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text: Chicken

characteristic: host common name

text: Prebiotic

characteristic: host diet treatment

characteristic: host disease status

text: Gallus gallus

characteristic: host scientific name

text: female

characteristic: host sex

characteristic: host storage container temperature

characteristic: host subject id

text: BEMT

text: PCR

text: D-rex protocol

text: Gallus gallus

characteristic: organism

text: HoloFood

text: HoloFood Chicken - Host Genome

text: Shield

text: E-matrix 2ml

text: UCPH

text: Gallus gallus

characteristic: title

value: UCPH

value: Lab Process ID

value: Sequencing company

value: BGI


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: UNIVERSITY OF COPENHAGEN

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

characteristic: adapters

characteristic: collection date

text: chicken

characteristic: common name

text: Chicken host genomic data from Caecum content; animal CC24.08 from cage CC24 with treatment CE

text: Spain

text: El Morell; Tarragona

text: Caecum content

text: Ross

text: Chicken

text: Prebiotic

text: Gallus gallus

text: female

characteristic: host taxid

characteristic: host total mass

text: BEMT

characteristic: library name

text: PCR

characteristic: library selection

text: D-rex protocol

characteristic: nucleic acid extraction

text: Gallus gallus

text: HoloFood

characteristic: project

text: HoloFood Chicken - Host Genome

characteristic: project name

characteristic: reference host genome for decontamination

text: Shield

characteristic: sample storage buffer

text: E-matrix 2ml

characteristic: sample storage container

text: UCPH

characteristic: sample storage location

characteristic: sample storage temperature

characteristic: sample volume or weight for DNA extraction

text: Gallus gallus

characteristic: sequencing method

characteristic: trial length

characteristic: trial timepoint

value: Sample code

value: Body site

value: Trial description


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: UNIVERSITY OF COPENHAGEN

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

characteristic: adapters

characteristic: collection date

text: chicken

characteristic: common name

text: Chicken host genomic data from Caecum content; animal CC24.12 from cage CC24 with treatment CE

characteristic: description

text: Spain

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: El Morell; Tarragona

characteristic: geographic location (region and locality)

text: Caecum content

characteristic: host body site

text: Ross

characteristic: host breed

text: Chicken

characteristic: host common name

text: Prebiotic

characteristic: host diet treatment

characteristic: host disease status

text: Gallus gallus

characteristic: host scientific name

text: female

characteristic: host sex

characteristic: host storage container temperature

characteristic: host subject id

text: BEMT

text: PCR

text: D-rex protocol

text: Gallus gallus

characteristic: organism

text: HoloFood

text: HoloFood Chicken - Host Genome

text: Shield

text: E-matrix 2ml

text: UCPH

text: Gallus gallus

characteristic: title

value: Project

value: Trial 3


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: UNIVERSITY OF COPENHAGEN

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

characteristic: adapters

characteristic: collection date

text: chicken

characteristic: common name

text: Chicken host genomic data from Ileum content; animal CC24.14 from cage CC24 with treatment CE

text: Spain

text: El Morell; Tarragona

text: Ileum content

text: Ross

text: Chicken

text: Prebiotic

text: Gallus gallus

text: female

characteristic: host taxid

characteristic: host total mass

text: BEMT

characteristic: library name

text: PCR

characteristic: library selection

text: D-rex protocol

characteristic: nucleic acid extraction

text: Gallus gallus

text: HoloFood

characteristic: project

text: HoloFood Chicken - Host Genome

characteristic: project name

characteristic: reference host genome for decontamination

text: Shield

characteristic: sample storage buffer

text: E-matrix 2ml

characteristic: sample storage container

text: UCPH

characteristic: sample storage location

characteristic: sample storage temperature

characteristic: sample volume or weight for DNA extraction

text: Gallus gallus

characteristic: sequencing method

characteristic: trial length

characteristic: trial timepoint

value: ileum content

value: Organism

value: Trial end


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: UNIVERSITY OF COPENHAGEN

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

characteristic: adapters

characteristic: collection date

text: chicken

characteristic: common name

text: Chicken host genomic data from Caecum content; animal CC24.14 from cage CC24 with treatment CE

characteristic: description

text: Spain

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: El Morell; Tarragona

characteristic: geographic location (region and locality)

