characteristic: ENA-FIRST-PUBLIC

characteristic: INSDC first public

text: public

characteristic: SRA accession

text: E-MTAB-11822:04_96_DC2650_WT8288-C04_D30

characteristic: Submitter Id

characteristic: age

text: ArrayExpress

characteristic: broker name

text: induced pluripotent stem cell

text: human

text: adult

text: normal

text: wild type genotype

text: Homo sapiens

text: Homo sapiens

text: blood

text: mononuclear cell

text: Homo sapiens

text: male


status: PUBLIC

tag: attribute

characteristic: ENA-CHECKLIST

characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: E-MTAB-11822:05_64_DC2673_WT8288-C04_D30

tag: Namespace:Nantes Universite, CHU Nantes, CNRS, INSERM, l’institut du thorax, F-44000 Nantes, France

unit: year

text: ArrayExpress

text: induced pluripotent stem cell

text: human

characteristic: common name

text: Protocols: Directed cardiac differentiations of hiPSCs were performed using the established matrix sandwich method (Es-Salah-Lamoureux et al., 2016). Briefly, when hiPSCs reached 90% confluency, an overlay of Growth Factor Reduced Matrigel (0.033 mg/ml, BD Corning) was added. Differentiation was initiated 24h later by culturing the cells in RPMI1640 medium (Life Technologies) supplemented with B27 (without insulin, Life Technologies), 2 mM L-glutamine (Life Technologies), 1% NEAA (Life Technologies), 100 ng/mL Activin A (Miltenyi Biotec), 1X Pen/Strep (Life Technologies) and 10 ng/mL FGF2 for 24 hours. On the next day, the medium was replaced by RPMI1640 medium supplemented with B27 without insulin, 2 mM L-glutamine, 1% NEAA, 10 ng/mL BMP4 (Miltenyi Biotec), 1X Pen/Strep and 5 ng/mL FGF2 for 4 days. By day 5, cells were cultured in RPMI1640 medium supplemented with B27 complete (Life Technologies), 2 mM L-glutamine, 1X Pen/Strep and 1% NEAA and changed every two days until day 30. For each hiPSC line, samples were harvested daily from D-1 to D30 of the cardiac differentiation protocol from three independent cardiac differentiations. Total RNA were extracted using the NucleoSpin RNA kit (MACHEREY-NAGEL) and their quality assessed by NanoDropTM 1000 Spectrophotometer (Thermo Fisher Scientific). 3’RNA libraries were prepared by GenoBiRD core facility according to their published method (Charpentier et al., 2021)

characteristic: description

text: adult

characteristic: developmental stage

text: normal

characteristic: disease

text: wild type genotype

characteristic: genotype

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: blood

characteristic: organism part

text: mononuclear cell

characteristic: progenitor cell type

text: Homo sapiens

text: male

characteristic: sex

characteristic: title


characteristic: ENA-FIRST-PUBLIC

text: Nantes Universite, CHU Nantes, CNRS, INSERM, l’institut du thorax, F-44000 Nantes, France

characteristic: INSDC first public

text: public

characteristic: SRA accession

characteristic: Submitter Id

characteristic: age

text: ArrayExpress

characteristic: broker name

text: induced pluripotent stem cell

text: human

text: adult

text: normal

text: wild type genotype

text: Homo sapiens

text: Homo sapiens

text: blood

text: mononuclear cell

text: Homo sapiens

text: male


characteristic: ENA-CHECKLIST

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: ETH ZURICH

characteristic: INSDC center name

characteristic: INSDC last update

text: public

characteristic: INSDC status

tag: Namespace:ETH ZURICH

text: Microbiota V3/V4 region 16S rRNA by universal primers

text: gut metagenome

text: gut metagenome


HGnegA

text: ETH ZURICH

text: public

text: HGnegA

text: Microbiota V3/V4 region 16S rRNA by universal primers, negative control

characteristic: description

text: gut metagenome

characteristic: organism

text: gut metagenome

text: HGnegA


text: STREPTOCOCCUS PNEUMONIAE

characteristic: ArrayExpress-SPECIES

text: SC

text: public

text: STREPTOCOCCUS PNEUMONIAE

characteristic: common name

text: Streptococcus pneumoniae TIGR4

text: Streptococcus pneumoniae TIGR4


text: public

tag: Namespace:Institute of Pharmacology, Heidelberg University, Heidelberg Ernst-Strungmann-Institute, Frankfurt am Main, Germany

