characteristic: ENA-CHECKLIST

text: D-BSSE, ETH ZURICH

text: public

tag: Namespace:D-BSSE, ETH ZURICH

text: ArrayExpress

text: retinal cell

text: human

characteristic: common name

text: Protocols: 1-3 organoids of the same batch were pooled and dissociated at multiple timepoints across the organoid developmental time course. Organoids were washed three times with HBSS without Ca2+/Mg2+ (STEMCELL technologies, 37250). Single cell suspensions were obtained by adapting the protocol described in (Cowan et al. 2020) and using a papain-based dissociation kit (Miltenyi Biotec, 130-092-628). Nuclei were loaded in a concentration that would result in a recovery of 10,000 nuclei. Stem cell lines were cultured in mTeSR1 (Stem Cell Technologies, 05851) with mTeSR1 supplement (Stem Cell Technologies, 05852) or mTeSR Plus (Stem Cell Technologies, 100-0274) with mTeSR Plus (Stem Cell Technologies, 100-0275) and supplemented with penicillin/streptomycin (P/S, 1:200, Gibco, 15140122) on matrigel-coated plates (Corning, 354277). Cells were split 1-2 times per week after dissociation with EDTA in DPBS (final concentration 0.5mM) (Gibco, 12605010). Media was supplemented with Rho-associated protein kinase (ROCK) inhibitor Y-27632 (final concentration 5μM, STEMCELL, 72302) the first day after thawing. To generate retinal organoids from the B7 and IMR90 lines, 600 cells were seeded in each micro-well of an agarose chamber (MicroTissues® 3D Petri Dish® micro-mold #Z764019). 409B2-iCas9 organoids were generated with 1500 cells per micro-well and treated with BMP4 (55ng/ml, Biotechne #314-BP) on day 6 with half medium change on day 9, 12 and15 (Kuwahara et al. 2015). Single cell ATAC-seq libraries were generated with the Chromium Single Cell ATAC V1.1 Library & Gel Bead Kit. Single cell ATAC-seq libraries were generated with the Chromium Single Cell ATAC V1.1 Library & Gel Bead Kit.

characteristic: description

text: adult

characteristic: developmental stage

text: normal

characteristic: disease

text: wild type genotype

characteristic: genotype

text: organoid

characteristic: growth condition

text: Homo sapiens

text: Homo sapiens

text: retina

characteristic: organism part

text: induced pluripotent stem cell

characteristic: progenitor cell type

text: skin

characteristic: progenitor organism part

text: Homo sapiens


status: PUBLIC

tag: attribute

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:Faculty of Biology Technion - Israel Institute of Technology

characteristic: Submitter Id

text: ArrayExpress

characteristic: broker name

text: human

text: Protocols: 80 million HCC827 cells (WT or RBM10-KO) were collected at each timepoint, snap-frozen in liquid nitrogen, and kept in -80°C prior to genomic DNA extraction. Genomic DNA extraction was performed with Blood & Cell Culture DNA Maxi Kit (Qiagen) according to the manufacturer’s instructions. gRNA inserts were amplified using two round of PCR reactions. First, a 600bp region of the lentiviral library vectors containing the sgRNA region was amplified using ordinary PCR with Q5 high-fidelity DNA polymerase for 25 cycles. A total of 120μg gDNA was used as template for each sample (60reactions: 2μg gDNA/50μl reaction). Second, the amplified PCR product was subjected to another PCR reaction with Illumina next-generation sequencing adaptors for 10 cycles and 200bp product was amplified.

text: adult

text: lung adenocarcinoma

text: CrisR/Cas9 mediated knockout of RBM10

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: lung

text: Homo sapiens

characteristic: title


characteristic: ENA-CHECKLIST

text: Faculty of Biology Technion - Israel Institute of Technology

text: public

text: ArrayExpress

text: human

characteristic: common name

characteristic: description

text: adult

characteristic: developmental stage

text: lung adenocarcinoma

characteristic: disease

text: CrisR/Cas9 mediated knockout of RBM10

characteristic: genotype

text: Homo sapiens

text: Homo sapiens

text: lung

text: Homo sapiens


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: public

text: ArrayExpress

text: human

text: adult

text: lung adenocarcinoma

text: wild type genotype

text: Homo sapiens

text: Homo sapiens

text: lung

characteristic: organism part

text: Homo sapiens


characteristic: External Id

text: The Kennel Club Genetics Centre

characteristic: INSDC center name

characteristic: INSDC first public

text: public

tag: Namespace:The Kennel Club Genetics Centre

text: Whippet

characteristic: breed

text: dog

text: Canis lupus familiaris

text: Canis lupus familiaris

text: Male

characteristic: sex

text: Whippet WGS


text: The Kennel Club Genetics Centre

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: Miniature Schnauzer

text: dog

text: Canis lupus familiaris

text: Canis lupus familiaris

text: Male

text: Miniature Schnauzer WGS


characteristic: ENA-CHECKLIST

text: The Kennel Club Genetics Centre

text: public

text: Spaniel (English Springer)

text: dog

characteristic: common name

text: Canis lupus familiaris

characteristic: organism

text: Canis lupus familiaris

text: Female

text: Spaniel (English Springer) WGS

characteristic: title


text: The Kennel Club Genetics Centre

text: public

text: Border Collie

text: dog

text: Canis lupus familiaris

text: Canis lupus familiaris

text: Female

text: Border Collie WGS


text: The Kennel Club Genetics Centre

text: public

text: Staffordshire Bull Terrier

text: dog

text: Canis lupus familiaris

text: Canis lupus familiaris

text: Female

text: Staffordshire Bull Terrier WGS


text: The Kennel Club Genetics Centre

text: public

text: Staffordshire Bull Terrier

text: dog

text: Canis lupus familiaris

text: Canis lupus familiaris

text: Male

text: Staffordshire Bull Terrier WGS


text: The Kennel Club Genetics Centre

text: public

text: Maltese

text: dog

text: Canis lupus familiaris

text: Canis lupus familiaris

text: Male

text: Maltese WGS


text: The Kennel Club Genetics Centre

text: public

text: Spaniel (English Springer)

text: dog

text: Canis lupus familiaris

text: Canis lupus familiaris

text: Male

text: Spaniel (English Springer) WGS


text: The Kennel Club Genetics Centre

text: public

text: Retriever (Labrador)

text: dog

text: Canis lupus familiaris

text: Canis lupus familiaris

text: Female

text: Retriever (Labrador) WGS


text: The Kennel Club Genetics Centre

text: public

text: Border Collie

text: dog

text: Canis lupus familiaris

text: Canis lupus familiaris

text: Male

text: Border Collie WGS


text: The Kennel Club Genetics Centre

text: public

text: Soft Coated Wheaten Terrier

text: dog

text: Canis lupus familiaris

text: Canis lupus familiaris

text: Male

text: Soft Coated Wheaten Terrier WGS


text: The Kennel Club Genetics Centre

text: public

text: Collie (Smooth)

text: dog

text: Canis lupus familiaris

text: Canis lupus familiaris

text: Male

text: Collie (Smooth) WGS


text: The Kennel Club Genetics Centre

text: public

text: Dachshund (Miniature Smooth Haired)

text: dog

text: Canis lupus familiaris

text: Canis lupus familiaris

text: Male

text: Dachshund (Miniature Smooth Haired) WGS


text: The Kennel Club Genetics Centre

text: public

text: French Bulldog

text: dog

text: Canis lupus familiaris

text: Canis lupus familiaris

text: Female

text: French Bulldog WGS


text: The Kennel Club Genetics Centre

text: public

text: Retriever (Nova Scotia Duck Tolling)

text: dog

text: Canis lupus familiaris

text: Canis lupus familiaris

text: Male

text: Retriever (Nova Scotia Duck Tolling) WGS


text: The Kennel Club Genetics Centre

text: public

text: Dachshund (Smooth Haired)

text: dog

text: Canis lupus familiaris

text: Canis lupus familiaris

text: Female

text: Dachshund (Smooth Haired) WGS


text: The Kennel Club Genetics Centre

text: public

text: Spaniel (Clumber)

text: dog

text: Canis lupus familiaris

text: Canis lupus familiaris

text: Female

text: Spaniel (Clumber) WGS


text: The Kennel Club Genetics Centre

text: public

text: Hungarian Vizsla

text: dog

text: Canis lupus familiaris

text: Canis lupus familiaris

text: Male

text: Hungarian Vizsla WGS


text: The Kennel Club Genetics Centre

text: public

text: Whippet

text: dog

text: Canis lupus familiaris

text: Canis lupus familiaris

text: Female

text: Whippet WGS


text: The Kennel Club Genetics Centre

text: public

text: Whippet

text: dog

text: Canis lupus familiaris

text: Canis lupus familiaris

text: Male

text: Whippet WGS


text: The Kennel Club Genetics Centre

text: public

text: Shih Tzu

text: dog

text: Canis lupus familiaris

text: Canis lupus familiaris

text: Male

text: Shih Tzu WGS


text: The Kennel Club Genetics Centre

text: public

text: Borzoi

text: dog

text: Canis lupus familiaris

text: Canis lupus familiaris

text: Male

text: Borzoi WGS


text: The Kennel Club Genetics Centre

text: public

text: German Shorthaired Pointer

text: dog

text: Canis lupus familiaris

text: Canis lupus familiaris

text: Female

text: German Shorthaired Pointer WGS


text: The Kennel Club Genetics Centre

text: public

text: Shetland Sheepdog

text: dog

text: Canis lupus familiaris

text: Canis lupus familiaris

text: Male

text: Shetland Sheepdog WGS


text: The Kennel Club Genetics Centre

text: public

text: Shetland Sheepdog

text: dog

text: Canis lupus familiaris

text: Canis lupus familiaris

text: Female

text: Shetland Sheepdog WGS


text: The Kennel Club Genetics Centre

text: public

text: Segugio Italiano

text: dog

text: Canis lupus familiaris

text: Canis lupus familiaris

text: Male

text: Segugio Italiano WGS


text: The Kennel Club Genetics Centre

text: public

text: Segugio Italiano

text: dog

text: Canis lupus familiaris

text: Canis lupus familiaris

text: Female

text: Segugio Italiano WGS


text: The Kennel Club Genetics Centre

text: public

text: Dachshund (Miniature Smooth Haired)