text: Caecum content

characteristic: host body site

text: Ross

characteristic: host breed

text: Chicken

characteristic: host common name

text: Prebiotic

characteristic: host diet treatment

characteristic: host disease status

text: Gallus gallus

characteristic: host scientific name

text: female

characteristic: host sex

characteristic: host storage container temperature

characteristic: host subject id

text: BEMT

text: PCR

text: D-rex protocol

text: Gallus gallus

characteristic: organism

text: HoloFood

text: HoloFood Chicken - Host Genome

text: Shield

text: E-matrix 2ml

text: UCPH

text: Gallus gallus

characteristic: title

value: Raw sequence name

value: caecum content

value: Pool

value: Index PCR cycles

value: ng used for library build


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: UNIVERSITY OF COPENHAGEN

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

characteristic: adapters

characteristic: collection date

text: chicken

characteristic: common name

text: Chicken host genomic data from Caecum content; animal CC24.17 from cage CC24 with treatment CE

text: Spain

text: El Morell; Tarragona

text: Caecum content

text: Ross

text: Chicken

text: Prebiotic

text: Gallus gallus

text: female

characteristic: host taxid

characteristic: host total mass

text: BEMT

characteristic: library name

text: PCR

characteristic: library selection

text: D-rex protocol

characteristic: nucleic acid extraction

text: Gallus gallus

text: HoloFood

characteristic: project

text: HoloFood Chicken - Host Genome

characteristic: project name

characteristic: reference host genome for decontamination

text: Shield

characteristic: sample storage buffer

text: E-matrix 2ml

characteristic: sample storage container

text: UCPH

characteristic: sample storage location

characteristic: sample storage temperature

characteristic: sample volume or weight for DNA extraction

text: Gallus gallus

characteristic: sequencing method

characteristic: trial length

characteristic: trial timepoint

value: Chicken

value: Experiment

value: genomics

value: HoloFood

value: Trial start


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: UNIVERSITY OF COPENHAGEN

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

characteristic: adapters

characteristic: collection date

text: chicken

characteristic: common name

text: Chicken host genomic data from Caecum content; animal CC24.18 from cage CC24 with treatment CE

characteristic: description

text: Spain

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: El Morell; Tarragona

characteristic: geographic location (region and locality)

text: Caecum content

characteristic: host body site

text: Ross

characteristic: host breed

text: Chicken

characteristic: host common name

text: Prebiotic

characteristic: host diet treatment

characteristic: host disease status

text: Gallus gallus

characteristic: host scientific name

text: female

characteristic: host sex

characteristic: host storage container temperature

characteristic: host subject id

text: BEMT

text: PCR

text: D-rex protocol

text: Gallus gallus

characteristic: organism

text: HoloFood

text: HoloFood Chicken - Host Genome

text: Shield

text: E-matrix 2ml

text: UCPH

text: Gallus gallus

characteristic: title

value: Sample code

value: Body site


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:The Gurdon Institute, University of Cambridge

characteristic: Submitter Id

text: ArrayExpress

characteristic: broker name

text: primordial germ cell

text: human

characteristic: common name

text: Protocols: Embryonic stem cells derived from WIS2 (https://hpscreg.eu/cell-line/WISe001-A, https://www.nature.com/articles/nature12745) with genetically targeted with a NANOS3-tdTomato reporter as described here: https://www.nature.com/articles/nature22812. hESCs are routinely maintained in E8 media and vitronectin coated plates. To induce PGCLCs, hESCs need to fist acquire competence for PGCLC-fate. For this hESCs are separated into single cells and cultured in the presence of Wnt and Activin. At the 12h stage pre-mesendoderm (PreME) cells are collected and cultured as embryoid bodies in the presence of BMP, SCF, LIF and EGF, which results in the specification of PGCLCs and other somatic cell types such (endoderm, mesoderm) and amnion (see more below for more details about culture mediums). For the basal medium, we used aRB27 medium which is composed of Advanced RPMI 1640 Medium (Thermo Fisher Scientific) supplemented with 1% B27 supplement (Thermo Fisher Scientific), 0.1 mM NEAA, 100 U ml−1 penicillin, 0.1 mg ml−1 streptomycin, 2 mM l-glutamine. aRB27 medium is supplemented with 100 ng ml−1 activin A (SCI), 3μM GSK3i and 10μM of ROCKi, 500 ng ml−1 BMP4 or BMP2 (SCI), 10 ng ml−1 human LIF (SCI), 100 ng ml−1 SCF, 50 ng ml−1 EGF (R&D Systems), and 10 μM ROCKi were added to aRB27 medium. Cells were dissociated using TrypLE, neutralised using MEF media and sorted to remove doublets and debries using a SONY SH800 sorter Single Cell 3' 10X V2 Single Cell 3' 10X V2

text: embryo

characteristic: developmental stage

text: normal

characteristic: disease

characteristic: genotype

text: 4i media

characteristic: growth condition

text: Homo sapiens

text: Homo sapiens

text: inner cell mass

characteristic: organism part

text: embryonic stem cell

characteristic: progenitor cell type

text: Homo sapiens


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: The Gurdon Institute, University of Cambridge

