text: UCSDMI

characteristic: INSDC first public

text: public

characteristic: Submitter Id

text: On shelf

text: 2018-05-11 11:30

text: Mouse 182 stool collection 12 of 21

characteristic: description

text: HFD

characteristic: diet

text: TRUE

text: Host-associated

text: Animal

text: Animal distal gut

text: urban biome

text: animal-associated habitat

text: feces

text: host-associated

text: 10 weeks

text: Air

text: Travis only for collections

text: ApoE KO

text: USA:CA:San Diego

text: Mus musculus

text: UBERON:feces

text: UBERON:feces

text: UBERON:feces

text: mouse

text: Adult

text: Mouse 182

text: g

characteristic: longitude

text: Mouse 182

text: mouse gut metagenome

text: UCSDMI

text: TRUE

text: feces

text: mouse gut metagenome

text: male

text: 10 week IH and IC


status: PUBLIC

tag: attribute

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: UCSDMI

characteristic: INSDC center name

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: On shelf

text: New lot of food

text: 2018-05-15 11:30

text: Mouse 182 stool collection 13 of 21

text: HFD

text: TRUE

characteristic: dob

characteristic: elevation

text: Host-associated

text: Animal

text: Animal distal gut

text: urban biome

text: animal-associated habitat

text: feces

text: host-associated

text: 10 weeks

text: Air

text: Orit only for collections

text: ApoE KO

characteristic: genotype

text: USA:CA:San Diego

text: Mus musculus

characteristic: host scientific name

text: UBERON:feces

text: UBERON:feces

text: UBERON:feces

text: mouse

text: Adult

text: Mouse 182

text: g

characteristic: latitude

text: Mouse 182

text: mouse gut metagenome

characteristic: organism

text: UCSDMI

text: TRUE

text: feces

text: mouse gut metagenome

text: male

characteristic: sex

text: 10 week IH and IC

characteristic: title


text: UCSDMI

characteristic: INSDC first public

text: public

characteristic: Submitter Id

text: On shelf

text: 2018-05-18 11:30

text: Mouse 182 stool collection 14 of 21

characteristic: description

text: HFD

characteristic: diet

text: TRUE

text: Host-associated

text: Animal

text: Animal distal gut

text: urban biome

text: animal-associated habitat

text: feces

text: host-associated

text: 10 weeks

text: Air

text: Orit only for collections

text: ApoE KO

text: USA:CA:San Diego

text: Mus musculus

text: UBERON:feces

text: UBERON:feces

text: UBERON:feces

text: mouse

text: Adult

text: Mouse 182

text: g

characteristic: longitude

text: Mouse 182

text: mouse gut metagenome

text: UCSDMI

text: TRUE

text: feces

text: mouse gut metagenome

text: male

text: 10 week IH and IC


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: UCSDMI

characteristic: INSDC center name

text: public

text: On shelf

text: 2018-05-22 11:30

text: Mouse 182 stool collection 15 of 21

text: HFD

text: TRUE

text: Host-associated

text: Animal

text: Animal distal gut

text: urban biome

text: animal-associated habitat

text: feces

text: host-associated

text: 10 weeks

text: Air

text: ApoE KO

text: USA:CA:San Diego

text: Mus musculus

text: UBERON:feces

text: UBERON:feces

text: UBERON:feces

text: mouse

text: Adult

text: Mouse 182

text: g

text: Mouse 182

text: mouse gut metagenome

text: UCSDMI

text: TRUE

text: feces

text: mouse gut metagenome

text: male

text: 10 week IH and IC


text: UCSDMI

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: On shelf

text: New bag of food

text: 2018-05-25 11:30

text: Mouse 182 stool collection 16 of 21

text: HFD

text: TRUE

characteristic: dob

characteristic: elevation

text: Host-associated

text: Animal

text: Animal distal gut

text: urban biome

text: animal-associated habitat

text: feces

text: host-associated

text: 10 weeks

text: Air

text: ApoE KO

text: USA:CA:San Diego

text: Mus musculus

text: UBERON:feces

text: UBERON:feces

text: UBERON:feces

text: mouse

text: Adult

text: Mouse 182

text: g

text: Mouse 182

text: mouse gut metagenome

text: UCSDMI

text: TRUE

text: feces

text: mouse gut metagenome

text: male

text: 10 week IH and IC


text: UCSDMI

text: public

text: On shelf

text: 2018-05-29 11:30

text: Mouse 182 stool collection 17 of 21

text: HFD

text: TRUE

text: Host-associated

text: Animal

text: Animal distal gut

text: urban biome

text: animal-associated habitat

text: feces

text: host-associated

text: 10 weeks

text: Air

text: ApoE KO

characteristic: genotype

text: USA:CA:San Diego

text: Mus musculus

characteristic: host scientific name

text: UBERON:feces

text: UBERON:feces

text: UBERON:feces

text: mouse

text: Adult

text: Mouse 182

text: g

characteristic: latitude

text: Mouse 182

text: mouse gut metagenome

characteristic: organism

text: UCSDMI

text: TRUE

text: feces

text: mouse gut metagenome

text: male

characteristic: sex

text: 10 week IH and IC


text: UCSDMI

characteristic: INSDC first public

text: public

characteristic: Submitter Id

text: On shelf

text: 2018-06-01 11:30

text: Mouse 182 stool collection 18 of 21

characteristic: description

text: HFD

characteristic: diet

text: TRUE

text: Host-associated

text: Animal

text: Animal distal gut

text: urban biome

text: animal-associated habitat

text: feces

text: host-associated

text: 10 weeks

text: Air

text: ApoE KO

text: USA:CA:San Diego

text: Mus musculus

text: UBERON:feces

text: UBERON:feces

text: UBERON:feces

text: mouse

text: Adult

text: Mouse 182

text: g

text: Mouse 182

text: mouse gut metagenome

text: UCSDMI

text: TRUE

text: feces

text: mouse gut metagenome

text: male

text: 10 week IH and IC

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: UCSDMI

text: public

text: On shelf

text: New bag of food

text: 2018-06-05 11:30

text: Mouse 182 stool collection 19 of 21

text: HFD

text: TRUE

text: Host-associated

text: Animal

text: Animal distal gut

text: urban biome

text: animal-associated habitat

text: feces

text: host-associated

text: 10 weeks

text: Air

text: ApoE KO

text: USA:CA:San Diego

text: Mus musculus

text: UBERON:feces

text: UBERON:feces

text: UBERON:feces

text: mouse

text: Adult

text: Mouse 182

text: g

characteristic: longitude

text: Mouse 182

text: mouse gut metagenome

text: UCSDMI

text: TRUE

text: feces

text: mouse gut metagenome

text: male

text: 10 week IH and IC


text: UCSDMI

characteristic: INSDC center name

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: On shelf

text: 2018-04-06 11:30

text: Mouse 182 stool collection 2 of 21

text: HFD

text: TRUE

characteristic: dob

text: Host-associated

text: Animal

text: Animal distal gut

text: urban biome

text: animal-associated habitat

text: feces

text: host-associated

text: 10 weeks

text: Air

text: ApoE KO

text: USA:CA:San Diego

text: Mus musculus

text: UBERON:feces

text: UBERON:feces

text: UBERON:feces

text: mouse

text: Adult

text: Mouse 182

text: g

text: Mouse 182

text: mouse gut metagenome

text: UCSDMI

text: TRUE

text: feces

text: mouse gut metagenome

text: male

text: 10 week IH and IC


text: UCSDMI

text: public

text: On shelf

text: 2018-06-08 11:30

text: Mouse 182 stool collection 20 of 21

text: HFD

text: TRUE

characteristic: elevation

text: Host-associated

text: Animal

text: Animal distal gut

text: urban biome

text: animal-associated habitat

text: feces

text: host-associated

text: 10 weeks

text: Air

text: Travis only for collections

text: ApoE KO

characteristic: genotype

text: USA:CA:San Diego

text: Mus musculus

characteristic: host scientific name

text: UBERON:feces

text: UBERON:feces

text: UBERON:feces

text: mouse

text: Adult

text: Mouse 182

text: g

characteristic: latitude

text: Mouse 182

text: mouse gut metagenome

characteristic: organism

text: UCSDMI

text: TRUE

text: feces

text: mouse gut metagenome

text: male

text: 10 week IH and IC


text: UCSDMI

characteristic: INSDC first public

text: public

characteristic: Submitter Id

text: On shelf

text: 2018-06-12 11:30

text: Mouse 182 stool collection 21 of 21

characteristic: description

text: HFD

characteristic: diet

text: TRUE

text: Host-associated

text: Animal

text: Animal distal gut

text: urban biome

text: animal-associated habitat

text: feces

text: host-associated

text: 10 weeks

text: Air

text: ApoE KO

text: USA:CA:San Diego

text: Mus musculus

text: UBERON:feces

text: UBERON:feces

text: UBERON:feces

text: mouse

text: Adult

text: Mouse 182

text: g

text: Mouse 182

text: mouse gut metagenome

text: UCSDMI

text: TRUE

text: feces

text: mouse gut metagenome

text: male

characteristic: sex

text: 10 week IH and IC


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: UCSDMI

text: public

text: On shelf

text: New bag of food

text: 2018-04-10 11:30

text: Mouse 182 stool collection 3 of 21

text: HFD

text: TRUE

text: Host-associated

text: Animal

text: Animal distal gut

text: urban biome

text: animal-associated habitat

text: feces

text: host-associated

text: 10 weeks

text: Air

text: ApoE KO

text: USA:CA:San Diego

text: Mus musculus

text: UBERON:feces

text: UBERON:feces

text: UBERON:feces

text: mouse

text: Adult

text: Mouse 182

text: g

text: Mouse 182

text: mouse gut metagenome

text: UCSDMI

text: TRUE

text: feces

text: mouse gut metagenome

text: male

text: 10 week IH and IC

characteristic: title


text: UCSDMI

characteristic: INSDC center name

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: On shelf

text: 2018-04-13 11:30

text: Mouse 182 stool collection 4 of 21

text: HFD

text: TRUE

text: Host-associated

text: Animal

text: Animal distal gut

text: urban biome

text: animal-associated habitat

text: feces

text: host-associated

text: 10 weeks

text: Air

text: Orit only for collections

text: ApoE KO

text: USA:CA:San Diego

text: Mus musculus

text: UBERON:feces

text: UBERON:feces

text: UBERON:feces

text: mouse

text: Adult

text: Mouse 182

text: g

characteristic: longitude

text: Mouse 182

text: mouse gut metagenome

text: UCSDMI

text: TRUE

text: feces

text: mouse gut metagenome

text: male

text: 10 week IH and IC


text: UCSDMI

text: public

text: On shelf

text: 2018-04-17 11:30

text: Mouse 182 stool collection 5 of 21

text: HFD

text: TRUE

characteristic: dob

characteristic: elevation

text: Host-associated

