E-MTAB-12447:Wild-type 2

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: E-MTAB-12447:Wild-type 2

text: ArrayExpress

text: house mouse

text: adult

text: normal

text: wild type genotype

text: not applicable

text: Mus musculus

text: Mus musculus

text: bone marrow

characteristic: organism part

text: Mus musculus

characteristic: strain

text: Wild-type 2


E-MTAB-12447:Wild-type 3

status: PUBLIC

tag: attribute

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-12447:Wild-type 3

tag: Namespace:Biotechnology and Biomedicine Center of the Academy of Sciences and Charles University in Vestec (BIOCEV); First Faculty of Medicine; Charles University, Czech Republic

characteristic: Submitter Id

unit: week

characteristic: age

text: ArrayExpress

characteristic: broker name

text: hematopoietic multipotent progenitor cell

text: house mouse

characteristic: common name

text: Protocols: A single cell suspension of bone marrow from 6 to 8-week-old mice were obtained by flushing tibias and femurs with 1 ml ice-cold Flow Cytometry Buffer (FCB, 1x PBS with 2mM EDTA and 0.5+ACU- biotin-free BSA) using 22-gauge needles. Bone marrow hematopoietic c-kit progenitors were enriched by BD Aria II SORP cell sorter using fluorescence-activated cell sorting with anti-CD117-BV421, anti-Sca1-PE, and anti-lineage (Ter119, Gr1, Mac1, B220, Cd3e) antibody cocktail. Total RNA from FACS-sorted hematopoietic cells was isolated using TRIzol Reagent (Invitrogen) following the manufacturer's RNA isolation protocol. For preparation of NGS libraries polyadenylated mRNA from FASC-sorted c-Kit cells enriched from starting material of 100ng total RNA was processed utilizing NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (New England Biolabs, MA, USA).

characteristic: description

text: adult

characteristic: developmental stage

text: normal

characteristic: disease

text: wild type genotype

characteristic: genotype

characteristic: individual

text: not applicable

characteristic: isolate

text: Mus musculus

characteristic: organism

text: Mus musculus

text: bone marrow

text: Mus musculus

text: Wild-type 3

characteristic: title


E-MTAB-12447:Wild-type 4

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: Biotechnology and Biomedicine Center of the Academy of Sciences and Charles University in Vestec (BIOCEV); First Faculty of Medicine; Charles University, Czech Republic

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: E-MTAB-12447:Wild-type 4

text: ArrayExpress

text: house mouse

text: adult

text: normal

text: wild type genotype

text: not applicable

text: Mus musculus

text: Mus musculus

text: bone marrow

characteristic: organism part

text: Mus musculus

characteristic: strain

text: Wild-type 4


E-MTAB-12448:Rps19R67∆/R67∆ 1

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-12448:Rps19R67∆/R67∆ 1

characteristic: Submitter Id

text: embryonic day 14.5

unit: day

characteristic: age

text: ArrayExpress

characteristic: broker name

text: house mouse

text: Protocols: Fetal liver from embryos from timed crossings of mating pairs of appropriate genotypes were harvested 14 days after detection of plugs (E14.5). Pregnant females were euthanized and they embryos extracted in ice-cold PBS. Fetal livers were collected in PBS and dissolved by pipetting and small aliquot was used for preparation of RNA in Trizol reagent within 1 hour after extraction of mouse embryos. Total RNA from freshly harvested fetal livers was isolated with Trizol reagent following manufacturer's protocol. 1µg of DNase I-treated RNA isolated from treated cells was used for poly-A mRNA isolation with the NEBNext Poly(A) mRNA Magnetic Isolation Module. Paired-end libraries were prepared using the NEBNext Ultra II Directional RNA Library Kit with NEBNext multiplex index oligos for Illumina (Dual Index Primers Set 1) (New England Biolabs).

text: embryo

text: Diamond-Blackfan anemia

text: not applicable

text: Mus musculus

text: Mus musculus

text: liver

text: Mus musculus

text: Rps19R67∆/R67∆ 1


E-MTAB-12448:Rps19R67∆/R67∆ 2

text: public

text: E-MTAB-12448:Rps19R67∆/R67∆ 2

text: embryonic day 14.5

text: ArrayExpress

text: house mouse

characteristic: common name

characteristic: description

text: embryo

characteristic: developmental stage

text: Diamond-Blackfan anemia

characteristic: disease

characteristic: genotype

characteristic: individual

text: not applicable

characteristic: isolate

text: Mus musculus

text: Mus musculus

text: liver

text: Mus musculus

text: Rps19R67∆/R67∆ 2


E-MTAB-12448:Rps19R67∆/R67∆ 3

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: E-MTAB-12448:Rps19R67∆/R67∆ 3

