characteristic: External Id

text: West of Scotland Specialist Virology Centre, NHSGGC / MRC-University of Glasgow Centre for Virus Research

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: COVID-19 Genomics UK Consortium

characteristic: collecting institution

characteristic: collection date

text: not provided

characteristic: collector name

text: not provided

characteristic: definition for seropositive sample

text: United Kingdom

characteristic: geographic location (country and/or sea)

text: Scotland

characteristic: geographic location (region and locality)

text: not provided

characteristic: host common name

text: not provided

characteristic: host health state

text: Human

characteristic: host scientific name

text: not provided

characteristic: host sex

text: not provided

characteristic: host subject id

text: not provided

characteristic: isolate

characteristic: sample capture status

text: not provided

characteristic: serotype (required for a seropositive sample)

text: not provided

characteristic: virus identifier


status: PUBLIC

tag: attribute

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC first public

text: public

characteristic: INSDC status

characteristic: SRA accession

tag: Namespace:Instituto de Investigacion Biosanitaria del Principado de Asturias (ISPA)

characteristic: Submitter Id

text: RNA

text: house mouse

characteristic: common name

text: RNA sample isolated from mouse hippocampus (Control condition)

characteristic: description

text: Mus musculus

characteristic: organism

text: Mus musculus

text: male

characteristic: sex

text: hippocampus

characteristic: title


text: Instituto de Investigacion Biosanitaria del Principado de Asturias (ISPA)

characteristic: INSDC last update

text: public

text: RNA

text: house mouse

text: Mus musculus

text: Mus musculus

text: male

text: hippocampus


text: public

text: RNA

text: house mouse

text: RNA sample isolated from mouse hippocampus (Resistance condition)

text: Mus musculus

text: Mus musculus

text: male

text: hippocampus


text: public

text: RNA

text: house mouse

text: RNA sample isolated from mouse hippocampus (Endurance condition)

text: Mus musculus

text: Mus musculus

text: male

text: hippocampus


text: public

tag: Namespace:CNRS - UMR 8126 University Paris-Saclay Gustave Roussy

text: ArrayExpress

characteristic: broker name

text: immortal cell line cell

text: human

text: Protocols: All samples correspond to human rhabdomyosarcoma TE671 cell line. The cells expressing shZNF55 and non targeting shCtl were compared. Cells were washed in PBS and were mixed with 500 µl of ice-cold MES lysis buffer, incubated for 5 min and centrifuged et 10 000 rpm for 5 min. The supernatant was collected and then diluted in 300 µl of LDS extraction buffer (glycerol 10%, Tris-Base (0.14 M), Tris-HCl (0.14M), LDS (2%), EDTA 500nM). The samples were shortly sonicated to reduce the viscosity and then centrifuged. The obtained supernatant was mixed with an equal volume of phenol:chloroform:isoamyl alcohol (25:24:1 [vol/vol]). The aqueous phase was retained by centrifugation, and then the dissolved DNA was precipitated with 0.1 volume of NaCl 2.5 M and 2.5 times greater volume of ice-cold ethanol. The samples were then centrifuged at 15000 × g for 15 min at 4°C. Finally, the pellet of DNA was washed with pre-cooled 70% ethanol and resuspended in 50 μL Milli-Q water. Concentration of the extracted DNA was measured using the Qubit instrument and the Qubit dsDNA HS Assay Kit (Thermo Fisher Scientific). The genomic DNA was sonicated (approximately 300-700 bp in size) and MIRA pull-down was performed using the Methyl Collector Ultra Kit (Active Motif) per manufacturer’s instructions starting with 1 µg of DNA and using high salt binding conditions. Extracted genomic DNA (gDNA) was sonicated in a Covaris S220 (LGC Genomics GmbH) to a mean fragment size of 180 bp. Fragment length distribution was assessed by microelectrophoresis using the Bioanalyseur 2100 (Agilent). Enriched DNA and Input DNA fragments were end-repaired, extended with an 'A' base on the 3′end, ligated with indexed paired-end adaptors (NEXTflex, Bioo Scientific) using the Bravo Platform (Agilent) and amplified by PCR for 10 cycles. The final libraries were purified with AMPure XP beads (Beckman Coulter).

text: adult

characteristic: developmental stage

text: embryonal rhabdomyosarcoma

characteristic: disease

text: control shRNA

characteristic: genotype

text: Homo sapiens

text: Homo sapiens

text: skeletal muscle tissue

characteristic: organism part

text: Homo sapiens


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: CNRS - UMR 8126 University Paris-Saclay Gustave Roussy

text: public

text: ArrayExpress

text: immortal cell line cell

text: human

text: adult

text: embryonal rhabdomyosarcoma

text: control shRNA

text: Homo sapiens

text: Homo sapiens

text: skeletal muscle tissue

text: Homo sapiens


characteristic: INSDC center name

characteristic: INSDC first public

text: public

characteristic: INSDC status

characteristic: SRA accession

text: ArrayExpress

text: immortal cell line cell

text: human

text: adult

text: embryonal rhabdomyosarcoma

text: ZNF555 shRNA

text: Homo sapiens

text: Homo sapiens

text: skeletal muscle tissue

text: Homo sapiens


text: HANYANG UNIVERSITY

text: public

tag: Namespace:HANYANG UNIVERSITY

characteristic: Submitter Id

characteristic: collection date

text: fecal environment

characteristic: environment (biome)

text: feces

characteristic: environment (feature)

text: feces

characteristic: environment (material)

text: South Korea

characteristic: geographic location (country and/or sea)

unit: DD

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: human-gut

characteristic: human gut environmental package

text: metagenome

characteristic: investigation type

text: human gut metagenome

characteristic: organism

text: Human gut microbiome

characteristic: project name

text: human gut metagenome

text: Illumina

characteristic: sequencing method

text: Human gut microbiome


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: STATION BIOLOGIQUE DE ROSCOFF

characteristic: INSDC center name

characteristic: INSDC last update

text: public

tag: Namespace:STATION BIOLOGIQUE DE ROSCOFF

text: Control

characteristic: description

text: Saccharina latissima

text: Saccharina latissima

characteristic: title


text: STATION BIOLOGIQUE DE ROSCOFF

characteristic: INSDC first public

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: Helgoland

text: Saccharina latissima

text: Saccharina latissima


text: STATION BIOLOGIQUE DE ROSCOFF

text: public

text: Norway

text: Saccharina latissima

text: Saccharina latissima


text: STATION BIOLOGIQUE DE ROSCOFF

text: public

text: Roscoff

text: Saccharina latissima

text: Saccharina latissima


text: STATION BIOLOGIQUE DE ROSCOFF

text: public

text: Svalbard

text: Saccharina latissima

text: Saccharina latissima


text: Indian Institute of Science

text: public

tag: Namespace:Indian Institute of Science

text: human

characteristic: common name

text: Exosome

text: male

characteristic: gender

text: Homo sapiens

text: WHO-PLAN A

characteristic: phenotype

text: Homo sapiens

text: Dengue infected patient


text: Indian Institute of Science

text: public

text: human

text: Exosome

text: male

text: Homo sapiens

characteristic: organism

text: WHO-PLAN B

text: Homo sapiens

text: Dengue infected patient


text: Indian Institute of Science

text: public

text: human

text: Exosome

text: male

text: Homo sapiens

text: WHO-PLAN C

text: Homo sapiens

text: Dengue infected patient


text: Indian Institute of Science

text: public

text: human

text: Exosome

text: male

text: Homo sapiens

text: Control

text: Homo sapiens

text: Dengue infected patient


text: Indian Institute of Science

text: public

text: human

text: cell culture

text: unknown

text: Homo sapiens

text: Lung cancer

text: Homo sapiens

text: Lung cancer cell culture


text: public

tag: Namespace:EMBL-EBI, WELLCOME TRUST GENOME CAMPUS, CAMBRIDGE

text: house mouse

text: Mus musculus

text: Mus musculus


text: EMBL-EBI, WELLCOME TRUST GENOME CAMPUS, CAMBRIDGE

text: public

text: house mouse

text: Mus musculus

text: Mus musculus


text: Indian Institute of Science

text: public

text: human

text: Serum

text: male

text: Homo sapiens

text: WHO-PLAN A

text: Homo sapiens

text: Dengue infected patient


text: Indian Institute of Science

text: public

text: human

text: Serum

text: male

text: Homo sapiens

text: WHO-PLAN B

text: Homo sapiens

text: Dengue infected patient


text: Indian Institute of Science

text: public

text: human

text: Serum

text: male

text: Homo sapiens

text: WHO-PLAN C

text: Homo sapiens

text: Dengue infected patient


text: Indian Institute of Science

text: public

text: human

text: Serum

text: male

text: Homo sapiens

text: Control

text: Homo sapiens

text: Dengue infected patient


text: MPIEVB

text: public

characteristic: antibiotics 6 months

characteristic: antibiotics 6 weeks

characteristic: cdai

characteristic: collection date

text: human

text: Maltese IBD study-cases treatment naive-fecal

text: fecal

characteristic: environment (biome)

text: stool

characteristic: environment (feature)

text: stool

characteristic: environment (material)

text: IBD

characteristic: experimental factor

text: Ulcerative colitis

characteristic: gastrointestinal tract disorder

text: Malta

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: Mater Dei Hospital, Triq Dun Karm, L-Imsida, MSD2090, Malta

characteristic: geographic location (region and locality)

characteristic: godin-leisure

characteristic: harvey-bradshaw

unit: years

characteristic: host age

text: stool

characteristic: host body product

text: stool

characteristic: host body site

characteristic: host body-mass index

text: diseased

characteristic: host disease status

unit: cm

characteristic: host height

text: Ulcerative colitis

characteristic: host phenotype

text: female

characteristic: host sex

characteristic: host subject id

unit: kg

characteristic: host total mass

text: human-gut

characteristic: human gut environmental package

characteristic: ibd subtype montreal classification

text: metagenome

characteristic: investigation type

characteristic: medication non ibd

characteristic: medication-azathioprine

characteristic: medication-infliximab

characteristic: medication-mesalazine

characteristic: medication-prednisolone

text: QIAamp DNA fast stool mini kit

characteristic: nucleic acid extraction

text: Homo sapiens

text: 27F-AGAGTTTGATCCTGGCTCAG; 338R-TGCTGCCTCCCGTAGGAGT

characteristic: pcr primers

text: Dysbiosis of the gut microbiota in Maltese patients with treatment naive Inflammatory Bowel Disease

characteristic: project name

unit: °C

characteristic: sample storage temperature

characteristic: sccai

text: Homo sapiens

text: ILLUMINA

characteristic: sequencing method

text: no

text: 16S rRNA

text: Maltese IBD study-cases treatment naive


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: MPIEVB

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

characteristic: antibiotics 6 months

characteristic: antibiotics 6 weeks

characteristic: cdai

characteristic: collection date

text: human

characteristic: common name

characteristic: description

text: fecal

characteristic: environment (biome)