text: Animal

text: Animal distal gut

text: urban biome

text: animal-associated habitat

text: feces

text: host-associated

text: 10 weeks

text: Air

text: Travis only for collections

text: ApoE KO

characteristic: genotype

text: USA:CA:San Diego

text: Mus musculus

characteristic: host scientific name

text: UBERON:feces

text: UBERON:feces

text: UBERON:feces

text: mouse

text: Adult

text: Mouse 182

text: g

characteristic: latitude

text: Mouse 182

text: mouse gut metagenome

text: UCSDMI

text: TRUE

text: feces

text: mouse gut metagenome

text: male

text: 10 week IH and IC


text: UCSDMI

characteristic: INSDC first public

text: public

characteristic: Submitter Id

text: On shelf

text: Mixed leftovers from 2 bags of food

text: 2018-04-20 11:30

text: Mouse 182 stool collection 6 of 21

characteristic: description

text: HFD

characteristic: diet

text: TRUE

text: Host-associated

text: Animal

text: Animal distal gut

text: urban biome

text: animal-associated habitat

text: feces

text: host-associated

text: 10 weeks

text: Air

text: ApoE KO

text: USA:CA:San Diego

text: Mus musculus

text: UBERON:feces

text: UBERON:feces

text: UBERON:feces

text: mouse

text: Adult

text: Mouse 182

text: g

text: Mouse 182

text: mouse gut metagenome

characteristic: organism

text: UCSDMI

text: TRUE

text: feces

text: mouse gut metagenome

text: male

text: 10 week IH and IC


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: UCSDMI

text: public

text: On shelf

text: New bag of food

text: 2018-04-24 11:30

text: Mouse 182 stool collection 7 of 21

text: HFD

text: TRUE

text: Host-associated

text: Animal

text: Animal distal gut

text: urban biome

text: animal-associated habitat

text: feces

text: host-associated

text: 10 weeks

text: Air

text: ApoE KO

text: USA:CA:San Diego

text: Mus musculus

text: UBERON:feces

text: UBERON:feces

text: UBERON:feces

text: mouse

text: Adult

text: Mouse 182

text: g

text: Mouse 182

text: mouse gut metagenome

text: UCSDMI

text: TRUE

text: feces

text: mouse gut metagenome

text: male

characteristic: sex

text: 10 week IH and IC


text: UCSDMI

characteristic: INSDC center name

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: On shelf

text: 2018-04-27 11:30

text: Mouse 182 stool collection 8 of 21

text: HFD

text: TRUE

text: Host-associated

text: Animal

text: Animal distal gut

text: urban biome

text: animal-associated habitat

text: feces

text: host-associated

text: 10 weeks

text: Air

text: Orit only for collections

text: ApoE KO

text: USA:CA:San Diego

text: Mus musculus

text: UBERON:feces

text: UBERON:feces

text: UBERON:feces

text: mouse

text: Adult

text: Mouse 182

text: g

text: Mouse 182

text: mouse gut metagenome

text: UCSDMI

text: TRUE

text: feces

text: mouse gut metagenome

text: male

characteristic: title

text: 10 week IH and IC


text: UCSDMI

text: public

text: On shelf

text: New bag of food

text: 2018-05-01 11:30

text: Mouse 182 stool collection 9 of 21

text: HFD

text: TRUE

characteristic: dob

characteristic: elevation

text: Host-associated

text: Animal

text: Animal distal gut

text: urban biome

text: animal-associated habitat

text: feces

text: host-associated

text: 10 weeks

text: Air

text: ApoE KO

characteristic: genotype

text: USA:CA:San Diego

text: Mus musculus

characteristic: host scientific name

text: UBERON:feces

text: UBERON:feces

text: UBERON:feces

text: mouse

text: Adult

text: Mouse 182

text: g

characteristic: longitude

text: Mouse 182

text: mouse gut metagenome

text: UCSDMI

text: TRUE

text: feces

text: mouse gut metagenome

text: male

text: 10 week IH and IC


text: UCSDMI

characteristic: INSDC first public

text: public

characteristic: Submitter Id

characteristic: description

text: TRUE

text: Control

text: Negative

text: Sterile water blank

text: urban biome

text: research facility

text: sterile water

text: misc environment

text: USA:CA:San Diego

text: g

characteristic: latitude

text: metagenome

text: UCSDMI

text: TRUE

text: control blank

text: metagenome

text: IH IC CR


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: UCSDMI

text: public

text: TRUE

text: Control

text: Negative

text: Sterile water blank

text: urban biome

text: research facility

text: sterile water

text: misc environment

text: USA:CA:San Diego

text: g

text: metagenome

characteristic: organism

text: UCSDMI

text: TRUE

text: control blank

text: metagenome

text: IH IC CR


characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC last update

text: public

tag: Namespace:Northumbria University / South Tees Hospitals NHS Foundation Trust / North Cumbria Integrated Care NHS Foundation Trust / North Tees and Hartlepool NHS Foundation Trust / Newcastle Hospitals NHS Foundation Trust

text: COVID-19 Genomics UK Consortium

characteristic: broker name

characteristic: collecting institution

characteristic: collection date

text: not provided

characteristic: collector name

text: not provided

characteristic: definition for seropositive sample

text: United Kingdom

characteristic: geographic location (country and/or sea)

text: England

characteristic: geographic location (region and locality)

text: not provided

characteristic: host common name

text: not provided

characteristic: host health state

text: Human

text: not provided

characteristic: host sex

text: not provided

characteristic: host subject id

text: not provided

characteristic: isolate

text: Severe acute respiratory syndrome coronavirus 2

characteristic: receipt date

text: active surveillance in response to outbreak

characteristic: sample capture status

text: not provided

characteristic: serotype (required for a seropositive sample)

text: not provided

characteristic: virus identifier


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Northumbria University / South Tees Hospitals NHS Foundation Trust / North Cumbria Integrated Care NHS Foundation Trust / North Tees and Hartlepool NHS Foundation Trust / Newcastle Hospitals NHS Foundation Trust

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: COVID-19 Genomics UK Consortium

text: not provided

text: not provided

text: United Kingdom

text: England

text: not provided

text: not provided

text: Human

characteristic: host scientific name

text: not provided

text: not provided

text: not provided

characteristic: organism

text: not provided

characteristic: title

text: not provided


text: Quadram Institute Bioscience

text: public

tag: Namespace:Quadram Institute Bioscience

text: COVID-19 Genomics UK Consortium

characteristic: broker name

text: Quadram Institute Bioscience

characteristic: collecting institution

characteristic: collection date

text: not provided

characteristic: collector name

text: not provided

characteristic: definition for seropositive sample

text: United Kingdom

characteristic: geographic location (country and/or sea)

text: England

characteristic: geographic location (region and locality)

text: not provided

characteristic: host common name

text: not provided

characteristic: host health state

text: Human

text: not provided

characteristic: host sex

text: not provided

characteristic: host subject id

text: not provided

characteristic: isolate

characteristic: receipt date

text: not provided

text: not provided


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

tag: Namespace:Dept. of Clinical and Molecular Medicine Norwegian University of Science and Technology (NTNU)

characteristic: Submitter Id

unit: day

characteristic: age

text: ArrayExpress

text: lymphocyte

text: house mouse

characteristic: common name

text: Protocols: Isolation of Lamina Propria lymphocytes was performed according to the protocol described in Webster et al, see reference below. Only modification was using PBS without calcium and magnesium instead of HBSS. After isolation according to the protocol, an extra step of cell sorting was done to remove any residual epithelial cell before performing scRNAseq on the CD45+ population. Briefly, isolated cells were incubated in PBS + 1%FBS + 2mM EDTA (flow buffer) along with DAPI, CD326 PE-Cy7 and CD45 PE-Cy5. Live CD45+ cells were selected on a DAPI- CD326- CD45+ basis and collected in RPMI 1640 + 10% FCS + 2mM Glutamine 2mM. Cells were then pelleted and resuspended in flow buffer at 1x10^6 cells/ml and brought to the genomics core on ice. Viability post-sorting was determined to be 85-90%. Untreated and antibiotics treated mice were isolated on different days, but sequenced at the same time. References: Webster HC, Andrusaite AT, Shergold AL, Milling SWF, Perona-Wright G. Isolation and functional characterisation of lamina propria leukocytes from helminth-infected, murine small intestine. J Immunol Methods. 2020 Feb;477:112702. doi: 10.1016/j.jim.2019.112702. Epub 2019 Nov 6. PMID: 31705860; PMCID: PMC6983935. Parental mice were treated ad libitum with a cocktail of antibiotics in drinking water freshly prepared every Monday, Wednesday and Friday. Ad libitum treatment of parental mice started 3-4 weeks before pup delivery and continued during the breastfeeding period. After weaning, pups were treated ad libitum with the same antibiotic cocktail up until tissue collection and cell isolation. Antibiotic cocktail: Ampicillin (1g/liter), Amoxicillin-Clavulanate (0,25g/liter), Neomycin (1g/liter), Gentamicin (1g/ liter), and Vancomycin (0.5g/liter) in drinking water. Added Sucralose (sweetener) 0,1g/liter to make the cocktail palatable. See nucleic acid library construction protocol Library preparation was done with 10X genomics Chromium Next GEM Single Cell 3′ GEM, Library & Gel Bead Kit v3.1

characteristic: description

text: adult

characteristic: developmental stage

text: Villin-Cre +; Lsd1f/f

characteristic: genotype

characteristic: immunophenotype

text: A

characteristic: individual

text: Mus musculus

text: Mus musculus

text: small intestine

characteristic: organism part

text: lamina propria of small intestine

characteristic: sampling site

text: Mus musculus

text: male

characteristic: sex

characteristic: strain


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Dept. of Clinical and Molecular Medicine Norwegian University of Science and Technology (NTNU)