text: embryonic day 14.5

text: ArrayExpress

text: house mouse

text: embryo

text: Diamond-Blackfan anemia

text: not applicable

text: Mus musculus

characteristic: organism

text: Mus musculus

text: liver

text: Mus musculus

text: Rps19R67∆/R67∆ 3

characteristic: title


E-MTAB-12448:Rps19R67∆/R67∆ Trp53−/− 1

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-12448:Rps19R67∆/R67∆ Trp53−/− 1

characteristic: Submitter Id

text: embryonic day 14.5

text: ArrayExpress

text: house mouse

text: embryo

text: Diamond-Blackfan anemia

text: Rps19R67∆/R67∆ Trp53−/−

text: not applicable

text: Mus musculus

text: Mus musculus

text: liver

characteristic: organism part

text: Mus musculus

characteristic: strain

text: Rps19R67∆/R67∆ Trp53−/− 1


E-MTAB-12448:Rps19R67∆/R67∆ Trp53−/− 2

text: public

text: E-MTAB-12448:Rps19R67∆/R67∆ Trp53−/− 2

text: embryonic day 14.5

characteristic: age

text: ArrayExpress

characteristic: broker name

text: house mouse

characteristic: common name

characteristic: description

text: embryo

characteristic: developmental stage

text: Diamond-Blackfan anemia

characteristic: disease

text: Rps19R67∆/R67∆ Trp53−/−

characteristic: genotype

text: not applicable

text: Mus musculus

text: Mus musculus

text: liver

text: Mus musculus

text: Rps19R67∆/R67∆ Trp53−/− 2


E-MTAB-12448:Rps19R67∆/R67∆ Trp53−/− 3

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: E-MTAB-12448:Rps19R67∆/R67∆ Trp53−/− 3

text: embryonic day 14.5

text: ArrayExpress

text: house mouse

text: embryo

text: Diamond-Blackfan anemia

text: Rps19R67∆/R67∆ Trp53−/−

characteristic: individual

text: not applicable

characteristic: isolate

text: Mus musculus

text: Mus musculus

text: liver

text: Mus musculus

text: Rps19R67∆/R67∆ Trp53−/− 3


E-MTAB-12448:Trp53−/− 1

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-12448:Trp53−/− 1

characteristic: Submitter Id

text: embryonic day 14.5

text: ArrayExpress

text: house mouse

text: embryo

text: normal

text: not applicable

text: Mus musculus

characteristic: organism

text: Mus musculus

text: liver

text: Mus musculus

text: Trp53−/− 1

characteristic: title


E-MTAB-12448:Trp53−/− 2

text: public

text: E-MTAB-12448:Trp53−/− 2

text: embryonic day 14.5

characteristic: age

text: ArrayExpress

characteristic: broker name

text: house mouse

characteristic: common name

characteristic: description

text: embryo

characteristic: developmental stage

text: normal

text: not applicable

text: Mus musculus

text: Mus musculus

text: liver

characteristic: organism part

text: Mus musculus

characteristic: strain

text: Trp53−/− 2


E-MTAB-12448:Trp53−/− 3

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: E-MTAB-12448:Trp53−/− 3

text: embryonic day 14.5

text: ArrayExpress

text: house mouse

text: embryo

text: normal

characteristic: disease

characteristic: genotype

text: not applicable

text: Mus musculus

text: Mus musculus

text: liver

text: Mus musculus

text: Trp53−/− 3


E-MTAB-12448:Wild-type 1

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-12448:Wild-type 1

characteristic: Submitter Id

text: embryonic day 14.5

text: ArrayExpress

text: house mouse

text: embryo

text: normal

text: wild type genotype

characteristic: individual

text: not applicable

characteristic: isolate

text: Mus musculus

text: Mus musculus

text: liver

text: Mus musculus

text: Wild-type 1


E-MTAB-12448:Wild-type 2

text: public

text: E-MTAB-12448:Wild-type 2

text: embryonic day 14.5

characteristic: age

text: ArrayExpress

characteristic: broker name

text: house mouse

characteristic: common name

characteristic: description

text: embryo

characteristic: developmental stage

text: normal

text: wild type genotype

text: not applicable

text: Mus musculus

characteristic: organism

text: Mus musculus

text: liver

text: Mus musculus

text: Wild-type 2

characteristic: title


E-MTAB-12448:Wild-type 3

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: E-MTAB-12448:Wild-type 3

text: embryonic day 14.5

text: ArrayExpress

text: house mouse

text: embryo

text: normal

text: wild type genotype

text: not applicable

text: Mus musculus

text: Mus musculus

text: liver

characteristic: organism part

text: Mus musculus

characteristic: strain

text: Wild-type 3


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Shanghai Tenth People's Hospital