text: ArrayExpress

text: iPSC line

text: neural crest progenitor

text: human

text: Protocols: clumps of 10-15 cells were picked individually and processed as a single sample see sample table see sample table Fastq files were aligned using the GRCh38.p12 assembly transcriptome acquired from GENCODE and the Salmon pseudoalignment package RNA was isolated and amplified using the SmartSeq2 protocol Libraries were generated using the Illumina TruSeq mRNA library prep kit.

text: doxycyclin-inducible Neurogenin 1 cassette

characteristic: genetic modification

text: doxycycline induction for 10 days

characteristic: growth condition

text: Homo sapiens

text: Homo sapiens

text: induced pluripotent stem cell

characteristic: progenitor cell type

text: Homo sapiens

characteristic: title


characteristic: ENA-FIRST-PUBLIC

text: Institute of Pharmacology, Heidelberg University, Heidelberg Ernst-Strungmann-Institute, Frankfurt am Main, Germany

characteristic: INSDC first public

text: public

characteristic: SRA accession

characteristic: Submitter Id

text: ArrayExpress

text: iPSC line

text: neural crest progenitor

text: human

text: doxycycline induction for 10 days

text: Homo sapiens

text: Homo sapiens

text: induced pluripotent stem cell

text: Homo sapiens


characteristic: ENA-CHECKLIST

characteristic: ENA-LAST-UPDATE

text: public

text: ArrayExpress

characteristic: broker name

text: iPSC line

text: neural crest progenitor

text: human

text: doxycycline induction for 23 days

text: Homo sapiens

text: Homo sapiens

text: induced pluripotent stem cell

text: Homo sapiens


characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC last update

text: public

text: ArrayExpress

text: iPSC line

text: neural crest progenitor

text: human

text: Protocols: 3.5cm dishes of differentiated sensory neurons were collected see sample table see sample table Fastq files were aligned using the GRCh38.p12 assembly transcriptome acquired from GENCODE and the Salmon pseudoalignment package RNA was isolated and amplified using the SmartSeq2 protocol Libraries were generated using the Illumina TruSeq mRNA library prep kit.

text: initial neural crest stage (day 0)

characteristic: infection

characteristic: lane

text: Homo sapiens

text: Homo sapiens

text: induced pluripotent stem cell

characteristic: replicate

text: Homo sapiens


text: public

characteristic: INSDC status

text: ArrayExpress

text: iPSC line

text: neural crest progenitor

text: human

characteristic: common name

characteristic: description

characteristic: genetic modification

text: doxycyclin treatment (days 0 - 10) followed by differentiation without induction of Ngn1 (days 12 onward)

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: induced pluripotent stem cell