text: public

text: ArrayExpress

text: primordial germ cell

text: human

characteristic: description

text: embryo

text: normal

text: definitive endoderm

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: inner cell mass

text: embryonic stem cell

text: Homo sapiens

text: DE

characteristic: title


E-MTAB-11283:In vivo PGC week 6.5

characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: E-MTAB-11283:In vivo PGC week 6.5

text: ArrayExpress

text: primordial germ cell

text: human

text: embryo

text: normal

text: primordial germ cell

text: Homo sapiens

text: Homo sapiens

text: inner cell mass

text: embryonic stem cell

text: Homo sapiens

text: In vivo PGC week 6.5


E-MTAB-11283:PGCLC 12h

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-11283:PGCLC 12h

characteristic: Submitter Id

text: ArrayExpress

characteristic: broker name

text: primordial germ cell

text: human

characteristic: common name

text: embryo

text: normal

text: embryoid body

text: Homo sapiens

text: Homo sapiens

text: inner cell mass

text: embryonic stem cell

text: Homo sapiens

text: PGCLC 12h


E-MTAB-11283:PGCLC 12h rep2

text: public

text: E-MTAB-11283:PGCLC 12h rep2

text: ArrayExpress

text: primordial germ cell

text: human

text: embryo

characteristic: developmental stage

text: normal

characteristic: disease

characteristic: genotype

text: embryoid body

characteristic: growth condition

text: Homo sapiens

text: Homo sapiens

text: inner cell mass

characteristic: organism part

text: embryonic stem cell

text: Homo sapiens

text: PGCLC 12h rep2


E-MTAB-11283:PGCLC 18h

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: public

text: E-MTAB-11283:PGCLC 18h

text: ArrayExpress

text: primordial germ cell

text: human

characteristic: description

text: embryo

text: normal

text: embryoid body

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: inner cell mass

text: embryonic stem cell

characteristic: progenitor cell type

text: Homo sapiens

text: PGCLC 18h


E-MTAB-11283:PGCLC 24h

characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: E-MTAB-11283:PGCLC 24h

text: ArrayExpress

text: primordial germ cell

text: human

text: embryo

text: normal

text: embryoid body

text: Homo sapiens

text: Homo sapiens

text: inner cell mass

text: embryonic stem cell

text: Homo sapiens

text: PGCLC 24h

characteristic: title


E-MTAB-11283:PGCLC 32h

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-11283:PGCLC 32h

characteristic: Submitter Id

text: ArrayExpress

characteristic: broker name

text: primordial germ cell

text: human

text: embryo

text: normal

text: embryoid body

text: Homo sapiens

text: Homo sapiens

text: inner cell mass

text: embryonic stem cell

text: Homo sapiens

text: PGCLC 32h


E-MTAB-11283:PGCLC 40h

text: public

text: E-MTAB-11283:PGCLC 40h

text: ArrayExpress

text: primordial germ cell

text: human

characteristic: common name

text: embryo

characteristic: developmental stage

text: normal

characteristic: disease

characteristic: genotype

text: embryoid body

characteristic: growth condition

text: Homo sapiens

text: Homo sapiens

text: inner cell mass

text: embryonic stem cell

text: Homo sapiens

text: PGCLC 40h


E-MTAB-11283:PGCLC d4 from 4I (rep2)

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: public

text: E-MTAB-11283:PGCLC d4 from 4I (rep2)

text: ArrayExpress

text: primordial germ cell

text: human

characteristic: description

text: embryo

text: normal

text: embryoid body

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: inner cell mass

characteristic: organism part

text: embryonic stem cell

text: Homo sapiens

text: PGCLC d4 from 4I (rep2)


E-MTAB-11283:PGCLC day 2

characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: E-MTAB-11283:PGCLC day 2