characteristic: INSDC center name

text: public

text: ArrayExpress

characteristic: broker name

text: lymphocyte

text: house mouse

text: adult

text: Villin-Cre -; Lsd1f/+

text: C

text: Mus musculus

characteristic: organism

text: Mus musculus

text: small intestine

text: lamina propria of small intestine

text: Mus musculus

text: male

characteristic: title


characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

characteristic: age

text: ArrayExpress

text: lymphocyte

text: house mouse

characteristic: common name

characteristic: description

text: adult

text: Villin-Cre +; Lsd1f/f

text: B

text: Mus musculus

text: Mus musculus

text: small intestine

text: lamina propria of small intestine

text: Mus musculus

text: female


text: public

text: ArrayExpress

text: lymphocyte

text: house mouse

text: adult

characteristic: developmental stage

text: Villin-Cre -; Lsd1f/+

characteristic: genotype

characteristic: immunophenotype

text: D

characteristic: individual

text: Mus musculus

text: Mus musculus

text: small intestine

characteristic: organism part

text: lamina propria of small intestine

characteristic: sampling site

text: Mus musculus

text: female

characteristic: sex

characteristic: strain


E-MTAB-10493:HFHS 1

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: XIAMEN UNIVERSITY

characteristic: INSDC center name

text: public

text: E-MTAB-10493:HFHS 1

tag: Namespace:XIAMEN UNIVERSITY

text: ArrayExpress

characteristic: broker name

text: crab-eating macaque

text: Protocols: The liver tissues were collected from Macaca fascicularis and frozen in liquid nitrogen immediately.The tissues were transfered to a freezer at -80 ℃ for storage. Total RNA was extracted using Trizol (Invitrogen, Carlsbad, CA, USA) according to the manufacturer’s instruction. In Brief, about 60 mg of tissues were ground into a powder in liquid nitrogen, and homogenized in the RNA extraction buffer for 2 min, followed by resting horizontally for 5 min. The mix was then centrifuged for 5 min with 12,000 ×g at 4°C, and the supernatant was transferred into a new tube with 0.3 mL chloroform/isoamyl alcohol (24:1). The mix was shacked vigorously for 15 s and centrifuged at 12,000 ×g for 10 min at 4°C. The upper aqueous phase was transferred into a new tube and mixed with an equal volume of isopropyl alcohol, followed by centrifugation at 13,600 rpm for 20 min at 4°C. Then the RNA pellet was washed twice with 1 ml 75% ethanol and centrifuged at 13,600 rpm for 3 min at 4°C to desert the residual ethanol. After 5-10 min of air dry in a biosafety cabinet, the RNA pellet was dissolved in 25µL~100µL of DEPC-treated water, followed by qualification and quantification using a NanoDrop and Agilent 2100 bioanalyzer (Thermo Fisher Scientific, MA, USA), respectively. Oligo(dT)-attached magnetic beads were applied to purify mRNA from the total RNA. Purified mRNA was fragmented into small pieces with fragment buffer. Then the first-strand cDNA was generated using random hexamer-primed reverse transcription, and the second-strand cDNA was synthesized. A-Tailing Mix and RNA Index Adapters were then added by incubation. The cDNA fragments were amplified by PCR, followed by purification by Ampure XP Beads, and then dissolved in EB solution. The product was validated on an Agilent Technologies 2100 bioanalyzer for quality control. The double-stranded PCR products were heated to denature and circularized by the splint oligo sequence to construct the final library.

text: adult

text: high fat high sugar diet

characteristic: diet

text: obesity

characteristic: disease

text: wild type genotype

text: Macaca fascicularis

characteristic: organism

text: Macaca fascicularis

text: liver

text: Macaca fascicularis

text: male

text: HFHS 1

characteristic: title


E-MTAB-10493:HFHS 2

text: XIAMEN UNIVERSITY

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-10493:HFHS 2

characteristic: Submitter Id

text: ArrayExpress

text: crab-eating macaque

characteristic: common name

characteristic: description

text: adult

characteristic: developmental stage

text: high fat high sugar diet

text: obesity

text: wild type genotype

characteristic: genotype

text: Macaca fascicularis

text: Macaca fascicularis

text: liver

text: Macaca fascicularis

text: male

text: HFHS 2


E-MTAB-10493:HFHS 3

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: XIAMEN UNIVERSITY

text: public

text: E-MTAB-10493:HFHS 3

text: ArrayExpress

text: crab-eating macaque

text: adult

text: high fat high sugar diet

text: obesity

text: wild type genotype

text: Macaca fascicularis

text: Macaca fascicularis

text: liver

characteristic: organism part

text: Macaca fascicularis

text: male

characteristic: sex

text: HFHS 3


E-MTAB-10493:NC 1

characteristic: External Id

text: XIAMEN UNIVERSITY

characteristic: INSDC center name

text: public

text: E-MTAB-10493:NC 1

text: ArrayExpress

characteristic: broker name

text: crab-eating macaque

text: adult

text: normal diet

characteristic: diet

text: normal

characteristic: disease

text: wild type genotype

text: Macaca fascicularis

text: Macaca fascicularis

text: liver

text: Macaca fascicularis

text: male

text: NC 1


E-MTAB-10493:NC 2

text: XIAMEN UNIVERSITY

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: E-MTAB-10493:NC 2

text: ArrayExpress

text: crab-eating macaque

text: adult

text: normal diet

text: normal

text: wild type genotype

text: Macaca fascicularis

characteristic: organism

text: Macaca fascicularis

text: liver

text: Macaca fascicularis

text: male

text: NC 2

characteristic: title


E-MTAB-10493:NC 3

text: XIAMEN UNIVERSITY

text: public

characteristic: SRA accession

text: E-MTAB-10493:NC 3

characteristic: Submitter Id

text: ArrayExpress

text: crab-eating macaque

characteristic: common name

characteristic: description

text: adult

characteristic: developmental stage

text: normal diet

text: normal

text: wild type genotype

text: Macaca fascicularis

text: Macaca fascicularis

text: liver

text: Macaca fascicularis

text: male

text: NC 3


E-MTAB-10493:sDM 1

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: XIAMEN UNIVERSITY

text: public

text: E-MTAB-10493:sDM 1

text: ArrayExpress

text: crab-eating macaque

text: adult

text: normal diet

text: diabetes mellitus

text: wild type genotype

characteristic: genotype

text: Macaca fascicularis

text: Macaca fascicularis

text: liver

characteristic: organism part

text: Macaca fascicularis

text: male

text: sDM 1


E-MTAB-10493:sDM 2

characteristic: External Id

text: XIAMEN UNIVERSITY

characteristic: INSDC center name

text: public

text: E-MTAB-10493:sDM 2

text: ArrayExpress

characteristic: broker name

text: crab-eating macaque

text: adult

text: normal diet

characteristic: diet

text: diabetes mellitus

text: wild type genotype

text: Macaca fascicularis

text: Macaca fascicularis

text: liver

text: Macaca fascicularis

text: male

characteristic: sex

text: sDM 2


E-MTAB-10493:sDM 3

text: XIAMEN UNIVERSITY

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: E-MTAB-10493:sDM 3

text: ArrayExpress

text: crab-eating macaque

text: adult

text: normal diet

text: diabetes mellitus

characteristic: disease

text: wild type genotype

text: Macaca fascicularis

characteristic: organism

text: Macaca fascicularis

text: liver

text: Macaca fascicularis

text: male

text: sDM 3


text: INSTITUT PASTEUR

text: public

characteristic: SRA accession

tag: Namespace:INSTITUT PASTEUR

characteristic: Submitter Id

text: University Hospital Reina Sofia (Córdoba, Spain)

characteristic: collecting institution

characteristic: collection date

text: CSF

characteristic: description

text: Spain

characteristic: geographic location (country and/or sea)

unit: DD

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: Córdoba, Córdoba

characteristic: geographic location (region and locality)

unit: year

characteristic: host age

text: Human

characteristic: host common name

text: diseased

characteristic: host health state

text: Homo sapiens

characteristic: host scientific name

text: male

characteristic: host sex

characteristic: host subject id

characteristic: isolate

text: Echovirus E11

characteristic: receipt date

text: Echovirus E11

characteristic: title

characteristic: virus identifier


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: INSTITUT PASTEUR

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

characteristic: collecting institution

text: CSF

text: Spain

text: Córdoba, Córdoba

text: Human

text: diseased

text: Homo sapiens

text: female

text: Echovirus E11

characteristic: organism

text: Echovirus E11


text: INSTITUT PASTEUR

text: public

characteristic: collection date

text: CSF

characteristic: description

text: Spain

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: Cordoba, La Victoria

characteristic: geographic location (region and locality)

characteristic: host age

text: Human

characteristic: host common name

text: diseased

characteristic: host health state

text: Homo sapiens

characteristic: host scientific name

text: female

characteristic: host sex

characteristic: host subject id

text: Echovirus E6

text: Echovirus E6


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: INSTITUT PASTEUR

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: CSF

text: Spain

text: Córdoba, Villafranca de Córdoba

text: Human

text: diseased

text: Homo sapiens

text: male

characteristic: isolate

text: Echovirus E6

characteristic: receipt date

text: Echovirus E6

characteristic: title

characteristic: virus identifier


text: INSTITUT PASTEUR

text: public

characteristic: SRA accession

characteristic: Submitter Id

characteristic: collecting institution

characteristic: collection date

text: CSF

characteristic: description

text: Spain

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: Córdoba, Córdoba

characteristic: geographic location (region and locality)

characteristic: host age

text: Human

characteristic: host common name

text: diseased

text: Homo sapiens

text: female

text: Echovirus E6

characteristic: organism

text: Echovirus E6


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: INSTITUT PASTEUR

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: CSF

text: Spain

text: Córdoba, Pedro Abad

text: Human

text: diseased

characteristic: host health state

text: Homo sapiens

characteristic: host scientific name

text: female

characteristic: host sex

characteristic: host subject id

text: Echovirus E6

text: Echovirus E6


text: INSTITUT PASTEUR

text: public

characteristic: SRA accession

characteristic: Submitter Id

characteristic: collecting institution

characteristic: collection date

text: CSF

characteristic: description

text: Spain

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: Córdoba, Posadas

text: Human

text: diseased

text: Homo sapiens

text: male

characteristic: isolate

text: Echovirus E30

characteristic: receipt date

text: Echovirus E30

characteristic: title

characteristic: virus identifier


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: INSTITUT PASTEUR

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: CSF

text: Spain

text: Córdoba, La Montiela

characteristic: geographic location (region and locality)

