse

text: SHIME environment

characteristic: environmental medium

text: Belgium

characteristic: geographic location (latitude)

text: human-gut

text: City

text: human gut metagenome

text: EOS-MiQuant

text: human gut metagenome

text: Illumina Miseq

text: 118; Donor 2; LT; P; Day 6; reverse


characteristic: ENA-CHECKLIST

text: GHENT UNIVERSITY

text: public

text: Digestive tract environment

text: Sample number 120; Donor 2; Short SHIME transit; Proximal colon; Day 7; reverse

text: SHIME environment

text: Belgium

characteristic: geographic location (longitude)

text: human-gut

characteristic: human gut environmental package

characteristic: investigation type

text: City

characteristic: local environmental context

text: human gut metagenome

text: EOS-MiQuant

characteristic: project name

text: human gut metagenome

text: Illumina Miseq

characteristic: sequencing method

text: 120; Donor 2; ST; P; Day 7; reverse

characteristic: title


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: GHENT UNIVERSITY

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: Digestive tract environment

text: Sample number 121; Donor 2; Short SHIME transit; Distal colon; Day 7; reverse

characteristic: description

text: SHIME environment

text: Belgium

characteristic: geographic location (country and/or sea)

text: human-gut

text: City

text: human gut metagenome

characteristic: organism

text: EOS-MiQuant

text: human gut metagenome

text: Illumina Miseq

text: 121; Donor 2; ST; D; Day 7; reverse


text: GHENT UNIVERSITY

characteristic: INSDC center name

characteristic: INSDC first public

text: public

characteristic: SRA accession

characteristic: Submitter Id

text: Digestive tract environment

characteristic: broad-scale environmental context

characteristic: collection date

text: Sample number 122; Donor 2; Medium SHIME transit; Proximal colon; Day 7; reverse

text: SHIME environment

characteristic: environmental medium

text: Belgium

characteristic: geographic location (latitude)

text: human-gut

text: City

text: human gut metagenome

text: EOS-MiQuant

text: human gut metagenome

text: Illumina Miseq

text: 122; Donor 2; MT; P; Day 7; reverse


characteristic: ENA-CHECKLIST

text: GHENT UNIVERSITY

text: public

text: Digestive tract environment

text: Sample number 126; Donor 2; Short SHIME transit; Proximal colon; Day 8; reverse

text: SHIME environment

text: Belgium

characteristic: geographic location (longitude)

text: human-gut

characteristic: human gut environmental package

characteristic: investigation type

text: City

characteristic: local environmental context

text: human gut metagenome

text: EOS-MiQuant

characteristic: project name

text: human gut metagenome

text: Illumina Miseq

characteristic: sequencing method

text: 126; Donor 2; ST; P; Day 8; reverse

characteristic: title


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: GHENT UNIVERSITY

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: Digestive tract environment

text: Sample number 127; Donor 2; Short SHIME transit; Distal colon; Day 8; reverse

characteristic: description

text: SHIME environment

text: Belgium

characteristic: geographic location (country and/or sea)

text: human-gut

text: City

text: human gut metagenome

characteristic: organism

text: EOS-MiQuant

text: human gut metagenome

text: Illumina Miseq

text: 127; Donor 2; ST; D; Day 8; reverse


text: GHENT UNIVERSITY

characteristic: INSDC center name

characteristic: INSDC first public

text: public

characteristic: SRA accession

characteristic: Submitter Id

text: Digestive tract environment

characteristic: broad-scale environmental context

characteristic: collection date

text: Sample number 13; Donor 1; Short SHIME transit; Proximal colon; Day 3; reverse

text: SHIME environment

characteristic: environmental medium

text: Belgium

characteristic: geographic location (latitude)

text: human-gut

text: City

text: human gut metagenome

text: EOS-MiQuant

text: human gut metagenome

text: Illumina Miseq

text: 13; Donor 1; ST; P; Day 3; reverse


characteristic: ENA-CHECKLIST

text: GHENT UNIVERSITY

text: public

text: Digestive tract environment

text: Sample number 132; Donor 2; Short SHIME transit; Proximal colon; Day 9; reverse

text: SHIME environment

text: Belgium

characteristic: geographic location (longitude)

text: human-gut

characteristic: human gut environmental package

characteristic: investigation type

text: City

characteristic: local environmental context

text: human gut metagenome

text: EOS-MiQuant

characteristic: project name

text: human gut metagenome

text: Illumina Miseq

characteristic: sequencing method

text: 132; Donor 2; ST; P; Day 9; reverse

characteristic: title


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: GHENT UNIVERSITY

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: Digestive tract environment

text: Sample number 133; Donor 2; Short SHIME transit; Distal colon; Day 9; reverse

characteristic: description

text: SHIME environment

text: Belgium

characteristic: geographic location (country and/or sea)

text: human-gut

text: City

text: human gut metagenome

characteristic: organism

text: EOS-MiQuant

text: human gut metagenome

text: Illumina Miseq

text: 133; Donor 2; ST; D; Day 9; reverse


text: GHENT UNIVERSITY

characteristic: INSDC center name

characteristic: INSDC first public

text: public

characteristic: SRA accession

characteristic: Submitter Id

text: Digestive tract environment

characteristic: broad-scale environmental context

characteristic: collection date

text: Sample number 137; Donor 2; Long SHIME transit; Distal colon; Day 9; reverse

text: SHIME environment

characteristic: environmental medium

text: Belgium

characteristic: geographic location (latitude)

text: human-gut

text: City

text: human gut metagenome

text: EOS-MiQuant

text: human gut metagenome

text: Illumina Miseq

text: 137; Donor 2; LT; D; Day 9; reverse


characteristic: ENA-CHECKLIST

text: GHENT UNIVERSITY

text: public

text: Digestive tract environment

text: Sample number 138; Donor 2; Short SHIME transit; Proximal colon; Day 10; reverse

text: SHIME environment

text: Belgium

characteristic: geographic location (longitude)

text: human-gut

characteristic: human gut environmental package

characteristic: investigation type

text: City

characteristic: local environmental context

text: human gut metagenome

text: EOS-MiQuant

characteristic: project name

text: human gut metagenome

text: Illumina Miseq

characteristic: sequencing method

text: 138; Donor 2; ST; P; Day 10; reverse

characteristic: title