text: Homo sapiens


characteristic: ENA-FIRST-PUBLIC

text: MRC Human Genetics Unit

characteristic: INSDC first public

text: public

tag: Namespace:MRC Human Genetics Unit

text: house mouse

text: ATAC-seq of mutant optic vesicle organoid 4b, replicate 1

text: germline

characteristic: germline

text: Mus musculus

text: Mus musculus

text: M

characteristic: sex

text: optical vesicle organoid

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-LAST-UPDATE

text: MRC Human Genetics Unit

text: public

characteristic: SRA accession

characteristic: Submitter Id

text: house mouse

text: ATAC-seq of mutant optic vesicle organoid 5c, replicate 1

text: germline

text: Mus musculus

text: Mus musculus

text: M

text: optical vesicle organoid


characteristic: External Id

text: MRC Human Genetics Unit

characteristic: INSDC center name

characteristic: INSDC last update

text: public

text: house mouse

text: ATAC-seq of mutant optic vesicle organoid 5c, replicate 2

text: germline

text: Mus musculus

text: Mus musculus

text: M

text: optical vesicle organoid


text: MRC Human Genetics Unit

text: public

characteristic: INSDC status

text: house mouse

text: ATAC-seq of wild type optic vesicle organoid 2c, replicate 1

text: germline

text: Mus musculus

text: Mus musculus

text: M

text: optical vesicle organoid


text: MRC Human Genetics Unit

text: public

text: house mouse

characteristic: common name

text: ATAC-seq of wild type optic vesicle organoid 2c, replicate 3

text: germline

text: Mus musculus

text: Mus musculus

text: M

text: optical vesicle organoid


text: MRC Human Genetics Unit

text: public

text: house mouse

text: ATAC-seq of wild type optic vesicle organoid 8c, replicate 1

characteristic: description

text: germline

text: Mus musculus

text: Mus musculus

text: M

text: optical vesicle organoid


text: MRC Human Genetics Unit

text: public

text: house mouse

text: ATAC-seq of wild type optic vesicle organoid 8c, replicate 2

text: germline

text: Mus musculus

text: Mus musculus

text: M

text: optical vesicle organoid


E-MTAB-12104:APS KO R1

text: public

text: E-MTAB-12104:APS KO R1

tag: Namespace:Novo Nordisk Foundation Center for Stem Cell Biology (DanStem). University of Copenhagen.

text: ArrayExpress

characteristic: broker name

text: epiblast stem cells

text: primitive streak

text: house mouse

text: Protocols: Cells were seeded on fibronectin-coated 6-well plates in N2B27 medium (DMEM-F12:Neurobasal, 1:1, N2, B27) supplemented with Activin A, FGF and XAV-939 and differentiated to all desired cell types as described in the publication. At 24h (EpiSC, PPS and APS) and 48h (mesoderm) cells were washed briefly and incubated with accutase for 3 min at 37C. After that time accutase was diluted with 3x volume N2B27, samples were centrifuged and the cell pellet was resuspended in lysis buffer (QIAGEN RNAeasy kit). RNA was extracted using QIAGEN RNAeasy kit according to manufacturer's indications. RNA concentration was quantified by NanoDrop and quality was verified with a Fragment analyzer. Library preparation was carried out using 0.5 μg of RNA with NEBNext Ultra II RNA library Prep Kit (New England BioLabs, E7770S) as per manufacturer’s instructions. Libraries were amplified for 4 total PCR cycles and purified with AMPure XP beads. DNA concentration was measured with a Qubit Fluorometer and fragment size was determined with a Fragment analyzer.

text: embryo

characteristic: developmental stage

text: normal

characteristic: disease

text: PGR knockout

characteristic: genotype

text: Mus musculus

text: Mus musculus

text: epiblast

characteristic: organism part

text: pluripotent stem cell

characteristic: progenitor cell type

text: Mus musculus

text: APS KO R1


E-MTAB-12104:APS KO R2

characteristic: ENA-FIRST-PUBLIC

text: Novo Nordisk Foundation Center for Stem Cell Biology (DanStem). University of Copenhagen.

characteristic: INSDC first public

text: public

text: E-MTAB-12104:APS KO R2

text: ArrayExpress

text: epiblast stem cells

text: primitive streak

text: house mouse

text: embryo

text: normal

text: PGR knockout

text: Mus musculus

characteristic: organism

text: Mus musculus

text: epiblast

text: pluripotent stem cell

text: Mus musculus

text: APS KO R2

characteristic: title


E-MTAB-12104:APS WT R1

characteristic: ENA-CHECKLIST

characteristic: ENA-LAST-UPDATE

text: public

characteristic: SRA accession

text: E-MTAB-12104:APS WT R1

characteristic: Submitter Id

text: ArrayExpress

text: epiblast stem cells

text: primitive streak

text: house mouse

text: embryo

text: normal

text: wild type genotype

text: Mus musculus

text: Mus musculus

text: epiblast

text: pluripotent stem cell

text: Mus musculus

text: APS WT R1


E-MTAB-12104:APS WT R2

characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: E-MTAB-12104:APS WT R2