text: stool

characteristic: environment (feature)

text: stool

characteristic: environment (material)

text: IBD

characteristic: experimental factor

text: Ulcerative colitis

characteristic: gastrointestinal tract disorder

text: Malta

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

characteristic: geographic location (region and locality)

characteristic: godin-leisure

characteristic: harvey-bradshaw

characteristic: host age

text: stool

characteristic: host body product

text: stool

characteristic: host body site

characteristic: host body-mass index

text: diseased

characteristic: host disease status

characteristic: host height

text: Ulcerative colitis

characteristic: host phenotype

text: male

characteristic: host sex

text: human-gut

text: metagenome

text: QIAamp DNA fast stool mini kit

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: ILLUMINA

text: yes

text: 16S rRNA

text: Maltese IBD study-cases treatment naive


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: MPIEVB

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

characteristic: antibiotics 6 months

characteristic: antibiotics 6 weeks

characteristic: cdai

characteristic: collection date

text: human

characteristic: common name

characteristic: description

text: fecal

characteristic: environment (biome)

text: stool

characteristic: environment (feature)

text: stool

characteristic: environment (material)

text: IBD

characteristic: experimental factor

text: Ulcerative colitis

text: Malta

text: stool

text: stool

text: diseased

text: Ulcerative colitis

text: male

characteristic: host subject id

characteristic: host total mass

text: human-gut

characteristic: human gut environmental package

characteristic: ibd subtype montreal classification

text: metagenome

characteristic: investigation type

characteristic: medication non ibd

characteristic: medication-azathioprine

characteristic: medication-infliximab

characteristic: medication-mesalazine

characteristic: medication-prednisolone

text: QIAamp DNA fast stool mini kit

characteristic: nucleic acid extraction

text: Homo sapiens

characteristic: pcr primers

characteristic: project name

characteristic: sample storage temperature

characteristic: sccai

text: Homo sapiens

text: ILLUMINA

characteristic: sequencing method

text: ex

text: 16S rRNA

text: Maltese IBD study-cases treatment naive


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: MPIEVB

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

characteristic: antibiotics 6 months

characteristic: antibiotics 6 weeks

characteristic: cdai

characteristic: collection date

text: human

characteristic: common name

characteristic: description

text: fecal

characteristic: environment (biome)

text: stool

characteristic: environment (feature)

text: stool

characteristic: environment (material)

text: IBD

characteristic: experimental factor

text: Crohn's Disease

characteristic: gastrointestinal tract disorder

text: Malta

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

characteristic: geographic location (region and locality)

characteristic: godin-leisure

characteristic: harvey-bradshaw

characteristic: host age

text: stool

characteristic: host body product

text: stool

characteristic: host body site

characteristic: host body-mass index

text: diseased

characteristic: host disease status

characteristic: host height

text: Crohn's Disease

characteristic: host phenotype

text: male

characteristic: host sex

text: human-gut

text: metagenome

text: QIAamp DNA fast stool mini kit

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: ILLUMINA

text: no

text: 16S rRNA

text: Maltese IBD study-cases treatment naive


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: MPIEVB

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

characteristic: antibiotics 6 months

characteristic: antibiotics 6 weeks

characteristic: cdai

characteristic: collection date

text: human

characteristic: common name

characteristic: description

text: fecal

characteristic: environment (biome)

text: stool

characteristic: environment (feature)

text: stool

characteristic: environment (material)

text: IBD

characteristic: experimental factor

text: Crohn's Disease

text: Malta

text: stool

text: stool

text: diseased

text: Crohn's Disease

text: female

characteristic: host subject id

characteristic: host total mass

text: human-gut

characteristic: human gut environmental package

characteristic: ibd subtype montreal classification

text: metagenome

characteristic: investigation type

characteristic: medication non ibd

characteristic: medication-azathioprine

characteristic: medication-infliximab

characteristic: medication-mesalazine

characteristic: medication-prednisolone

text: QIAamp DNA fast stool mini kit

characteristic: nucleic acid extraction

text: Homo sapiens

characteristic: pcr primers

characteristic: project name

characteristic: sample storage temperature

characteristic: sccai

text: Homo sapiens

text: ILLUMINA

characteristic: sequencing method

text: no

text: 16S rRNA

text: Maltese IBD study-cases treatment naive


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: MPIEVB

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

characteristic: antibiotics 6 months

characteristic: antibiotics 6 weeks

characteristic: cdai

characteristic: collection date

text: human

characteristic: common name

characteristic: description

text: fecal

characteristic: environment (biome)

text: stool

characteristic: environment (feature)

text: stool

characteristic: environment (material)

text: IBD

characteristic: experimental factor

text: Crohn's Disease

characteristic: gastrointestinal tract disorder

text: Malta

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

characteristic: geographic location (region and locality)

characteristic: godin-leisure

characteristic: harvey-bradshaw

characteristic: host age

text: stool

characteristic: host body product

text: stool

characteristic: host body site

characteristic: host body-mass index

text: diseased

characteristic: host disease status

characteristic: host height

text: Crohn's Disease

characteristic: host phenotype

text: female

characteristic: host sex

text: human-gut

text: metagenome

text: QIAamp DNA fast stool mini kit

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: ILLUMINA

text: yes

text: 16S rRNA

text: Maltese IBD study-cases treatment naive


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: MPIEVB

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

characteristic: antibiotics 6 months

characteristic: antibiotics 6 weeks

characteristic: cdai

characteristic: collection date

text: human

characteristic: common name

characteristic: description

text: fecal

characteristic: environment (biome)

text: stool

characteristic: environment (feature)

text: stool

characteristic: environment (material)

text: IBD

characteristic: experimental factor

text: Ulcerative colitis

text: Malta

text: stool

text: stool

text: diseased

text: Ulcerative colitis

text: male

characteristic: host subject id

characteristic: host total mass

text: human-gut

characteristic: human gut environmental package

characteristic: ibd subtype montreal classification

text: metagenome

characteristic: investigation type

characteristic: medication non ibd

characteristic: medication-azathioprine

characteristic: medication-infliximab

characteristic: medication-mesalazine

characteristic: medication-prednisolone

text: QIAamp DNA fast stool mini kit

characteristic: nucleic acid extraction

text: Homo sapiens

characteristic: pcr primers

characteristic: project name

characteristic: sample storage temperature

characteristic: sccai

text: Homo sapiens

text: ILLUMINA

characteristic: sequencing method

text: no

text: 16S rRNA

text: Maltese IBD study-cases treatment naive


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: MPIEVB

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

characteristic: antibiotics 6 months

characteristic: antibiotics 6 weeks

characteristic: cdai

characteristic: collection date

text: human

characteristic: common name

characteristic: description

text: fecal

characteristic: environment (biome)

text: stool

characteristic: environment (feature)

text: stool

characteristic: environment (material)

text: IBD

characteristic: experimental factor

text: Crohn's Disease

characteristic: gastrointestinal tract disorder

text: Malta

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

characteristic: geographic location (region and locality)

characteristic: godin-leisure

characteristic: harvey-bradshaw

characteristic: host age

text: stool

characteristic: host body product

text: stool

characteristic: host body site

characteristic: host body-mass index

text: diseased

characteristic: host disease status

characteristic: host height

text: Crohn's Disease

characteristic: host phenotype

text: female

characteristic: host sex

text: human-gut

text: metagenome

text: QIAamp DNA fast stool mini kit

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: ILLUMINA

text: ex

text: 16S rRNA

text: Maltese IBD study-cases treatment naive


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: MPIEVB

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

characteristic: antibiotics 6 months

characteristic: antibiotics 6 weeks

characteristic: cdai

characteristic: collection date

text: human

characteristic: common name

characteristic: description

text: fecal

characteristic: environment (biome)

text: stool

characteristic: environment (feature)

text: stool

characteristic: environment (material)

text: IBD

characteristic: experimental factor

text: Ulcerative colitis

text: Malta

text: stool

text: stool

text: diseased

text: Ulcerative colitis

text: female

characteristic: host subject id

characteristic: host total mass

text: human-gut

characteristic: human gut environmental package

characteristic: ibd subtype montreal classification

text: metagenome

characteristic: investigation type

characteristic: medication non ibd

characteristic: medication-azathioprine

characteristic: medication-infliximab

characteristic: medication-mesalazine

characteristic: medication-prednisolone

text: QIAamp DNA fast stool mini kit

characteristic: nucleic acid extraction

text: Homo sapiens

characteristic: pcr primers

characteristic: project name

characteristic: sample storage temperature

characteristic: sccai

text: Homo sapiens

text: ILLUMINA

characteristic: sequencing method

text: yes

text: 16S rRNA

text: Maltese IBD study-cases treatment naive


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: MPIEVB

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

characteristic: antibiotics 6 months

characteristic: antibiotics 6 weeks

characteristic: cdai

characteristic: collection date

text: human

characteristic: common name

characteristic: description

text: fecal

characteristic: environment (biome)

text: stool

characteristic: environment (feature)

text: stool

characteristic: environment (material)

text: IBD

characteristic: experimental factor

text: Crohn's Disease

characteristic: gastrointestinal tract disorder

text: Malta

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

characteristic: geographic location (region and locality)

characteristic: godin-leisure

characteristic: harvey-bradshaw

characteristic: host age

text: stool

characteristic: host body product

text: stool

characteristic: host body site

characteristic: host body-mass index

text: diseased

characteristic: host disease status

characteristic: host height

text: Crohn's Disease

characteristic: host phenotype

text: male

characteristic: host sex

text: human-gut

text: metagenome

text: QIAamp DNA fast stool mini kit

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: ILLUMINA

text: yes

text: 16S rRNA

text: Maltese IBD study-cases treatment naive


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: MPIEVB

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

characteristic: antibiotics 6 months

characteristic: antibiotics 6 weeks

characteristic: cdai

characteristic: collection date

text: human

characteristic: common name

characteristic: description

text: fecal

characteristic: environment (biome)

text: stool

characteristic: environment (feature)

text: stool

characteristic: environment (material)

text: IBD

characteristic: experimental factor

text: Crohn's Disease

text: Malta

text: stool

text: stool

text: diseased

text: Crohn's Disease

text: male

characteristic: host subject id

characteristic: host total mass

text: human-gut

characteristic: human gut environmental package

characteristic: ibd subtype montreal classification

text: metagenome

characteristic: investigation type

characteristic: medication non ibd

characteristic: medication-azathioprine

characteristic: medication-infliximab

characteristic: medication-mesalazine

characteristic: medication-prednisolone

text: QIAamp DNA fast stool mini kit

characteristic: nucleic acid extraction

text: Homo sapiens

characteristic: pcr primers

characteristic: project name

characteristic: sample storage temperature

characteristic: sccai

text: Homo sapiens

text: ILLUMINA

characteristic: sequencing method

text: ex

text: 16S rRNA

text: Maltese IBD study-cases treatment naive


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: MPIEVB

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

characteristic: antibiotics 6 months

characteristic: antibiotics 6 weeks

characteristic: cdai

characteristic: collection date

text: human

characteristic: common name

characteristic: description

text: fecal

characteristic: environment (biome)