characteristic: host age

text: Human

characteristic: host common name

text: diseased

text: Homo sapiens

text: male

text: Echovirus E30

characteristic: organism

text: Echovirus E30


text: INSTITUT PASTEUR

text: public

characteristic: SRA accession

characteristic: Submitter Id

characteristic: collecting institution

characteristic: collection date

text: CSF

characteristic: description

text: Spain

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: Córdoba, Córdoba

text: Human

text: diseased

characteristic: host health state

text: Homo sapiens

characteristic: host scientific name

text: female

characteristic: host sex

characteristic: host subject id

text: Echovirus E13

text: Echovirus E13


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: INSTITUT PASTEUR

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: CSF

text: Spain

text: Córdoba, Almodovar del Rio

text: Human

text: diseased

text: Homo sapiens

text: male

characteristic: isolate

text: Echovirus E30

characteristic: receipt date

text: Echovirus E30

characteristic: title

characteristic: virus identifier


text: public

characteristic: SRA accession

characteristic: Submitter Id

characteristic: age

text: ArrayExpress

characteristic: broker name

text: house mouse

characteristic: common name

text: Protocols: RNA was extracted (see nucleic acid extraction protocol) from small intestinal organoids (see growth protocol) grown from mice with a epithelial specific LSD1 knock out (Villin-Cre+; Lsd1f/f) and wt mice (Villin-Cre -; Lsd1f/f). RNAseq was performed on organoids after 4 passages since isolation from intestines. Crypts from small intestine were isolated according to a published protocol by Sato and Clevers, see reference below. In summary, the small intestine of mouse was washed in ice-cold PBS and opened longitudinally. A microscopy cover slip was used to gently scrape of excess mucus and villus before the intestine was cut into 2-4 mm pieces. The fragments were resuspended in 30 mL ice-cold PBS and pipetted up and down with a 10 mL pipette. Supernatant was discarded and this step was repeated 5-10 times until the supernatant was clear. The fragments were incubated in 2 mM EDTA in PBS at 4 °C for 30 min with gentle rocking. The supernatant was removed, 20 mL of ice-cold PBS was added and the fragments were pipetted up and down. This washing step was repeated until the crypt fraction appeared as seen in a microscope. The 1-3 consecutive crypt fractions were passed through a 70 um cell strainer and collected into a FCS coated 50 mL tube. The crypts were spun down at 300 x g for 5 min and washed once in 10 mL ice cold PBS at 200 x g for 5 min. Approximately 200-500 crypts were resuspended in 50 uL Matrigel and kept at 4 °C. 50 uL of the matrigel solution were added to the center of a pre-warmed 24 well plate and quickly transferred to an incubator at 37 degrees with 5 % CO2. After 5 min the pellet had solidified and 500 uL of basal culture medium was added and the plate was put back into the incubator. Basal culture medium consisted of advanced Dulbecco's modified Eagle medium - F12 supplemented with penicillin/streptomycin, 10 mM HEPES, 2 mM Glutamax, 1x N2 [ThermoFisher Scientific 100X, 17502048], 1x B-27 [ThermoFisher Scientific 50X, 17504044], and 1x N-acetyl-L-cysteine [Sigma, A7250]) and overlaid with ENR factors containing 50 ng/ml of murine EGF [Thermo Fisher Scientific, PMG8041], 20 % condition medium (CM) from a cell line producing R-Spondin (kind gift from Calvin Kuo, Stanford University School of Medicine, Stanford, CA, USA) and 10 % Noggin-CM (a kind gift from Hans Clevers, Hubrecht Institute, Utrecht, The Netherlands). The culture medium was replaced every 2-3 days. Organoids were passaged by disrupting them with strong mechanical pipetting, letting the solution cool on ice before centrifuging at 200 x g, 5 min at 4 °C and resuspending in matrigel. References:Sato, Toshiro and Hans Clevers (2013). “Primary Mouse Small Intestinal Epithelial Cell Cultures”. In:Epithelial Cell Culture Protocols: Second Edition. Ed. by Scott H. Randell and M. Leslie Fulcher. Methods in Molecular Biology. Totowa, NJ: Humana Press, pp. 319-328.isbn: 978-1-62703-125-7.doi:10.1007/978-1-62703-125-7_19.527url:https://doi.org/10.1007/978-1-62703-125-7_19. RNA was isolated with the RNeasy Plus Micro Kit (QIAGEN) Library preparation was done with NEB Next(R) Ultra(TM) RNA Library Prep Kit

characteristic: description

text: adult

characteristic: developmental stage

text: normal

characteristic: disease

text: Villin-Cre+; Lsd1f/f

characteristic: genotype

text: organoid culture

characteristic: growth condition

text: Mus musculus

characteristic: organism

text: Mus musculus

text: epithelium of crypt of Lieberkuhn of small intestine

characteristic: organism part

text: villin-induced Lsd1 homozygous knockout

characteristic: phenotype

text: Mus musculus

text: male

characteristic: sex

characteristic: strain


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: ArrayExpress

text: house mouse

text: adult

text: normal

text: Villin-Cre+; Lsd1f/f

text: organoid culture

text: Mus musculus

text: Mus musculus

text: villin-induced Lsd1 homozygous knockout

text: Mus musculus

text: female

characteristic: title


text: public

characteristic: SRA accession

characteristic: Submitter Id

characteristic: age

text: ArrayExpress

characteristic: broker name

text: house mouse

characteristic: common name

characteristic: description

text: adult

characteristic: developmental stage

text: normal

characteristic: disease

text: Villin-Cre-; Lsd1f/f

text: organoid culture

text: Mus musculus

text: Mus musculus

text: wild type

text: Mus musculus

text: male


characteristic: ENA-CHECKLIST

text: public

text: ArrayExpress

text: house mouse

text: adult

text: normal

text: Villin-Cre-; Lsd1f/+

characteristic: genotype

text: organoid culture

characteristic: growth condition

text: Mus musculus

characteristic: organism

text: Mus musculus

characteristic: organism part

text: wild type

characteristic: phenotype

text: Mus musculus

text: male

characteristic: sex

characteristic: strain


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

text: ArrayExpress

text: house mouse

text: Ampicillin; 1g/liter, Amoxicillin-Clavulanate; 0,25g/liter, Neomycin; 1g/liter, Gentamicin; 1g/ liter, and Vancomycin; 0.5g/liter

characteristic: compound

text: Protocols: The proximal half of mouse small intestine was isolated and washed with ice-cold PBS until luminal contents were cleared. The intestine was opened longitudinally, villi scraped off and collected, after scraping remaining tissue was cut into ~2mm pieces. Collected villi were resuspended in cold PBS and filtered through a 70 μm cell strainer to remove cell debris. Afterwards a wash of PBS was performed to remove remaining debris and mucus. To collect the villi fraction the filter was inverted, eluted with PBS and centrifuged at 300 g, 5 minutes, 4°C. Crypts were isolated according to Sato and Clevers protocol, see reference below. Briefly, the 2 mm intestinal fragments were washed 5 times with PBS. Tissue pieces were incubated with 2 mM EDTA in ice-cold PBS for 30-60 minutes with gentle rocking. The supernatant was removed, 20 mL of ice-cold PBS was added and the fragments were pipetted up and down. This washing step was repeated until the crypt fraction appeared under microscopic examinations seen in a microscope. The 1-3 consecutive crypt fractions were passed through a 70 μm cell strainer and collected into a FCS coated 50 mL tube. The crypts were spun down at 300 x g for 5 min and washed once in 10 mL ice cold PBS at 200 x g for 5 min. References:Sato, Toshiro and Hans Clevers (2013). “Primary Mouse Small Intestinal Epithelial Cell Cultures”. In:Epithelial Cell Culture Protocols: Second Edition. Ed. by Scott H. Randell and M. Leslie Fulcher. Methods in Molecular Biology. Totowa, NJ: Humana Press, pp. 319-328.isbn: 978-1-62703-125-7.doi:10.1007/978-1-62703-125-7_19.527url:https://doi.org/10.1007/978-1-62703-125-7_19. Parental mice were treated ad libitum with a cocktail of antibiotics in drinking water freshly prepared every Monday, Wednesday and Friday. Ad libitum treatment of parental mice started 3-4 weeks before pup delivery and continued during the breastfeeding period. After weaning, pups were treated ad libitum with the same antibiotic cocktail up until tissue collection and cell isolation. . Antibiotic cocktail: Ampicillin (1g/liter), Amoxicillin-Clavulanate (0,25g/liter), Neomycin (1g/liter), Gentamicin (1g/ liter), and Vancomycin (0.5g/liter) in drinking water. Added Sucralose (sweetener) 0,1g/liter to make the cocktail palatable. RNA was isolated with the RNeasy Plus Mini Kit (QIAGEN) Library preparation was done with NEB Next(R) Ultra(TM) RNA Library Prep Kit