text: dog

text: Canis lupus familiaris

text: Canis lupus familiaris

text: Female

text: Dachshund (Miniature Smooth Haired) WGS


text: The Kennel Club Genetics Centre

text: public

text: Shih Tzu

text: dog

text: Canis lupus familiaris

text: Canis lupus familiaris

text: Female

text: Shih Tzu WGS


text: The Kennel Club Genetics Centre

text: public

text: Miniature Schnauzer

text: dog

text: Canis lupus familiaris

text: Canis lupus familiaris

text: Male

text: Miniature Schnauzer WGS


text: The Kennel Club Genetics Centre

text: public

text: Miniature Schnauzer

text: dog

text: Canis lupus familiaris

text: Canis lupus familiaris

text: Female

text: Miniature Schnauzer WGS


text: NOFIMA

text: public

text: Atlantic

text: ArrayExpress

characteristic: broker name

text: Atlantic salmon

text: Protocols: The samples were collected from a fish trial described and reported earlier*. The trial conducted experimental induction of amoebic gill disease and thereafter treatment with peracetic acid of Atlantic salmon smolts weighing 80-90 g. The samples were collected from the group that was not infected and treated. Briefly, the fish were reared in 800 L tank operating in a flow through system under the following conditions: water flow rate in the tanks was 6-7 L/min, the water temperature at 14.5°C, oxygen at >85% saturation, salinity at 35 ppt, photoperiod set at 24 light: 0 darkness, and continuous feeding regime with a commercial diet (Skretting Nutra Olympic 3 mm, Averøy, Norway) administered through a belt feeder. Six fish with almost identical weight (82 ± 5.5 g) were dip netted from the tank and humanely euthanised with a bath overdose of Benzoak Vet (ACD Pharmaceuticals AS, Leknes, Norway). Gills from the second gill arch and olfactory rosette, both from the left side, were dissected and suspended in RNAlater (Ambion©, Connecticut, USA), kept at room temperature for 12 h for penetration and afterwards stored at -80°C until RNA isolation. *Lazado, D.A. Strand, M.W. Breiland, F. Furtado, G. Timmerhaus, M.C. Gjessing, S. Hytterød, G. Merkin, L.-F. Pedersen, K. Pittman, Mucosal immune and stress responses of Neoparamoeba perurans-infected Atlantic salmon (Salmo salar) treated with peracetic acid shed light on the host-parasite-oxidant interactions, Frontiers in Immunology, 13 (2022) 948897. Total RNA was isolated from the gills and olfactory rosette using the Agencourt RNAdvance™ Tissue Total RNA Purification Kit (Beckman Coulter Inc., CA, USA) with the aid of Biomek 4000 automated workbench station (Beckman Coulter, Inc., CA, United States). The purified RNA was quantified using NanoDrop 8000 Spectrophotometer (ThermoFisher Scientific, United States) and integrity was further evaluated using the Agilent® 2100 Bioanalyzer™ RNA 6000 Nano Kit (Agilent Technology Inc., Santa Clara, CA, USA). All samples had an RNA Integrity Number (RIN) above 8.0. Total RNA samples were sent to the Norwegian Sequencing Center (UiO, Norway). RNA libraries were prepared using strand specific TruSeq RNA Library Prep Kit (Illumina, CA, USA).

characteristic: description

text: smolt

characteristic: developmental stage

text: normal

characteristic: disease

text: wild type genotype

characteristic: genotype

characteristic: individual

text: Salmo salar

text: Salmo salar

text: gill filament

text: Salmo salar


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: NOFIMA

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: Atlantic

text: ArrayExpress

text: Atlantic salmon

text: smolt

text: normal

text: wild type genotype

text: Salmo salar

text: Salmo salar

text: olfactory rosette

characteristic: organism part

text: Salmo salar


characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

tag: Namespace:London School of Hygiene and Tropical Medicine

characteristic: Submitter Id

text: malaria parasite P. falciparum

text: Plasmodium falciparum whole-genome sequence

text: Morodjambougou (Ou�less�bougou)

characteristic: geographic location (region and locality)

text: Plasmodium falciparum

text: Plasmodium falciparum


characteristic: ENA-CHECKLIST

text: London School of Hygiene and Tropical Medicine

text: public

text: malaria parasite P. falciparum

characteristic: common name

text: Morodjambougou (Ou�less�bougou)

text: Plasmodium falciparum

characteristic: organism

text: Plasmodium falciparum

characteristic: title


text: public

text: malaria parasite P. falciparum

characteristic: description

text: N'Korobougou (Ou�less�bougou)

text: Plasmodium falciparum

text: Plasmodium falciparum


text: public

text: malaria parasite P. falciparum

text: Tenemambougou (Ou�less�bougou)

text: Plasmodium falciparum

text: Plasmodium falciparum


text: public

text: malaria parasite P. falciparum

text: Zelani (Ou�less�bougou)

text: Plasmodium falciparum

text: Plasmodium falciparum


text: public

text: malaria parasite P. falciparum

text: N'Tentoukoro (Ou�less�bougou)

text: Plasmodium falciparum

text: Plasmodium falciparum


text: public

text: malaria parasite P. falciparum

text: Moussadjiebougou (Ou�less�bougou)

text: Plasmodium falciparum

text: Plasmodium falciparum


text: public

text: malaria parasite P. falciparum

text: Soussounkoro (Ou�less�bougou)

text: Plasmodium falciparum

text: Plasmodium falciparum


text: public

text: malaria parasite P. falciparum

text: Djalakoro-Djitoumou (Ou�less�bougou)

text: Plasmodium falciparum

text: Plasmodium falciparum


text: public

text: malaria parasite P. falciparum

text: Sikoro-Djitoumou (Ou�less�bougou)

text: Plasmodium falciparum

text: Plasmodium falciparum


text: public

text: malaria parasite P. falciparum

text: Tamala (Ou�less�bougou)

text: Plasmodium falciparum

text: Plasmodium falciparum


text: public

text: malaria parasite P. falciparum

text: M'Pana (Ou�less�bougou)

text: Plasmodium falciparum

text: Plasmodium falciparum


text: D-BSSE, ETH ZURICH

text: public

text: ArrayExpress

characteristic: broker name

text: retinal cell

text: human

text: Protocols: 1-3 organoids of the same batch were pooled and dissociated at multiple timepoints across the organoid developmental time course. Organoids were washed three times with HBSS without Ca2+/Mg2+ (STEMCELL technologies, 37250). Single cell suspensions were obtained by adapting the protocol described in (Cowan et al. 2020) and using a papain-based dissociation kit (Miltenyi Biotec, 130-092-628). Stem cell lines were cultured in mTeSR1 (Stem Cell Technologies, 05851) with mTeSR1 supplement (Stem Cell Technologies, 05852) or mTeSR Plus (Stem Cell Technologies, 100-0274) with mTeSR Plus (Stem Cell Technologies, 100-0275) and supplemented with penicillin/streptomycin (P/S, 1:200, Gibco, 15140122) on matrigel-coated plates (Corning, 354277). Cells were split 1-2 times per week after dissociation with EDTA in DPBS (final concentration 0.5mM) (Gibco, 12605010). Media was supplemented with Rho-associated protein kinase (ROCK) inhibitor Y-27632 (final concentration 5μM, STEMCELL, 72302) the first day after thawing. To generate retinal organoids from the B7 and IMR90 lines, 600 cells were seeded in each micro-well of an agarose chamber (MicroTissues® 3D Petri Dish® micro-mold #Z764019). 409B2-iCas9 organoids were generated with 1500 cells per micro-well and treated with BMP4 (55ng/ml, Biotechne #314-BP) on day 6 with half medium change on day 9, 12 and15 (Kuwahara et al. 2015). 8,000 cells were targeted and when the cell number was not sufficient, all cells were loaded. Single cell RNA-seq libraries were generated with the Chromium Single Cell 3’ V3.1 Library & Gel Bead Kit. Single cell encapsulation and library preparation were performed according to the manufacturer's protocol. Single cell RNA-seq libraries were generated with the Chromium Single Cell 3’ V3.1 Library & Gel Bead Kit. Single cell encapsulation and library preparation were performed according to the manufacturer's protocol.