text: stool

characteristic: environment (feature)

text: stool

characteristic: environment (material)

text: IBD

characteristic: experimental factor

text: Ulcerative colitis

characteristic: gastrointestinal tract disorder

text: Malta

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

characteristic: geographic location (region and locality)

characteristic: godin-leisure

characteristic: harvey-bradshaw

characteristic: host age

text: stool

characteristic: host body product

text: stool

characteristic: host body site

characteristic: host body-mass index

text: diseased

characteristic: host disease status

characteristic: host height

text: Ulcerative colitis

characteristic: host phenotype

text: female

characteristic: host sex

text: human-gut

text: metagenome

text: QIAamp DNA fast stool mini kit

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: ILLUMINA

text: ex

text: 16S rRNA

text: Maltese IBD study-cases treatment naive


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: Baldridge_ORCHARD_10_E5_SIC_index_0537_SIC_index_0545_AGCAGATAC_CTGCTGATA_S151_L001

tag: Namespace:WASHINGTON UNIVERSITY SCHOOL OF MEDICINE

characteristic: Submitter Id

text: house mouse

characteristic: common name

characteristic: description

text: Mus musculus

text: Mus musculus

characteristic: title


text: WASHINGTON UNIVERSITY SCHOOL OF MEDICINE

text: public

text: Baldridge_ORCHARD_10_F5_SIC_index_0538_SIC_index_0545_TGCAAACAG_CTGCTGATA_S152_L001

text: house mouse

text: Mus musculus

text: Mus musculus


text: public

text: Baldridge_ORCHARD_10_G5_SIC_index_0539_SIC_index_0545_TGTGAGGCT_CTGCTGATA_S153_L001

text: house mouse

text: Mus musculus

text: Mus musculus


text: public

text: Baldridge_ORCHARD_10_H5_SIC_index_0540_SIC_index_0545_TTCGCAACG_CTGCTGATA_S154_L001

text: house mouse

text: Mus musculus

text: Mus musculus


text: public

text: Baldridge_ORCHARD_1_A1_SIC_index_0496_SIC_index_0541_TCACTACAG_GGCAAGACT_S115_L001

text: house mouse

text: Mus musculus

text: Mus musculus


text: public

text: Baldridge_ORCHARD_1_B1_SIC_index_0497_SIC_index_0541_GAGATGAAA_GGCAAGACT_S116_L001

text: house mouse

text: Mus musculus

text: Mus musculus


text: public

text: Baldridge_ORCHARD_1_C1_SIC_index_0498_SIC_index_0541_TTGAGAGTG_GGCAAGACT_S117_L001

text: house mouse

text: Mus musculus

text: Mus musculus


text: public

text: Baldridge_ORCHARD_1_D1_SIC_index_0499_SIC_index_0541_TAGTGCCAG_GGCAAGACT_S118_L001

text: house mouse

text: Mus musculus

text: Mus musculus


text: public

text: Baldridge_ORCHARD_2_E1_SIC_index_0537_SIC_index_0541_AGCAGATAC_GGCAAGACT_S119_L001

text: house mouse

text: Mus musculus

text: Mus musculus


text: public

text: Baldridge_ORCHARD_2_F1_SIC_index_0538_SIC_index_0541_TGCAAACAG_GGCAAGACT_S120_L001

text: house mouse

text: Mus musculus

text: Mus musculus


text: public

text: Baldridge_ORCHARD_2_G1_SIC_index_0539_SIC_index_0541_TGTGAGGCT_GGCAAGACT_S121_L001

text: house mouse

text: Mus musculus

text: Mus musculus


text: public

text: Baldridge_ORCHARD_2_H1_SIC_index_0540_SIC_index_0541_TTCGCAACG_GGCAAGACT_S122_L001

text: house mouse

text: Mus musculus

text: Mus musculus


text: public

text: Baldridge_ORCHARD_3_A2_SIC_index_0496_SIC_index_0542_TCACTACAG_CCTGACGGC_S123_L001

text: house mouse

text: Mus musculus

text: Mus musculus


text: public

text: Baldridge_ORCHARD_3_B2_SIC_index_0497_SIC_index_0542_GAGATGAAA_CCTGACGGC_S124_L001

text: house mouse

text: Mus musculus

text: Mus musculus


text: public

text: Baldridge_ORCHARD_3_C2_SIC_index_0498_SIC_index_0542_TTGAGAGTG_CCTGACGGC_S125_L001

text: house mouse

text: Mus musculus

text: Mus musculus


text: public

text: Baldridge_ORCHARD_3_D2_SIC_index_0499_SIC_index_0542_TAGTGCCAG_CCTGACGGC_S126_L001

text: house mouse

text: Mus musculus

text: Mus musculus


text: public

text: Baldridge_ORCHARD_4_E2_SIC_index_0537_SIC_index_0542_AGCAGATAC_CCTGACGGC_S127_L001

text: house mouse

text: Mus musculus

text: Mus musculus


text: WASHINGTON UNIVERSITY SCHOOL OF MEDICINE

text: public

text: Baldridge_ORCHARD_4_F2_SIC_index_0538_SIC_index_0542_TGCAAACAG_CCTGACGGC_S128_L001

text: house mouse

text: Mus musculus

text: Mus musculus


text: public

text: Baldridge_ORCHARD_4_G2_SIC_index_0539_SIC_index_0542_TGTGAGGCT_CCTGACGGC_S129_L001

text: house mouse

text: Mus musculus

text: Mus musculus


text: public

text: Baldridge_ORCHARD_4_H2_SIC_index_0540_SIC_index_0542_TTCGCAACG_CCTGACGGC_S130_L001

text: house mouse

text: Mus musculus

text: Mus musculus


text: public

text: Baldridge_ORCHARD_5_A3_SIC_index_0496_SIC_index_0543_TCACTACAG_CAAACCTGC_S131_L001

text: house mouse

text: Mus musculus

text: Mus musculus


text: public

text: Baldridge_ORCHARD_5_B3_SIC_index_0497_SIC_index_0543_GAGATGAAA_CAAACCTGC_S132_L001

text: house mouse

text: Mus musculus

text: Mus musculus


text: public

text: Baldridge_ORCHARD_5_C3_SIC_index_0498_SIC_index_0543_TTGAGAGTG_CAAACCTGC_S133_L001

text: house mouse

text: Mus musculus

text: Mus musculus


text: public

text: Baldridge_ORCHARD_5_D3_SIC_index_0499_SIC_index_0543_TAGTGCCAG_CAAACCTGC_S134_L001

text: house mouse

text: Mus musculus

text: Mus musculus


text: public

text: Baldridge_ORCHARD_6_E3_SIC_index_0537_SIC_index_0543_AGCAGATAC_CAAACCTGC_S135_L001

text: house mouse

text: Mus musculus

text: Mus musculus


text: public

text: Baldridge_ORCHARD_6_F3_SIC_index_0538_SIC_index_0543_TGCAAACAG_CAAACCTGC_S136_L001

text: house mouse

text: Mus musculus

text: Mus musculus


text: public

text: Baldridge_ORCHARD_6_G3_SIC_index_0539_SIC_index_0543_TGTGAGGCT_CAAACCTGC_S137_L001

text: house mouse

text: Mus musculus

text: Mus musculus


text: public

text: Baldridge_ORCHARD_6_H3_SIC_index_0540_SIC_index_0543_TTCGCAACG_CAAACCTGC_S138_L001

text: house mouse

text: Mus musculus

text: Mus musculus


text: public

text: Baldridge_ORCHARD_7_A4_SIC_index_0496_SIC_index_0544_TCACTACAG_ACATGCGAT_S139_L001

text: house mouse

text: Mus musculus

text: Mus musculus


text: public

text: Baldridge_ORCHARD_7_B4_SIC_index_0497_SIC_index_0544_GAGATGAAA_ACATGCGAT_S140_L001

text: house mouse

text: Mus musculus

text: Mus musculus


text: public

text: Baldridge_ORCHARD_7_C4_SIC_index_0498_SIC_index_0544_TTGAGAGTG_ACATGCGAT_S141_L001

text: house mouse

text: Mus musculus

text: Mus musculus


text: public

text: Baldridge_ORCHARD_7_D4_SIC_index_0499_SIC_index_0544_TAGTGCCAG_ACATGCGAT_S142_L001

text: house mouse

text: Mus musculus

text: Mus musculus


text: public

text: Baldridge_ORCHARD_8_E4_SIC_index_0537_SIC_index_0544_AGCAGATAC_ACATGCGAT_S143_L001

text: house mouse

text: Mus musculus

text: Mus musculus


text: WASHINGTON UNIVERSITY SCHOOL OF MEDICINE

text: public

text: Baldridge_ORCHARD_8_F4_SIC_index_0538_SIC_index_0544_TGCAAACAG_ACATGCGAT_S144_L001

text: house mouse

text: Mus musculus

text: Mus musculus


text: public

text: Baldridge_ORCHARD_8_G4_SIC_index_0539_SIC_index_0544_TGTGAGGCT_ACATGCGAT_S145_L001

text: house mouse

text: Mus musculus

text: Mus musculus


text: public

text: Baldridge_ORCHARD_8_H4_SIC_index_0540_SIC_index_0544_TTCGCAACG_ACATGCGAT_S146_L001

text: house mouse

text: Mus musculus

text: Mus musculus


text: public

text: Baldridge_ORCHARD_9_A5_SIC_index_0496_SIC_index_0545_TCACTACAG_CTGCTGATA_S147_L001

text: house mouse

text: Mus musculus

text: Mus musculus


text: public

text: Baldridge_ORCHARD_9_B5_SIC_index_0497_SIC_index_0545_GAGATGAAA_CTGCTGATA_S148_L001

text: house mouse

text: Mus musculus

text: Mus musculus


text: public

text: Baldridge_ORCHARD_9_C5_SIC_index_0498_SIC_index_0545_TTGAGAGTG_CTGCTGATA_S149_L001

text: house mouse

text: Mus musculus

text: Mus musculus


text: public

text: Baldridge_ORCHARD_9_D5_SIC_index_0499_SIC_index_0545_TAGTGCCAG_CTGCTGATA_S150_L001

text: house mouse

text: Mus musculus

text: Mus musculus


text: public

tag: Namespace:West of Scotland Specialist Virology Centre, NHSGGC / MRC-University of Glasgow Centre for Virus Research

text: COVID-19 Genomics UK Consortium

characteristic: broker name

characteristic: collecting institution

characteristic: collection date

text: not provided

characteristic: collector name

text: not provided

characteristic: definition for seropositive sample

text: United Kingdom

characteristic: geographic location (country and/or sea)

text: Scotland

characteristic: geographic location (region and locality)

text: not provided

characteristic: host common name

text: not provided

characteristic: host health state

text: Human

characteristic: host scientific name

text: not provided

text: not provided

characteristic: host subject id

text: not provided

characteristic: isolate

text: Severe acute respiratory syndrome coronavirus 2

text: active surveillance in response to outbreak

characteristic: sample capture status

text: not provided

characteristic: serotype (required for a seropositive sample)

text: not provided

characteristic: virus identifier


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: West of Scotland Specialist Virology Centre, NHSGGC / MRC-University of Glasgow Centre for Virus Research