text: ArrayExpress

text: primordial germ cell

text: human

text: embryo

text: normal

text: embryoid body

text: Homo sapiens

text: Homo sapiens

text: inner cell mass

text: embryonic stem cell

characteristic: progenitor cell type

text: Homo sapiens

text: PGCLC day 2


E-MTAB-11283:PGCLC day 4

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-11283:PGCLC day 4

characteristic: Submitter Id

text: ArrayExpress

text: primordial germ cell

text: human

text: embryo

text: normal

text: embryoid body

text: Homo sapiens

text: Homo sapiens

text: inner cell mass

text: embryonic stem cell

text: Homo sapiens

text: PGCLC day 4

characteristic: title


E-MTAB-11547:JA1 A1163 noDrug rep1

text: UNIVERSITY OF MANCHESTER

text: public

text: E-MTAB-11547:JA1 A1163 noDrug rep1

tag: Namespace:UNIVERSITY OF MANCHESTER

text: ArrayExpress

characteristic: broker name

text: Protocols: Mycelium were harvested (avoiding conidia as much as possible) from plates without voriconazole disc (No Drug), from the area equidistant from the border of the plate and the inhibition halo (Low Drug) and the colonies in the halo (Supra-MIC = Persistence). Persister colonies were combined from 20 plates per replicate in order to obtain sufficient material for RNA extraction. Additionally, mycelia were harvested from A1160 with No and Low Drug in the same conditions. Mycelia were scratched using a spatula and immediately frozen and grounded in liquid nitrogen. Two independent replicates were assayed per isolate and condition. Spores were inoculated on top of a 0.45 µm pore nylon membrane placed on an RPMI solid plate. The disc with voriconazole (0.8 mg/mL) was placed on the membrane and incubated for 5 days at 37°C. Standard halos of inhibition formed on the membrane, and persister colonies appeared for the PD-47-104 strain, but not for the A1160 strain. RNA was extracted and purified with the Plant RNeasy Mini Kit (Qiagen) following the manufacturer’s instructions for filamentous fungi, and using on-column DNase treatment. Library preparation of samples was performed using the Illumina Stranded mRNA Prep. Ligation kit (Illumina, Inc.)

text: wild type genotype

characteristic: genotype

text: RPMI medium solid plate

text: Aspergillus fumigatus

text: Aspergillus fumigatus

text: whole organism

text: Aspergillus fumigatus

characteristic: strain

text: JA1 A1163 noDrug rep1


E-MTAB-11547:JA6 A1163 noDrug rep2

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: UNIVERSITY OF MANCHESTER

text: public

text: E-MTAB-11547:JA6 A1163 noDrug rep2

text: ArrayExpress

text: wild type genotype

text: RPMI medium solid plate

characteristic: growth condition

text: Aspergillus fumigatus

text: Aspergillus fumigatus

text: whole organism

text: Aspergillus fumigatus

text: JA6 A1163 noDrug rep2


E-MTAB-11547:JA3 104 noDrug rep1

text: UNIVERSITY OF MANCHESTER

text: public

text: E-MTAB-11547:JA3 104 noDrug rep1

text: ArrayExpress

characteristic: description

text: wild type genotype

text: RPMI medium solid plate

text: Aspergillus fumigatus

characteristic: organism

text: Aspergillus fumigatus

text: whole organism

characteristic: organism part

text: Aspergillus fumigatus

text: JA3 104 noDrug rep1


E-MTAB-11547:JA8 104 noDrug rep2

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: UNIVERSITY OF MANCHESTER

characteristic: INSDC center name

text: public

text: E-MTAB-11547:JA8 104 noDrug rep2

text: ArrayExpress

text: wild type genotype

text: RPMI medium solid plate

text: Aspergillus fumigatus

text: Aspergillus fumigatus

text: whole organism

text: Aspergillus fumigatus

text: JA8 104 noDrug rep2


E-MTAB-11547:JA2 A1163 lowDrug rep1

text: UNIVERSITY OF MANCHESTER

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: E-MTAB-11547:JA2 A1163 lowDrug rep1

text: ArrayExpress

text: wild type genotype

text: RPMI medium solid plate

text: Aspergillus fumigatus

text: Aspergillus fumigatus

text: whole organism

text: Aspergillus fumigatus

text: JA2 A1163 lowDrug rep1


E-MTAB-11547:JA7 A1163 lowDrug rep2

text: UNIVERSITY OF MANCHESTER

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-11547:JA7 A1163 lowDrug rep2