text: public

characteristic: INSDC status

characteristic: SRA accession

tag: Namespace:Shanghai Tenth People's Hospital

characteristic: Submitter Id

text: ArrayExpress

text: Protocols: Strains were maintained at -80˚C. Strains were streaked on YPD plates. The plates were incubated at 37˚C overnight. Then several colonies were picked up and suspended in DDW. Cell density was adjusted to 10,000 cells/ml, then 100µl of cell suspension was plated on YPD plates. The plates were incubated at 37˚C overnight. Colonies were picked up and suspended in DDW, then cell pellets were obtained by centrifuging at highest speed for 1min. We used the phenol-chloroform method to extract Genomic DNA. Cell pellets were suspended in 200µl of lysis buffer, add 100µl of acid washed glass beads, and 0,2ml phenol:chloroform:isoamyl alcohol (25:24:1). Vortex for 30min at 4˚C. Add 200µl TE pH7.5. Centrifuge for 5min at maximum speed. Transfer aqueous layer to a new 1.5ml EP tube. Add 1ml 100% ethanol. Precipitate 1h at -20˚C. Pellet DNA by centrifuging for 10min at maximum speed. Discard the supernatant. Add 400µl TE pH 7.5. Add 3ul of RNase A (10mg/ml). Incubate at 37˚C for 30min. Add 10µl of 3M NaOAc and 1ml of 100% ethanol. Mix by inversion. Precipitate 30min at -20˚C. Pellet DNA by centrifuging for 10min at maximum speed. Discard supernatant. Air-dry the pellet overnight. Resuspend in 50µl water. 1µg Genomic DNA was randomly fragmented by Covaris, followed by fragments selection by Agencourt AMPure XP-Medium kit to an average size of 200~400 bp. Selected fragments were end repaired and 3\adenylate, then the adaptors were ligated to the end of these 3\adenylate fragments. The products were amplified by PCR and purified by the Agencourt AMPure XP-Medium kit. The purified double stranded PCR products were heat denatured to single strand, then circularised by the splint oligo sequence. The single strand circle DNA (ssCirDNA) were formatted as the final library and qualified by QC.

characteristic: genotype

text: YPD broth

characteristic: growth condition

text: euploid revertant

characteristic: karyotype

text: Candida albicans

text: Candida albicans

text: whole organism

text: Candida albicans


text: Shanghai Tenth People's Hospital

text: public

text: ArrayExpress

characteristic: broker name

characteristic: description

text: YPD broth

text: aneuploid

text: Candida albicans

characteristic: organism

text: Candida albicans

text: whole organism

text: Candida albicans


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: IRCCS Humanitas Research Hospital

text: public

tag: Namespace:IRCCS Humanitas Research Hospital

text: house mouse

characteristic: common name

text: control replicate 1

text: Mus musculus

text: Mus musculus

characteristic: title


text: IRCCS Humanitas Research Hospital

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: house mouse

text: control replicate 2

text: Mus musculus

text: Mus musculus


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: IRCCS Humanitas Research Hospital