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: COVID-19 Genomics UK Consortium

text: not provided

text: not provided

text: United Kingdom

text: Scotland

text: not provided

text: not provided

text: Human

text: not provided

characteristic: host sex

text: not provided

text: not provided

characteristic: organism

text: not provided

text: not provided


text: Hebrew University, genetics department.

text: public

tag: Namespace:Hebrew University, genetics department.

text: ArrayExpress

characteristic: broker name

text: human

characteristic: common name

text: Protocols: Cells were trypsinized and collected 10% FBS Sin1 at 50uM Ladostigil 5.4uM RNeasy Plus Universal Mini Kit (QIAGEN) KAPA Stranded mRNA-Seq Kit

characteristic: description

text: neuroblastoma

characteristic: disease

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: bone marrow

characteristic: organism part

text: Homo sapiens

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: public

tag: Namespace:Universite Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette cedex, France

text: ArrayExpress

text: Protocols: Following a 75 minutes shift at 37°C, after reaching exponential phase at 25°C in YPD, cells were cross-linked with 1% formaldehyde during 10 minutes. DNA was extracted using the Auto iPure V2 kit from Diagenode, following the manufacturer recommendations. Library construction was done according to the takara SMARTER thruplex (takara bio) protocol, following manufacturer's recommendation. Libraries were sized with AMPure beads (Beckman-coulter) to a final size of 325bp.

text: exponential phase

characteristic: developmental stage

text: MATα ade2-1 lys2-801uag ura3-52 trp1-∆63 his3-∆200 leu2-∆ HIS3::3HA::RAD26 MED17::13Myc::TRP1 kin28::KanMX6 CEN kin28-ts16 LEU2

characteristic: genotype

text: YPD media

characteristic: growth condition

text: not applicable

characteristic: isolate

text: Saccharomyces cerevisiae S288C

text: Saccharomyces cerevisiae S288C

text: whole organism

text: temperature sensitive Kin28

characteristic: phenotype

text: Saccharomyces cerevisiae S288C


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Universite Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette cedex, France

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: ArrayExpress

text: exponential phase

text: MATα ade2-1 lys2-801uag ura3-52 trp1-∆63 his3-∆200 leu2-∆ HIS3::3HA::RAD26 MED17::13Myc::TRP1 kin28::KanMX6 CEN KIN28 LEU2

text: YPD media

text: not applicable

text: Saccharomyces cerevisiae S288C

text: Saccharomyces cerevisiae S288C

text: whole organism

text: wild type

text: Saccharomyces cerevisiae S288C


text: public

characteristic: Submitter Id

text: ArrayExpress

characteristic: broker name

characteristic: description

text: exponential phase

text: YPD media

text: not applicable

text: Saccharomyces cerevisiae S288C

characteristic: organism

text: Saccharomyces cerevisiae S288C

text: whole organism

text: temperature sensitive Kin28

text: Saccharomyces cerevisiae S288C


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: public

text: ArrayExpress

text: exponential phase

text: MATα ade2-1 lys2-801uag ura3-52 trp1-∆63 his3-∆200 leu2-∆ RAD10::3HA::HIS3 MED17::13Myc::TRP1 kin28::KanMX6 CEN kin28-ts16 LEU2

text: YPD media

text: not applicable

text: Saccharomyces cerevisiae S288C

text: Saccharomyces cerevisiae S288C

text: whole organism

characteristic: organism part

text: temperature sensitive Kin28

text: Saccharomyces cerevisiae S288C

characteristic: title


text: public

text: ArrayExpress

text: exponential phase

characteristic: developmental stage

text: MATα ade2-1 lys2-801uag ura3-52 trp1-∆63 his3-∆200 leu2-∆ RAD10::3HA::HIS3 MED17::13Myc::TRP1 kin28::KanMX6 CEN KIN28 LEU2

characteristic: genotype

text: YPD media

characteristic: growth condition

text: not applicable

characteristic: isolate

text: Saccharomyces cerevisiae S288C

text: Saccharomyces cerevisiae S288C

text: whole organism

text: wild type

text: Saccharomyces cerevisiae S288C


characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC center name

text: public

text: ArrayExpress

text: exponential phase

text: MATa ura3-52 his3-Δ200 ade2-101uaa trp1-Δ63 lys2-801uag leu2-Δ1 RAD1::3HA::HIS3 MED17::13Myc::TRP1 kin28::KanMX6 CEN kin28ts16 LEU2

text: YPD media

text: not applicable

text: Saccharomyces cerevisiae S288C

text: Saccharomyces cerevisiae S288C

text: whole organism

text: temperature sensitive Kin28

characteristic: phenotype

text: Saccharomyces cerevisiae S288C


characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: ArrayExpress

text: exponential phase

text: MATa ura3-52 his3-Δ200 ade2-101uaa trp1-Δ63 lys2-801uag leu2-Δ1 RAD1::3HA::HIS3 MED17::13Myc::TRP1 kin28::KanMX6 CEN KIN28 LEU2

text: YPD media

text: not applicable

text: Saccharomyces cerevisiae S288C

text: Saccharomyces cerevisiae S288C

text: whole organism

text: wild type

text: Saccharomyces cerevisiae S288C


text: public

characteristic: Submitter Id

text: ArrayExpress

characteristic: broker name

characteristic: description

text: exponential phase

text: YPD media

text: not applicable

text: Saccharomyces cerevisiae S288C

characteristic: organism

text: Saccharomyces cerevisiae S288C

text: whole organism

text: temperature sensitive Kin28

text: Saccharomyces cerevisiae S288C


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: public

text: ArrayExpress

text: exponential phase

text: YPD media

text: not applicable

text: Saccharomyces cerevisiae S288C

text: Saccharomyces cerevisiae S288C

text: whole organism

characteristic: organism part

text: wild type

text: Saccharomyces cerevisiae S288C

characteristic: title


text: public

tag: Namespace:INSERM U1242 OSS (Oncogenesis, Stress and Signaling) - Universite de Rennes1

text: ArrayExpress

text: human

characteristic: common name

text: Protocols: Whole blood samples were collected before the first administration of any cytotoxic agent from patients with a histologically or cytologically confirmed CD56+ chemotherapy-naïve SCLC. Patients were eligible to a systemic treatment and were part of a larger ongoing prospective non-interventional study conducted at Rennes University Hospital. Any active neoplasia other than SCLC or known HIV, HCV or HBV infection, was considered as an exclusion criterion. Isolation of CD56+CTCs from whole blood sample. CTC00 enrichment was performed using the EasySep™ Direct Human CTC Enrichment Kit (StemCell Technologies®) according to manufacturer instruction. Approximately 10 ml of the heparin blood samples was gently mixed and incubated with CTC enrichment cocktail at room temperature for 5 min in constant mixing. After dilution of 1:2 in PBS 2%-BSA the blood was incubated with buffer EasySep and RapidSpheres™ (StemCell,Canada) in “Big Easy” StemCell magnet for 10 minutes. The cells suspension was collected and the same immunomagnetic depletion step was repeated. Final cell suspension was centrifuged and the pellet resuspended in 70µL of PBS 2% BSA, 100 000 PBMC were added (see below for isolation method). Cell suspension was washed in PBS 2% BSA and incubated with saturating concentrations of fluorescent‐labelled antibodies against human CD56, CD45 and Cd235a (Milteny®) for 15 min at 4°C. Cells were then washed with PBS 2%-BSA, analyzed and sorted by flow cytometry using a FACSAria II (Becton Dickinson). For whole exome sequencing, the population of interest was gated according to its CD56/CD45 criteria to avoid NK lymphocytes (CD56+/CD45+) contamination. Cells CD56 + and CD45- were sorted, centrifuged, and immediately frozen at -80°C. Data were analyzed with FlowJow software. PBMC isolation from whole blood samples. The blood sample collected in EDTA-K2 tube (1x5mL tubes) was diluted in an equal volume of PBS 2% BSA. Five milliters of Ficoll-Paque™ (Milteny®) was carefully added on the suspension, then centrifuged 20 minutes at 1200 x g at room temperature without brake. The mononuclear cell layer was carefully aspirated and diluted with an equal volume of PBS 2% BSA. For whole exome sequencing, the suspension was centrifuged, washed in PBS 2% BSA and immediately frozen at -80°C. Genomic DNA (DNAg) of CTCs were prepared using the REPLI-g Single Cell Kit (Quiagen, Germany) according to manufacturer's recommendations. DNAg from PBMC were prepared using QIAamp DNA Mini Kit (Quiagen, Germany) according to manufacturer's recommendations. Tumor biopsies were deparaffinized with Deparaffinization Solution (Qiagen, Germany) at 56°C for 3 minutes. DNA was extracted using QIAamp DNA FFPE Tissue Kit (Quiagen, Germany) according to manufacturer's recommendations. DNAg from PBMC were prepared using QIAamp DNA Mini Kit (Quiagen, Germany) according to manufacturer's recommendations. Total genomic DNA library was prepared, at each step a control quality of process was performed (Fragment Analyzer and qPCR assays). The steps from library preparation, exome capture and sequencing were performed by Integragen SA (Evry, France) according to manufacturer’s instruction and relative protocols (SureSelect, Agilent) without modification except for library preparation performed with NEBNext® Ultra II kit (New England Biolabs®). Genomic DNA is captured using Agilent in-solution enrichment methodology with their biotinylated oligonucleotides probes library (SureSelect Clinical Research Exome V2, Agilent Technologies).

text: adult

characteristic: developmental stage

text: small cell lung carcinoma

characteristic: disease

text: unsorted

characteristic: immunophenotype

characteristic: individual

text: not applicable

characteristic: isolate

text: Homo sapiens

text: Homo sapiens

text: lung

text: neoplasm

characteristic: sampling site

text: at initial diagnosis

characteristic: sampling time point

text: Homo sapiens

text: FFPE

characteristic: specimen with known storage state


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: INSERM U1242 OSS (Oncogenesis, Stress and Signaling) - Universite de Rennes1