text: 38 weeks

characteristic: developmental stage

text: normal

characteristic: disease

text: wild type genotype

characteristic: genotype

text: retinal organoid

characteristic: growth condition

text: Homo sapiens

text: Homo sapiens

text: retina

text: induced pluripotent stem cell

characteristic: progenitor cell type

text: skin

characteristic: progenitor organism part

text: Homo sapiens


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: D-BSSE, ETH ZURICH

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: ArrayExpress

text: retinal cell

text: human

text: 40 weeks

text: normal

text: wild type genotype

text: retinal organoid

text: Homo sapiens

text: Homo sapiens

text: retina

characteristic: organism part

text: induced pluripotent stem cell

text: skin

text: Homo sapiens


characteristic: ENA-CHECKLIST

text: D-BSSE, ETH ZURICH

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: ArrayExpress

text: retinal cell

text: human

characteristic: common name

text: 34 weeks

text: normal

text: wild type genotype

text: retinal organoid

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: retina

text: induced pluripotent stem cell

text: skin

text: Homo sapiens


text: D-BSSE, ETH ZURICH

text: public

text: ArrayExpress

characteristic: broker name

text: retinal cell

text: human

characteristic: description

text: 28 weeks

characteristic: developmental stage

text: normal

characteristic: disease

text: wild type genotype

characteristic: genotype

text: retinal organoid

text: Homo sapiens

text: Homo sapiens

text: retina

text: induced pluripotent stem cell

text: skin

text: Homo sapiens

characteristic: title


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: D-BSSE, ETH ZURICH

text: public

text: ArrayExpress

text: retinal cell

text: human

text: 18 weeks

text: normal

text: wild type genotype

text: retinal organoid

characteristic: growth condition

text: Homo sapiens

text: Homo sapiens

text: retina

text: induced pluripotent stem cell

characteristic: progenitor cell type

text: skin

characteristic: progenitor organism part

text: Homo sapiens


characteristic: ENA-CHECKLIST

text: D-BSSE, ETH ZURICH

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: ArrayExpress

text: retinal cell

text: human

text: 24 weeks

text: normal

text: wild type genotype

text: retinal organoid

text: Homo sapiens

text: Homo sapiens

text: retina

characteristic: organism part

text: induced pluripotent stem cell

text: skin

text: Homo sapiens


text: D-BSSE, ETH ZURICH

text: public

characteristic: SRA accession

characteristic: Submitter Id

text: ArrayExpress

characteristic: broker name

text: retinal cell

text: human

characteristic: common name

characteristic: description

text: 30 weeks

text: normal

text: wild type genotype

text: retinal organoid

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: retina

text: induced pluripotent stem cell

text: skin

text: Homo sapiens


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: D-BSSE, ETH ZURICH

text: public

text: ArrayExpress

text: retinal cell

text: human

text: 6 weeks

characteristic: developmental stage

text: normal

characteristic: disease

text: wild type genotype

characteristic: genotype

text: retinal organoid

text: Homo sapiens

text: Homo sapiens

text: retina

text: induced pluripotent stem cell

text: skin

text: Homo sapiens

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: External Id

text: D-BSSE, ETH ZURICH

characteristic: INSDC center name

text: public

text: ArrayExpress

text: retinal cell

text: human

text: 8 weeks

text: normal

text: wild type genotype

text: retinal organoid

characteristic: growth condition

text: Homo sapiens

text: Homo sapiens

text: retina

text: induced pluripotent stem cell

characteristic: progenitor cell type

text: skin

characteristic: progenitor organism part

text: Homo sapiens


text: D-BSSE, ETH ZURICH

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: ArrayExpress

text: retinal cell

text: human

text: 10 weeks

text: normal

text: wild type genotype

text: retinal organoid

text: Homo sapiens

text: Homo sapiens

text: retina

characteristic: organism part

text: induced pluripotent stem cell

text: skin

text: Homo sapiens


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: D-BSSE, ETH ZURICH

text: public

text: ArrayExpress

characteristic: broker name

text: retinal cell

text: human

characteristic: common name

characteristic: description

text: 13 weeks

text: normal

text: wild type genotype

text: retinal organoid

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: retina

text: induced pluripotent stem cell

text: skin

text: Homo sapiens


characteristic: ENA-CHECKLIST

characteristic: External Id

text: D-BSSE, ETH ZURICH

text: public

text: ArrayExpress

text: retinal cell

text: human

text: 16 weeks

characteristic: developmental stage

text: normal

characteristic: disease

text: wild type genotype

characteristic: genotype

text: retinal organoid

text: Homo sapiens

text: Homo sapiens

text: retina

text: induced pluripotent stem cell

text: skin

text: Homo sapiens

characteristic: title


text: D-BSSE, ETH ZURICH

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: ArrayExpress

text: retinal cell

text: human

text: 11 weeks

text: normal

text: wild type genotype

text: retinal organoid

characteristic: growth condition

text: Homo sapiens

text: Homo sapiens

text: retina

text: induced pluripotent stem cell

characteristic: progenitor cell type

text: skin

characteristic: progenitor organism part

text: Homo sapiens


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: public

characteristic: INSDC status

characteristic: SRA accession

tag: Namespace:Laboratory of Neuroepigenetics, Brain Research Institute, Medical faculty of the University of Zurich and Institute for Neuroscience, Department of Health Science and Technology, ETH Zurich, Switzerland

characteristic: Submitter Id

unit: day

characteristic: age

text: ArrayExpress

text: spermatogonium

text: house mouse

text: Protocols: For pup testis, dissociated cells were stained with BV421-conjugated anti-β2M, biotin-conjugated anti-THY1 (53-2.1), and PE-conjugated anti-αv-integrin (RMV-7) antibodies. THY1 was detected by staining with Alexa Fluor 488-Sav. For adult testes, cells were stained with anti-α6-integrin (CD49f; GoH3), BV421-conjugated anti-β2 microglobulin (β2M; S19.8), and R-phycoerythrin (PE)-conjugated anti-THY1 (CD90.2; 30H-12) antibodies. α6-Integrin was detected by Alexa Fluor 488-SAv after staining with biotin-conjugated rat anti-mouse IgG1/2a (G28-5) antibody. Prior to FACS, 1 μg/ml propidium iodide (Sigma) was added to the cell suspensions to discriminate dead cells. All antibody incubations were performed in PBS-S for at least 30 min at 4oC followed by washing in PBS-S. Antibodies were obtained from BD Biosciences (San Jose, United States) unless otherwise stated. Cell sorting was performed at 4oC on a FACS Aria III 5L using an 85μm nozzle at the Cytometry Facility of University of Zurich. RNA sequencing libraries were prepared using the SMARTer Stranded Total RNA-Seq Kit v3 (Takara, Cat# 634486) following the recommended protocol with minor adjustments. Adult spermatogonial cells libraries were prepared using the option to start with 1000 cells. Cells were sheared for 6 minutes at 85 °C. After reverse transcription, samples were barcoded using the SMARTer Unique Dual Index Kit (Takara, Cat# 634452). Five PCR cycles were performed and the PCR products were purified using AMPure XP reagent (Beckman Coulter Life Sciences, Cat# A63881; bead:sample ratio 0.8X). Ribosomal cDNA was depleted following the protocol and final library amplification was performed with twelve PCR cycles. Libraries were purified twice using AMPure XP reagent (bead:sample ratio 1X) and eluted in Tris buffer.Concentration and fragment length distribution of all samples were measured using Qubit 2.0 (Invitrogen) and Bioanalyzer (Agilent). Samples were pooled at the equal molarity, as determined in a 100 - 800 bp window on the Bioanalyzer.

text: normal

text: wild type genotype

text: Mus musculus

text: Mus musculus

text: testis

characteristic: organism part

text: Mus musculus

text: male

characteristic: sex

characteristic: strain


characteristic: ENA-CHECKLIST

characteristic: External Id

text: Laboratory of Neuroepigenetics, Brain Research Institute, Medical faculty of the University of Zurich and Institute for Neuroscience, Department of Health Science and Technology, ETH Zurich, Switzerland

text: public

text: ArrayExpress

characteristic: broker name

text: spermatogonium

text: house mouse

characteristic: common name

characteristic: description

text: normal

characteristic: disease

text: wild type genotype

characteristic: genotype

text: Mus musculus

characteristic: organism

text: Mus musculus

text: testis

text: Mus musculus

text: male


characteristic: ENA-FIRST-PUBLIC

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

unit: week

text: ArrayExpress

text: spermatogonium

text: house mouse

text: Protocols: For pup testis, dissociated cells were stained with BV421-conjugated anti-β2M, biotin-conjugated anti-THY1 (53-2.1), and PE-conjugated anti-αv-integrin (RMV-7) antibodies. THY1 was detected by staining with Alexa Fluor 488-Sav. For adult testes, cells were stained with anti-α6-integrin (CD49f; GoH3), BV421-conjugated anti-β2 microglobulin (β2M; S19.8), and R-phycoerythrin (PE)-conjugated anti-THY1 (CD90.2; 30H-12) antibodies. α6-Integrin was detected by Alexa Fluor 488-SAv after staining with biotin-conjugated rat anti-mouse IgG1/2a (G28-5) antibody. Prior to FACS, 1 μg/ml propidium iodide (Sigma) was added to the cell suspensions to discriminate dead cells. All antibody incubations were performed in PBS-S for at least 30 min at 4oC followed by washing in PBS-S. Antibodies were obtained from BD Biosciences (San Jose, United States) unless otherwise stated. Cell sorting was performed at 4oC on a FACS Aria III 5L using an 85μm nozzle at the Cytometry Facility of University of Zurich. For OmniATAC on PND15 spermatogonia, 25’000 cells were collected in a separate tube, pelleted by centrifugation and immediately processed using the OmniATAC library preparation protocol (Corces et al., 2017). For OmniATAC on adult spermatogonia, 5000 cells from each animal were collected in a separate tube and further processed using the same protocol. Chromatin accessibility was profiled from PND15 and adult spermatogonial cells. The libraries were prepared according to the Omni-ATAC protocol, starting from 25 000 PND15 and 5000 adult sorted spermatogonia, respectively (Corces et al., 2017). Briefly, sorted cells were lysed in cold lysis buffer (10 mM Tris-HCl pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% NP40, 0.1% Tween-20, and 0.01% digitonin) and the nuclei were pelleted and transposed using the Nextera Tn5 (Illumina) for 30 min at 37oC in a thermomixer with shaking at 1000 rpm. The transposed fragments were purified using the MinElute Reaction Cleanup Kit (Qiagen). Following purification, libraries were generated by PCR amplification using the NEBNext High-Fidelity 2X PCR Master Mix (New England Biolabs), and purified using Agencourt AMPure XP magnetic beads (Beckman Coulter) in order to remove primer dimers (78bp) and large fragments of 1000-10,000 bp in length. Library quality was assessed on an Agilent High Sensitivity DNA chip using the Bioanalyzer 2100 (Agilent Technologies). 6 samples were sequenced from PND15 and 5 from adult spermatogonial cells.

text: normal

text: wild type genotype

text: Mus musculus

text: Mus musculus

text: testis

text: Mus musculus

text: male

characteristic: title


characteristic: ENA-LAST-UPDATE

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

characteristic: age

text: ArrayExpress

text: spermatogonium

text: house mouse

text: normal

text: wild type genotype

text: Mus musculus

text: Mus musculus

text: testis

text: Mus musculus

text: male


characteristic: ENA-CHECKLIST

characteristic: External Id

text: HELMHOLTZ CENTRE FOR INFECTION RESEARCH

text: public

tag: Namespace:HELMHOLTZ CENTRE FOR INFECTION RESEARCH

text: Many fragments with little to no review of assembly other than reporting of standard assembly statistics

characteristic: assembly quality

text: metaSPAdes

characteristic: assembly software

text: default

characteristic: binning parameters

characteristic: binning software

text: mouse digestive system

characteristic: broad-scale environmental context

characteristic: collection date

characteristic: completeness score

text: CheckM

characteristic: completeness software

characteristic: contamination score

text: This sample represents a Metagenome-assembled genome assembled from the metagenomic run ERR982822 of study ERP011540.