text: ArrayExpress

text: wild type genotype

text: RPMI medium solid plate

text: Aspergillus fumigatus

text: Aspergillus fumigatus

text: whole organism

text: Aspergillus fumigatus

text: JA7 A1163 lowDrug rep2


E-MTAB-11547:JA10 104 highDrug rep2

text: UNIVERSITY OF MANCHESTER

text: public

text: E-MTAB-11547:JA10 104 highDrug rep2

characteristic: Submitter Id

text: ArrayExpress

text: wild type genotype

text: RPMI medium solid plate

text: Aspergillus fumigatus

text: Aspergillus fumigatus

text: whole organism

text: Aspergillus fumigatus

text: JA10 104 highDrug rep2

characteristic: title


E-MTAB-11547:JA4 104 lowDrug rep1

text: UNIVERSITY OF MANCHESTER

text: public

text: E-MTAB-11547:JA4 104 lowDrug rep1

text: ArrayExpress

characteristic: broker name

text: wild type genotype

characteristic: genotype

text: RPMI medium solid plate

text: Aspergillus fumigatus

text: Aspergillus fumigatus

text: whole organism

text: Aspergillus fumigatus

text: JA4 104 lowDrug rep1


E-MTAB-11547:JA5 104 highDrug rep1

characteristic: ENA-CHECKLIST

text: UNIVERSITY OF MANCHESTER

text: public

text: E-MTAB-11547:JA5 104 highDrug rep1

text: ArrayExpress

text: wild type genotype

text: RPMI medium solid plate

text: Aspergillus fumigatus

text: Aspergillus fumigatus

text: whole organism

text: Aspergillus fumigatus

characteristic: strain

text: JA5 104 highDrug rep1


E-MTAB-11547:JA9 104 lowDrug rep2

characteristic: ENA-FIRST-PUBLIC

text: UNIVERSITY OF MANCHESTER

text: public

text: E-MTAB-11547:JA9 104 lowDrug rep2

text: ArrayExpress

text: wild type genotype

text: RPMI medium solid plate

characteristic: growth condition

text: Aspergillus fumigatus

text: Aspergillus fumigatus

text: whole organism

text: Aspergillus fumigatus

text: JA9 104 lowDrug rep2


text: public

tag: Namespace:Centre for Interdisciplinary Research in Animal Health (CIISA), Faculty of Veterinary Medicine, University of Lisbon, Lisbon, Portugal

text: Portugal

characteristic: geographic location (country and/or sea)

text: healthy

characteristic: host health state

text: Felis silvestris catus

characteristic: host scientific name

characteristic: isolate

text: Feaces

text: Escherichia coli

characteristic: organism

text: Escherichia coli

characteristic: serovar


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Centre for Interdisciplinary Research in Animal Health (CIISA), Faculty of Veterinary Medicine, University of Lisbon, Lisbon, Portugal

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: Portugal

text: healthy

text: homo sapiens sapiens

text: Feaces

text: Escherichia coli

text: Escherichia coli


text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: Portugal

text: healthy

text: Canis lupus familiaris

text: Feaces

text: Escherichia coli

text: Escherichia coli

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: public

text: United Kingdom

text: healthy

text: Canis lupus familiaris

text: Feaces

text: Escherichia coli

text: Escherichia coli


text: public

text: United Kingdom

characteristic: geographic location (country and/or sea)

text: healthy

text: homo sapiens sapiens

text: Feaces

text: Escherichia coli

text: Escherichia coli


text: public

tag: Namespace:Blizard Institute, Queen Mary University of London

unit: year

characteristic: age

text: ArrayExpress

characteristic: broker name

text: cattle

characteristic: common name

text: Protocols: Whole heart samples were obtained immediately post-mortem, and blood was removed by direct perfusion of the liver with buffered salt solution (PBS) and/or washing of finely diced tissue (<0.5 cm3) with PBS. Whole-heart minced tissue was cross-linked in 1% formaldehyde solution for 20 minutes, and quenched by addition of 250 mM glycine for 10 minutes. Cross-linked tissue samples were washed with PBS and frozen at -80C until further use. Chromatin was prepared from cross-linked tissue samples following published protocols (Schmidt et al 2009). Chromatin samples were sonicated to 200-400bp fragments using a Q500 QSonica sonicator fitted with a 4417 (1/16 inch) tip. Chromatin from 100-500 mg of dounced heart tissue was used for each ChIP experiment, using antibodies against H3K4me3 (millipore 05-1339), H3K27ac (abcam ab4729) and H3K4me1 (abcam ab8895); and automated 96-well protocols in an Agilent Bravo liquid handling robot {Aldridge, 2013}. The allocation of libraries to each 96-well plate followed a randomised block design tested for lack of overt spatial effects with the Osat R package (Yan 2021). Libraries were prepared from up to 10ng of ChIP input using ThruPLEX® DNA-seq kit (Rubicon Genomics) in a 96-well format, following manufacturer’s guidelines and using 8-15 amplification cycles. Libraries were pooled in equimolar concentrations for Illumina sequencing by library quantification with KAPA Library Quantification Kit (Kapa Biosystems, KK4824) and Roche LightCycler® 480 (Roche), in accordance with manufacturer’s guidelines

characteristic: description

text: adult

characteristic: developmental stage

text: normal

characteristic: disease

text: wild type genotype

characteristic: genotype

characteristic: individual

text: Bos taurus

text: Bos taurus

text: heart

characteristic: organism part

text: Bos taurus

text: male

characteristic: sex


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Blizard Institute, Queen Mary University of London