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: ArrayExpress

text: human

text: Protocols: Whole blood samples were collected before the first administration of any cytotoxic agent from patients with a histologically or cytologically confirmed CD56+ chemotherapy-naïve SCLC. Patients were eligible to a systemic treatment and were part of a larger ongoing prospective non-interventional study conducted at Rennes University Hospital. Any active neoplasia other than SCLC or known HIV, HCV or HBV infection, was considered as an exclusion criterion. Isolation of CD56+CTCs from whole blood sample. CTC00 enrichment was performed using the EasySep™ Direct Human CTC Enrichment Kit (StemCell Technologies®) according to manufacturer instruction. Approximately 10 ml of the heparin blood samples was gently mixed and incubated with CTC enrichment cocktail at room temperature for 5 min in constant mixing. After dilution of 1:2 in PBS 2%-BSA the blood was incubated with buffer EasySep and RapidSpheres™ (StemCell,Canada) in “Big Easy” StemCell magnet for 10 minutes. The cells suspension was collected and the same immunomagnetic depletion step was repeated. Final cell suspension was centrifuged and the pellet resuspended in 70µL of PBS 2% BSA, 100 000 PBMC were added (see below for isolation method). Cell suspension was washed in PBS 2% BSA and incubated with saturating concentrations of fluorescent‐labelled antibodies against human CD56, CD45 and Cd235a (Milteny®) for 15 min at 4°C. Cells were then washed with PBS 2%-BSA, analyzed and sorted by flow cytometry using a FACSAria II (Becton Dickinson). For whole exome sequencing, the population of interest was gated according to its CD56/CD45 criteria to avoid NK lymphocytes (CD56+/CD45+) contamination. Cells CD56 + and CD45- were sorted, centrifuged, and immediately frozen at -80°C. Data were analyzed with FlowJow software. PBMC isolation from whole blood samples. The blood sample collected in EDTA-K2 tube (1x5mL tubes) was diluted in an equal volume of PBS 2% BSA. Five milliters of Ficoll-Paque™ (Milteny®) was carefully added on the suspension, then centrifuged 20 minutes at 1200 x g at room temperature without brake. The mononuclear cell layer was carefully aspirated and diluted with an equal volume of PBS 2% BSA. For whole exome sequencing, the suspension was centrifuged, washed in PBS 2% BSA and immediately frozen at -80°C. DNAg from PBMC were prepared using QIAamp DNA Mini Kit (Quiagen, Germany) according to manufacturer's recommendations. Tumor biopsies were deparaffinized with Deparaffinization Solution (Qiagen, Germany) at 56°C for 3 minutes. DNA was extracted using QIAamp DNA FFPE Tissue Kit (Quiagen, Germany) according to manufacturer's recommendations. Total genomic DNA library was prepared, at each step a control quality of process was performed (Fragment Analyzer and qPCR assays). The steps from library preparation, exome capture and sequencing were performed by Integragen SA (Evry, France) according to manufacturer’s instruction and relative protocols (SureSelect, Agilent) without modification except for library preparation performed with NEBNext® Ultra II kit (New England Biolabs®). Genomic DNA is captured using Agilent in-solution enrichment methodology with their biotinylated oligonucleotides probes library (SureSelect Clinical Research Exome V2, Agilent Technologies).

text: adult

text: small cell lung carcinoma

text: CD56 positive

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: blood

text: circulating tumor cells

text: at initial diagnosis

text: Homo sapiens

text: frozen sample


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: public

text: ArrayExpress

characteristic: broker name

text: human

characteristic: common name

characteristic: description

text: adult

text: small cell lung carcinoma

text: CD56 positive

text: not applicable

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: blood

characteristic: organism part

text: circulating tumor cells

text: at relapse

text: Homo sapiens

text: frozen sample

characteristic: title


text: public

text: ArrayExpress

text: human

text: Protocols: Whole blood samples were collected before the first administration of any cytotoxic agent from patients with a histologically or cytologically confirmed CD56+ chemotherapy-naïve SCLC. Patients were eligible to a systemic treatment and were part of a larger ongoing prospective non-interventional study conducted at Rennes University Hospital. Any active neoplasia other than SCLC or known HIV, HCV or HBV infection, was considered as an exclusion criterion. Isolation of CD56+CTCs from whole blood sample. CTC00 enrichment was performed using the EasySep™ Direct Human CTC Enrichment Kit (StemCell Technologies®) according to manufacturer instruction. Approximately 10 ml of the heparin blood samples was gently mixed and incubated with CTC enrichment cocktail at room temperature for 5 min in constant mixing. After dilution of 1:2 in PBS 2%-BSA the blood was incubated with buffer EasySep and RapidSpheres™ (StemCell,Canada) in “Big Easy” StemCell magnet for 10 minutes. The cells suspension was collected and the same immunomagnetic depletion step was repeated. Final cell suspension was centrifuged and the pellet resuspended in 70µL of PBS 2% BSA, 100 000 PBMC were added (see below for isolation method). Cell suspension was washed in PBS 2% BSA and incubated with saturating concentrations of fluorescent‐labelled antibodies against human CD56, CD45 and Cd235a (Milteny®) for 15 min at 4°C. Cells were then washed with PBS 2%-BSA, analyzed and sorted by flow cytometry using a FACSAria II (Becton Dickinson). For whole exome sequencing, the population of interest was gated according to its CD56/CD45 criteria to avoid NK lymphocytes (CD56+/CD45+) contamination. Cells CD56 + and CD45- were sorted, centrifuged, and immediately frozen at -80°C. Data were analyzed with FlowJow software. Genomic DNA (DNAg) of CTCs were prepared using the REPLI-g Single Cell Kit (Quiagen, Germany) according to manufacturer's recommendations. DNAg from PBMC were prepared using QIAamp DNA Mini Kit (Quiagen, Germany) according to manufacturer's recommendations. Tumor biopsies were deparaffinized with Deparaffinization Solution (Qiagen, Germany) at 56°C for 3 minutes. DNA was extracted using QIAamp DNA FFPE Tissue Kit (Quiagen, Germany) according to manufacturer's recommendations. DNAg from PBMC were prepared using QIAamp DNA Mini Kit (Quiagen, Germany) according to manufacturer's recommendations. Tumor biopsies were deparaffinized with Deparaffinization Solution (Qiagen, Germany) at 56°C for 3 minutes. DNA was extracted using QIAamp DNA FFPE Tissue Kit (Quiagen, Germany) according to manufacturer's recommendations. Total genomic DNA library was prepared, at each step a control quality of process was performed (Fragment Analyzer and qPCR assays). The steps from library preparation, exome capture and sequencing were performed by Integragen SA (Evry, France) according to manufacturer’s instruction and relative protocols (SureSelect, Agilent) without modification except for library preparation performed with NEBNext® Ultra II kit (New England Biolabs®). Genomic DNA is captured using Agilent in-solution enrichment methodology with their biotinylated oligonucleotides probes library (SureSelect Clinical Research Exome V2, Agilent Technologies).

text: adult

characteristic: developmental stage

text: small cell lung carcinoma

characteristic: disease

text: unsorted

characteristic: immunophenotype

characteristic: individual

text: not applicable

characteristic: isolate

text: Homo sapiens

text: Homo sapiens

text: blood

text: peripheral blood mononuclear cell

characteristic: sampling site

text: at initial diagnosis

characteristic: sampling time point

text: Homo sapiens

text: frozen sample

characteristic: specimen with known storage state


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

characteristic: Submitter Id

text: ArrayExpress

text: human

text: adult

text: small cell lung carcinoma

text: unsorted

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: lung

text: neoplasm

text: at initial diagnosis

text: Homo sapiens

text: FFPE


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: UNIVERSITY OF SHEFFIELD

text: public

tag: Namespace:UNIVERSITY OF SHEFFIELD

text: ArrayExpress

characteristic: broker name

text: motor neuron

text: human

characteristic: common name

text: Protocols: Cells were harvested on day 34 of differentiation using Accutase and spun in 15ml falcon tubes at 400g for 4 minutes. Prior to RNA extraction pellets were stored at -80 degrees celsius. Neurons were differentiated to limb innervating motor neurons using optimized protocol Total RNA was extracted using Norgen Total RNA extraction plus following manufactures instructions. RNA quality was checked using Nanodrop Lite (Thermofisher) and quantity was checked using Qubit 3.0 (Life Technologies) A total amount of 1 μg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEBNext First Strand Synthesis Reaction Buffer (5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase (RNase H-). Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 150~200 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then 3 μl USER Enzyme (NEB, USA) was used with size-selected, adaptorligated cDNA at 37 °C for 15 min followed by 5 min at 95 °C before PCR. Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system.