text: ArrayExpress

text: epiblast stem cells

text: primitive streak

text: house mouse

text: embryo

text: normal

text: wild type genotype

text: Mus musculus

text: Mus musculus

text: epiblast

text: pluripotent stem cell

text: Mus musculus

text: APS WT R2


E-MTAB-12104:CM KO R1

text: public

text: E-MTAB-12104:CM KO R1

text: ArrayExpress

characteristic: broker name

text: epiblast stem cells

text: cardiac mesoderm

text: house mouse

characteristic: common name

characteristic: description

text: embryo

characteristic: developmental stage

text: normal

text: PGR knockout

text: Mus musculus

text: Mus musculus

text: epiblast

text: pluripotent stem cell

text: Mus musculus

text: CM KO R1


E-MTAB-12104:CM KO R2

text: public

text: E-MTAB-12104:CM KO R2

text: ArrayExpress

text: epiblast stem cells

text: cardiac mesoderm

text: house mouse

text: embryo

text: normal

characteristic: disease

text: PGR knockout

characteristic: genotype

text: Mus musculus

text: Mus musculus

text: epiblast

characteristic: organism part

text: pluripotent stem cell

characteristic: progenitor cell type

text: Mus musculus

text: CM KO R2


E-MTAB-12104:CM WT R1

characteristic: ENA-FIRST-PUBLIC

characteristic: INSDC first public

text: public

text: E-MTAB-12104:CM WT R1

text: ArrayExpress

text: epiblast stem cells

text: cardiac mesoderm

text: house mouse

text: embryo

text: normal

text: wild type genotype

text: Mus musculus

characteristic: organism

text: Mus musculus

text: epiblast

text: pluripotent stem cell

text: Mus musculus

text: CM WT R1

characteristic: title


E-MTAB-12104:CM WT R2

characteristic: ENA-CHECKLIST

characteristic: ENA-LAST-UPDATE

text: public

characteristic: SRA accession

text: E-MTAB-12104:CM WT R2

characteristic: Submitter Id

text: ArrayExpress

text: epiblast stem cells

text: cardiac mesoderm

text: house mouse

text: embryo

text: normal

text: wild type genotype

text: Mus musculus

text: Mus musculus

text: epiblast

text: pluripotent stem cell

text: Mus musculus

text: CM WT R2


E-MTAB-12104:EpiSC KO R1

characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: E-MTAB-12104:EpiSC KO R1

text: ArrayExpress

text: epiblast stem cells

text: pluripotent stem cell

text: house mouse

text: embryo

text: normal

text: PGR knockout

text: Mus musculus

text: Mus musculus

text: epiblast

text: pluripotent stem cell

text: Mus musculus

text: EpiSC KO R1


E-MTAB-12104:EpiSC KO R2

text: public

text: E-MTAB-12104:EpiSC KO R2

text: ArrayExpress

characteristic: broker name

text: epiblast stem cells

text: pluripotent stem cell

text: house mouse

characteristic: common name

characteristic: description

text: embryo

characteristic: developmental stage

text: normal

text: PGR knockout

text: Mus musculus

text: Mus musculus

text: epiblast

text: pluripotent stem cell

text: Mus musculus

text: EpiSC KO R2


E-MTAB-12104:EpiSC WT R1

text: public

text: E-MTAB-12104:EpiSC WT R1

text: ArrayExpress

text: epiblast stem cells

text: pluripotent stem cell

text: house mouse

text: embryo

text: normal

characteristic: disease

text: wild type genotype

characteristic: genotype

text: Mus musculus

text: Mus musculus

text: epiblast

characteristic: organism part

text: pluripotent stem cell

characteristic: progenitor cell type

text: Mus musculus

text: EpiSC WT R1


E-MTAB-12104:EpiSC WT R2

characteristic: ENA-FIRST-PUBLIC

characteristic: INSDC first public

text: public

text: E-MTAB-12104:EpiSC WT R2

text: ArrayExpress

text: epiblast stem cells

text: pluripotent stem cell

text: house mouse

text: embryo

text: normal

text: wild type genotype

text: Mus musculus

characteristic: organism

text: Mus musculus

text: epiblast

text: pluripotent stem cell

text: Mus musculus

text: EpiSC WT R2

characteristic: title


E-MTAB-12104:ExM KO R1

characteristic: ENA-CHECKLIST

characteristic: ENA-LAST-UPDATE

text: public

characteristic: SRA accession

text: E-MTAB-12104:ExM KO R1

characteristic: Submitter Id

text: ArrayExpress

text: epiblast stem cells

text: extraembryonic mesoderm

text: house mouse

text: embryo

text: normal

text: PGR knockout

text: Mus musculus

text: Mus musculus

text: epiblast

text: pluripotent stem cell

text: Mus musculus

text: ExM KO R1


E-MTAB-12104:ExM KO R2

characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: E-MTAB-12104:ExM KO R2