text: public

text: house mouse

text: control replicate 3

text: Mus musculus

text: Mus musculus


text: IRCCS Humanitas Research Hospital

text: public

characteristic: INSDC status

characteristic: SRA accession

text: house mouse

text: control replicate 4

text: Mus musculus

text: Mus musculus


text: IRCCS Humanitas Research Hospital

text: public

characteristic: Submitter Id

text: house mouse

text: silenced OPN replicate 2

text: Mus musculus

text: Mus musculus


text: IRCCS Humanitas Research Hospital

text: public

text: house mouse

text: silenced OPN replicate 3

text: Mus musculus

text: Mus musculus


text: IRCCS Humanitas Research Hospital

text: public

text: house mouse

text: silenced OPN replicate 4

text: Mus musculus

text: Mus musculus


text: AALBORG UNIVERSITY

text: public

text: ena-SAMPLE-TAB-21-12-2022-08:36:52:425-65516

tag: Namespace:AALBORG UNIVERSITY

text: uncultured bacterium

text: uncultured bacterium


text: AALBORG UNIVERSITY

text: public

text: ena-SAMPLE-TAB-21-12-2022-08:36:52:425-65517

text: uncultured bacterium

text: uncultured bacterium


text: AALBORG UNIVERSITY

text: public

text: ena-SAMPLE-TAB-21-12-2022-08:36:52:426-65518

text: uncultured bacterium

text: uncultured bacterium


text: AALBORG UNIVERSITY

text: public

text: ena-SAMPLE-TAB-21-12-2022-08:36:52:426-65519

text: uncultured bacterium

text: uncultured bacterium


text: AALBORG UNIVERSITY

text: public

text: ena-SAMPLE-TAB-21-12-2022-08:36:52:426-65520

text: uncultured bacterium

text: uncultured bacterium


text: AALBORG UNIVERSITY

text: public

text: ena-SAMPLE-TAB-21-12-2022-08:36:52:426-65521

text: uncultured bacterium

text: uncultured bacterium


text: AALBORG UNIVERSITY

text: public

text: ena-SAMPLE-TAB-21-12-2022-08:36:52:426-65522

text: uncultured bacterium

text: uncultured bacterium


text: AALBORG UNIVERSITY

text: public

text: ena-SAMPLE-TAB-21-12-2022-08:36:52:426-65523

text: uncultured bacterium

text: uncultured bacterium


text: AALBORG UNIVERSITY

text: public

text: ena-SAMPLE-TAB-21-12-2022-08:36:52:426-65526

text: uncultured bacterium

text: uncultured bacterium


text: AALBORG UNIVERSITY

text: public

text: ena-SAMPLE-TAB-21-12-2022-08:36:52:426-65527

text: uncultured bacterium

text: uncultured bacterium


text: AALBORG UNIVERSITY

text: public

text: ena-SAMPLE-TAB-21-12-2022-08:36:52:426-65528

text: uncultured bacterium

text: uncultured bacterium


text: AALBORG UNIVERSITY

text: public

text: ena-SAMPLE-TAB-21-12-2022-08:36:52:426-65529

text: uncultured bacterium

text: uncultured bacterium


text: AALBORG UNIVERSITY

text: public

text: ena-SAMPLE-TAB-21-12-2022-08:36:52:426-65530

text: uncultured bacterium

text: uncultured bacterium


text: AALBORG UNIVERSITY

text: public

text: ena-SAMPLE-TAB-21-12-2022-08:36:52:426-65531

text: uncultured bacterium

text: uncultured bacterium


text: AALBORG UNIVERSITY

text: public

text: ena-SAMPLE-TAB-21-12-2022-08:36:52:426-65532

text: uncultured bacterium

text: uncultured bacterium


text: AALBORG UNIVERSITY

text: public

text: ena-SAMPLE-TAB-21-12-2022-08:36:52:426-65533

text: uncultured bacterium

text: uncultured bacterium


text: AALBORG UNIVERSITY

text: public

text: ena-SAMPLE-TAB-21-12-2022-08:36:52:426-65534

text: uncultured bacterium

text: uncultured bacterium


text: AALBORG UNIVERSITY

text: public

text: ena-SAMPLE-TAB-21-12-2022-08:36:52:426-65535

text: uncultured bacterium

text: uncultured bacterium


text: AALBORG UNIVERSITY

text: public

text: ena-SAMPLE-TAB-21-12-2022-08:36:52:426-65536

text: uncultured bacterium

text: uncultured bacterium


text: AALBORG UNIVERSITY

text: public

text: ena-SAMPLE-TAB-21-12-2022-08:36:52:426-65537

text: uncultured bacterium

text: uncultured bacterium


text: AALBORG UNIVERSITY

text: public

text: ena-SAMPLE-TAB-21-12-2022-08:36:52:426-65538

text: uncultured bacterium

text: uncultured bacterium


text: AALBORG UNIVERSITY

text: public

text: ena-SAMPLE-TAB-21-12-2022-08:36:52:426-65539

text: uncultured bacterium

text: uncultured bacterium


text: AALBORG UNIVERSITY

text: public

text: ena-SAMPLE-TAB-21-12-2022-08:36:52:426-65540

text: uncultured bacterium