characteristic: description

text: embryo

text: normal

text: homology-directed repair CRISPR

characteristic: genetic modification

text: MFN2 R94Q/+

characteristic: genotype

characteristic: growth condition

text: 46, XY

characteristic: karyotype

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: blastocyst

characteristic: organism part

text: Charcot-Marie-Tooth disease type 2

characteristic: phenotype

text: embryonic stem cell

characteristic: progenitor cell type

text: Homo sapiens

text: male

characteristic: sex

unit: day

characteristic: time

characteristic: title


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: UNIVERSITY OF SHEFFIELD

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: ArrayExpress

text: motor neuron

text: human

text: embryo

characteristic: developmental stage

text: normal

characteristic: disease

text: homology-directed repair CRISPR

text: MFN2 R94Q/+

text: differentiated to limb innervating motor neuron

text: 46, XY

text: Homo sapiens

text: Homo sapiens

text: blastocyst

text: Charcot-Marie-Tooth disease type 2

text: embryonic stem cell

text: Homo sapiens

text: male


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: UNIVERSITY OF SHEFFIELD

text: public

text: ArrayExpress

characteristic: broker name

text: motor neuron

text: human

characteristic: common name

characteristic: description

text: embryo

text: normal

text: mock homology-directed repair CRISPR

characteristic: genetic modification

text: wild type genotype

characteristic: genotype

characteristic: growth condition

text: 46, XY

characteristic: karyotype

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: blastocyst

text: wild type

text: embryonic stem cell

text: Homo sapiens

text: male


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: UNIVERSITY OF SHEFFIELD

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: ArrayExpress

text: motor neuron

text: human

text: embryo

text: normal

text: homology-directed repair CRISPR

text: MFN2 R94Q/R94Q

text: 46, XY

text: Homo sapiens

text: Homo sapiens

text: blastocyst

characteristic: organism part

text: Charcot-Marie-Tooth disease type 2

characteristic: phenotype

text: embryonic stem cell

characteristic: progenitor cell type

text: Homo sapiens

text: male

characteristic: sex

characteristic: time

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: UNIVERSITY OF SHEFFIELD

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: ArrayExpress

characteristic: broker name

text: motor neuron

text: human

characteristic: common name

text: embryo

characteristic: developmental stage

text: normal

characteristic: disease

text: wild type genotype

text: 46, XY

text: Homo sapiens

text: Homo sapiens

text: blastocyst

text: wild type

text: embryonic stem cell

text: Homo sapiens

text: male


characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC first public

text: public

tag: Namespace:Istituto di Ricerche Farmacologiche Mario Negri IRCCS

text: ArrayExpress

characteristic: cell line

text: human

text: Protocols: Breast cancer cell lines were grown in DMEM-F12 medium in the presence of 5% fetal calf serum. To obtain circDOCK1 over-expressing cellular populations, the DNA coding for circDOCK1 was cloned into the pCDNA3 plasmid, which was transfected in the MDA-MB-157 and MDA-MB-231 breast cancer cell-lines using the FuGENE6 (Promega). Neomycin resistant cell clones were selected in the presence of G418 (MDA-MB-157 cells = 400 µg/ml; MDA-MB-231 cells = 500 µg/ml) for two weeks. Approximately 20 G418 resistant clones were isolated from each cell line and the levels of circDOCK1 expression were examined by RT-PCR. At least 3 clones with highest amounts of circDOCK1 RNA expression were expanded from each cell line and used for further experiments. To obtain negative control clones, the cells were transfected with void vectors and at least 3 of G418 resistant clones were isolated and used for determination of basal levels of circDOCK1. To obtain circDOCK1 silencing, CAMA1 cells were infected with lenti-viral particles containing 2 independent circDOCK1 targeting sh-constructs cloned in the plasmid pINDUCER10 (Addgene, Watertown, MA), and the cellular pools obtained the sh constructs were selected in the presence of puromycin (1 µg/ml) for two weeks. Puromycin resistant cell pools were then divided into two groups and they were treated in the absence (as controls) or in the presence of 0.5 µg/ml of doxycycline for four days to induce the shRNAs. Cells with reduced levels of circDOCK1 expression respect to the basal conditions (controls) were expanded and used for further experiments. For the RNAseq analysis of circDOCK1 overexpressing clones and the respective control clones, three paired biological replicates of each cell-line were grown in the presence of G418. For the silencing constructs, three biological replicates of cells were treated for 4 days in the presence or absence of doxycycline. Collection of 5-10 million cells in PDS, and resuspension of the pellet in a buffer. RNA was extracted with the mRNeasy Mini Kit (QIAGEN). TruSeq Stranded Total RNA Sample Preparation Guide

characteristic: description

text: breast cancer

text: doxycyline-inducible expression of circDOCK1 shRNA 2

characteristic: genotype

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: mammary gland

text: Homo sapiens


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: Istituto di Ricerche Farmacologiche Mario Negri IRCCS

text: public

text: ArrayExpress

text: human

text: breast cancer

text: Homo sapiens

text: Homo sapiens

text: mammary gland

characteristic: organism part

text: Homo sapiens

characteristic: title


characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: ArrayExpress

text: human

text: breast cancer

text: doxycyline-inducible expression of circDOCK1 shRNA 3

text: Homo sapiens

text: Homo sapiens

text: mammary gland

text: Homo sapiens


text: public

text: ArrayExpress

characteristic: broker name

text: human

characteristic: common name

text: breast cancer

characteristic: disease

text: circDOCK1 overexpression

text: Homo sapiens

text: Homo sapiens

text: mammary gland

text: Homo sapiens


characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC center name

text: public

text: ArrayExpress

text: human

text: breast cancer

text: pcDNA3 empty vector

text: Homo sapiens

text: Homo sapiens

text: mammary gland

text: Homo sapiens


text: LSHTM

characteristic: INSDC first public

text: public

text: Chlamydia trachomatis

text: Chlamydia trachomatis

text: Genomics of Ocular Chlamydia trachomatis in Moshi District, Tanzania


E-MTAB-10870:Sample 1

text: public

text: E-MTAB-10870:Sample 1

tag: Namespace:Hagai Lab The Shmunis School of Biomedicine and Cancer Research Faculty of Life Sciences Tel Aviv University

text: ArrayExpress

text: fibroblast

text: Kuhl's pipistrelle

text: Protocols: All fibroblast derived cell lines were treated with different stimuli for 4 hours. Cells were washed with PBS and then lysed in RNA Lysis Buffer (Zymo Research). Cells were stimulated with 1 ug/mL of High-Molecular Weight poly(I:C) (InvivoGen, Cat. Code: tlrl-pic), transfected with 2 uL/mL Lipofectamin 2000 (Thermo Fisher Scientific), for 4 hours before collection. Total RNA was extracted using the Quick-RNA MicroPrep kit (Zymo Research, Cat. No. R1051). Libraries were produced using the Kapa Stranded mRNA-seq Kit (24RXN) (KK8420 ROCHE-07962193001) with the KAPA Unique Dual-Indexed Adapter Plate (KK8726-08861862001) and KAPA Adapter Dilution Buffer (KK8721-08278539001), starting with 500 ng of total RNA (samples #1-4 were started with 275-337 ng total). For all samples, except sample #39, fragmentation was performed as recommended for 7 minutes. Fragmentation for sample #39 was set to 5 minutes (RIN 6.0). UDI adapters were diluted to 350nM as instructed in the protocol. Final cDNA amplification was performed with 13 PCR cycles. Libraries were normalized and pooled at 10 nM.

characteristic: description

text: adult

characteristic: developmental stage

text: normal

text: wild type genotype

characteristic: genotype

text: Pipistrellus kuhlii

text: Pipistrellus kuhlii

text: dermis

text: Pipistrellus kuhlii

text: female

characteristic: sex

text: Sample 1


E-MTAB-10870:Sample 10

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: Hagai Lab The Shmunis School of Biomedicine and Cancer Research Faculty of Life Sciences Tel Aviv University

text: public

text: E-MTAB-10870:Sample 10

text: ArrayExpress

text: fibroblast

text: Egyptian rousette

text: adult

text: normal

text: wild type genotype

text: Rousettus aegyptiacus

characteristic: organism

text: Rousettus aegyptiacus

text: dermis

characteristic: organism part

text: Rousettus aegyptiacus

text: male

text: Sample 10


E-MTAB-10870:Sample 11

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-10870:Sample 11

text: ArrayExpress

text: fibroblast

text: Egyptian rousette

text: adult

text: normal

text: wild type genotype

text: Rousettus aegyptiacus

text: Rousettus aegyptiacus

text: dermis

text: Rousettus aegyptiacus

text: female

text: Sample 11

characteristic: title


E-MTAB-10870:Sample 12

text: public

text: E-MTAB-10870:Sample 12

characteristic: Submitter Id

text: ArrayExpress

characteristic: broker name

text: fibroblast

text: Egyptian rousette

characteristic: common name

text: adult

text: normal

characteristic: disease

text: wild type genotype

text: Rousettus aegyptiacus

text: Rousettus aegyptiacus

text: dermis

text: Rousettus aegyptiacus

text: female

text: Sample 12


E-MTAB-10870:Sample 13

characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: E-MTAB-10870:Sample 13

text: ArrayExpress

text: fibroblast

text: Kuhl's pipistrelle

text: adult

text: normal

text: wild type genotype

text: Pipistrellus kuhlii

text: Pipistrellus kuhlii

text: dermis

text: Pipistrellus kuhlii

text: male

text: Sample 13


E-MTAB-10870:Sample 14

text: public

text: E-MTAB-10870:Sample 14

text: ArrayExpress

text: fibroblast

text: Kuhl's pipistrelle

characteristic: description

text: adult

characteristic: developmental stage

text: normal

text: wild type genotype

characteristic: genotype

text: Pipistrellus kuhlii

text: Pipistrellus kuhlii

text: dermis

text: Pipistrellus kuhlii

text: male

characteristic: sex

text: Sample 14


E-MTAB-10870:Sample 15

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: public

text: E-MTAB-10870:Sample 15

text: ArrayExpress

text: fibroblast

text: Kuhl's pipistrelle

text: adult

text: normal

text: wild type genotype

text: Pipistrellus kuhlii

characteristic: organism

text: Pipistrellus kuhlii

text: dermis

characteristic: organism part

text: Pipistrellus kuhlii

text: male

text: Sample 15


E-MTAB-10870:Sample 16

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-10870:Sample 16

text: ArrayExpress

text: fibroblast

text: Kuhl's pipistrelle

text: adult

text: normal

text: wild type genotype

text: Pipistrellus kuhlii

text: Pipistrellus kuhlii

text: dermis

text: Pipistrellus kuhlii

text: male

text: Sample 16

characteristic: title


E-MTAB-10870:Sample 17

text: public

text: E-MTAB-10870:Sample 17

characteristic: Submitter Id

text: ArrayExpress

characteristic: broker name

text: fibroblast

text: Egyptian rousette

characteristic: common name

text: adult

text: normal

characteristic: disease

text: wild type genotype

text: Rousettus aegyptiacus

text: Rousettus aegyptiacus

text: dermis

text: Rousettus aegyptiacus

text: male

text: Sample 17


E-MTAB-10870:Sample 18

characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: E-MTAB-10870:Sample 18

text: ArrayExpress

text: fibroblast

text: Egyptian rousette

text: adult

text: normal

text: wild type genotype

text: Rousettus aegyptiacus

text: Rousettus aegyptiacus

text: dermis

text: Rousettus aegyptiacus

text: male

text: Sample 18


E-MTAB-10870:Sample 19

text: public

text: E-MTAB-10870:Sample 19

text: ArrayExpress

text: fibroblast

text: Egyptian rousette

characteristic: description

text: adult

characteristic: developmental stage

text: normal

text: wild type genotype

characteristic: genotype

text: Rousettus aegyptiacus

text: Rousettus aegyptiacus

text: dermis

text: Rousettus aegyptiacus

text: female

characteristic: sex

text: Sample 19


E-MTAB-10870:Sample 2

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: public

text: E-MTAB-10870:Sample 2

text: ArrayExpress

text: fibroblast

text: Kuhl's pipistrelle

text: adult

text: normal

text: wild type genotype

text: Pipistrellus kuhlii

characteristic: organism

text: Pipistrellus kuhlii

text: dermis

characteristic: organism part

text: Pipistrellus kuhlii

text: female

text: Sample 2


E-MTAB-10870:Sample 20

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-10870:Sample 20

text: ArrayExpress

text: fibroblast

text: Egyptian rousette

text: adult

text: normal

text: wild type genotype

text: Rousettus aegyptiacus

text: Rousettus aegyptiacus

text: dermis

text: Rousettus aegyptiacus

text: female

text: Sample 20

characteristic: title


E-MTAB-10870:Sample 21

text: public

text: E-MTAB-10870:Sample 21

characteristic: Submitter Id

text: ArrayExpress

characteristic: broker name

text: fibroblast

text: Egyptian rousette

characteristic: common name

text: adult

text: normal

characteristic: disease

text: wild type genotype

text: Rousettus aegyptiacus

text: Rousettus aegyptiacus

text: dermis

text: Rousettus aegyptiacus

text: male

text: Sample 21


E-MTAB-10870:Sample 22

characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: E-MTAB-10870:Sample 22