text: feces

characteristic: environmental medium

text: Denmark

characteristic: geographic location (country and/or sea)

unit: DD

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: metagenome-assembled genome

characteristic: investigation type

text: mouse gut metagenome

text: mouse gut

characteristic: local environmental context

text: mouse gut metagenome

characteristic: metagenomic source

text: Faecalibaculum rodentium

text: High fat feeding rather than obesity drives taxonomical and functional changes in the gut microbiota in mice

characteristic: project name

characteristic: sample derived from

text: Faecalibaculum rodentium

text: Illumina HiSeq 2000

characteristic: sequencing method

text: multi-marker approach

characteristic: taxonomic identity marker

text: Metagenome-assembled genome: extra-ERR982822.25_1677794515


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: HELMHOLTZ CENTRE FOR INFECTION RESEARCH

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

characteristic: assembly quality

text: metaSPAdes

characteristic: assembly software

text: default

characteristic: binning parameters

characteristic: binning software

text: mouse digestive system

text: CheckM

characteristic: description

text: feces

text: Denmark

text: metagenome-assembled genome

text: mouse gut metagenome

text: mouse gut

text: mouse gut metagenome

text: uncultured Alphaproteobacteria bacterium

characteristic: organism

text: Illumina HiSeq 2000

text: multi-marker approach

text: Metagenome-assembled genome: extra-ERR982822.26_1677794515

characteristic: title


characteristic: ENA-CHECKLIST

text: HELMHOLTZ CENTRE FOR INFECTION RESEARCH

text: public

text: metaSPAdes

text: default

text: mouse digestive system

characteristic: broad-scale environmental context

characteristic: collection date

characteristic: completeness score

text: CheckM

characteristic: completeness software

characteristic: contamination score

text: feces

characteristic: environmental medium

text: Denmark

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: metagenome-assembled genome

characteristic: investigation type

text: mouse gut metagenome

text: mouse gut

characteristic: local environmental context

text: mouse gut metagenome

characteristic: metagenomic source

text: Akkermansia muciniphila

characteristic: project name

characteristic: sample derived from

text: Akkermansia muciniphila

text: Illumina HiSeq 2000

characteristic: sequencing method

text: multi-marker approach

characteristic: taxonomic identity marker

text: Metagenome-assembled genome: extra-ERR982822.28_1677794516


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: HELMHOLTZ CENTRE FOR INFECTION RESEARCH

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

characteristic: assembly quality

text: metaSPAdes

characteristic: assembly software

text: default

characteristic: binning parameters

characteristic: binning software

text: mouse digestive system

text: CheckM

characteristic: description

text: feces

text: Denmark

text: metagenome-assembled genome

text: mouse gut metagenome

text: mouse gut

text: mouse gut metagenome

text: Muribaculaceae bacterium

characteristic: organism

text: Muribaculaceae bacterium

text: Illumina HiSeq 2000

text: multi-marker approach

text: Metagenome-assembled genome: extra-ERR982822.30_1677794516

characteristic: title


characteristic: ENA-CHECKLIST

text: HELMHOLTZ CENTRE FOR INFECTION RESEARCH

text: public

text: metaSPAdes

text: default

text: mouse digestive system

characteristic: broad-scale environmental context

characteristic: collection date

characteristic: completeness score

text: CheckM

characteristic: completeness software

characteristic: contamination score

text: feces

characteristic: environmental medium

text: Denmark

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: metagenome-assembled genome

characteristic: investigation type

text: mouse gut metagenome

text: mouse gut

characteristic: local environmental context

text: mouse gut metagenome

characteristic: metagenomic source

text: uncultured Odoribacter sp.

characteristic: project name

characteristic: sample derived from

text: uncultured Odoribacter sp.

text: Illumina HiSeq 2000

characteristic: sequencing method

text: multi-marker approach

characteristic: taxonomic identity marker

text: Metagenome-assembled genome: extra-ERR982822.31_1677794516


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: HELMHOLTZ CENTRE FOR INFECTION RESEARCH

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

characteristic: assembly quality

text: metaSPAdes

characteristic: assembly software

text: default

characteristic: binning parameters

characteristic: binning software

text: mouse digestive system

text: CheckM

characteristic: description

text: feces

text: Denmark

text: metagenome-assembled genome

text: mouse gut metagenome

text: mouse gut

text: mouse gut metagenome

text: Bacteroides uniformis dnLKV2

characteristic: organism

text: Bacteroides uniformis dnLKV2

text: Illumina HiSeq 2000

text: multi-marker approach

text: Metagenome-assembled genome: extra-ERR982822.32_1677794517

characteristic: title


characteristic: ENA-CHECKLIST

text: HELMHOLTZ CENTRE FOR INFECTION RESEARCH

text: public

text: metaSPAdes

text: default

text: mouse digestive system

characteristic: broad-scale environmental context

characteristic: collection date

characteristic: completeness score

text: CheckM

characteristic: completeness software

characteristic: contamination score

text: feces

characteristic: environmental medium

text: Denmark

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: metagenome-assembled genome

characteristic: investigation type

text: mouse gut metagenome

text: mouse gut

characteristic: local environmental context

text: mouse gut metagenome

characteristic: metagenomic source

text: uncultured Lachnospiraceae bacterium

characteristic: project name

characteristic: sample derived from

text: uncultured Lachnospiraceae bacterium

text: Illumina HiSeq 2000

characteristic: sequencing method

text: multi-marker approach

characteristic: taxonomic identity marker

text: Metagenome-assembled genome: extra-ERR982822.34_1677794518


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: HELMHOLTZ CENTRE FOR INFECTION RESEARCH

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

characteristic: assembly quality

text: metaSPAdes

characteristic: assembly software

text: default

characteristic: binning parameters

characteristic: binning software

text: mouse digestive system

text: CheckM

characteristic: description

text: feces

text: Denmark

text: metagenome-assembled genome

text: mouse gut metagenome

text: mouse gut

text: mouse gut metagenome

text: Muribaculaceae bacterium

characteristic: organism

text: Muribaculaceae bacterium

text: Illumina HiSeq 2000

text: multi-marker approach

text: Metagenome-assembled genome: extra-ERR982822.35_1677794518

characteristic: title


characteristic: ENA-CHECKLIST

text: HELMHOLTZ CENTRE FOR INFECTION RESEARCH

text: public

text: metaSPAdes

text: default

text: mouse digestive system

characteristic: broad-scale environmental context

characteristic: collection date

characteristic: completeness score

text: CheckM

characteristic: completeness software

characteristic: contamination score

text: feces

characteristic: environmental medium

text: Denmark

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: metagenome-assembled genome

characteristic: investigation type

text: mouse gut metagenome

text: mouse gut

characteristic: local environmental context

text: mouse gut metagenome

characteristic: metagenomic source

text: uncultured Christensenellaceae bacterium

characteristic: project name

characteristic: sample derived from

text: Illumina HiSeq 2000

characteristic: sequencing method

text: multi-marker approach

characteristic: taxonomic identity marker

text: Metagenome-assembled genome: extra-ERR982822.36_1677794518


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: HELMHOLTZ CENTRE FOR INFECTION RESEARCH

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

characteristic: assembly quality

text: metaSPAdes

characteristic: assembly software

text: default

characteristic: binning parameters

characteristic: binning software

text: mouse digestive system

text: CheckM

characteristic: description

text: feces

text: Denmark

text: metagenome-assembled genome

text: mouse gut metagenome

text: mouse gut

text: mouse gut metagenome

text: uncultured Lachnospiraceae bacterium

characteristic: organism

text: uncultured Lachnospiraceae bacterium

text: Illumina HiSeq 2000

text: multi-marker approach

text: Metagenome-assembled genome: extra-ERR982822.38_1677794519

characteristic: title


characteristic: ENA-CHECKLIST

text: HELMHOLTZ CENTRE FOR INFECTION RESEARCH

text: public

text: metaSPAdes

text: default

text: mouse digestive system

characteristic: broad-scale environmental context

characteristic: collection date

characteristic: completeness score

text: CheckM

characteristic: completeness software

characteristic: contamination score

text: feces

characteristic: environmental medium

text: Denmark

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: metagenome-assembled genome

characteristic: investigation type

text: mouse gut metagenome

text: mouse gut

characteristic: local environmental context

text: mouse gut metagenome

characteristic: metagenomic source

text: uncultured Muribaculaceae bacterium

characteristic: project name

characteristic: sample derived from

text: uncultured Muribaculaceae bacterium

text: Illumina HiSeq 2000

characteristic: sequencing method

text: multi-marker approach

characteristic: taxonomic identity marker

text: Metagenome-assembled genome: extra-ERR982822.40_1677794519


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: HELMHOLTZ CENTRE FOR INFECTION RESEARCH

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

characteristic: assembly quality

text: metaSPAdes

characteristic: assembly software

text: default

characteristic: binning parameters

characteristic: binning software

text: mouse digestive system

text: CheckM

text: This sample represents a Metagenome-assembled genome assembled from the metagenomic run ERR982823 of study ERP011540.

characteristic: description

text: feces

text: Denmark

text: metagenome-assembled genome

text: mouse gut metagenome

text: mouse gut

text: mouse gut metagenome

text: uncultured Acetatifactor sp.

characteristic: organism

text: uncultured Acetatifactor sp.