text: adult

text: normal

text: Villin-Cre+; Lsd1f/f

characteristic: individual

text: Mus musculus

text: Mus musculus

text: epithelium of crypt of Lieberkuhn

text: villin-induced Lsd1 homozygous knockout

text: small intestine

characteristic: sampling site

text: Mus musculus

text: female

characteristic: title


characteristic: ENA-CHECKLIST

text: public

characteristic: SRA accession

characteristic: Submitter Id

characteristic: age

text: ArrayExpress

characteristic: broker name

text: house mouse

characteristic: common name

characteristic: description

text: adult

characteristic: developmental stage

text: normal

characteristic: disease

text: Villin-Cre-; Lsd1f/f

characteristic: genotype

text: Mus musculus

text: Mus musculus

text: epithelium of crypt of Lieberkuhn

text: wild type

text: small intestine

text: Mus musculus

text: female


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: ArrayExpress

text: house mouse

text: adult

text: normal

text: Villin-Cre-; Lsd1f/-

text: Mus musculus

characteristic: organism

text: Mus musculus

text: epithelium of crypt of Lieberkuhn

characteristic: organism part

text: wild type

characteristic: phenotype

text: small intestine

text: Mus musculus

text: female

characteristic: sex

characteristic: strain


characteristic: ENA-CHECKLIST

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

characteristic: age

text: ArrayExpress

text: house mouse

characteristic: compound

text: adult

text: normal

text: Villin-Cre-; Lsd1f/-

characteristic: individual

text: Mus musculus

text: Mus musculus

text: epithelium of crypt of Lieberkuhn

text: wild type

text: small intestine

characteristic: sampling site

text: Mus musculus

text: male

characteristic: title


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC center name

text: public

text: ArrayExpress

characteristic: broker name

text: house mouse

characteristic: common name

characteristic: description

text: adult

characteristic: developmental stage

text: normal

characteristic: disease

text: Villin-Cre+; Lsd1f/f

characteristic: genotype

text: Mus musculus

text: Mus musculus

text: epithelium of intestinal villus

text: villin-induced Lsd1 homozygous knockout

text: small intestine

text: Mus musculus

text: female


characteristic: ENA-CHECKLIST

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: ArrayExpress

text: house mouse

text: adult

text: normal

text: Villin-Cre-; Lsd1f/f

text: Mus musculus

characteristic: organism

text: Mus musculus

text: epithelium of intestinal villus

characteristic: organism part

text: wild type

characteristic: phenotype

text: small intestine

text: Mus musculus

text: female

characteristic: sex

characteristic: strain


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC center name

text: public

characteristic: Submitter Id

characteristic: age

text: ArrayExpress

text: house mouse

characteristic: compound

text: adult

text: normal

text: Villin-Cre-; Lsd1f/+

characteristic: individual

text: Mus musculus

text: Mus musculus

text: epithelium of intestinal villus

text: wild type

text: small intestine

characteristic: sampling site

text: Mus musculus

text: female

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: ArrayExpress

characteristic: broker name

text: house mouse

characteristic: common name

characteristic: description

text: adult

characteristic: developmental stage

text: normal

characteristic: disease

text: Villin-Cre-; Lsd1f/+

characteristic: genotype

text: Mus musculus

text: Mus musculus

text: epithelium of intestinal villus

text: wild type

text: small intestine

text: Mus musculus

text: male


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC center name

text: public

characteristic: SRA accession

text: ArrayExpress

text: house mouse

text: Protocols: The proximal half of mouse small intestine was isolated and washed with ice-cold PBS until luminal contents were cleared. The intestine was opened longitudinally, villi scraped off and collected, after scraping remaining tissue was cut into ~2mm pieces. Collected villi were resuspended in cold PBS and filtered through a 70 μm cell strainer to remove cell debris. Afterwards a wash of PBS was performed to remove remaining debris and mucus. To collect the villi fraction the filter was inverted, eluted with PBS and centrifuged at 300 g, 5 minutes, 4°C. Crypts were isolated according to Sato and Clevers protocol, see reference below. Briefly, the 2mm intestinal fragments were washed 5 times with PBS. Tissue pieces were incubated with 2 mM EDTA in ice-cold PBS for 30-60 minutes with gentle rocking. The supernatant was removed, 20 mL of ice-cold PBS was added and the fragments were pipetted up and down. This washing step was repeated until the crypt fraction appeared under microscopic examination. The 1-3 consecutive crypt fractions were passed through a 70 μm cell strainer and collected into a FCS coated 50 mL tube. The crypts were spun down at 300 x g for 5 min and washed once in 10 mL ice cold PBS at 200 x g for 5 min. References:Sato, Toshiro and Hans Clevers (2013). “Primary Mouse Small Intestinal Epithelial Cell Cultures”. In:Epithelial Cell Culture Protocols: Second Edition. Ed. by Scott H. Randell and M. Leslie Fulcher. Methods in Molecular Biology. Totowa, NJ: Humana Press, pp. 319-328.isbn: 978-1-62703-125-7.doi:10.1007/978-1-62703-125-7_19.527url:https://doi.org/10.1007/978-1-62703-125-7_19. RNA was isolated with the RNeasy Plus Mini Kit (QIAGEN) Library preparation was done with NEB Next(R) Ultra(TM) RNA Library Prep Kit

text: adult

text: normal

text: Villin-Cre+; Lsd1f/f

text: Mus musculus

characteristic: organism

text: Mus musculus

text: epithelium of crypt of Lieberkuhn

characteristic: organism part

text: villin-induced Lsd1 homozygous knockout

characteristic: phenotype

text: small intestine

text: Mus musculus

text: male

characteristic: sex

characteristic: strain


characteristic: ENA-CHECKLIST

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: Submitter Id

characteristic: age

text: ArrayExpress

text: house mouse

text: adult

text: normal

text: Villin-Cre+; Lsd1f/f

characteristic: individual

text: Mus musculus

text: Mus musculus

text: epithelium of crypt of Lieberkuhn

text: villin-induced Lsd1 homozygous knockout

text: small intestine

characteristic: sampling site

text: Mus musculus

text: female

characteristic: title


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: public

text: ArrayExpress

characteristic: broker name

text: house mouse

characteristic: common name

characteristic: description

text: adult

characteristic: developmental stage

text: normal

characteristic: disease

text: Villin-Cre-; Lsd1f/f

characteristic: genotype

text: Mus musculus

text: Mus musculus

text: epithelium of crypt of Lieberkuhn

text: wild type

text: small intestine

text: Mus musculus

text: female


characteristic: ENA-CHECKLIST

characteristic: INSDC center name

characteristic: INSDC first public

text: public

characteristic: SRA accession

text: ArrayExpress

text: house mouse

text: adult

text: normal

text: Villin-Cre-; Lsd1f/f

text: Mus musculus

characteristic: organism

text: Mus musculus

text: epithelium of crypt of Lieberkuhn

characteristic: organism part

text: wild type

characteristic: phenotype

text: small intestine

text: Mus musculus

text: male

characteristic: sex

characteristic: strain


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: Submitter Id

characteristic: age

text: ArrayExpress

text: house mouse

text: adult

text: normal

text: Villin-Cre+; Lsd1f/f

characteristic: individual

text: Mus musculus

text: Mus musculus

text: epithelium of intestinal villus

text: villin-induced Lsd1 homozygous knockout

text: small intestine

characteristic: sampling site

text: Mus musculus

text: male

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: External Id

characteristic: INSDC center name

text: public

text: ArrayExpress

characteristic: broker name

text: house mouse

characteristic: common name

characteristic: description

text: adult

characteristic: developmental stage

text: normal

characteristic: disease

text: Villin-Cre+; Lsd1f/f

characteristic: genotype

text: Mus musculus

text: Mus musculus

text: epithelium of intestinal villus

text: villin-induced Lsd1 homozygous knockout

text: small intestine

text: Mus musculus

text: female


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: INSDC first public

text: public

characteristic: SRA accession

text: ArrayExpress

text: house mouse

text: adult

text: normal

text: Villin-Cre-; Lsd1f/f

text: Mus musculus

characteristic: organism

text: Mus musculus

text: epithelium of intestinal villus

characteristic: organism part

text: wild type

characteristic: phenotype

text: small intestine

text: Mus musculus

text: female

characteristic: sex

characteristic: strain


characteristic: ENA-CHECKLIST

characteristic: External Id

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: Submitter Id

characteristic: age

text: ArrayExpress

text: house mouse

text: adult

text: normal

text: Villin-Cre-; Lsd1f/f

characteristic: individual

text: Mus musculus

text: Mus musculus

text: epithelium of intestinal villus

text: wild type

text: small intestine

characteristic: sampling site

text: Mus musculus

text: male

characteristic: title


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: University of Strasbourg

characteristic: INSDC center name

text: public

tag: Namespace:University of Strasbourg

text: DSM 42138

text: Streptomyces bryophytorum DSM 42138/NEAU-HZ10 is a mesophilic bacterium that was isolated from moss

characteristic: description

text: China

characteristic: geographic location (country and/or sea)

text: Heilongjiang Province, Wuchang

characteristic: geographic location (region and locality)

text: Bryophyta

characteristic: host scientific name

text: Moss

text: 44° 15' N, 127° 54' E

text: Streptomyces bryophytorum

text: Streptomyces bryophytorum

text: Streptomyces bryophytorum DSM 42138 whole genome


text: INSTITUT PASTEUR

characteristic: INSDC first public

text: public

characteristic: SRA accession

characteristic: collecting institution

characteristic: collection date

text: Spain

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

characteristic: host age

text: Human

characteristic: host common name

text: diseased

characteristic: host health state

text: Homo sapiens

text: female

characteristic: host sex

characteristic: host subject id

characteristic: isolate

text: Echovirus E30

characteristic: organism

characteristic: receipt date

text: Echovirus E30

characteristic: virus identifier


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Melanoma Institute Australia

characteristic: INSDC center name

characteristic: INSDC last update

text: public

characteristic: INSDC status

tag: Namespace:Melanoma Institute Australia

characteristic: Submitter Id

text: human

characteristic: common name

characteristic: description

text: Homo sapiens

text: Homo sapiens

characteristic: title


characteristic: INSDC first public

text: public

characteristic: SRA accession

tag: Namespace:Institute of Molecular Microbiology and Biotechnology

characteristic: collection date

text: Amplicon sequencing of the microbial biofilm on polyethylene at Ems river.

text: water

characteristic: environment (biome)

text: river

characteristic: environment (feature)

text: polyethylene

characteristic: environment (material)

text: Germany

characteristic: geographic location (country and/or sea)

unit: m

characteristic: geographic location (depth)

characteristic: geographic location (elevation)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: metagenome

characteristic: investigation type

text: microbial mat/biofilm

characteristic: microbial mat/biofilm environmental package

text: metagenome

characteristic: project name

text: metagenome

text: Illumina MiSeq

characteristic: sequencing method

text: Ems river PE


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Institute of Molecular Microbiology and Biotechnology

characteristic: INSDC center name

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: Submitter Id

text: Amplicon sequencing of the microbial biofilm on polyethylene terephthalate at Ems river.

characteristic: description

text: water

text: river

text: polyethylene terephthalate

text: Germany

text: metagenome

text: microbial mat/biofilm

text: metagenome

characteristic: organism

text: metagenome

text: Illumina MiSeq

text: Ems river PET


characteristic: INSDC first public

text: public

characteristic: SRA accession

characteristic: collection date

text: Amplicon sequencing of the microbial biofilm on polystyrene at Ems river.

text: water

characteristic: environment (biome)

text: river

characteristic: environment (feature)

text: polystyrene

characteristic: environment (material)

text: Germany

characteristic: geographic location (country and/or sea)

characteristic: geographic location (depth)

characteristic: geographic location (elevation)

text: metagenome

text: microbial mat/biofilm

text: metagenome

text: metagenome

text: Illumina MiSeq

text: Ems river PS

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: public

text: Amplicon sequencing of the microbial biofilm on polyethylene at Ems lake.

text: water

text: lake

text: polyethylene

text: Germany

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: metagenome

characteristic: investigation type

text: microbial mat/biofilm

characteristic: microbial mat/biofilm environmental package

text: metagenome

characteristic: project name

text: metagenome

text: Illumina MiSeq

characteristic: sequencing method

text: Ems lake PE


characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

characteristic: collection date

text: Amplicon sequencing of the microbial biofilm on polyethylene terephthalate at Ems lake.

characteristic: description

text: water

characteristic: environment (biome)

text: lake

text: polyethylene terephthalate

text: Germany

text: metagenome

text: microbial mat/biofilm

text: metagenome

characteristic: organism

text: metagenome

text: Illumina MiSeq

text: Ems lake PET


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: public

text: Amplicon sequencing of the microbial biofilm on polystyrene at Ems lake.

text: water

text: lake

characteristic: environment (feature)

text: polystyrene

characteristic: environment (material)

text: Germany

characteristic: geographic location (country and/or sea)

characteristic: geographic location (depth)

characteristic: geographic location (elevation)

text: metagenome

text: microbial mat/biofilm

text: metagenome

text: metagenome

text: Illumina MiSeq

text: Ems lake PS

characteristic: title


characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: Amplicon sequencing of the microbial biofilm on polyethylene at Rieselfelder.