text: ArrayExpress

text: epiblast stem cells

text: extraembryonic mesoderm

text: house mouse

text: embryo

text: normal

text: PGR knockout

text: Mus musculus

text: Mus musculus

text: epiblast

text: pluripotent stem cell

text: Mus musculus

text: ExM KO R2


E-MTAB-12104:ExM WT R1

text: public

text: E-MTAB-12104:ExM WT R1

text: ArrayExpress

characteristic: broker name

text: epiblast stem cells

text: extraembryonic mesoderm

text: house mouse

characteristic: common name

characteristic: description

text: embryo

characteristic: developmental stage

text: normal

text: wild type genotype

text: Mus musculus

text: Mus musculus

text: epiblast

text: pluripotent stem cell

text: Mus musculus

text: ExM WT R1


E-MTAB-12104:ExM WT R2

text: public

text: E-MTAB-12104:ExM WT R2

text: ArrayExpress

text: epiblast stem cells

text: extraembryonic mesoderm

text: house mouse

text: embryo

text: normal

characteristic: disease

text: wild type genotype

characteristic: genotype

text: Mus musculus

text: Mus musculus

text: epiblast

characteristic: organism part

text: pluripotent stem cell

characteristic: progenitor cell type

text: Mus musculus

text: ExM WT R2


E-MTAB-12104:PM KO R1

characteristic: ENA-FIRST-PUBLIC

characteristic: INSDC first public

text: public

text: E-MTAB-12104:PM KO R1

text: ArrayExpress

text: epiblast stem cells

text: paraxial mesoderm

text: house mouse

text: embryo

text: normal

text: PGR knockout

text: Mus musculus

characteristic: organism

text: Mus musculus

text: epiblast

text: pluripotent stem cell

text: Mus musculus

text: PM KO R1

characteristic: title


E-MTAB-12104:PM KO R2

characteristic: ENA-CHECKLIST

characteristic: ENA-LAST-UPDATE

text: public

characteristic: SRA accession

text: E-MTAB-12104:PM KO R2

characteristic: Submitter Id

text: ArrayExpress

text: epiblast stem cells

text: paraxial mesoderm

text: house mouse

text: embryo

text: normal

text: PGR knockout

text: Mus musculus

text: Mus musculus

text: epiblast

text: pluripotent stem cell

text: Mus musculus

text: PM KO R2


E-MTAB-12104:PM WT R1

characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: E-MTAB-12104:PM WT R1