text: uncultured bacterium


text: AALBORG UNIVERSITY

text: public

text: ena-SAMPLE-TAB-21-12-2022-08:36:52:426-65541

text: uncultured bacterium

text: uncultured bacterium


text: AALBORG UNIVERSITY

text: public

text: ena-SAMPLE-TAB-21-12-2022-08:36:52:426-65542

text: uncultured bacterium

text: uncultured bacterium


text: AALBORG UNIVERSITY

text: public

text: ena-SAMPLE-TAB-21-12-2022-08:36:52:426-65543

text: uncultured bacterium

text: uncultured bacterium


text: AALBORG UNIVERSITY

text: public

text: ena-SAMPLE-TAB-21-12-2022-08:36:52:426-65544

text: uncultured bacterium

text: uncultured bacterium


text: AALBORG UNIVERSITY

text: public

text: ena-SAMPLE-TAB-21-12-2022-08:36:52:426-65545

text: uncultured bacterium

text: uncultured bacterium


text: AALBORG UNIVERSITY

text: public

text: ena-SAMPLE-TAB-21-12-2022-08:36:52:426-65546

text: uncultured bacterium

text: uncultured bacterium


text: AALBORG UNIVERSITY

text: public

text: ena-SAMPLE-TAB-21-12-2022-08:36:52:426-65547

text: uncultured bacterium

text: uncultured bacterium


text: AALBORG UNIVERSITY

text: public

text: ena-SAMPLE-TAB-21-12-2022-08:36:52:426-65548

text: uncultured bacterium

text: uncultured bacterium


text: AALBORG UNIVERSITY

text: public

text: ena-SAMPLE-TAB-21-12-2022-08:36:52:426-65549

text: uncultured bacterium

text: uncultured bacterium


text: AALBORG UNIVERSITY

text: public

text: ena-SAMPLE-TAB-21-12-2022-08:36:52:426-65550

text: uncultured bacterium

text: uncultured bacterium


text: AALBORG UNIVERSITY

text: public

text: ena-SAMPLE-TAB-21-12-2022-08:36:52:426-65551

text: uncultured bacterium

text: uncultured bacterium


text: WAGENINGEN UNIVERSITY

text: public

tag: Namespace:WAGENINGEN UNIVERSITY

text: White-fronted goose

text: Genomic Data

text: Anser albifrons

text: Anser albifrons


text: WAGENINGEN UNIVERSITY

text: public

text: Domestic goose

text: Genomic Data

text: Anser anser

text: Anser anser


text: WAGENINGEN UNIVERSITY

text: public

text: Lesser white-fronted goose

text: Genomic Data

text: Anser erythropus

text: Anser erythropus


text: WAGENINGEN UNIVERSITY

text: public

text: Pink-footed goose

text: Genomic Data

text: Anser brachyrhynchus

text: Anser brachyrhynchus


text: WAGENINGEN UNIVERSITY

text: public

text: Genomic Data

text: Branta bernicla

text: Branta bernicla


text: WAGENINGEN UNIVERSITY

text: public

text: Canada goose

text: Genomic Data

text: Branta canadensis

text: Branta canadensis


text: WAGENINGEN UNIVERSITY

text: public

text: barnacle goose

text: Genomic Data

text: Branta leucopsis

text: Branta leucopsis


text: public

tag: Namespace:INDIAN INSTITUTE OF SCIENCE EDUCATION AND RESEARCH, BHOPAL

text: chicken

text: Broiler

text: Bhopal Madhya Pradesh India

text: 23.2599° N, 77.4126° E

text: Gallus gallus

text: Gallus gallus

text: Liver


text: Evolutionary Biology Centre

text: public

tag: Namespace:Evolutionary Biology Centre

text: Callosobruchus analis

text: Callosobruchus analis

text: m160605_052229_42237_c101040332550000001823233112031640_s1_p0.1.bax.h5


text: Evolutionary Biology Centre

text: public

text: Callosobruchus analis

text: Callosobruchus analis

text: m160605_052229_42237_c101040332550000001823233112031640_s1_p0.2.bax.h5


text: Evolutionary Biology Centre

text: public

text: Callosobruchus analis

text: Callosobruchus analis

text: m160605_052229_42237_c101040332550000001823233112031640_s1_p0.3.bax.h5


text: Evolutionary Biology Centre

text: public

text: Callosobruchus analis

text: Callosobruchus analis

text: m160605_052229_42237_c101040332550000001823233112031640_s1_p0.bas.h5


text: Evolutionary Biology Centre

text: public

text: Callosobruchus analis

text: Callosobruchus analis

text: m160605_094218_42237_c101040332550000001823233112031641_s1_p0.1.bax.h5


text: Evolutionary Biology Centre

text: public

text: Callosobruchus analis

text: Callosobruchus analis

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text: Evolutionary Biology Centre

text: public

text: Callosobruchus analis

text: Callosobruchus analis

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text: Evolutionary Biology Centre