text: Illumina HiSeq 2000

text: multi-marker approach

text: Metagenome-assembled genome: extra-ERR982823.1_1677794519

characteristic: title


characteristic: ENA-CHECKLIST

text: HELMHOLTZ CENTRE FOR INFECTION RESEARCH

text: public

text: Many fragments with little to no review of assembly other than reporting of standard assembly statistics

text: metaSPAdes

text: default

text: mouse digestive system

characteristic: broad-scale environmental context

characteristic: collection date

characteristic: completeness score

text: CheckM

characteristic: completeness software

characteristic: contamination score

text: feces

characteristic: environmental medium

text: Denmark

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: metagenome-assembled genome

characteristic: investigation type

text: mouse gut metagenome

text: mouse gut

characteristic: local environmental context

text: mouse gut metagenome

characteristic: metagenomic source

text: uncultured Odoribacter sp.

characteristic: project name

characteristic: sample derived from

text: uncultured Odoribacter sp.

text: Illumina HiSeq 2000

characteristic: sequencing method

text: multi-marker approach

characteristic: taxonomic identity marker

text: Metagenome-assembled genome: extra-ERR982823.2_1677794519


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: HELMHOLTZ CENTRE FOR INFECTION RESEARCH

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

characteristic: assembly quality

text: metaSPAdes

characteristic: assembly software

text: default

characteristic: binning parameters

characteristic: binning software

text: mouse digestive system

text: CheckM

characteristic: description

text: feces

text: Denmark

text: metagenome-assembled genome

text: mouse gut metagenome

text: mouse gut

text: mouse gut metagenome

text: uncultured Alistipes sp.

characteristic: organism

text: High fat feeding rather than obesity drives taxonomical and functional changes in the gut microbiota in mice

text: uncultured Alistipes sp.

text: Illumina HiSeq 2000

text: multi-marker approach

text: Metagenome-assembled genome: extra-ERR982823.3_1677794520

characteristic: title


characteristic: ENA-CHECKLIST

text: HELMHOLTZ CENTRE FOR INFECTION RESEARCH

text: public

text: metaSPAdes

text: default

text: mouse digestive system

characteristic: broad-scale environmental context

characteristic: collection date

characteristic: completeness score

text: CheckM

characteristic: completeness software

characteristic: contamination score

text: feces

characteristic: environmental medium

text: Denmark

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: metagenome-assembled genome

characteristic: investigation type

text: mouse gut metagenome

text: mouse gut

characteristic: local environmental context

text: mouse gut metagenome

characteristic: metagenomic source

text: uncultured Eubacterium sp.

characteristic: project name

characteristic: sample derived from

text: uncultured Eubacterium sp.

text: Illumina HiSeq 2000

characteristic: sequencing method

text: multi-marker approach

characteristic: taxonomic identity marker

text: Metagenome-assembled genome: extra-ERR982823.4_1677794523


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: HELMHOLTZ CENTRE FOR INFECTION RESEARCH

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

characteristic: assembly quality

text: metaSPAdes

characteristic: assembly software

text: default

characteristic: binning parameters

characteristic: binning software

text: mouse digestive system

text: CheckM

characteristic: description

text: feces

text: Denmark

text: metagenome-assembled genome

text: mouse gut metagenome

text: mouse gut

text: mouse gut metagenome

text: uncultured Muribaculaceae bacterium

characteristic: organism

text: uncultured Muribaculaceae bacterium

text: Illumina HiSeq 2000

text: multi-marker approach

text: Metagenome-assembled genome: extra-ERR982823.10_1677794523

characteristic: title


characteristic: ENA-CHECKLIST

text: HELMHOLTZ CENTRE FOR INFECTION RESEARCH

text: public

text: metaSPAdes

text: default

text: mouse digestive system

characteristic: broad-scale environmental context

characteristic: collection date

characteristic: completeness score

text: CheckM

characteristic: completeness software

characteristic: contamination score

text: feces

characteristic: environmental medium

text: Denmark

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: metagenome-assembled genome

characteristic: investigation type

text: mouse gut metagenome

text: mouse gut

characteristic: local environmental context

text: mouse gut metagenome

characteristic: metagenomic source

text: uncultured Acetatifactor sp.

characteristic: project name

characteristic: sample derived from

text: uncultured Acetatifactor sp.

text: Illumina HiSeq 2000

characteristic: sequencing method

text: multi-marker approach

characteristic: taxonomic identity marker

text: Metagenome-assembled genome: extra-ERR982823.14_1677794523


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: HELMHOLTZ CENTRE FOR INFECTION RESEARCH

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

characteristic: assembly quality

text: metaSPAdes

characteristic: assembly software

text: default

characteristic: binning parameters

characteristic: binning software

text: mouse digestive system

text: CheckM

characteristic: description

text: feces

text: Denmark

text: metagenome-assembled genome

text: mouse gut metagenome

text: mouse gut

text: mouse gut metagenome

text: Bacteroidales bacterium

characteristic: organism

text: Bacteroidales bacterium

text: Illumina HiSeq 2000

text: multi-marker approach

text: Metagenome-assembled genome: extra-ERR982823.15_1677794524

characteristic: title


characteristic: ENA-CHECKLIST

text: HELMHOLTZ CENTRE FOR INFECTION RESEARCH

text: public

text: metaSPAdes

text: default

text: mouse digestive system

characteristic: broad-scale environmental context

characteristic: collection date

characteristic: completeness score

text: CheckM

characteristic: completeness software

characteristic: contamination score

text: feces

characteristic: environmental medium

text: Denmark

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: metagenome-assembled genome

characteristic: investigation type

text: mouse gut metagenome

text: mouse gut

characteristic: local environmental context

text: mouse gut metagenome

characteristic: metagenomic source

text: uncultured Eubacteriales bacterium

characteristic: project name

characteristic: sample derived from

text: uncultured Eubacteriales bacterium

text: Illumina HiSeq 2000

characteristic: sequencing method

text: multi-marker approach

characteristic: taxonomic identity marker

text: Metagenome-assembled genome: extra-ERR982823.16_1677794524


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: HELMHOLTZ CENTRE FOR INFECTION RESEARCH

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

characteristic: assembly quality

text: metaSPAdes

characteristic: assembly software

text: default

characteristic: binning parameters

characteristic: binning software

text: mouse digestive system

text: CheckM

characteristic: description

text: feces

text: Denmark

text: metagenome-assembled genome

text: mouse gut metagenome

text: mouse gut

text: mouse gut metagenome

text: Akkermansia muciniphila

characteristic: organism

text: Akkermansia muciniphila

text: Illumina HiSeq 2000

text: multi-marker approach

text: Metagenome-assembled genome: extra-ERR982823.21_1677794524

characteristic: title


characteristic: ENA-CHECKLIST

text: HELMHOLTZ CENTRE FOR INFECTION RESEARCH

text: public

text: metaSPAdes

text: default

text: mouse digestive system

characteristic: broad-scale environmental context

characteristic: collection date

characteristic: completeness score

text: CheckM

characteristic: completeness software

characteristic: contamination score

text: feces

characteristic: environmental medium

text: Denmark

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: metagenome-assembled genome

characteristic: investigation type

text: mouse gut metagenome

text: mouse gut

characteristic: local environmental context

text: mouse gut metagenome

characteristic: metagenomic source

text: Limosilactobacillus reuteri

characteristic: project name

characteristic: sample derived from

text: Limosilactobacillus reuteri

text: Illumina HiSeq 2000

characteristic: sequencing method

text: multi-marker approach

characteristic: taxonomic identity marker

text: Metagenome-assembled genome: extra-ERR982823.22_1677794525


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: HELMHOLTZ CENTRE FOR INFECTION RESEARCH

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

characteristic: assembly quality

text: metaSPAdes

characteristic: assembly software

text: default

characteristic: binning parameters

characteristic: binning software

text: mouse digestive system

text: CheckM

characteristic: description

text: feces

text: Denmark

text: metagenome-assembled genome

text: mouse gut metagenome

text: mouse gut

text: mouse gut metagenome

text: Lactobacillaceae bacterium

characteristic: organism

text: Lactobacillaceae bacterium

text: Illumina HiSeq 2000

text: multi-marker approach

text: Metagenome-assembled genome: extra-ERR982823.23_1677794525

characteristic: title


characteristic: ENA-CHECKLIST

text: HELMHOLTZ CENTRE FOR INFECTION RESEARCH

text: public

text: metaSPAdes

text: default

text: mouse digestive system

characteristic: broad-scale environmental context

characteristic: collection date

characteristic: completeness score

text: CheckM

characteristic: completeness software

characteristic: contamination score

text: feces

characteristic: environmental medium

text: Denmark

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: metagenome-assembled genome

characteristic: investigation type

text: mouse gut metagenome

text: mouse gut

characteristic: local environmental context

text: mouse gut metagenome

characteristic: metagenomic source

text: uncultured Lachnospiraceae bacterium

characteristic: project name

characteristic: sample derived from

text: uncultured Lachnospiraceae bacterium

text: Illumina HiSeq 2000

characteristic: sequencing method

text: multi-marker approach

characteristic: taxonomic identity marker

text: Metagenome-assembled genome: extra-ERR982823.25_1677794525


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: HELMHOLTZ CENTRE FOR INFECTION RESEARCH

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

characteristic: assembly quality

text: metaSPAdes

characteristic: assembly software

text: default

characteristic: binning parameters

characteristic: binning software

text: mouse digestive system

text: CheckM

characteristic: description

text: feces

text: Denmark

text: metagenome-assembled genome

text: mouse gut metagenome

text: mouse gut

text: mouse gut metagenome

text: Bacteroidales bacterium

characteristic: organism

text: Bacteroidales bacterium

text: Illumina HiSeq 2000

text: multi-marker approach

text: Metagenome-assembled genome: extra-ERR982823.30_1677794525

characteristic: title


characteristic: ENA-CHECKLIST

text: HELMHOLTZ CENTRE FOR INFECTION RESEARCH

text: public

text: metaSPAdes

text: default

text: mouse digestive system

characteristic: broad-scale environmental context

characteristic: collection date

characteristic: completeness score

text: CheckM

characteristic: completeness software

characteristic: contamination score

text: feces

characteristic: environmental medium

text: Denmark

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: metagenome-assembled genome

characteristic: investigation type

text: mouse gut metagenome

text: mouse gut

characteristic: local environmental context

text: mouse gut metagenome

characteristic: metagenomic source

text: uncultured Mailhella sp.