text: water

text: lake

text: polyethylene

text: Germany

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: metagenome

characteristic: investigation type

text: microbial mat/biofilm

characteristic: microbial mat/biofilm environmental package

text: metagenome

characteristic: project name

text: metagenome

text: Illumina MiSeq

characteristic: sequencing method

text: Rieselfelder PE


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: public

characteristic: SRA accession

characteristic: Submitter Id

characteristic: collection date

text: Amplicon sequencing of the microbial biofilm on polyethylene terephthalate at Rieselfelder.

characteristic: description

text: water

characteristic: environment (biome)

text: lake

text: polyethylene terephthalate

text: Germany

text: metagenome

text: microbial mat/biofilm

text: metagenome

characteristic: organism

text: metagenome

text: Illumina MiSeq

text: Rieselfelder PET


characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: Amplicon sequencing of the microbial biofilm on polystyrene at Rieselfelder.

text: water

text: lake

characteristic: environment (feature)

text: polystyrene

characteristic: environment (material)

text: Germany

characteristic: geographic location (country and/or sea)

characteristic: geographic location (depth)

characteristic: geographic location (elevation)

text: metagenome

text: microbial mat/biofilm

text: metagenome

text: metagenome

text: Illumina MiSeq

text: Rieselfelder PS

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: public

tag: Namespace:Centrum Medyczne Ksztalcenia Podyplomowego

text: house mouse

characteristic: common name

text: eko

characteristic: genotype

text: Mus musculus

text: Mus musculus


text: Centrum Medyczne Ksztalcenia Podyplomowego

text: public

characteristic: SRA accession

characteristic: Submitter Id

text: house mouse

text: eko

text: Mus musculus

characteristic: organism

text: Mus musculus


characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: house mouse

text: CONTROL

text: Mus musculus

text: Mus musculus


text: UTRECHT UNIVERSITY

text: public

characteristic: INSDC status

tag: Namespace:UTRECHT UNIVERSITY

text: Illumina sequencing of 21S00955-1

characteristic: description

text: Netherlands

text: bovine

text: Campylobacter fetus

text: Campylobacter fetus

text: Illumina sequencing of 21S00955-1


text: IRSICAIXA

text: public

text: V3-V4 16s RNA gene region from tissue samples of colorectal cancer patients

text: human gut metagenome

text: human gut metagenome


text: IRSICAIXA

text: public

text: human gut metagenome

text: human gut metagenome

text: CNT-PCR


text: Northumbria University / South Tees Hospitals NHS Foundation Trust / North Cumbria Integrated Care NHS Foundation Trust / North Tees and Hartlepool NHS Foundation Trust / Newcastle Hospitals NHS Foundation Trust

text: public

text: COVID-19 Genomics UK Consortium

characteristic: broker name

characteristic: collecting institution

characteristic: collection date

text: not provided

characteristic: collector name

text: not provided

characteristic: definition for seropositive sample

text: United Kingdom

characteristic: geographic location (country and/or sea)

text: England

characteristic: geographic location (region and locality)

text: not provided

characteristic: host common name

text: not provided

characteristic: host health state

text: Human

characteristic: host scientific name

text: not provided

characteristic: host sex

text: not provided

characteristic: host subject id

text: not provided

characteristic: isolate

text: Severe acute respiratory syndrome coronavirus 2

characteristic: receipt date

text: active surveillance in response to outbreak

characteristic: sample capture status

text: not provided

characteristic: serotype (required for a seropositive sample)

text: not provided

characteristic: virus identifier


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: University of Birmingham

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

tag: Namespace:University of Birmingham

characteristic: Submitter Id

text: COVID-19 Genomics UK Consortium

characteristic: broker name

text: University of Birmingham

text: not provided

text: not provided

text: United Kingdom

text: England

text: not provided

text: not provided

text: Human

text: not provided

text: not provided

text: not provided

characteristic: organism

text: not provided

characteristic: title

text: not provided


text: public

tag: Namespace:Virology Department, Sheffield Teaching Hospitals NHS Foundation Trust/Department of Infection, Immunity and Cardiovascular Disease, The Medical School, University of Sheffield

text: COVID-19 Genomics UK Consortium

characteristic: collecting institution

characteristic: collection date

text: not provided

characteristic: collector name

text: not provided

characteristic: definition for seropositive sample

text: United Kingdom

characteristic: geographic location (country and/or sea)

text: England

characteristic: geographic location (region and locality)

text: not provided

characteristic: host common name

text: not provided

characteristic: host health state

text: Human

characteristic: host scientific name

text: not provided

characteristic: host sex

text: not provided

characteristic: host subject id

text: not provided

characteristic: isolate

characteristic: receipt date

text: not provided

text: not provided


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Virology Department, Sheffield Teaching Hospitals NHS Foundation Trust/Department of Infection, Immunity and Cardiovascular Disease, The Medical School, University of Sheffield

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: COVID-19 Genomics UK Consortium

text: not provided

text: not provided

text: United Kingdom

text: England

text: not provided

text: not provided

text: Human

text: not provided

text: not provided

text: not provided

characteristic: sample capture status

text: not provided

characteristic: serotype (required for a seropositive sample)

text: not provided

characteristic: virus identifier


COG-UK/BIRM-BCFDJU

text: University of Birmingham

text: public

text: COG-UK/BIRM-BCFDJU

text: COVID-19 Genomics UK Consortium

characteristic: broker name

text: University of Birmingham

characteristic: collecting institution

characteristic: collection date

text: not provided

characteristic: collector name

text: not provided

characteristic: definition for seropositive sample

text: United Kingdom

characteristic: geographic location (country and/or sea)

text: England

characteristic: geographic location (region and locality)

text: not provided

characteristic: host common name

text: not provided

characteristic: host health state

text: Human

characteristic: host scientific name

text: not provided

characteristic: host sex

text: not provided

text: not provided

characteristic: organism

text: not provided

text: COG-UK/BIRM-BCFDJU

characteristic: title

text: not provided


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: THE RAMACIOTTI CENTRE, NSW, AUSTRALIA

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

tag: Namespace:THE RAMACIOTTI CENTRE, NSW, AUSTRALIA

characteristic: Submitter Id

text: human

characteristic: common name

text: Homo sapiens

text: Homo sapiens

text: Human K562


text: UNSW Sydeny, School of Medical Sciences

text: public

tag: Namespace:UNSW Sydeny, School of Medical Sciences

text: Norway rat

text: Rattus norvegicus

text: Rattus norvegicus

text: Fecal


text: Universite Toulouse III - Paul Sabatier

text: public

tag: Namespace:Universite Toulouse III - Paul Sabatier

characteristic: collection date

text: midwife toad

text: mountain habitat

characteristic: environment (biome)

text: lake

characteristic: environment (feature)

text: water

characteristic: environment (material)

text: France

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: host-associated

characteristic: host-associated environmental package

characteristic: investigation type

text: Alytes obstetricans

text: tadpoles skin microbiome

characteristic: project name

text: Alytes obstetricans

text: Next Generation Sequencing Illumina

characteristic: sequencing method

characteristic: target gene


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Quadram Institute Bioscience

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: COVID-19 Genomics UK Consortium

characteristic: broker name

text: Quadram Institute Bioscience

characteristic: collecting institution

text: not provided

characteristic: collector name

text: not provided

characteristic: definition for seropositive sample

text: United Kingdom

text: England

characteristic: geographic location (region and locality)

text: not provided

characteristic: host common name

text: not provided

characteristic: host health state

text: Human

characteristic: host scientific name

text: not provided

characteristic: host sex

text: not provided

characteristic: host subject id

text: not provided

characteristic: isolate

characteristic: organism

characteristic: receipt date

characteristic: sample capture status

text: not provided

characteristic: serotype (required for a seropositive sample)

characteristic: title

text: not provided

characteristic: virus identifier


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: NEWCASTLE UNIVERSITY, UK

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

tag: Namespace:NEWCASTLE UNIVERSITY, UK

characteristic: Submitter Id

text: human

characteristic: common name

text: Homo sapiens

text: Homo sapiens

text: Wt U2OS


tag: attribute

text: NEWCASTLE UNIVERSITY, UK

text: public

text: human

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: Wt U2OS with CHK1i


text: NEWCASTLE UNIVERSITY, UK

text: public

text: human

text: Homo sapiens

text: Homo sapiens

text: CHK1i resistant U2OS


text: NEWCASTLE UNIVERSITY, UK

text: public

text: human

text: Homo sapiens

text: Homo sapiens

text: CHK1i resistant U2OS with CHK1i


text: NEWCASTLE UNIVERSITY, UK

text: public

text: house mouse

text: Mus musculus

text: Mus musculus

text: WT


text: NEWCASTLE UNIVERSITY, UK

text: public

text: house mouse

text: Mus musculus

text: Mus musculus

text: WT with CHK1i


text: NEWCASTLE UNIVERSITY, UK

text: public

text: house mouse

text: Mus musculus

text: Mus musculus


text: NEWCASTLE UNIVERSITY, UK

text: public

text: house mouse

text: Mus musculus

text: Mus musculus

text: T505A with CHK1i


text: NEWCASTLE UNIVERSITY, UK

text: public

text: house mouse

text: Mus musculus

text: Mus musculus

text: cREL


text: NEWCASTLE UNIVERSITY, UK

text: public

text: house mouse

text: Mus musculus

text: Mus musculus

text: cREL with CHK1i


text: public

tag: Namespace:Northumbria University / South Tees Hospitals NHS Foundation Trust / North Cumbria Integrated Care NHS Foundation Trust / North Tees and Hartlepool NHS Foundation Trust / Newcastle Hospitals NHS Foundation Trust

text: COVID-19 Genomics UK Consortium

characteristic: broker name

characteristic: collecting institution

characteristic: collection date

text: not provided

characteristic: collector name

text: not provided

characteristic: definition for seropositive sample

text: United Kingdom

characteristic: geographic location (country and/or sea)

text: England

characteristic: geographic location (region and locality)

text: not provided

characteristic: host common name

text: not provided

characteristic: host health state

text: Human

characteristic: host scientific name

text: not provided

characteristic: host sex

text: not provided

characteristic: host subject id

text: not provided

characteristic: isolate

characteristic: receipt date

text: not provided

text: not provided


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

tag: Namespace:Originating lab: Wales Specialist Virology Centre Sequencing lab: Pathogen Genomics Unit