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text: Callosobruchus analis

text: Callosobruchus analis

text: m160605_094218_42237_c101040332550000001823233112031641_s1_p0.bas.h5


text: Evolutionary Biology Centre

text: public

text: Callosobruchus analis

text: Callosobruchus analis

text: m160605_140222_42237_c101040332550000001823233112031642_s1_p0.1.bax.h5


text: Evolutionary Biology Centre

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text: Callosobruchus analis

text: Callosobruchus analis

text: m160605_140222_42237_c101040332550000001823233112031642_s1_p0.2.bax.h5


text: Evolutionary Biology Centre

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text: Callosobruchus analis

text: Callosobruchus analis

text: m160605_140222_42237_c101040332550000001823233112031642_s1_p0.3.bax.h5


text: Evolutionary Biology Centre

text: public

text: Callosobruchus analis

text: Callosobruchus analis

text: m160605_140222_42237_c101040332550000001823233112031642_s1_p0.bas.h5


text: Evolutionary Biology Centre

text: public

text: Callosobruchus analis

text: Callosobruchus analis

text: m160604_052516_42237_c101040102550000001823233112031633_s1_p0.1.bax.h5


text: Evolutionary Biology Centre

text: public

text: Callosobruchus analis

text: Callosobruchus analis

text: m160604_052516_42237_c101040102550000001823233112031633_s1_p0.2.bax.h5


text: Evolutionary Biology Centre

text: public

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Chia

text: OREGON STATE UNIVERSITY

text: public

text: Chia

tag: Namespace:OREGON STATE UNIVERSITY

characteristic: air temperature regimen

characteristic: collection date

characteristic: culture rooting medium

text: Seeds of Chia (S. hispanica L.) were bought online from Ancient Naturals, LLC, Salba Corp., N.A., were sown in autoclaved soils, and watered thoroughly under controlled greenhouse conditions. Young leaf samples were collected from 2-week-old seedlings that were pretreated in the dark for 2 days. Samples were immediately frozen in liquid nitrogen and stored at ?80�C.

text: 356 Mbp

characteristic: estimated size

text: USA

characteristic: geographic location (country and/or sea)

unit: DD

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: glasshouse

characteristic: growth facility

text: Leaf tissue

characteristic: isolation and growth condition

characteristic: light regimen

characteristic: mineral nutrient regimen

characteristic: number of replicons

text: Salvia hispanica

text: Chia

characteristic: organism common name

characteristic: plant developmental stage

characteristic: plant growth medium

characteristic: plant structure

characteristic: plant treatment

text: Diploid

characteristic: ploidy

text: From seed

characteristic: propagation

characteristic: rooting conditions

characteristic: rooting medium carbon

characteristic: rooting medium macronutrients

characteristic: rooting medium micronutrients

characteristic: rooting medium organic supplements

characteristic: rooting medium pH

characteristic: rooting medium regulators

characteristic: rooting medium solidifier

characteristic: sample disease status

text: healthy

characteristic: sample health state

text: Salvia hispanica

characteristic: soil pH

characteristic: soil_taxonomic/FAO classification

characteristic: source material identifiers

characteristic: subspecific genetic lineage name

characteristic: subspecific genetic lineage rank

text: Chia genome

characteristic: watering regimen


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: AALBORG UNIVERSITY

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: ena-SAMPLE-TAB-05-01-2023-08:33:44:562-108424