characteristic: project name

characteristic: sample derived from

text: uncultured Mailhella sp.

text: Illumina HiSeq 2000

characteristic: sequencing method

text: multi-marker approach

characteristic: taxonomic identity marker

text: Metagenome-assembled genome: extra-ERR982823.31_1677794526


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: HELMHOLTZ CENTRE FOR INFECTION RESEARCH

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

characteristic: assembly quality

text: metaSPAdes

characteristic: assembly software

text: default

characteristic: binning parameters

characteristic: binning software

text: mouse digestive system

text: CheckM

text: This sample represents a Metagenome-assembled genome assembled from the metagenomic run ERR982823 of study ERP011540.

characteristic: description

text: feces

text: Denmark

text: metagenome-assembled genome

text: mouse gut metagenome

text: mouse gut

text: mouse gut metagenome

text: Faecalibaculum rodentium

characteristic: organism

text: Faecalibaculum rodentium

text: Illumina HiSeq 2000

text: multi-marker approach

text: Metagenome-assembled genome: extra-ERR982823.32_1677794526

characteristic: title


characteristic: ENA-CHECKLIST

text: HELMHOLTZ CENTRE FOR INFECTION RESEARCH

text: public

text: Many fragments with little to no review of assembly other than reporting of standard assembly statistics

text: metaSPAdes

text: default

text: mouse digestive system

characteristic: broad-scale environmental context

characteristic: collection date

characteristic: completeness score

text: CheckM

characteristic: completeness software

characteristic: contamination score

text: feces

characteristic: environmental medium

text: Denmark

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: metagenome-assembled genome

characteristic: investigation type

text: mouse gut metagenome

text: mouse gut

characteristic: local environmental context

text: mouse gut metagenome

characteristic: metagenomic source

text: uncultured Oscillospiraceae bacterium

characteristic: project name

characteristic: sample derived from

text: uncultured Oscillospiraceae bacterium

text: Illumina HiSeq 2000

characteristic: sequencing method

text: multi-marker approach

characteristic: taxonomic identity marker

text: Metagenome-assembled genome: extra-ERR982823.33_1677794526


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: HELMHOLTZ CENTRE FOR INFECTION RESEARCH

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

characteristic: assembly quality

text: metaSPAdes

characteristic: assembly software

text: default

characteristic: binning parameters

characteristic: binning software

text: mouse digestive system

text: CheckM

characteristic: description

text: feces

text: Denmark

text: metagenome-assembled genome

text: mouse gut metagenome

text: mouse gut

text: mouse gut metagenome

text: uncultured Lachnospiraceae bacterium

characteristic: organism

text: High fat feeding rather than obesity drives taxonomical and functional changes in the gut microbiota in mice

text: uncultured Lachnospiraceae bacterium

text: Illumina HiSeq 2000

text: multi-marker approach

text: Metagenome-assembled genome: extra-ERR982823.35_1677794527

characteristic: title


characteristic: ENA-CHECKLIST

text: HELMHOLTZ CENTRE FOR INFECTION RESEARCH

text: public

text: metaSPAdes

text: default

text: mouse digestive system

characteristic: broad-scale environmental context

characteristic: collection date

characteristic: completeness score

text: CheckM

characteristic: completeness software

characteristic: contamination score

text: feces

characteristic: environmental medium

text: Denmark

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: metagenome-assembled genome

characteristic: investigation type

text: mouse gut metagenome

text: mouse gut

characteristic: local environmental context

text: mouse gut metagenome

characteristic: metagenomic source

text: Lachnospiraceae bacterium

characteristic: project name

characteristic: sample derived from

text: Lachnospiraceae bacterium

text: Illumina HiSeq 2000

characteristic: sequencing method

text: multi-marker approach

characteristic: taxonomic identity marker

text: Metagenome-assembled genome: extra-ERR982823.36_1677794527


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: HELMHOLTZ CENTRE FOR INFECTION RESEARCH

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

characteristic: assembly quality

text: metaSPAdes

characteristic: assembly software

text: default

characteristic: binning parameters

characteristic: binning software

text: mouse digestive system

text: CheckM

characteristic: description

text: feces

text: Denmark

text: metagenome-assembled genome

text: mouse gut metagenome

text: mouse gut

text: mouse gut metagenome

text: uncultured Lachnospiraceae bacterium

characteristic: organism

text: uncultured Lachnospiraceae bacterium

text: Illumina HiSeq 2000

text: multi-marker approach

text: Metagenome-assembled genome: extra-ERR982823.37_1677794527

characteristic: title


characteristic: ENA-CHECKLIST

text: HELMHOLTZ CENTRE FOR INFECTION RESEARCH

text: public

text: metaSPAdes

text: default

text: mouse digestive system

characteristic: broad-scale environmental context

characteristic: collection date

characteristic: completeness score

text: CheckM

characteristic: completeness software

characteristic: contamination score

text: feces

characteristic: environmental medium

text: Denmark

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: metagenome-assembled genome

characteristic: investigation type

text: mouse gut metagenome

text: mouse gut

characteristic: local environmental context

text: mouse gut metagenome

characteristic: metagenomic source

text: Lactobacillus johnsonii

characteristic: project name

characteristic: sample derived from

text: Lactobacillus johnsonii

text: Illumina HiSeq 2000

characteristic: sequencing method

text: multi-marker approach

characteristic: taxonomic identity marker

text: Metagenome-assembled genome: extra-ERR982823.39_1677794528


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: HELMHOLTZ CENTRE FOR INFECTION RESEARCH

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

characteristic: assembly quality

text: metaSPAdes

characteristic: assembly software

text: default

characteristic: binning parameters

characteristic: binning software

text: mouse digestive system

text: CheckM

characteristic: description

text: feces

text: Denmark

text: metagenome-assembled genome

text: mouse gut metagenome

text: mouse gut

text: mouse gut metagenome

text: uncultured Lachnospiraceae bacterium

characteristic: organism

text: uncultured Lachnospiraceae bacterium

text: Illumina HiSeq 2000

text: multi-marker approach

text: Metagenome-assembled genome: extra-ERR982823.41_1677794528

characteristic: title


characteristic: ENA-CHECKLIST

text: HELMHOLTZ CENTRE FOR INFECTION RESEARCH

text: public

text: metaSPAdes

text: default

text: mouse digestive system

characteristic: broad-scale environmental context

characteristic: collection date

characteristic: completeness score

text: CheckM

characteristic: completeness software

characteristic: contamination score

text: feces

characteristic: environmental medium

text: Denmark

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: metagenome-assembled genome

characteristic: investigation type

text: mouse gut metagenome

text: mouse gut

characteristic: local environmental context

text: mouse gut metagenome

characteristic: metagenomic source

text: Clostridia bacterium

characteristic: project name

characteristic: sample derived from

text: Clostridia bacterium

text: Illumina HiSeq 2000

characteristic: sequencing method

text: multi-marker approach

characteristic: taxonomic identity marker

text: Metagenome-assembled genome: extra-ERR982823.42_1677794528


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: HELMHOLTZ CENTRE FOR INFECTION RESEARCH

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

characteristic: assembly quality

text: metaSPAdes

characteristic: assembly software

text: default

characteristic: binning parameters

characteristic: binning software

text: mouse digestive system

text: CheckM

characteristic: description

text: feces

text: Denmark

text: metagenome-assembled genome

text: mouse gut metagenome

text: mouse gut

text: mouse gut metagenome

text: Ligilactobacillus murinus

characteristic: organism

text: Ligilactobacillus murinus

text: Illumina HiSeq 2000

text: multi-marker approach

text: Metagenome-assembled genome: extra-ERR982823.44_1677794528

characteristic: title


characteristic: ENA-CHECKLIST

text: HELMHOLTZ CENTRE FOR INFECTION RESEARCH

text: public

text: metaSPAdes

text: default

text: mouse digestive system

characteristic: broad-scale environmental context

characteristic: collection date

characteristic: completeness score

text: CheckM

characteristic: completeness software

characteristic: contamination score

text: feces

characteristic: environmental medium

text: Denmark

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: metagenome-assembled genome

characteristic: investigation type

text: mouse gut metagenome

text: mouse gut

characteristic: local environmental context

text: mouse gut metagenome

characteristic: metagenomic source

text: Phocaeicola vulgatus

characteristic: project name

characteristic: sample derived from

text: Phocaeicola vulgatus

text: Illumina HiSeq 2000

characteristic: sequencing method

text: multi-marker approach

characteristic: taxonomic identity marker

text: Metagenome-assembled genome: extra-ERR982823.46_1677794529


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: HELMHOLTZ CENTRE FOR INFECTION RESEARCH

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

characteristic: assembly quality

text: metaSPAdes

characteristic: assembly software

text: default

characteristic: binning parameters

characteristic: binning software

text: mouse digestive system

text: CheckM

characteristic: description

text: feces

text: Denmark

text: metagenome-assembled genome

text: mouse gut metagenome

text: mouse gut

text: mouse gut metagenome

text: uncultured Lachnospiraceae bacterium

characteristic: organism

text: uncultured Lachnospiraceae bacterium

text: Illumina HiSeq 2000

text: multi-marker approach

text: Metagenome-assembled genome: extra-ERR982823.51_1677794529

characteristic: title


characteristic: ENA-CHECKLIST

text: HELMHOLTZ CENTRE FOR INFECTION RESEARCH

text: public

text: metaSPAdes

text: default

text: mouse digestive system

characteristic: broad-scale environmental context

characteristic: collection date

characteristic: completeness score

text: CheckM

characteristic: completeness software

characteristic: contamination score

text: feces

characteristic: environmental medium

text: Denmark

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: metagenome-assembled genome

characteristic: investigation type

text: mouse gut metagenome

text: mouse gut

characteristic: local environmental context

text: mouse gut metagenome

characteristic: metagenomic source

text: Mucispirillum schaedleri ASF457

characteristic: project name

characteristic: sample derived from

text: Mucispirillum schaedleri ASF457

text: Illumina HiSeq 2000

characteristic: sequencing method

text: multi-marker approach

characteristic: taxonomic identity marker

text: Metagenome-assembled genome: extra-ERR982823.52_1677794529


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: HELMHOLTZ CENTRE FOR INFECTION RESEARCH