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: ArrayExpress

text: cattle

text: adult

text: normal

text: wild type genotype

text: Bos taurus

characteristic: organism

text: Bos taurus

text: heart

text: Bos taurus

text: male


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: public

characteristic: SRA accession

characteristic: Submitter Id

characteristic: age

text: ArrayExpress

text: white-tufted-ear marmoset

text: adult

text: normal

text: wild type genotype

text: Callithrix jacchus

text: Callithrix jacchus

text: heart

text: Callithrix jacchus

text: female

characteristic: title


text: public

text: ArrayExpress

characteristic: broker name

text: white-tufted-ear marmoset

characteristic: common name

characteristic: description

text: adult

characteristic: developmental stage

text: wild type genotype

characteristic: genotype

text: Callithrix jacchus

text: Callithrix jacchus

text: heart

text: Callithrix jacchus

text: male


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: public

text: 1 year

text: ArrayExpress

text: white-tufted-ear marmoset

text: adult

text: normal

characteristic: disease

text: wild type genotype

characteristic: individual

text: Callithrix jacchus

text: Callithrix jacchus

text: heart

characteristic: organism part

text: Callithrix jacchus

text: male

characteristic: sex


characteristic: ENA-CHECKLIST

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: ArrayExpress

text: white-tufted-ear marmoset

text: adult

text: normal

text: wild type genotype

text: Callithrix jacchus

characteristic: organism

text: Callithrix jacchus

text: heart

text: Callithrix jacchus

text: male


characteristic: ENA-FIRST-PUBLIC

text: public

characteristic: SRA accession

characteristic: Submitter Id

characteristic: age

text: ArrayExpress

characteristic: broker name

text: dog

text: adult

text: normal

text: wild type genotype

text: Canis lupus familiaris

text: Canis lupus familiaris

text: heart

text: Canis lupus familiaris

text: male

characteristic: title


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: public

unit: month

text: ArrayExpress

text: dog

characteristic: common name

characteristic: description

text: adult

characteristic: developmental stage

text: normal

text: wild type genotype

characteristic: genotype

text: Canis lupus familiaris

text: Canis lupus familiaris

text: heart

text: Canis lupus familiaris

text: male


characteristic: ENA-CHECKLIST

characteristic: INSDC center name

text: public

text: ArrayExpress

text: horse

text: adult

text: normal

characteristic: disease

text: wild type genotype

characteristic: individual

text: Equus caballus

text: Equus caballus

text: heart

characteristic: organism part

text: Equus caballus

text: male

characteristic: sex


characteristic: ENA-FIRST-PUBLIC

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: ArrayExpress

text: domestic cat

text: adult

text: normal

text: wild type genotype

text: Felis catus

characteristic: organism

text: Felis catus

text: heart

text: Felis catus

text: male


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: public

characteristic: Submitter Id

characteristic: age

text: ArrayExpress

characteristic: broker name

text: domestic cat

text: adult

text: normal

text: wild type genotype

text: Felis catus

text: Felis catus

text: heart

text: Felis catus

text: female

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: INSDC center name

text: public

text: ArrayExpress

text: Rhesus monkey

characteristic: common name

characteristic: description

text: adult

characteristic: developmental stage

text: normal

text: wild type genotype

characteristic: genotype

text: Mulberry

text: Macaca mulatta

text: Macaca mulatta

text: heart

text: Macaca mulatta

text: male


characteristic: ENA-FIRST-PUBLIC

characteristic: INSDC first public

text: public

text: ArrayExpress

text: Rhesus monkey

text: adult

text: normal

characteristic: disease

text: wild type genotype

text: Jeremy

characteristic: individual

text: Macaca mulatta

text: Macaca mulatta

text: heart

characteristic: organism part

text: Macaca mulatta

text: male

characteristic: sex


characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: ArrayExpress

text: Rhesus monkey

text: adult

text: normal

text: wild type genotype

text: Dean

text: Macaca mulatta

characteristic: organism

text: Macaca mulatta

text: heart

text: Macaca mulatta

text: male


characteristic: ENA-CHECKLIST

characteristic: INSDC center name

text: public

characteristic: Submitter Id

unit: week

characteristic: age

text: ArrayExpress

characteristic: broker name

text: house mouse

text: adult

text: normal

text: wild type genotype

text: Mus musculus

text: Mus musculus

text: heart

text: Mus musculus

text: male

characteristic: title


characteristic: ENA-FIRST-PUBLIC

characteristic: INSDC first public

text: public

text: 1 year

text: ArrayExpress

text: rabbit

characteristic: common name

characteristic: description