characteristic: Submitter Id

characteristic: description

text: anaerobic digester metagenome

characteristic: organism

text: anaerobic digester metagenome

text: Metagenome

characteristic: title


text: public

tag: Namespace:UNIVERSITY OF COPENHAGEN, SECTION OF MICROBIOLOGY

text: gut metagenome

text: gut metagenome


text: UNIVERSITY OF COPENHAGEN, SECTION OF MICROBIOLOGY

text: public

text: gut metagenome

text: gut metagenome


text: public

text: Negative

text: gut metagenome

text: gut metagenome


text: public

text: Positive

text: gut metagenome

text: gut metagenome


text: public

text: Controls

text: gut metagenome

text: gut metagenome


text: public

tag: Namespace:CENTRE FOR GENOMIC RESEARCH UNIVERSITY OF LIVERPOOL

text: Genome for Buchnera aphidicola from Macrosiphum euphorbiae

text: Buchnera aphidicola

text: Buchnera aphidicola

text: Me Buchnera aphidicola


text: Shanghai Tenth People's Hospital

text: public

text: ArrayExpress

characteristic: broker name

text: Protocols: Strains were maintained at -80˚C. Strains were streaked on YPD plates. The plates were incubated at 37˚C overnight. Then several colonies were picked up and suspended in DDW. Cell density was adjusted to 10,000 cells/ml, then 100µl of cell suspension was plated on YPD plates. The plates were incubated at 37˚C overnight. Colonies were picked up and suspended in DDW, then cell pellets were obtained by centrifuging at highest speed for 1min. We used the phenol-chloroform method to extract Genomic DNA. Cell pellets were suspended in 200µl of lysis buffer, add 100µl of acid washed glass beads, and 0,2ml phenol:chloroform:isoamyl alcohol (25:24:1). Vortex for 30min at 4˚C. Add 200µl TE pH7.5. Centrifuge for 5min at maximum speed. Transfer aqueous layer to a new 1.5ml EP tube. Add 1ml 100% ethanol. Precipitate 1h at -20˚C. Pellet DNA by centrifuging for 10min at maximum speed. Discard the supernatant. Add 400µl TE pH 7.5. Add 3ul of RNase A (10mg/ml). Incubate at 37˚C for 30min. Add 10µl of 3M NaOAc and 1ml of 100% ethanol. Mix by inversion. Precipitate 30min at -20˚C. Pellet DNA by centrifuging for 10min at maximum speed. Discard supernatant. Air-dry the pellet overnight. Resuspend in 50µl water. 1µg Genomic DNA was randomly fragmented by Covaris, followed by fragments selection by Agencourt AMPure XP-Medium kit to an average size of 200~400 bp. Selected fragments were end repaired and 3\"adenylate, then the adaptors were ligated to the end of these 3\"adenylate fragments. The products were amplified by PCR and purified by the Agencourt AMPure XP-Medium kit. The purified double stranded PCR products were heat denatured to single strand, then circularised by the splint oligo sequence. The single strand circle DNA (ssCirDNA) were formatted as the final library and qualified by QC.

text: wild type genotype

characteristic: genotype

text: YPD broth

characteristic: growth condition

text: not applicable

characteristic: isolate

text: [Candida] glabrata

text: [Candida] glabrata

text: whole organism

characteristic: organism part

text: [Candida] glabrata


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: Shanghai Tenth People's Hospital

text: public

text: ArrayExpress

text: YPD broth

text: not applicable

text: [Candida] glabrata

text: [Candida] glabrata

text: whole organism

text: [Candida] glabrata


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Shanghai Tenth People's Hospital

text: public

text: ArrayExpress

text: Protocols: Strains were maintained at -80˚C. Strains were streaked on YPD plates. The plates were incubated at 37˚C overnight. Then several colonies were picked up and suspended in DDW. Cell density was adjusted to 10,000 cells/ml, then 100µl of cell suspension was plated on YPD plates. The plates were incubated at 37˚C overnight. Colonies were picked up and suspended in DDW, then cell pellets were obtained by centrifuging at highest speed for 1min. We used the phenol-chloroform method to extract Genomic DNA. Cell pellets were suspended in 200µl of lysis buffer, add 100µl of acid washed glass beads, and 0,2ml phenol:chloroform:isoamyl alcohol (25:24:1). Vortex for 30min at 4˚C. Add 200µl TE pH7.5. Centrifuge for 5min at maximum speed. Transfer aqueous layer to a new 1.5ml EP tube. Add 1ml 100% ethanol. Precipitate 1h at -20˚C. Pellet DNA by centrifuging for 10min at maximum speed. Discard the supernatant. Add 400µl TE pH 7.5. Add 3ul of RNase A (10mg/ml). Incubate at 37˚C for 30min. Add 10µl of 3M NaOAc and 1ml of 100% ethanol. Mix by inversion. Precipitate 30min at -20˚C. Pellet DNA by centrifuging for 10min at maximum speed. Discard supernatant. Air-dry the pellet overnight. Resuspend in 50µl water. 1µg Genomic DNA was randomly fragmented by Covaris, followed by fragments selection by Agencourt AMPure XP-Medium kit to an average size of 200~400 bp. Selected fragments were end repaired and 3\adenylate, then the adaptors were ligated to the end of these 3\adenylate fragments. The products were amplified by PCR and purified by the Agencourt AMPure XP-Medium kit. The purified double stranded PCR products were heat denatured to single strand, then circularised by the splint oligo sequence. The single strand circle DNA (ssCirDNA) were formatted as the final library and qualified by QC.

text: wild type genotype

text: YPD plate

text: Cryptococcus neoformans var. grubii H99

text: Cryptococcus neoformans var. grubii H99

text: whole organism

text: Cryptococcus neoformans var. grubii H99

characteristic: strain


text: Shanghai Tenth People's Hospital

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: ArrayExpress

text: YPD plate

text: Cryptococcus neoformans var. grubii H99

text: Cryptococcus neoformans var. grubii H99

text: Cryptococcus neoformans var. grubii H99


text: Shanghai Tenth People's Hospital

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: ArrayExpress

text: Aneuploid

text: YPD plate

text: Cryptococcus neoformans var. grubii H99

text: Cryptococcus neoformans var. grubii H99

text: Cryptococcus neoformans var. grubii H99


text: Uppsala University

text: public

tag: Namespace:Uppsala University

text: small freshwater lake biome (ENVO:00000892)