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

characteristic: assembly quality

text: metaSPAdes

characteristic: assembly software

text: default

characteristic: binning parameters

characteristic: binning software

text: mouse digestive system

text: CheckM

characteristic: description

text: feces

text: Denmark

text: metagenome-assembled genome

text: mouse gut metagenome

text: mouse gut

text: mouse gut metagenome

text: uncultured Dorea sp.

characteristic: organism

text: uncultured Dorea sp.

text: Illumina HiSeq 2000

text: multi-marker approach

text: Metagenome-assembled genome: extra-ERR982823.53_1677794530

characteristic: title


characteristic: ENA-CHECKLIST

text: HELMHOLTZ CENTRE FOR INFECTION RESEARCH

text: public

text: metaSPAdes

text: default

text: mouse digestive system

characteristic: broad-scale environmental context

characteristic: collection date

characteristic: completeness score

text: CheckM

characteristic: completeness software

characteristic: contamination score

text: feces

characteristic: environmental medium

text: Denmark

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: metagenome-assembled genome

characteristic: investigation type

text: mouse gut metagenome

text: mouse gut

characteristic: local environmental context

text: mouse gut metagenome

characteristic: metagenomic source

text: uncultured Angelakisella sp.

characteristic: project name

characteristic: sample derived from

text: uncultured Angelakisella sp.

text: Illumina HiSeq 2000

characteristic: sequencing method

text: multi-marker approach

characteristic: taxonomic identity marker

text: Metagenome-assembled genome: extra-ERR982823.54_1677794530


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: HELMHOLTZ CENTRE FOR INFECTION RESEARCH

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

characteristic: assembly quality

text: metaSPAdes

characteristic: assembly software

text: default

characteristic: binning parameters

characteristic: binning software

text: mouse digestive system

text: CheckM

text: This sample represents a Metagenome-assembled genome assembled from the metagenomic run ERR982823 of study ERP011540.

characteristic: description

text: feces

text: Denmark

text: metagenome-assembled genome

text: mouse gut metagenome

text: mouse gut

text: mouse gut metagenome

text: uncultured Lachnospiraceae bacterium

characteristic: organism

text: uncultured Lachnospiraceae bacterium

text: Illumina HiSeq 2000

text: multi-marker approach

text: Metagenome-assembled genome: extra-ERR982823.57_1677794531

characteristic: title


characteristic: ENA-CHECKLIST

text: HELMHOLTZ CENTRE FOR INFECTION RESEARCH

text: public

text: Many fragments with little to no review of assembly other than reporting of standard assembly statistics

text: metaSPAdes

text: default

text: mouse digestive system

characteristic: broad-scale environmental context

characteristic: collection date

characteristic: completeness score

text: CheckM

characteristic: completeness software

characteristic: contamination score

text: feces

characteristic: environmental medium

text: Denmark

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: metagenome-assembled genome

characteristic: investigation type

text: mouse gut metagenome

text: mouse gut

characteristic: local environmental context

text: mouse gut metagenome

characteristic: metagenomic source

text: uncultured Acetatifactor sp.

characteristic: project name

characteristic: sample derived from

text: uncultured Acetatifactor sp.

text: Illumina HiSeq 2000

characteristic: sequencing method

text: multi-marker approach

characteristic: taxonomic identity marker

text: Metagenome-assembled genome: extra-ERR982823.58_1677794532


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: HELMHOLTZ CENTRE FOR INFECTION RESEARCH

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

characteristic: assembly quality

text: metaSPAdes

characteristic: assembly software

text: default

characteristic: binning parameters

characteristic: binning software

text: mouse digestive system

text: CheckM

characteristic: description

text: feces

text: Denmark

text: metagenome-assembled genome

text: mouse gut metagenome

text: mouse gut

text: mouse gut metagenome

text: Thomasclavelia cocleata

characteristic: organism

text: High fat feeding rather than obesity drives taxonomical and functional changes in the gut microbiota in mice

text: Thomasclavelia cocleata

text: Illumina HiSeq 2000

text: multi-marker approach

text: Metagenome-assembled genome: extra-ERR982823.61_1677794532

characteristic: title


characteristic: ENA-CHECKLIST

text: HELMHOLTZ CENTRE FOR INFECTION RESEARCH

text: public

text: metaSPAdes

text: default

text: mouse digestive system

characteristic: broad-scale environmental context

characteristic: collection date

characteristic: completeness score

text: CheckM

characteristic: completeness software

characteristic: contamination score

text: This sample represents a Metagenome-assembled genome assembled from the metagenomic run ERR982824 of study ERP011540.

text: feces

characteristic: environmental medium

text: Denmark

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: metagenome-assembled genome

characteristic: investigation type

text: mouse gut metagenome

text: mouse gut

characteristic: local environmental context

text: mouse gut metagenome

characteristic: metagenomic source

text: uncultured Mailhella sp.

characteristic: project name

characteristic: sample derived from

text: uncultured Mailhella sp.

text: Illumina HiSeq 2000

characteristic: sequencing method

text: multi-marker approach

characteristic: taxonomic identity marker

text: Metagenome-assembled genome: extra-ERR982824.2_1677794532


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: HELMHOLTZ CENTRE FOR INFECTION RESEARCH

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

characteristic: assembly quality

text: metaSPAdes

characteristic: assembly software

text: default

characteristic: binning parameters

characteristic: binning software

text: mouse digestive system

text: CheckM

characteristic: description

text: feces

text: Denmark

text: metagenome-assembled genome

text: mouse gut metagenome

text: mouse gut

text: mouse gut metagenome

text: Akkermansia muciniphila

characteristic: organism

text: Akkermansia muciniphila

text: Illumina HiSeq 2000

text: multi-marker approach

text: Metagenome-assembled genome: extra-ERR982824.4_1677794533

characteristic: title


characteristic: ENA-CHECKLIST

text: HELMHOLTZ CENTRE FOR INFECTION RESEARCH

text: public

text: metaSPAdes

text: default

text: mouse digestive system

characteristic: broad-scale environmental context

characteristic: collection date

characteristic: completeness score

text: CheckM

characteristic: completeness software

characteristic: contamination score

text: feces

characteristic: environmental medium

text: Denmark

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: metagenome-assembled genome

characteristic: investigation type

text: mouse gut metagenome

text: mouse gut

characteristic: local environmental context

text: mouse gut metagenome

characteristic: metagenomic source

text: uncultured Eubacterium sp.

characteristic: project name

characteristic: sample derived from

text: uncultured Eubacterium sp.

text: Illumina HiSeq 2000

characteristic: sequencing method

text: multi-marker approach

characteristic: taxonomic identity marker

text: Metagenome-assembled genome: extra-ERR982824.5_1677794533


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: HELMHOLTZ CENTRE FOR INFECTION RESEARCH

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

characteristic: assembly quality

text: metaSPAdes

characteristic: assembly software

text: default

characteristic: binning parameters

characteristic: binning software

text: mouse digestive system

text: CheckM

characteristic: description

text: feces

text: Denmark

text: metagenome-assembled genome

text: mouse gut metagenome

text: mouse gut

text: mouse gut metagenome

text: Thomasclavelia cocleata

characteristic: organism

text: Thomasclavelia cocleata

text: Illumina HiSeq 2000

text: multi-marker approach

text: Metagenome-assembled genome: extra-ERR982824.6_1677794533

characteristic: title


characteristic: ENA-CHECKLIST

text: HELMHOLTZ CENTRE FOR INFECTION RESEARCH

text: public

text: metaSPAdes

text: default

text: mouse digestive system

characteristic: broad-scale environmental context

characteristic: collection date

characteristic: completeness score

text: CheckM

characteristic: completeness software

characteristic: contamination score

text: feces

characteristic: environmental medium

text: Denmark

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: metagenome-assembled genome

characteristic: investigation type

text: mouse gut metagenome

text: mouse gut

characteristic: local environmental context

text: mouse gut metagenome

characteristic: metagenomic source

text: Ligilactobacillus murinus

characteristic: project name

characteristic: sample derived from

text: Ligilactobacillus murinus

text: Illumina HiSeq 2000

characteristic: sequencing method

text: multi-marker approach

characteristic: taxonomic identity marker

text: Metagenome-assembled genome: extra-ERR982824.7_1677794533


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: HELMHOLTZ CENTRE FOR INFECTION RESEARCH

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

characteristic: assembly quality

text: metaSPAdes

characteristic: assembly software

text: default

characteristic: binning parameters

characteristic: binning software

text: mouse digestive system

text: CheckM

characteristic: description

text: feces

text: Denmark

text: metagenome-assembled genome

text: mouse gut metagenome

text: mouse gut

text: mouse gut metagenome

text: Bacteroidales bacterium

characteristic: organism

text: Bacteroidales bacterium

text: Illumina HiSeq 2000

text: multi-marker approach

text: Metagenome-assembled genome: extra-ERR982824.10_1677794534

characteristic: title


characteristic: ENA-CHECKLIST

text: HELMHOLTZ CENTRE FOR INFECTION RESEARCH

text: public

text: metaSPAdes

text: default

text: mouse digestive system

characteristic: broad-scale environmental context

characteristic: collection date

characteristic: completeness score

text: CheckM

characteristic: completeness software

characteristic: contamination score

text: feces

characteristic: environmental medium

text: Denmark

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: metagenome-assembled genome

characteristic: investigation type

text: mouse gut metagenome

text: mouse gut

characteristic: local environmental context

text: mouse gut metagenome

characteristic: metagenomic source

text: uncultured Lachnospiraceae bacterium

characteristic: project name

characteristic: sample derived from

text: uncultured Lachnospiraceae bacterium

text: Illumina HiSeq 2000

characteristic: sequencing method

text: multi-marker approach

characteristic: taxonomic identity marker

text: Metagenome-assembled genome: extra-ERR982824.11_1677794534


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: HELMHOLTZ CENTRE FOR INFECTION RESEARCH