characteristic: Submitter Id

text: COVID-19 Genomics UK Consortium

text: not provided

text: not provided

text: United Kingdom

text: Wales

text: not provided

text: not provided

text: Human

text: not provided

text: not provided

text: not provided

characteristic: sample capture status

text: not provided

characteristic: serotype (required for a seropositive sample)

characteristic: title

text: not provided

characteristic: virus identifier


text: public

tag: Namespace:State Key Laboratory of Crop Stress Adaptation and Improvement, State Key Laboratory of Cotton Biology, School of Life Sciences, Henan University

characteristic: age

text: ArrayExpress

characteristic: broker name

text: thale cress

characteristic: common name

characteristic: cultivar

text: Protocols: 7-day-old plant seedlings were collected and flash frozen on liquid nitrogen, and total RNA was harvested using Trizol reagent. Seedlings were grown on 1/2 MS medium at 22 °C under 12/12 h day/night cycles, and the intensity of the light was set at 150 μE. TRIZOL reagent was used to extract the total RNA of the plant samples. 1)There are two methods to treat total RNA.Oligo(dT) magnetic beads are used to selec tmRNA with poly A tail,or hybridize the rRNA with DNA probe and digest the DNA/RNA hybrid strand,followed by DNaseI reaction to remove DNA probe. Then obtain the target RNA after purification.2)Fragment the target RNA and reverse transcription to double-strand cDNA (dscDNA)by N6 random primer.3)Endrepair the dscDNA with phosphateat 5'end and stickiness'A'at 3'end,then ligate and adapt or with stickiness 'T'at3'end to the dscDNA.4)Two specific primers are used to amplify the ligation product.5)Denature the PCR product by heat and the single strand DNA is cyclized by splint oligo and DNA ligase.6)Perform sequencing on prepared library.

characteristic: description

text: seedling development stage

characteristic: developmental stage

text: amiR-TSB1 transgenic

characteristic: genotype

text: Arabidopsis thaliana

characteristic: organism

text: Arabidopsis thaliana

text: whole organism

characteristic: organism part

text: Arabidopsis thaliana


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: State Key Laboratory of Crop Stress Adaptation and Improvement, State Key Laboratory of Cotton Biology, School of Life Sciences, Henan University

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: ArrayExpress

text: thale cress

text: seedling development stage

text: amiR-TSB1 transgenic

text: Arabidopsis thaliana

text: Arabidopsis thaliana

text: whole organism

text: Arabidopsis thaliana


text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: ArrayExpress

text: thale cress

text: seedling development stage

text: wild type genotype

text: Arabidopsis thaliana

text: Arabidopsis thaliana

text: whole organism

text: Arabidopsis thaliana

characteristic: title


characteristic: GISAID Accession ID

text: University Hospital Basel

text: public

text: hCoV-19/Switzerland/SO-UHB-42850063/2021

tag: Namespace:University Hospital Basel

text: SIB

characteristic: broker name

text: Synlab Suisse SA, Luzern, Switzerland

characteristic: collecting institution

characteristic: collection date

text: Tim Roloff, Madlen Stange, Helena MB Seth-Smith, Alfredo Mari, Karoline Leuzinger, Julia Bielicki, Manuel Battegay, Hans Hirsch, Adrian Egli

characteristic: collector name

text: Switzerland

characteristic: geographic location (country and/or sea)

text: SO

characteristic: geographic location (region and locality)

text: Human

characteristic: host common name

text: restricted access

characteristic: host health state

text: Homo sapiens

characteristic: host scientific name

text: restricted access

characteristic: host sex

text: restricted access

characteristic: host subject id

characteristic: isolate

characteristic: sample capture status


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

tag: Namespace:Center for Integrative Genetics (CIGENE), Department of Animal and Aquacultural Sciences, Faculty for BioSciences, The Norwegian University of Life Sciences (NMBU)

unit: week

characteristic: age

text: ArrayExpress

text: Atlantic salmon

characteristic: common name

text: Protocols: This experiment was set up to evaluate the effect of the duration of a short photoperiod (winter-like conditions, 8 hours light, 14 hours dark) on the smolt transcriptome in liver and gill. Fish were kept at constant light before fish were split between treatment tank or control tanks. Treatment tanks either experienced 2 weeks of short photoperiod or 8 weeks of short photoperiod. The control fish were kept in constant winter-like conditions. After winter, the fish were brought back to constant light for 4 weeks. Sampling was done before transition to short photoperiod, at the end of winter period and four weeks after transition back to constant light. Control fish were sampled at the same time points as the treatment group. Protocol for the RNeasy Plus Universal Kit (QIAGEN) TruSeq Stranded mRNA Sample Prep HS Protocol (Illumina)

characteristic: description

text: Salmo salar

characteristic: organism

text: Salmo salar

text: gill

characteristic: organism part

text: LP

characteristic: photoperiod

text: Salmo salar

text: Aquagen

characteristic: strain

text: Pre-winter

characteristic: time point


characteristic: ENA-CHECKLIST

text: Center for Integrative Genetics (CIGENE), Department of Animal and Aquacultural Sciences, Faculty for BioSciences, The Norwegian University of Life Sciences (NMBU)

text: public

characteristic: Submitter Id

text: ArrayExpress

characteristic: broker name

text: Atlantic salmon

text: Salmo salar

text: Salmo salar

text: gill

text: LP

text: Salmo salar

text: Aquagen

text: Pre-winter

characteristic: title


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC center name

text: public

text: ArrayExpress

text: Atlantic salmon

text: Salmo salar

text: Salmo salar

text: gill

text: SP

text: Salmo salar

text: Aquagen

text: 2WW spring control


characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: ArrayExpress

text: Atlantic salmon

text: Salmo salar

text: Salmo salar

text: gill

text: LP

text: Salmo salar

text: Aquagen

text: 2WW spring


text: public

characteristic: age

text: ArrayExpress

text: Atlantic salmon

characteristic: common name

characteristic: description

text: Salmo salar

characteristic: organism

text: Salmo salar

text: gill

text: SP

text: Salmo salar

text: Aquagen

text: winter 8 weeks


text: public

text: ArrayExpress

text: Atlantic salmon

text: Salmo salar

text: Salmo salar

text: gill

characteristic: organism part

text: SP

characteristic: photoperiod

text: Salmo salar

text: Aquagen

characteristic: strain

text: Winter first week

characteristic: time point


characteristic: ENA-CHECKLIST

text: public

characteristic: Submitter Id

text: ArrayExpress

characteristic: broker name

text: Atlantic salmon

text: Salmo salar

text: Salmo salar

text: gill

text: SP

text: Salmo salar

text: Aquagen

text: 8WW spring control

characteristic: title


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC center name

text: public

text: ArrayExpress

text: Atlantic salmon

text: Salmo salar

text: Salmo salar

text: gill

text: LP

text: Salmo salar

text: Aquagen

text: 8 WW spring


characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: ArrayExpress

text: Atlantic salmon

text: Salmo salar

text: Salmo salar

text: gill

text: SP

text: Salmo salar

text: Aquagen

text: Winter second week


text: public

characteristic: age

text: ArrayExpress

text: Atlantic salmon

characteristic: common name

characteristic: description

text: Salmo salar

characteristic: organism

text: Salmo salar

text: liver

text: LP

text: Salmo salar

text: Aquagen

text: Pre-winter


text: public

text: ArrayExpress

text: Atlantic salmon

text: Salmo salar

text: Salmo salar

text: liver

characteristic: organism part

text: SP

characteristic: photoperiod

text: Salmo salar

text: Aquagen

characteristic: strain

text: 2WW spring control

characteristic: time point


characteristic: ENA-CHECKLIST

text: public

characteristic: Submitter Id

text: ArrayExpress

characteristic: broker name

text: Atlantic salmon

text: Salmo salar

text: Salmo salar

text: liver

text: LP

text: Salmo salar

text: Aquagen

text: 2WW spring

characteristic: title


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC center name

text: public

text: ArrayExpress

text: Atlantic salmon

text: Salmo salar

text: Salmo salar

text: liver

text: SP

text: Salmo salar

text: Aquagen

text: winter 8 weeks


characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: ArrayExpress

text: Atlantic salmon

text: Salmo salar

text: Salmo salar

text: liver

text: SP

text: Salmo salar

text: Aquagen

text: Winter first week


text: public

characteristic: age

text: ArrayExpress

text: Atlantic salmon

characteristic: common name

characteristic: description

text: Salmo salar

characteristic: organism

text: Salmo salar

text: liver

text: SP

text: Salmo salar

text: Aquagen

text: 8WW spring control


text: public

text: ArrayExpress

text: Atlantic salmon

text: Salmo salar

text: Salmo salar

text: liver

characteristic: organism part

text: LP

characteristic: photoperiod

text: Salmo salar

text: Aquagen

characteristic: strain

text: 8 WW spring

characteristic: time point


characteristic: ENA-CHECKLIST

text: public

characteristic: Submitter Id

text: ArrayExpress

characteristic: broker name

text: Atlantic salmon

text: Salmo salar

text: Salmo salar

text: liver

text: SP

text: Salmo salar

text: Aquagen

text: Winter second week

characteristic: title


E-MTAB-10529:ATDC5 t=0 sample 1

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC center name

text: public

text: E-MTAB-10529:ATDC5 t=0 sample 1

tag: Namespace:Laboratory for Experimental Orthopedics | Department of Orthopedic Surgery | Maastricht UMC+, Maastricht, the Netherlands