text: ArrayExpress

text: fibroblast

text: Egyptian rousette

text: adult

text: normal

text: wild type genotype

text: Rousettus aegyptiacus

text: Rousettus aegyptiacus

text: dermis

text: Rousettus aegyptiacus

text: male

text: Sample 22


E-MTAB-10870:Sample 23

text: public

text: E-MTAB-10870:Sample 23

text: ArrayExpress

text: fibroblast

text: Egyptian rousette

characteristic: description

text: adult

characteristic: developmental stage

text: normal

text: wild type genotype

characteristic: genotype

text: Rousettus aegyptiacus

text: Rousettus aegyptiacus

text: dermis

text: Rousettus aegyptiacus

text: male

characteristic: sex

text: Sample 23


E-MTAB-10870:Sample 24

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: public

text: E-MTAB-10870:Sample 24

text: ArrayExpress

text: fibroblast

text: Egyptian rousette

text: adult

text: normal

text: wild type genotype

text: Rousettus aegyptiacus

characteristic: organism

text: Rousettus aegyptiacus

text: dermis

characteristic: organism part

text: Rousettus aegyptiacus

text: male

text: Sample 24


E-MTAB-10870:Sample 25

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-10870:Sample 25

text: ArrayExpress

text: fibroblast

text: Egyptian rousette

text: adult

text: normal

text: wild type genotype

text: Rousettus aegyptiacus

text: Rousettus aegyptiacus

text: dermis

text: Rousettus aegyptiacus

text: female

text: Sample 25

characteristic: title


E-MTAB-10870:Sample 26

text: public

text: E-MTAB-10870:Sample 26

characteristic: Submitter Id

text: ArrayExpress

characteristic: broker name

text: fibroblast

text: Egyptian rousette

characteristic: common name

text: adult

text: normal

characteristic: disease

text: wild type genotype

text: Rousettus aegyptiacus

text: Rousettus aegyptiacus

text: dermis

text: Rousettus aegyptiacus

text: female

text: Sample 26


E-MTAB-10870:Sample 27

characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: E-MTAB-10870:Sample 27

text: ArrayExpress

text: fibroblast

text: Egyptian rousette

text: adult

text: normal

text: wild type genotype

text: Rousettus aegyptiacus

text: Rousettus aegyptiacus

text: dermis

text: Rousettus aegyptiacus

text: female

text: Sample 27


E-MTAB-10870:Sample 28

text: public

text: E-MTAB-10870:Sample 28

text: ArrayExpress

text: fibroblast

text: Egyptian rousette

characteristic: description

text: adult

characteristic: developmental stage

text: normal

text: wild type genotype

characteristic: genotype

text: Rousettus aegyptiacus

text: Rousettus aegyptiacus

text: dermis

text: Rousettus aegyptiacus

text: female

characteristic: sex

text: Sample 28


E-MTAB-10870:Sample 29

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: public

text: E-MTAB-10870:Sample 29

text: ArrayExpress

text: fibroblast

text: Kuhl's pipistrelle

text: adult

text: normal

text: wild type genotype

text: Pipistrellus kuhlii

characteristic: organism

text: Pipistrellus kuhlii

text: dermis

characteristic: organism part

text: Pipistrellus kuhlii

text: female

text: Sample 29


E-MTAB-10870:Sample 3

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-10870:Sample 3

text: ArrayExpress

text: fibroblast

text: Kuhl's pipistrelle

text: adult

text: normal

text: wild type genotype

text: Pipistrellus kuhlii

text: Pipistrellus kuhlii

text: dermis

text: Pipistrellus kuhlii

text: female

text: Sample 3

characteristic: title


E-MTAB-10870:Sample 30

text: public

text: E-MTAB-10870:Sample 30

characteristic: Submitter Id

text: ArrayExpress

characteristic: broker name

text: fibroblast

text: Kuhl's pipistrelle

characteristic: common name

text: adult

text: normal

characteristic: disease

text: wild type genotype

text: Pipistrellus kuhlii

text: Pipistrellus kuhlii

text: dermis

text: Pipistrellus kuhlii

text: female

text: Sample 30


E-MTAB-10870:Sample 31

characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: E-MTAB-10870:Sample 31

text: ArrayExpress

text: fibroblast

text: Kuhl's pipistrelle

text: adult

text: normal

text: wild type genotype

text: Pipistrellus kuhlii

text: Pipistrellus kuhlii

text: dermis

text: Pipistrellus kuhlii

text: female

text: Sample 31


E-MTAB-10870:Sample 32

text: public

text: E-MTAB-10870:Sample 32

text: ArrayExpress

text: fibroblast

text: Kuhl's pipistrelle

characteristic: description

text: adult

characteristic: developmental stage

text: normal

text: wild type genotype

characteristic: genotype

text: Pipistrellus kuhlii

text: Pipistrellus kuhlii

text: dermis

text: Pipistrellus kuhlii

text: female

characteristic: sex

text: Sample 32


E-MTAB-10870:Sample 33

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: public

text: E-MTAB-10870:Sample 33

text: ArrayExpress

text: fibroblast

text: Kuhl's pipistrelle

text: adult

text: normal

text: wild type genotype

text: Pipistrellus kuhlii

characteristic: organism

text: Pipistrellus kuhlii

text: dermis

characteristic: organism part

text: Pipistrellus kuhlii

text: female

text: Sample 33


E-MTAB-10870:Sample 34

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-10870:Sample 34

text: ArrayExpress

text: fibroblast

text: Kuhl's pipistrelle

text: adult

text: normal

text: wild type genotype

text: Pipistrellus kuhlii

text: Pipistrellus kuhlii

text: dermis

text: Pipistrellus kuhlii

text: female

text: Sample 34

characteristic: title


E-MTAB-10870:Sample 35

text: public

text: E-MTAB-10870:Sample 35

characteristic: Submitter Id

text: ArrayExpress

characteristic: broker name

text: fibroblast

text: Kuhl's pipistrelle

characteristic: common name

text: adult

text: normal

characteristic: disease

text: wild type genotype

text: Pipistrellus kuhlii

text: Pipistrellus kuhlii

text: dermis

text: Pipistrellus kuhlii

text: female

text: Sample 35


E-MTAB-10870:Sample 36

characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: E-MTAB-10870:Sample 36

text: ArrayExpress

text: fibroblast

text: Kuhl's pipistrelle

text: adult

text: normal

text: wild type genotype

text: Pipistrellus kuhlii

text: Pipistrellus kuhlii

text: dermis

text: Pipistrellus kuhlii

text: female

text: Sample 36


E-MTAB-10870:Sample 37

text: public

text: E-MTAB-10870:Sample 37

text: ArrayExpress

text: fibroblast

text: Egyptian rousette

characteristic: description

text: adult

characteristic: developmental stage

text: normal

text: wild type genotype

characteristic: genotype

text: Rousettus aegyptiacus

text: Rousettus aegyptiacus

text: dermis

text: Rousettus aegyptiacus

text: female

characteristic: sex

text: Sample 37


E-MTAB-10870:Sample 38

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: public

text: E-MTAB-10870:Sample 38

text: ArrayExpress

text: fibroblast

text: Egyptian rousette

text: adult

text: normal

text: wild type genotype

text: Rousettus aegyptiacus

characteristic: organism

text: Rousettus aegyptiacus

text: dermis

characteristic: organism part

text: Rousettus aegyptiacus

text: female

text: Sample 38


E-MTAB-10870:Sample 39

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-10870:Sample 39

text: ArrayExpress

text: fibroblast

text: Egyptian rousette

text: adult

text: normal

text: wild type genotype

text: Rousettus aegyptiacus

text: Rousettus aegyptiacus

text: dermis

text: Rousettus aegyptiacus

text: female

text: Sample 39

characteristic: title


E-MTAB-10870:Sample 4

text: public

text: E-MTAB-10870:Sample 4

characteristic: Submitter Id

text: ArrayExpress

characteristic: broker name

text: fibroblast

text: Kuhl's pipistrelle

characteristic: common name

text: adult

text: normal

characteristic: disease

text: wild type genotype

text: Pipistrellus kuhlii

text: Pipistrellus kuhlii

text: dermis

text: Pipistrellus kuhlii

text: female

text: Sample 4


E-MTAB-10870:Sample 40

characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: E-MTAB-10870:Sample 40

text: ArrayExpress

text: fibroblast

text: Egyptian rousette

text: adult

text: normal

text: wild type genotype

text: Rousettus aegyptiacus

text: Rousettus aegyptiacus

text: dermis

text: Rousettus aegyptiacus

text: female

text: Sample 40


E-MTAB-10870:Sample 41

text: public

text: E-MTAB-10870:Sample 41

text: ArrayExpress

text: fibroblast

text: Kuhl's pipistrelle

characteristic: description

text: adult

characteristic: developmental stage

text: normal

text: wild type genotype

characteristic: genotype

text: Pipistrellus kuhlii

text: Pipistrellus kuhlii

text: dermis

text: Pipistrellus kuhlii

text: male

characteristic: sex

text: Sample 41


E-MTAB-10870:Sample 42

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: public

text: E-MTAB-10870:Sample 42

text: ArrayExpress

text: fibroblast

text: Kuhl's pipistrelle

text: adult

text: normal

text: wild type genotype

text: Pipistrellus kuhlii

characteristic: organism

text: Pipistrellus kuhlii

text: dermis

characteristic: organism part

text: Pipistrellus kuhlii

text: male

text: Sample 42


E-MTAB-10870:Sample 43

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-10870:Sample 43

text: ArrayExpress

text: fibroblast

text: Kuhl's pipistrelle

text: adult

text: normal

text: wild type genotype

text: Pipistrellus kuhlii

text: Pipistrellus kuhlii

text: dermis

text: Pipistrellus kuhlii

text: male

text: Sample 43

characteristic: title


E-MTAB-10870:Sample 44

text: public

text: E-MTAB-10870:Sample 44

characteristic: Submitter Id

text: ArrayExpress

characteristic: broker name

text: fibroblast

text: Egyptian rousette

characteristic: common name

text: adult

text: normal

characteristic: disease

text: wild type genotype

text: Rousettus aegyptiacus

text: Rousettus aegyptiacus

text: dermis

text: Rousettus aegyptiacus

text: female

text: Sample 44


E-MTAB-10870:Sample 45

characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: E-MTAB-10870:Sample 45