text: ArrayExpress

text: epiblast stem cells

text: paraxial mesoderm

text: house mouse

text: embryo

text: normal

text: wild type genotype

text: Mus musculus

text: Mus musculus

text: epiblast

text: pluripotent stem cell

text: Mus musculus

text: PM WT R1


E-MTAB-12104:PM WT R2

text: public

text: E-MTAB-12104:PM WT R2

text: ArrayExpress

characteristic: broker name

text: epiblast stem cells

text: paraxial mesoderm

text: house mouse

characteristic: common name

characteristic: description

text: embryo

characteristic: developmental stage

text: normal

text: wild type genotype

text: Mus musculus

text: Mus musculus

text: epiblast

text: pluripotent stem cell

text: Mus musculus

text: PM WT R2


E-MTAB-12104:PPS KO R1

text: public

text: E-MTAB-12104:PPS KO R1

text: ArrayExpress

text: epiblast stem cells

text: primitive streak

text: house mouse

text: embryo

text: normal

characteristic: disease

text: PGR knockout

characteristic: genotype

text: Mus musculus

text: Mus musculus

text: epiblast

characteristic: organism part

text: pluripotent stem cell

characteristic: progenitor cell type

text: Mus musculus

text: PPS KO R1


E-MTAB-12104:PPS KO R2

characteristic: ENA-FIRST-PUBLIC

characteristic: INSDC first public

text: public

text: E-MTAB-12104:PPS KO R2

text: ArrayExpress

text: epiblast stem cells

text: primitive streak

text: house mouse

text: embryo

text: normal

text: PGR knockout

text: Mus musculus

characteristic: organism

text: Mus musculus

text: epiblast

text: pluripotent stem cell

text: Mus musculus

text: PPS KO R2

characteristic: title


E-MTAB-12104:PPS WT R1

characteristic: ENA-CHECKLIST

characteristic: ENA-LAST-UPDATE

text: public

characteristic: SRA accession

text: E-MTAB-12104:PPS WT R1

characteristic: Submitter Id

text: ArrayExpress

text: epiblast stem cells

text: primitive streak

text: house mouse

text: embryo

text: normal

text: wild type genotype

text: Mus musculus

text: Mus musculus

text: epiblast

text: pluripotent stem cell

text: Mus musculus

text: PPS WT R1


E-MTAB-12104:PPS WT R2

characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: E-MTAB-12104:PPS WT R2

text: ArrayExpress

text: epiblast stem cells

text: primitive streak

text: house mouse

text: embryo

text: normal

text: wild type genotype

text: Mus musculus

text: Mus musculus

text: epiblast

text: pluripotent stem cell

text: Mus musculus

text: PPS WT R2


text: Fidock Lab

text: public

tag: Namespace:Fidock Lab

text: control

characteristic: description

text: asexual blood stage

text: Plasmodium falciparum NF54

text: David Fidock

characteristic: provider

text: Plasmodium falciparum NF54

characteristic: strain

text: NF54 Control


text: Fidock Lab

text: public

text: wildtype

text: asexual blood stage

text: Plasmodium falciparum NF54

text: David Fidock

text: Plasmodium falciparum NF54

text: NF54 Wildtype


text: Fidock Lab

text: public

text: sample 1 with G358S haplotype

text: asexual blood stage

text: Plasmodium falciparum NF54

text: David Fidock

text: Plasmodium falciparum NF54

text: NF54 Sample 1


text: Fidock Lab

text: public

text: sample 2 with G358S haplotype

text: asexual blood stage

text: Plasmodium falciparum NF54

text: David Fidock

text: Plasmodium falciparum NF54

text: NF54 Sample 2


text: Ragimbeau

text: public

text: PFM sweep metagenomics from Bird

text: Yes

text: Luxembourg

characteristic: geographic location (country and/or sea)

text: Dudelange

characteristic: geographic location (region and locality)

text: Cygnus

characteristic: host scientific name

text: Bird

text: Campylobacter jejuni

text: Campylobacter jejuni


characteristic: ENA-FIRST-PUBLIC

text: Ragimbeau

characteristic: INSDC first public

text: public

text: PFM sweep metagenomics from Bird

text: Yes

text: Luxembourg

text: Dudelange

text: Corvus corone

text: Bird

text: Campylobacter jejuni

text: Campylobacter jejuni


text: Ragimbeau

text: public

text: PFM sweep metagenomics from Bird

text: Yes

text: Luxembourg

text: Dudelange

text: Pica pica

text: Bird

text: Campylobacter jejuni

characteristic: organism

text: Campylobacter jejuni

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-LAST-UPDATE

text: Ragimbeau

text: public

text: PFM sweep metagenomics from Bird

text: Yes

text: Luxembourg

text: Dudelange

text: Corvus monedula

text: Bird

text: Campylobacter jejuni

text: Campylobacter jejuni


text: Ragimbeau

text: public

characteristic: SRA accession

characteristic: Submitter Id

text: PFM sweep metagenomics from Bird

text: Yes

text: Luxembourg

text: Dudelange

text: Falco

text: Bird

text: Campylobacter jejuni

text: Campylobacter jejuni


characteristic: External Id

text: Ragimbeau

characteristic: INSDC center name

text: public

text: PFM sweep metagenomics from Bird

text: Yes

text: Luxembourg

text: Dudelange

text: Apus apus

text: Bird

text: Campylobacter jejuni

text: Campylobacter jejuni


text: Ragimbeau

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: PFM sweep metagenomics from Bird