text: ArrayExpress

text: chondrocyte

text: house mouse

text: Protocols: Cells were harvested for RNA isolation with TRIzol reagent (Invitrogen). ATDC5 cells (RIKEN BRC, Japan) were cultured in a humidified atmosphere at 37oC, 5% CO2 in proliferation medium (DMEM/F12 (Invitrogen, Carlsbad, CA, USA), 5% FCS (Sigma-Aldrich, St. Louis, MO, USA) and 1% antibiotic/antimycotic (Invitrogen). Cells were plated at 6,400 cells/cm2. After 24 hours chondrogenic differentiation was initiated by changing the medium to differentiation medium (proliferation medium supplemented with 10 μg/ml insulin (Sigma-Aldrich), 10 μg/ml transferrin (Roche, Basel, Switzerland) and 30 nM sodium selenite (Sigma-Aldrich)). Differentiation medium was refreshed every two days for the first 10 days, and each day after day 10, until cells were harvested at indicated time points. RNA was isolated from the TRIzol samples by collecting the aqueous phase after phase separation. RNA was precipitated with isopropanol (30 minutes, -80oC) and centrifuged for 30 minutes at 20,000 x g, 4oC. RNA pellets were washed with 80% ethanol and potential DNA contamination was removed by DNase I (Roche) treatment (1 hour, 37oC). After subsequent ethanol precipitation, RNA was dissolved in 15 μL DNase/RNase free water (Eurogentec, Seraing, Belgium). RNA quantity and purity were determined spectrophotometrically (Biodrop, Isogen Life Sciences, Utrecht, the Netherlands). SnoRNA expression during ATDC5 differentiation was analyzed by small RNA Next Generation Sequencing (NGS) of samples acquired from day 0 (progenitor stage), day 7 (chondrogenic stage) and day 14 (hypertrophic stage). Total RNA was isolated and after library preparation (NEBNext library generation kit, New England Biolabs (NEB), Ipswich, MA, USA) inserts <200 nt were selected using an automated gel cutter. One µg of total RNA was converted into NGS libraries using the NEBNext library generation kit (NEB), using a protocol (Exiqon, Vedbæk, Denmark) to increase the 5’ and 3’ ligation of modified small RNA ends. Each individual RNA sample had adapters ligated to its 3’ and 5’ ends and was converted to cDNA. Then, the cDNA was pre-amplified with specific primers containing sample specific indexes (Exiqon). After a 15 cycle pre-PCR the libraries were purified on QiaQuick column (Qiagen, Hilden, Germany) and the insert efficiency was evaluated on a Bioanalyzer 2100 instrument (Agilent, Santa Clara, CA, USA) on a high sensitivity DNA chip (Agilent). The cDNA libraries were size fractioned on a LabChip XT (Caliper Life Sciences, Waltham, MA, USA) and 15-200 bp inserts were excised according to the manufacturer’s protocol (Caliper). Samples were then quantified using qPCR and a concentration standard. Based on the quality of the inserts and the concentration measurements the libraries were pooled in equimolar concentrations. The library pool was quantified with qPCR and an optimal concentration of the library pool (Illumina) was used to generate the clusters on the surface of a flowcell before sequencing (using v3 sequencing methodology according to the manufacturer’s instructions).

text: mouse postnatal

characteristic: developmental stage

text: baseline

characteristic: growth condition

text: Mus musculus

text: Mus musculus

text: biological replicate

characteristic: replicate

text: Mus musculus

text: ATDC5 t=0 sample 1


E-MTAB-10529:ATDC5 t=0 sample 2

text: Laboratory for Experimental Orthopedics | Department of Orthopedic Surgery | Maastricht UMC+, Maastricht, the Netherlands

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-10529:ATDC5 t=0 sample 2

text: ArrayExpress

text: chondrocyte

text: house mouse

characteristic: common name

characteristic: description

text: mouse postnatal

text: baseline

text: Mus musculus

text: Mus musculus

text: biological replicate

text: Mus musculus

text: ATDC5 t=0 sample 2


E-MTAB-10529:ATDC5 t=0 sample 3

characteristic: ENA-CHECKLIST

text: public

text: E-MTAB-10529:ATDC5 t=0 sample 3

text: ArrayExpress

text: chondrocyte

text: house mouse

text: mouse postnatal

text: baseline

text: Mus musculus

characteristic: organism

text: Mus musculus

text: biological replicate

text: Mus musculus

text: ATDC5 t=0 sample 3


E-MTAB-10529:ATDC5 t=14 sample 1

text: public

text: E-MTAB-10529:ATDC5 t=14 sample 1

characteristic: Submitter Id

text: ArrayExpress

characteristic: broker name

text: chondrocyte

text: house mouse

text: mouse postnatal

text: differentiation

text: Mus musculus

text: Mus musculus

text: biological replicate

text: Mus musculus

text: ATDC5 t=14 sample 1


E-MTAB-10529:ATDC5 t=14 sample 2

characteristic: ENA-FIRST-PUBLIC

text: public

text: E-MTAB-10529:ATDC5 t=14 sample 2

text: ArrayExpress

text: chondrocyte

text: house mouse

text: mouse postnatal

text: differentiation

text: Mus musculus

text: Mus musculus

text: biological replicate

text: Mus musculus

text: ATDC5 t=14 sample 2

characteristic: title


E-MTAB-10529:ATDC5 t=4 sample 3

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: public

text: E-MTAB-10529:ATDC5 t=4 sample 3

text: ArrayExpress

text: chondrocyte

text: house mouse

text: mouse postnatal

text: differentiation

text: Mus musculus

text: Mus musculus

text: biological replicate

text: Mus musculus

text: ATDC5 t=4 sample 3


E-MTAB-10529:ATDC5 t=7 sample 2

characteristic: INSDC center name

text: public

text: E-MTAB-10529:ATDC5 t=7 sample 2

text: ArrayExpress

text: chondrocyte

text: house mouse

text: mouse postnatal

characteristic: developmental stage

text: differentiation

text: Mus musculus

text: Mus musculus

text: biological replicate

text: Mus musculus

text: ATDC5 t=7 sample 2


E-MTAB-10529:ATDC5 t=7 sample 1

text: public

text: E-MTAB-10529:ATDC5 t=7 sample 1

text: ArrayExpress

text: chondrocyte

text: house mouse

text: mouse postnatal

text: differentiation

characteristic: growth condition

text: Mus musculus

text: Mus musculus

text: biological replicate

characteristic: replicate

text: Mus musculus

text: ATDC5 t=7 sample 1


E-MTAB-10529:ATDC5 t=7 sample 3

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: E-MTAB-10529:ATDC5 t=7 sample 3

text: ArrayExpress

text: chondrocyte

text: house mouse

text: mouse postnatal

text: differentiation

text: Mus musculus

text: Mus musculus

text: biological replicate

text: Mus musculus

text: ATDC5 t=7 sample 3


text: public

characteristic: INSDC status

characteristic: SRA accession

text: COVID-19 Genomics UK Consortium

characteristic: collecting institution

characteristic: collection date

text: not provided

characteristic: collector name

text: not provided

characteristic: definition for seropositive sample

text: United Kingdom

characteristic: geographic location (country and/or sea)

text: England

characteristic: geographic location (region and locality)

text: not provided

characteristic: host common name

text: not provided

characteristic: host health state

text: Human

characteristic: host scientific name

text: not provided

characteristic: host sex

text: not provided

characteristic: host subject id

text: not provided

characteristic: isolate

characteristic: receipt date

characteristic: sample capture status

text: not provided

characteristic: serotype (required for a seropositive sample)

text: not provided

characteristic: virus identifier


COG-UK/PHWC-PYFGOI

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Originating lab: Wales Specialist Virology Centre Sequencing lab: Pathogen Genomics Unit

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: COG-UK/PHWC-PYFGOI

characteristic: Submitter Id

text: COVID-19 Genomics UK Consortium

characteristic: broker name

text: not provided

text: not provided

text: United Kingdom

text: Wales

text: not provided

text: not provided

text: Human

text: not provided

text: not provided

text: not provided

characteristic: organism

text: not provided

text: COG-UK/PHWC-PYFGOI

characteristic: title

text: not provided


text: Quadram Institute Bioscience

text: public

tag: Namespace:Quadram Institute Bioscience

text: COVID-19 Genomics UK Consortium

text: Quadram Institute Bioscience

characteristic: collecting institution

characteristic: collection date

text: not provided

characteristic: collector name

text: not provided

characteristic: definition for seropositive sample

text: United Kingdom

characteristic: geographic location (country and/or sea)

text: England

characteristic: geographic location (region and locality)

text: not provided

characteristic: host common name

text: not provided

characteristic: host health state

text: Human

characteristic: host scientific name

text: not provided

characteristic: host sex

text: not provided

characteristic: host subject id

text: not provided

characteristic: isolate

characteristic: receipt date

text: not provided

text: not provided


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-10519:FCA55_Male_antenna_adult_5dWT_Luo_sample2_S23

tag: Namespace:VIB Center for Brain & Disease Research, KU Leuven, Leuven 3000, Belgium

characteristic: Submitter Id

characteristic: age

text: ArrayExpress

text: fruit fly

characteristic: common name

text: Protocols: tissue dissection 10x Genomics v3 chemistry 10x Genomics v3 chemistry

characteristic: description

text: adult

characteristic: developmental stage

text: wild type genotype

characteristic: genotype

characteristic: individual

text: Drosophila melanogaster

text: Drosophila melanogaster

text: antenna

characteristic: organism part

text: Drosophila melanogaster

text: male

characteristic: sex

characteristic: strain


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: VIB Center for Brain & Disease Research, KU Leuven, Leuven 3000, Belgium

text: public

text: E-MTAB-10519:FCA55_Male_antenna_adult_5dWT_Luo_sample2_S29

text: ArrayExpress

characteristic: broker name

text: fruit fly

text: adult

text: wild type genotype

text: Drosophila melanogaster

characteristic: organism

text: Drosophila melanogaster

text: antenna

text: Drosophila melanogaster

text: male

characteristic: title


characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-10519:FCA55_Male_antenna_adult_5dWT_Luo_sample2_S33

text: ArrayExpress

text: fruit fly

text: adult

text: wild type genotype

text: Drosophila melanogaster

text: Drosophila melanogaster

text: antenna

text: Drosophila melanogaster

text: male


text: public

text: E-MTAB-10519:FCA56_Female_antenna_adult_5dWT_Luo_sample2_S52

characteristic: Submitter Id

characteristic: age

text: ArrayExpress

text: fruit fly

characteristic: common name

characteristic: description

text: adult

characteristic: developmental stage

text: wild type genotype

characteristic: genotype

text: Drosophila melanogaster

text: Drosophila melanogaster

text: antenna

text: Drosophila melanogaster

text: female


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: public

text: E-MTAB-10519:FCA56_Female_antenna_adult_5dWT_Luo_sample2_S53

text: ArrayExpress

text: fruit fly

text: adult

text: wild type genotype

characteristic: individual

text: Drosophila melanogaster

text: Drosophila melanogaster

text: antenna

characteristic: organism part

text: Drosophila melanogaster

text: female

characteristic: sex

characteristic: strain


characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC center name

text: public

text: E-MTAB-10519:FCA56_Female_antenna_adult_5dWT_Luo_sample2_S54

text: ArrayExpress

characteristic: broker name

text: fruit fly

text: adult

text: wild type genotype

text: Drosophila melanogaster

characteristic: organism

text: Drosophila melanogaster

text: antenna

text: Drosophila melanogaster

text: female

characteristic: title


characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-10519:FCA43_Male_antenna_adult_5dWT_Luo_sample1_S58

characteristic: Submitter Id

characteristic: age

text: ArrayExpress

text: fruit fly

text: adult

text: wild type genotype

text: Drosophila melanogaster

text: Drosophila melanogaster

text: antenna

text: Drosophila melanogaster

text: male