text: adult

characteristic: developmental stage

text: normal

text: wild type genotype

characteristic: genotype

text: Oryctolagus cuniculus

text: Oryctolagus cuniculus

text: heart

text: Oryctolagus cuniculus

text: male


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: public

text: ArrayExpress

text: rabbit

text: adult

text: normal

characteristic: disease

text: wild type genotype

characteristic: individual

text: Oryctolagus cuniculus

text: Oryctolagus cuniculus

text: heart

characteristic: organism part

text: Oryctolagus cuniculus

text: male

characteristic: sex


characteristic: ENA-CHECKLIST

characteristic: INSDC center name

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: ArrayExpress

text: Norway rat

text: adult

text: normal

text: wild type genotype

text: Rattus norvegicus

characteristic: organism

text: Rattus norvegicus

text: heart

text: Rattus norvegicus

text: male


characteristic: ENA-FIRST-PUBLIC

characteristic: INSDC first public

text: public

characteristic: Submitter Id

characteristic: age

text: ArrayExpress

characteristic: broker name

text: pig

text: adult

text: normal

text: wild type genotype

text: Sus scrofa

text: Sus scrofa

text: heart

text: Sus scrofa

text: male

characteristic: title


E-MTAB-11550:Sample 1

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: public

text: E-MTAB-11550:Sample 1

tag: Namespace:Retroviral Immunology The Francis Crick Institute

text: ArrayExpress

text: HARA

text: epithelial cell

text: human

characteristic: common name

text: Protocols: Calbindin-deficient HARA 3D5 cells were generated by Cas9-mediated mutation of the CALB1 gene, encoding Calbindin. HARA.LTR7-GFP+ and HARA.LTR7-GFP- cells were generated by introduction of a HERVH LTR7-GFP reporter into parental HARA (Calbindin-sufficient) cells, using the Sleeping Beauty transposon system. Cells transduced and expressing the reporter were distinguished from cells either not transduced or not expressing GFP expression. GFP+ and GFP- cells were enriched by cell sorting and kept as separate sublines. Introduction of the HERVH LTR7-GFP reporter does not directly affect Calbindin expression, but GFP reporter expression is a marker for and correlates with Calbindin expression. All four cell populations, were grown in vitro and were processed as one batch at the same time, with cell viability between 89% and 93%. RNA was isolated and reverse transcribed with the 10× 3’-mRNA Seq (v3) kit (10× Genomics). Library prep was performed using the the 10× 3’-mRNA Seq (v3) kit (10× Genomics).

characteristic: description

text: adult

characteristic: developmental stage

text: squamous cell lung carcinoma

text: Japanese

characteristic: ethnic group

text: wild type genotype

characteristic: genotype

text: Homo sapiens

text: Homo sapiens

text: lung

text: wild type

characteristic: phenotype

text: pleural effusion

characteristic: sampling site

text: Homo sapiens

text: male

text: Sample 1


E-MTAB-11550:Sample 2

characteristic: ENA-CHECKLIST

text: Retroviral Immunology The Francis Crick Institute

characteristic: INSDC center name

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-11550:Sample 2

text: ArrayExpress

text: HARA

text: epithelial cell

text: human

text: adult

text: squamous cell lung carcinoma

characteristic: disease

text: Japanese

text: CRISPR-Cas9 mediated mutation of CALB1

characteristic: genetic modification

text: Homo sapiens

text: Homo sapiens

text: lung

characteristic: organism part

text: calbindin deficient

text: pleural effusion

text: Homo sapiens

text: male

characteristic: sex

text: Sample 2


E-MTAB-11550:Sample 3

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC first public

text: public

text: E-MTAB-11550:Sample 3

characteristic: Submitter Id

characteristic: age

text: ArrayExpress

characteristic: broker name

text: HARA

text: epithelial cell

text: human

text: adult

text: squamous cell lung carcinoma

text: Japanese

text: HERVH LTR7-GFP transduction

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: lung

text: wild type

text: pleural effusion

text: Homo sapiens

text: male

text: Sample 3

characteristic: title


E-MTAB-11550:Sample 4

characteristic: ENA-CHECKLIST

characteristic: INSDC center name

text: public

text: E-MTAB-11550:Sample 4

text: ArrayExpress

text: HARA

text: epithelial cell

text: human

characteristic: common name

characteristic: description

text: adult

characteristic: developmental stage

text: squamous cell lung carcinoma

text: Japanese

characteristic: ethnic group

text: HERVH LTR7-GFP transduction

characteristic: genotype

text: Homo sapiens

text: Homo sapiens

text: lung

text: GFP expression

characteristic: phenotype

text: pleural effusion

characteristic: sampling site

text: Homo sapiens

text: male

text: Sample 4


text: Caenorhabditis sp. 8 KK-2021

characteristic: ArrayExpress-SPECIES

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: SC

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: Caenorhabditis sp. 8 KK-2021