text: Yes

text: Luxembourg

text: Dudelange

text: Turdus

text: Bird

text: Campylobacter jejuni

text: Campylobacter jejuni


text: Ragimbeau

text: public

text: PFM sweep metagenomics from Bird

characteristic: description

text: Yes

text: Luxembourg

text: Dudelange

text: Columba

text: Bird

text: Campylobacter jejuni

text: Campylobacter jejuni


text: Ragimbeau

text: public

text: PFM sweep metagenomics from Bird

text: Yes

text: Luxembourg

text: Dudelange

text: Buteo buteo

text: Bird

text: Campylobacter jejuni

text: Campylobacter jejuni


text: Ragimbeau

text: public

text: PFM sweep metagenomics from Bird

text: Yes

text: Luxembourg

text: Wasserbillig

text: Anas

text: Bird

text: Campylobacter jejuni

text: Campylobacter jejuni


text: Ragimbeau

text: public

text: PFM sweep metagenomics from Bird

text: Yes

text: Luxembourg

text: Wasserbillig

text: Alopochen aegyptiacus

text: Bird

text: Campylobacter jejuni

text: Campylobacter jejuni


text: Ragimbeau

text: public

text: PFM sweep metagenomics from Bird

text: Yes

text: Luxembourg

text: Uerbersyren

text: Emberiza citrinella

text: Bird

text: Campylobacter jejuni

text: Campylobacter jejuni


text: Ragimbeau

text: public

text: PFM sweep metagenomics from Bird

text: Yes

text: Luxembourg

text: Uerbersyren

text: Sylvia atricapilla

text: Bird

text: Campylobacter jejuni

text: Campylobacter jejuni


text: Ragimbeau

text: public

text: PFM sweep metagenomics from Bird

text: Yes

text: Luxembourg

text: Dudelange

text: Asio otus

text: Bird

text: Campylobacter jejuni

text: Campylobacter jejuni


text: Ragimbeau

text: public

text: PFM sweep metagenomics from Bird

text: Yes

text: Luxembourg

text: Dudelange

text: Sturnus

text: Bird

text: Campylobacter jejuni

text: Campylobacter jejuni


text: Ragimbeau

text: public

text: PFM sweep metagenomics from Bird

text: Yes

text: Luxembourg

text: Dudelange

text: Parus major

text: Bird

text: Campylobacter jejuni

text: Campylobacter jejuni


text: Ragimbeau

text: public

text: PFM sweep metagenomics from Bird

text: Yes

text: Luxembourg

text: Dudelange

text: Dendrocopos major

text: Bird

text: Campylobacter jejuni

text: Campylobacter jejuni


text: Ragimbeau

text: public

text: PFM sweep metagenomics from Bird

text: Yes

text: Luxembourg

text: Uerbersyren

text: Prunella modularis

text: Bird

text: Campylobacter jejuni

text: Campylobacter jejuni


text: Ragimbeau

text: public

text: PFM sweep metagenomics from Bird

text: Yes

text: Luxembourg

text: Dudelange

text: Garrulus

text: Bird

text: Campylobacter jejuni

text: Campylobacter jejuni


text: Ragimbeau

text: public

text: PFM sweep metagenomics from Bird

text: Yes

text: Luxembourg

text: Dudelange

text: Fringilla coelebs

text: Bird

text: Campylobacter jejuni

text: Campylobacter jejuni


text: Ragimbeau

text: public

text: PFM sweep metagenomics from Bird

text: Yes

text: Luxembourg

text: Dudelange

text: Corvus monedula

text: Bird

text: Campylobacter jejuni

text: Campylobacter jejuni


text: Ragimbeau

text: public

text: PFM sweep metagenomics from Bird

text: Yes

text: Luxembourg

text: Dudelange

text: Passer

text: Bird

text: Campylobacter jejuni

text: Campylobacter jejuni


text: Ragimbeau

text: public

text: PFM sweep metagenomics from Bird

text: Yes

text: Luxembourg

text: Dudelange

text: Pica pica

text: Bird

text: Campylobacter jejuni

text: Campylobacter jejuni


text: Ragimbeau

text: public

text: PFM sweep metagenomics from Mammals

text: Yes

text: Luxembourg

text: Dudelange

text: Procyon

text: Mammals

text: Campylobacter jejuni

text: Campylobacter jejuni


text: Ragimbeau

text: public

text: PFM sweep metagenomics from Surface water

text: Yes

text: Luxembourg

text: Moselle (Wasserbillig)