text: ArrayExpress

text: fibroblast

text: Egyptian rousette

text: adult

text: normal

text: wild type genotype

text: Rousettus aegyptiacus

text: Rousettus aegyptiacus

text: dermis

text: Rousettus aegyptiacus

text: female

text: Sample 45


E-MTAB-10870:Sample 46

text: public

text: E-MTAB-10870:Sample 46

text: ArrayExpress

text: fibroblast

text: Egyptian rousette

characteristic: description

text: adult

characteristic: developmental stage

text: normal

text: wild type genotype

characteristic: genotype

text: Rousettus aegyptiacus

text: Rousettus aegyptiacus

text: dermis

text: Rousettus aegyptiacus

text: male

characteristic: sex

text: Sample 46


E-MTAB-10870:Sample 47

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: public

text: E-MTAB-10870:Sample 47

text: ArrayExpress

text: fibroblast

text: Egyptian rousette

text: adult

text: normal

text: wild type genotype

text: Rousettus aegyptiacus

characteristic: organism

text: Rousettus aegyptiacus

text: dermis

characteristic: organism part

text: Rousettus aegyptiacus

text: male

text: Sample 47


E-MTAB-10870:Sample 48

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-10870:Sample 48

text: ArrayExpress

text: fibroblast

text: Egyptian rousette

text: adult

text: normal

text: wild type genotype

text: Rousettus aegyptiacus

text: Rousettus aegyptiacus

text: dermis

text: Rousettus aegyptiacus

text: male

text: Sample 48

characteristic: title


E-MTAB-10870:Sample 49

text: public

text: E-MTAB-10870:Sample 49

characteristic: Submitter Id

text: ArrayExpress

characteristic: broker name

text: fibroblast

text: Egyptian rousette

characteristic: common name

text: adult

text: normal

characteristic: disease

text: wild type genotype

text: Rousettus aegyptiacus

text: Rousettus aegyptiacus

text: dermis

text: Rousettus aegyptiacus

text: male

text: Sample 49


E-MTAB-10870:Sample 5

characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: E-MTAB-10870:Sample 5

text: ArrayExpress

text: fibroblast

text: Egyptian rousette

text: adult

text: normal

text: wild type genotype

text: Rousettus aegyptiacus

text: Rousettus aegyptiacus

text: dermis

text: Rousettus aegyptiacus

text: male

text: Sample 5


E-MTAB-10870:Sample 6

text: public

text: E-MTAB-10870:Sample 6

text: ArrayExpress

text: fibroblast

text: Egyptian rousette

characteristic: description

text: adult

characteristic: developmental stage

text: normal

text: wild type genotype

characteristic: genotype

text: Rousettus aegyptiacus

text: Rousettus aegyptiacus

text: dermis

text: Rousettus aegyptiacus

text: male

characteristic: sex

text: Sample 6


E-MTAB-10870:Sample 7

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: public

text: E-MTAB-10870:Sample 7

text: ArrayExpress

text: fibroblast

text: Egyptian rousette

text: adult

text: normal

text: wild type genotype

text: Rousettus aegyptiacus

characteristic: organism

text: Rousettus aegyptiacus

text: dermis

characteristic: organism part

text: Rousettus aegyptiacus

text: male

text: Sample 7


E-MTAB-10870:Sample 8

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-10870:Sample 8

text: ArrayExpress

text: fibroblast

text: Egyptian rousette

text: adult

text: normal

text: wild type genotype

text: Rousettus aegyptiacus

text: Rousettus aegyptiacus

text: dermis

text: Rousettus aegyptiacus

text: male

text: Sample 8

characteristic: title


E-MTAB-10870:Sample 9

text: public

text: E-MTAB-10870:Sample 9

characteristic: Submitter Id

text: ArrayExpress

characteristic: broker name

text: fibroblast

text: Egyptian rousette

characteristic: common name

text: adult

text: normal

characteristic: disease

text: wild type genotype

text: Rousettus aegyptiacus

text: Rousettus aegyptiacus

text: dermis

text: Rousettus aegyptiacus

text: male

text: Sample 9


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: West of Scotland Specialist Virology Centre, NHSGGC / MRC-University of Glasgow Centre for Virus Research

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: COVID-19 Genomics UK Consortium

characteristic: collecting institution

characteristic: collection date

text: not provided

characteristic: collector name

text: not provided

characteristic: definition for seropositive sample

text: United Kingdom

characteristic: geographic location (country and/or sea)

text: Scotland

characteristic: geographic location (region and locality)

text: not provided

characteristic: host common name

text: not provided

characteristic: host health state

text: Human

characteristic: host scientific name

text: not provided

characteristic: host sex

text: not provided

characteristic: host subject id

text: not provided

characteristic: isolate

text: Severe acute respiratory syndrome coronavirus 2

text: active surveillance in response to outbreak

characteristic: sample capture status

text: not provided

characteristic: serotype (required for a seropositive sample)

text: not provided

characteristic: virus identifier


SAMI00000016-Test Case Sample1 Title

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: KLE TEch

characteristic: INSDC center name

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: SAMI00000016-Test Case Sample1 Title

tag: Namespace:KLE TEch

characteristic: Submitter Id

text: mango

characteristic: common name

text: Test Case Sample1 Desc

characteristic: description

text: Mangifera indica

characteristic: organism

text: Mangifera indica

text: Test Case Sample1 Title

characteristic: title


SAMI00000017-Test Case Sample2 Title

text: KLE TEch

characteristic: INSDC first public

text: public

text: SAMI00000017-Test Case Sample2 Title

text: mango

text: Test Case Sample2 Desc

text: Mangifera indica

text: Mangifera indica

text: Test Case Sample2 Title


characteristic: GISAID Accession ID

text: Dutch COVID-19 response team

text: public

tag: Namespace:Dutch COVID-19 response team

text: ERASMUS MC, UNIVERISTY MEDICAL CENTER

characteristic: broker name

text: not provided

characteristic: collecting institution

characteristic: collection date

text: Dutch COVID-19 response team

characteristic: collector name

text: Human coronavirus 2019

text: A SARS-CoV-2 specfic multiplex PCR for Nanopore sequencing was performed, similar to amplicon-based approaches as previously described. In short, primers for 86 overlapping amplicons spanning the entire genome were designed using primal. The amplicon length was set to 500bp with 75bp overlap between the different amplicons. The libraries were generated using the native barcode kits from Nanopore (EXP-NBD104 and EXP-NBD114 and SQK-LSK109) and sequenced on a R9.4 flow cell multiplexing up to 24 samples per sequence run. Raw data was demultiplexed, amplicon primers were trimmed and human data was removed by mapping against the human reference genome.

text: Netherlands

characteristic: geographic location (country and/or sea)

text: Human

characteristic: host common name

text: not collected

characteristic: host health state

text: Homo sapiens

characteristic: host scientific name

text: not provided

characteristic: host sex

text: restricted access

characteristic: host subject id

characteristic: isolate

text: not collected

characteristic: isolation source host associated

text: ReCoDID COVID-19 pilot study

characteristic: project name

characteristic: sample capture status

characteristic: sample derived from

text: Dutch COVID-19 response sample sequencing

type: derived from


tag: attribute

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:Institute for Research on Cancer and Aging, Nice (IRCAN) Inserm U1081 - CNRS UMR 7284 University Cote d'Azur

characteristic: Submitter Id

text: ArrayExpress

text: embryonic stem cell

text: human

characteristic: common name

text: Protocols: Cells were grown and collected from culture dishes. HFF-1 and derivatives were transduced by the Sleeping Beauty transposon vector, described in Grabunzija et al. 2013 (doi: 10.1093/nar/gks1305). The PEli003-A cells were reprogrammed with CytoTune®-iPS 2.0 Sendai Reprogramming Kit (Thermo Fisher Scientific) supplying the four Yamanaka factors, OCT4, SOX2, KLF4 and c-MYC. The other cell lines were transduced with lentivirus vestors as described in Haase et al. 2009 (doi: 10.1016/j.stem.2009.08.021). Genomic DNA was extracted and prepared using QIAGEN DNeasy Blood & Tissue Kit, according to manufacturer's protocol In brief, bs-ATLAS-seq follows these steps: fragmentation of genomic DNA by sonication, ligation of a methylated adapter, bisulfite treatment of linker-ligated DNA, suppression PCR-amplification of L1 5' junctions, and asymmetric Illumina paired-end sequencing (90 bp + 210 bp). Read #1 starts from a random position (sonicated DNA break), while read #2 starts from a fixed sequence in L1 5' UTR (internal promoter). With this design, read #2 covers the 15 most 5’ CpG sites (1-207, relative to L1HS consensus sequence). Read #1 has the same orientation as the L1 element.

characteristic: description

text: embryo

characteristic: developmental stage

text: normal

characteristic: disease

text: wild type genotype

characteristic: genotype

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: blastocyst

characteristic: organism part

characteristic: passage number

text: bs-ATLAS-seq

characteristic: protocol

text: technical replicate

characteristic: replicate

text: unmodified

characteristic: reprogramming factors

text: Homo sapiens

text: female

characteristic: sex

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Institute for Research on Cancer and Aging, Nice (IRCAN) Inserm U1081 - CNRS UMR 7284 University Cote d'Azur

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: ArrayExpress

characteristic: broker name

text: embryonic stem cell

text: human

text: embryo

text: normal

text: wild type genotype

text: Homo sapiens

text: Homo sapiens

text: blastocyst

text: bs-ATLAS-seq

text: unmodified

text: Homo sapiens

text: female


text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: ArrayExpress

text: hCBEC

text: cord blood-derived endothelial cell

text: human

characteristic: common name

characteristic: description

text: neonate

characteristic: developmental stage

text: normal

characteristic: disease

text: wild type genotype

characteristic: genotype

text: Homo sapiens

text: Homo sapiens

text: blastocyst

text: bs-ATLAS-seq

text: unmodified

text: Homo sapiens

text: male


text: public

text: ArrayExpress

text: induced pluripotent stem cell

text: human

text: neonate

text: normal

text: transduced with lentiviral vectors pSIN-EF2-Oct-Pur, pSIN-EF2-Sox2-Pur, pSIN-EF2-Nanog-Pur, and pSIN-EF2-LIN28-Pur

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: blastocyst

characteristic: organism part

characteristic: passage number

text: bs-ATLAS-seq

characteristic: protocol

text: technical replicate

characteristic: replicate

text: reprogrammed by OCT-4, SOX2, NANOG, LIN28

characteristic: reprogramming factors

text: Homo sapiens

text: male

characteristic: sex

characteristic: title


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

text: ArrayExpress

characteristic: broker name

text: induced pluripotent stem cell

text: human

text: neonate

text: normal

text: Homo sapiens

text: Homo sapiens

text: blastocyst

text: bs-ATLAS-seq

text: Homo sapiens

text: male


text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: ArrayExpress

text: foreskin fibroblast

text: human

characteristic: common name

characteristic: description

text: neonate

characteristic: developmental stage

text: normal

characteristic: disease

text: wild type genotype

characteristic: genotype

text: Homo sapiens

text: Homo sapiens

text: prepuce of penis

text: bs-ATLAS-seq

text: unmodified

text: Homo sapiens

text: male


text: public

text: ArrayExpress

text: induced pluripotent stem cell

text: human

text: neonate

text: normal

text: transduced with Sleeping Beauty transposon vector pT2-OSKM

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: prepuce of penis

characteristic: organism part

characteristic: passage number

text: bs-ATLAS-seq

characteristic: protocol

text: reprogrammed by OCT-4, SOX2, KLF4, c-MYC

characteristic: reprogramming factors

text: Homo sapiens

text: male

characteristic: sex

characteristic: title