text: Caenorhabditis sp. 8 KK-2011

text: Caenorhabditis sp. 8 KK-2011


text: Acrobeloides maximus

characteristic: External Id

text: SC

characteristic: INSDC first public

text: public

characteristic: Submitter Id

text: Acrobeloides maximus

text: Acrobeloides maximus

characteristic: organism

text: Acrobeloides maximus


text: Caenorhabditis sinica

characteristic: ENA-CHECKLIST

text: SC

characteristic: INSDC center name

text: public

text: Caenorhabditis sinica

characteristic: common name

text: Caenorhabditis sinica

text: Caenorhabditis sinica

characteristic: title


text: public

tag: Namespace:Cambridge Department of Veterinary Medicine

text: Maximilian Stammnitz

text: Tasmanian devil

characteristic: coverage

characteristic: description

text: Australia

characteristic: geographic location (country and/or sea)

text: St. Marys, Tasmania

characteristic: geographic location (region and locality)

text: 41.5801277 S 148.1862030 E

text: Sarcophilus harrisii

text: tetraploid

characteristic: ploidy

characteristic: purity

text: Sarcophilus harrisii

text: female

characteristic: sex

text: tumour biopsy


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: Cambridge Department of Veterinary Medicine

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: Maximilian Stammnitz

text: Tasmanian devil

text: Australia

text: Fentonbury, Tasmania

text: 42.6510201 S 146.7679749 E

text: Sarcophilus harrisii

text: diploid

text: Sarcophilus harrisii

text: female

text: tumour biopsy


characteristic: External Id

characteristic: INSDC first public

text: public

characteristic: SRA accession

characteristic: Submitter Id

text: Maximilian Stammnitz

text: Tasmanian devil

text: Australia

text: Gladstone, Tasmania

text: 40.9599609 S 148.0095978 E

text: Sarcophilus harrisii

text: diploid

text: Sarcophilus harrisii

text: female

text: tumour biopsy


characteristic: ENA-CHECKLIST

characteristic: INSDC center name

text: public

text: Maximilian Stammnitz

text: Tasmanian devil

characteristic: common name

text: Australia

text: Mangalore, Tasmania

text: 42.6543541 S 147.2405396 E

text: Sarcophilus harrisii

characteristic: organism

text: tetraploid

text: Sarcophilus harrisii

text: female

text: tumour biopsy


text: public

text: Maximilian Stammnitz

text: Tasmanian devil

characteristic: coverage

characteristic: description

text: Australia

characteristic: geographic location (country and/or sea)

text: Kempton, Tasmania

text: 42.5291455 S 147.1996036 E

text: Sarcophilus harrisii

text: diploid

text: Sarcophilus harrisii

text: female

text: tumour biopsy

characteristic: title


text: public

text: Maximilian Stammnitz

text: Tasmanian devil

text: Australia

text: Freycinet, Tasmania

characteristic: geographic location (region and locality)

text: 42.1421700 S 148.2960510 E

text: Sarcophilus harrisii

text: diploid

characteristic: ploidy

characteristic: purity

text: Sarcophilus harrisii

text: female

characteristic: sex

text: tumour biopsy


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: Maximilian Stammnitz

text: Tasmanian devil

text: Australia

text: West Pencil Pine, Tasmania

text: 41.5950272 S 145.9286214 E

text: Sarcophilus harrisii

text: diploid

text: Sarcophilus harrisii

text: female

text: tumour biopsy


characteristic: External Id

characteristic: INSDC first public

text: public

characteristic: SRA accession

characteristic: Submitter Id

text: Maximilian Stammnitz

text: Tasmanian devil

text: Australia

text: Upper Natone, Tasmania

text: 41.2297321 S 145.9003633 E

text: Sarcophilus harrisii

text: diploid

text: Sarcophilus harrisii

text: female

text: tumour biopsy


characteristic: ENA-CHECKLIST

characteristic: INSDC center name

text: public

text: Maximilian Stammnitz

text: Tasmanian devil

characteristic: common name

text: Australia

text: Forestier, Tasmania

text: 42.9419441 S 147.9141693 E

text: Sarcophilus harrisii

characteristic: organism

text: diploid

text: Sarcophilus harrisii

text: female

text: tumour biopsy


text: public

text: Maximilian Stammnitz

text: Tasmanian devil

characteristic: coverage

characteristic: description

text: Australia

characteristic: geographic location (country and/or sea)

text: Lovely Banks, Tasmania

text: 42.4441277 S 147.2266246 E

text: Sarcophilus harrisii

text: diploid

text: Sarcophilus harrisii

text: female

text: tumour biopsy

characteristic: title


text: public

text: Maximilian Stammnitz

text: Tasmanian devil

text: Australia

text: Buckland, Tasmania

characteristic: geographic location (region and locality)

text: 42.6076202 S 147.7173157 E

text: Sarcophilus harrisii

text: diploid

characteristic: ploidy

characteristic: purity

text: Sarcophilus harrisii

text: female

characteristic: sex

text: tumour biopsy