characteristic: broad-scale environmental context

characteristic: collection date

unit: m

characteristic: depth

text: FACS-isolated single mixotrophic flagellate cells

characteristic: description

text: lake water (ENVO:04000007)

characteristic: environmental medium

text: Sweden

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: oligotrophic lake (ENVO:01000774)

characteristic: local environmental context

text: GATCG; GGAGA; ATACC; CCGTT

characteristic: multiplex identifiers

text: lake water metagenome

characteristic: organism

text: 574*F (CGGTAAYTCCAGCTCYV) and 1132R (CCGTCAATTHCTTYAART)

characteristic: pcr primers

text: mixocapture

characteristic: project name

text: lake water metagenome

text: Illumina MiSeq

characteristic: sequencing method

text: 18S rRNA

characteristic: target gene

characteristic: target subfragment

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Uppsala University

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

characteristic: broad-scale environmental context

text: bulk extraction replicate 1 duplicate 1

text: lake water (ENVO:04000007)

text: Sweden

text: oligotrophic lake (ENVO:01000774)

text: lake water metagenome

text: mixocapture

text: lake water metagenome

text: Illumina MiSeq

text: 18S rRNA


text: Uppsala University

text: public

characteristic: collection date

characteristic: depth

text: bulk extraction replicate 1 duplicate 2

characteristic: description

text: lake water (ENVO:04000007)

characteristic: environmental medium

text: Sweden

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: oligotrophic lake (ENVO:01000774)

characteristic: local environmental context

text: lake water metagenome

characteristic: organism

characteristic: pcr primers

text: mixocapture

text: lake water metagenome

text: Illumina MiSeq

text: 18S rRNA


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Uppsala University

characteristic: INSDC center name

text: public

text: bulk extraction replicate 2 duplicate 1

text: lake water (ENVO:04000007)

text: Sweden

text: oligotrophic lake (ENVO:01000774)

text: lake water metagenome

text: mixocapture

characteristic: project name

text: lake water metagenome

text: Illumina MiSeq

characteristic: sequencing method

text: 18S rRNA

characteristic: target gene

characteristic: target subfragment

characteristic: title


text: Uppsala University

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

characteristic: broad-scale environmental context

characteristic: collection date

characteristic: depth

text: bulk extraction replicate 2 duplicate 2

characteristic: description

text: lake water (ENVO:04000007)

characteristic: environmental medium

text: Sweden

text: oligotrophic lake (ENVO:01000774)

text: lake water metagenome

text: mixocapture

text: lake water metagenome

text: Illumina MiSeq

text: 18S rRNA


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Uppsala University

text: public

text: bulk extraction replicate 3 duplicate 1

text: lake water (ENVO:04000007)

text: Sweden

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: oligotrophic lake (ENVO:01000774)

characteristic: local environmental context

text: lake water metagenome

characteristic: organism

characteristic: pcr primers

text: mixocapture

text: lake water metagenome

text: Illumina MiSeq

text: 18S rRNA


text: Uppsala University

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: bulk extraction replicate 3 duplicate 2

text: lake water (ENVO:04000007)

text: Sweden

text: oligotrophic lake (ENVO:01000774)

text: lake water metagenome

text: mixocapture

characteristic: project name

text: lake water metagenome

text: Illumina MiSeq

characteristic: sequencing method

text: 18S rRNA

characteristic: target gene

characteristic: target subfragment

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: THE JACKSON LABORATORY

text: public

text: Instrument

characteristic: Instrument

tag: Namespace:THE JACKSON LABORATORY

characteristic: Submitter Id

text: human

characteristic: common name

text: JAX_HiFi_HG01457_m64119_210723_055657.bam

text: size fractionation

text: GENOMIC

text: WGS

text: Homo sapiens

text: Homo sapiens


text: THE JACKSON LABORATORY

characteristic: INSDC center name

text: public

text: Instrument

text: human

text: JAX_HiFi_HG00096_m64039_220218_071556.bam

text: size fractionation

text: GENOMIC

text: WGS

text: Homo sapiens

characteristic: organism

text: Homo sapiens


text: THE JACKSON LABORATORY

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: Instrument

text: human

text: JAX_HiFi_HG00096_m64039_220211_040031.bam

text: size fractionation

text: GENOMIC

text: WGS

text: Homo sapiens

text: Homo sapiens


text: THE JACKSON LABORATORY

text: public

characteristic: INSDC status

text: Instrument

characteristic: SRA accession

text: human

text: JAX_HiFi_HG00096_m64119_220224_171953.bam

text: size fractionation

text: GENOMIC

text: WGS

text: Homo sapiens

text: Homo sapiens


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