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

characteristic: assembly quality

text: metaSPAdes

characteristic: assembly software

text: default

characteristic: binning parameters

characteristic: binning software

text: mouse digestive system

text: CheckM

characteristic: description

text: feces

text: Denmark

text: metagenome-assembled genome

text: mouse gut metagenome

text: mouse gut

text: mouse gut metagenome

text: Bacteroidales bacterium

characteristic: organism

text: Bacteroidales bacterium

text: Illumina HiSeq 2000

text: multi-marker approach

text: Metagenome-assembled genome: extra-ERR982824.13_1677794534

characteristic: title


characteristic: ENA-CHECKLIST

text: HELMHOLTZ CENTRE FOR INFECTION RESEARCH

text: public

text: metaSPAdes

text: default

text: mouse digestive system

characteristic: broad-scale environmental context

characteristic: collection date

characteristic: completeness score

text: CheckM

characteristic: completeness software

characteristic: contamination score

text: feces

characteristic: environmental medium

text: Denmark

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: metagenome-assembled genome

characteristic: investigation type

text: mouse gut metagenome

text: mouse gut

characteristic: local environmental context

text: mouse gut metagenome

characteristic: metagenomic source

text: uncultured Odoribacter sp.

characteristic: project name

characteristic: sample derived from

text: uncultured Odoribacter sp.

text: Illumina HiSeq 2000

characteristic: sequencing method

text: multi-marker approach

characteristic: taxonomic identity marker

text: Metagenome-assembled genome: extra-ERR982824.15_1677794535


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: HELMHOLTZ CENTRE FOR INFECTION RESEARCH

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

characteristic: assembly quality

text: metaSPAdes

characteristic: assembly software

text: default

characteristic: binning parameters

characteristic: binning software

text: mouse digestive system

text: CheckM

characteristic: description

text: feces

text: Denmark

text: metagenome-assembled genome

text: mouse gut metagenome

text: mouse gut

text: mouse gut metagenome

text: uncultured Oscillospiraceae bacterium

characteristic: organism

text: uncultured Oscillospiraceae bacterium

text: Illumina HiSeq 2000

text: multi-marker approach

text: Metagenome-assembled genome: extra-ERR982824.16_1677794535

characteristic: title


characteristic: ENA-CHECKLIST

text: HELMHOLTZ CENTRE FOR INFECTION RESEARCH

text: public

text: metaSPAdes

text: default

text: mouse digestive system

characteristic: broad-scale environmental context

characteristic: collection date

characteristic: completeness score

text: CheckM

characteristic: completeness software

characteristic: contamination score

text: feces

characteristic: environmental medium

text: Denmark

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: metagenome-assembled genome

characteristic: investigation type

text: mouse gut metagenome

text: mouse gut

characteristic: local environmental context

text: mouse gut metagenome

characteristic: metagenomic source

text: uncultured Muribaculaceae bacterium

characteristic: project name

characteristic: sample derived from

text: uncultured Muribaculaceae bacterium

text: Illumina HiSeq 2000

characteristic: sequencing method

text: multi-marker approach

characteristic: taxonomic identity marker

text: Metagenome-assembled genome: extra-ERR982824.17_1677794535


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: HELMHOLTZ CENTRE FOR INFECTION RESEARCH

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

characteristic: assembly quality

text: metaSPAdes

characteristic: assembly software

text: default

characteristic: binning parameters

characteristic: binning software

text: mouse digestive system

text: CheckM

characteristic: description

text: feces

text: Denmark

text: metagenome-assembled genome

text: mouse gut metagenome

text: mouse gut

text: mouse gut metagenome

text: uncultured Acetatifactor sp.

characteristic: organism

text: uncultured Acetatifactor sp.

text: Illumina HiSeq 2000

text: multi-marker approach

text: Metagenome-assembled genome: extra-ERR982824.18_1677794535

characteristic: title


characteristic: ENA-CHECKLIST

text: HELMHOLTZ CENTRE FOR INFECTION RESEARCH

text: public

text: Many fragments with little to no review of assembly other than reporting of standard assembly statistics

text: metaSPAdes

text: default

text: mouse digestive system

characteristic: broad-scale environmental context

characteristic: collection date

characteristic: completeness score

text: CheckM

characteristic: completeness software

characteristic: contamination score

text: feces

characteristic: environmental medium

text: Denmark

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: metagenome-assembled genome

characteristic: investigation type

text: mouse gut metagenome

text: mouse gut

characteristic: local environmental context

text: mouse gut metagenome

characteristic: metagenomic source

text: uncultured Lachnospiraceae bacterium

characteristic: project name

characteristic: sample derived from

text: uncultured Lachnospiraceae bacterium

text: Illumina HiSeq 2000

characteristic: sequencing method

text: multi-marker approach

characteristic: taxonomic identity marker

text: Metagenome-assembled genome: extra-ERR982824.20_1677794536


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: HELMHOLTZ CENTRE FOR INFECTION RESEARCH

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

characteristic: assembly quality

text: metaSPAdes

characteristic: assembly software

text: default

characteristic: binning parameters

characteristic: binning software

text: mouse digestive system

text: CheckM

characteristic: description

text: feces

text: Denmark

text: metagenome-assembled genome

text: mouse gut metagenome

text: mouse gut

text: mouse gut metagenome

text: Muribaculaceae bacterium

characteristic: organism

text: High fat feeding rather than obesity drives taxonomical and functional changes in the gut microbiota in mice

text: Muribaculaceae bacterium

text: Illumina HiSeq 2000

text: multi-marker approach

text: Metagenome-assembled genome: extra-ERR982824.24_1677794536

characteristic: title


characteristic: ENA-CHECKLIST

text: HELMHOLTZ CENTRE FOR INFECTION RESEARCH

text: public

text: metaSPAdes

text: default

text: mouse digestive system

characteristic: broad-scale environmental context

characteristic: collection date

characteristic: completeness score

text: CheckM

characteristic: completeness software

characteristic: contamination score

text: This sample represents a Metagenome-assembled genome assembled from the metagenomic run ERR982824 of study ERP011540.

text: feces

characteristic: environmental medium

text: Denmark

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: metagenome-assembled genome

characteristic: investigation type

text: mouse gut metagenome

text: mouse gut

characteristic: local environmental context

text: mouse gut metagenome

characteristic: metagenomic source

text: uncultured Eubacteriales bacterium

characteristic: project name

characteristic: sample derived from

text: uncultured Eubacteriales bacterium

text: Illumina HiSeq 2000

characteristic: sequencing method

text: multi-marker approach

characteristic: taxonomic identity marker

text: Metagenome-assembled genome: extra-ERR982824.25_1677794536


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: HELMHOLTZ CENTRE FOR INFECTION RESEARCH

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

characteristic: assembly quality

text: metaSPAdes

characteristic: assembly software

text: default

characteristic: binning parameters

characteristic: binning software

text: mouse digestive system

text: CheckM

characteristic: description

text: feces

text: Denmark

text: metagenome-assembled genome

text: mouse gut metagenome

text: mouse gut

text: mouse gut metagenome

text: Parabacteroides goldsteinii

characteristic: organism

text: Parabacteroides goldsteinii

text: Illumina HiSeq 2000

text: multi-marker approach

text: Metagenome-assembled genome: extra-ERR982824.26_1677794537

characteristic: title


characteristic: ENA-CHECKLIST

text: HELMHOLTZ CENTRE FOR INFECTION RESEARCH

text: public

text: metaSPAdes

text: default

text: mouse digestive system

characteristic: broad-scale environmental context

characteristic: collection date

characteristic: completeness score

text: CheckM

characteristic: completeness software

characteristic: contamination score

text: feces

characteristic: environmental medium

text: Denmark

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: metagenome-assembled genome

characteristic: investigation type

text: mouse gut metagenome

text: mouse gut

characteristic: local environmental context

text: mouse gut metagenome

characteristic: metagenomic source

text: Lachnospiraceae bacterium

characteristic: project name

characteristic: sample derived from

text: Lachnospiraceae bacterium

text: Illumina HiSeq 2000

characteristic: sequencing method

text: multi-marker approach

characteristic: taxonomic identity marker

text: Metagenome-assembled genome: extra-ERR982824.27_1677794537


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: HELMHOLTZ CENTRE FOR INFECTION RESEARCH

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

characteristic: assembly quality

text: metaSPAdes

characteristic: assembly software

text: default

characteristic: binning parameters

characteristic: binning software

text: mouse digestive system

text: CheckM

characteristic: description

text: feces

text: Denmark

text: metagenome-assembled genome

text: mouse gut metagenome

text: mouse gut

text: mouse gut metagenome

text: uncultured Lachnospiraceae bacterium

characteristic: organism

text: uncultured Lachnospiraceae bacterium

text: Illumina HiSeq 2000

text: multi-marker approach

text: Metagenome-assembled genome: extra-ERR982824.29_1677794538

characteristic: title


characteristic: ENA-CHECKLIST

text: HELMHOLTZ CENTRE FOR INFECTION RESEARCH

text: public

text: metaSPAdes

text: default

text: mouse digestive system

characteristic: broad-scale environmental context

characteristic: collection date

characteristic: completeness score

text: CheckM

characteristic: completeness software

characteristic: contamination score

text: feces

characteristic: environmental medium

text: Denmark

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: metagenome-assembled genome

characteristic: investigation type

text: mouse gut metagenome

text: mouse gut

characteristic: local environmental context

text: mouse gut metagenome

characteristic: metagenomic source

text: uncultured Acetatifactor sp.

characteristic: project name

characteristic: sample derived from

text: uncultured Acetatifactor sp.

text: Illumina HiSeq 2000

characteristic: sequencing method

text: multi-marker approach

characteristic: taxonomic identity marker

text: Metagenome-assembled genome: extra-ERR982824.32_1677794538