text: Surface water

text: Campylobacter jejuni

text: Campylobacter jejuni


text: Ragimbeau

text: public

text: Yes

text: Luxembourg

text: Alzette Schifflange

text: Surface water

text: Campylobacter jejuni

text: Campylobacter jejuni


text: Ragimbeau

text: public

text: Yes

text: Luxembourg

text: Alzette Hesperange Amont step

text: Surface water

text: Campylobacter jejuni

text: Campylobacter jejuni


text: Ragimbeau

text: public

text: Yes

text: Luxembourg

text: Alzette Hesperange Aval step

text: Surface water

text: Campylobacter jejuni

text: Campylobacter jejuni


text: Ragimbeau

text: public

text: Yes

text: Luxembourg

text: Sûre (Wasserbillig)

text: Surface water

text: Campylobacter jejuni

text: Campylobacter jejuni


text: Ragimbeau

text: public

text: Yes

text: Luxembourg

text: Alzette Huncherange

text: Surface water

text: Campylobacter jejuni

text: Campylobacter jejuni


text: public

tag: Namespace:Novo Nordisk Foundation Center for Stem Cell Biology (DanStem), University of Copenhagen

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characteristic: broker name

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text: Protocols: EpiSCs were seeded at ~6 × 103 cells/cm2 in six-well cell-culture plates pre-coated with 15 µg/ml human Fibronectin, and differentiated to PS as described in the article. At desired time-points, cells were dissociated using Accutase (Thermo Fisher Scientific, 00-4555-56) for 3 min at 37 °C and counted. 500,000 cells per condition were washed with ice-cold FACS buffer (10% (v/v) FBS in PBS) and resuspended into 1 ml ice-cold FACS buffer containing 1 µg/ml DAPI.Cells were washed with 500 μl ice-cold FACS buffer, centrifuged again at 350 × g for 3 min and resuspended into 250 μl ice-cold FACS buffer containing 1 µg/ml DAPI. Singlecells from in vitro-differentiated cells were sorted into Eppendorf Polypropylene U-shaped 384-well Twin Tec PCR Microplates (Thermo Fisher Scientific, 10573035), containing 2 μl of lysis solution (0.2% (v/v) Triton X-100) supplemented with 0.4 U/μl RNasin Ribonuclease Inhibitor (Promega, N2515) and 400 nM indexed RT primer from group 1 (1-96 barcodes) or group 2 (97-192 barcodes)63 Cells were washed with 500 μl ice-cold FACS buffer, centrifuged again at 350 × g for 3 min and resuspended into 250 μl ice-cold FACS buffer containing 1 µg/ml DAPI. Singlecells from in vitro-differentiated cells were sorted into Eppendorf Polypropylene U-shaped 384-well Twin Tec PCR Microplates (Thermo Fisher Scientific, 10573035), containing 2 μl of lysis solution (0.2% (v/v) Triton X-100) supplemented with 0.4 U/μl RNasin Ribonuclease Inhibitor (Promega, N2515) and 400 nM indexed RT primer from group 1 (1-96 barcodes) or group 2 (97-192 barcodes). Additionally, 71 WT EpiSCs were sorted into each plate, as spike-in control for batch-effect correction. Capture plates were prepared on the Bravo automated liquid handling robot station (Agilent) using 384-filtered tips (Agilent, 19133-142). Index sorting was performed using a FACS Aria III cell sorter (BD Biosciences) at the DanStem Flow Cytometry Platform (University of Copenhagen, Copenhagen, Denmark), sorting live cells as singlets. Immediately after sorting, plates were spun down, snap-frozen on dry ice and stored at −80 °C until further processing. Semi-automated library preparation was performed, using 10-12 total cycles of PCR amplification and AMPure XP beads (Beckman Coulter Life Sciences, A63881) for purification63. DNA concentration was measured with a Qubit Fluorometer (Thermo Fisher Scientific, Q32854) and fragment size was determined with a Fragment analyzer (Agilent).

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