characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: James Hutton Institute

text: public

text: rangeland biome

text: 2018/06/25 - Stream Sed upper 2

text: stream sediment

text: United Kingdom

text: not collected

text: not collected

characteristic: geographic location (region and locality)

text: stream sediment

characteristic: local environmental context

text: Escherichia coli

characteristic: organism

characteristic: project name

text: Escherichia coli


status: PUBLIC

tag: attribute

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: James Hutton Institute

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

tag: Namespace:James Hutton Institute

characteristic: Submitter Id

text: rangeland biome

characteristic: broad-scale environmental context

characteristic: collection date

text: 2018/08/27 - Sheep 3

characteristic: description

text: animal manure

characteristic: environmental medium

text: United Kingdom

characteristic: geographic location (country and/or sea)

text: not collected

unit: DD

characteristic: geographic location (latitude)

text: not collected

characteristic: geographic location (longitude)

text: Catchment of Tarland Burn, North East Scotland

text: feces

text: Escherichia coli

text: E. coli isolates from the Tarland catchment, Scotland

text: Escherichia coli

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: James Hutton Institute

text: public

text: rangeland biome

text: 2018/07/02 - Sheep 1

text: animal manure

text: United Kingdom

text: not collected

text: not collected

characteristic: geographic location (region and locality)

text: feces

characteristic: local environmental context

text: Escherichia coli

characteristic: organism

characteristic: project name

text: Escherichia coli


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: James Hutton Institute

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: rangeland biome

text: 2018/07/02 - Sheep 3

text: animal manure

text: United Kingdom

text: not collected

text: not collected

text: feces

text: Escherichia coli

text: Escherichia coli


text: James Hutton Institute

text: public

characteristic: SRA accession

characteristic: Submitter Id

text: rangeland biome

characteristic: broad-scale environmental context

characteristic: collection date

text: 2018/09/03 - Cow 6

characteristic: description

text: animal manure

characteristic: environmental medium

text: United Kingdom

text: not collected

text: not collected

text: feces

text: Escherichia coli

text: Escherichia coli


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: James Hutton Institute

text: public

text: rangeland biome

text: 2018/07/30 - Cow 4

text: animal manure

text: United Kingdom

characteristic: geographic location (country and/or sea)

text: not collected

characteristic: geographic location (latitude)

text: not collected

characteristic: geographic location (longitude)

text: feces

text: Escherichia coli

text: Escherichia coli

characteristic: title


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: James Hutton Institute

text: public

text: rangeland biome

text: 2018/07/02 - Cow 5

text: animal manure

text: United Kingdom

text: not collected

text: not collected

characteristic: geographic location (region and locality)

text: feces

characteristic: local environmental context

text: Escherichia coli

characteristic: organism

characteristic: project name

text: Escherichia coli


text: James Hutton Institute

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: rangeland biome

text: 2018/07/02 - Sheep 2

text: animal manure

text: United Kingdom

text: not collected

text: not collected

text: feces

text: Escherichia coli

text: Escherichia coli


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: James Hutton Institute

text: public

text: rangeland biome

characteristic: broad-scale environmental context

characteristic: collection date

text: 2018/07/23 - Cow 5

characteristic: description

text: animal manure

characteristic: environmental medium

text: United Kingdom

text: not collected

text: not collected

text: feces

text: Escherichia coli

text: Escherichia coli


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: James Hutton Institute

text: public

text: rangeland biome

text: 2018/07/30 - Sheep 2

text: animal manure

text: United Kingdom

characteristic: geographic location (country and/or sea)

text: not collected

characteristic: geographic location (latitude)

text: not collected

characteristic: geographic location (longitude)

text: feces

text: Escherichia coli

text: Escherichia coli

characteristic: title


text: James Hutton Institute

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: rangeland biome

text: 2018/07/09 - Cow 6

text: animal manure

text: United Kingdom

text: not collected

text: not collected

characteristic: geographic location (region and locality)

text: feces

characteristic: local environmental context

text: Escherichia coli

characteristic: organism

characteristic: project name

text: Escherichia coli


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: James Hutton Institute

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: rangeland biome

text: 2018/09/03 - Cow 8

text: animal manure

text: United Kingdom

text: not collected

text: not collected

text: feces

text: Escherichia coli

text: Escherichia coli


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: James Hutton Institute

text: public

text: rangeland biome

characteristic: broad-scale environmental context

characteristic: collection date

text: 2018/06/25 - Sheep 1

characteristic: description

text: animal manure

characteristic: environmental medium

text: United Kingdom

text: not collected

text: not collected

text: feces

text: Escherichia coli

text: Escherichia coli


text: James Hutton Institute

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: rangeland biome

text: 2017/10/23 - Soil 4

text: soil

text: United Kingdom

characteristic: geographic location (country and/or sea)

text: not collected

characteristic: geographic location (latitude)

text: not collected

characteristic: geographic location (longitude)

text: soil

text: Escherichia coli

text: Escherichia coli

characteristic: title


E-MTAB-13384:Sample 1

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: public

text: E-MTAB-13384:Sample 1

tag: Namespace:Institute of Cardiovascular Regeneration Centre of Molecular Medicine Goethe-University Frankfurt

unit: month

characteristic: age

text: ArrayExpress

characteristic: broker name

text: cardiac muscle cell

text: not collected

text: house mouse

characteristic: common name

text: Protocols: DNMT3AR882H knock-in (KI) mice were generated by the Mouse Biology Program (MBP) of the University of California (Davis, CA) as previously described34. The DNMT3Afl-R882H-fl mice were crossed to B6.Cg-Tg(Mx1-cre)1Cgn/J mice (referred to as Mx1-Cre)57 or to tamoxifen-inducible transgenic B6.129-Gt(ROSA)26Sortm1(cre/ERT2)Tyj/J mice (referred to as R26-CreERT2 Cre recombinase - estrogen receptor T2)58. C57BL/6N (CD45.2 or Ly5.2) and B6.SJL-PtprcaPepcb/BoyJ (CD45.1 or Ly5.1) mice were obtained from Charles River Laboratory. Primary bone marrow cells of age-matched Mx1-Cre+/DNMT3Afl-R882H-fl and Mx1-Cre-/DNMT3Afl-R882H-fl donor mice (Ly5.2) were collected between 14 to 28 days after the last pI:pC injection (Amersham; 400μg/mouse intraperitoneally for 3 nonconsecutive days) to ensure that signaling activation and cytotoxic effects mediated by pI:pC were minimized. To validate excision efficiency, genomic DNA from blood or harvested cells was subjected to PCR. Recipient mice were lethally (7.5 Gy total body irradiation) irradiated using X-Ray Irradiation System MultuRad 160 (Faxitron Bioptics LLC, USA). Recipient mice were maintained on Cyprofloxacin drinking water (40/mg/kg, Fresenius Kabi Deutschland GmbH, Bad Homburg) for one week before and two weeks after transplantation and allowed to engraft for 6 weeks, before being used for analysis. For transplantation, donor bone marrow cells from primary +/m (Ly5.2+) or wild-type +/+ (Ly5.2+) mice were transplanted into lethally irradiated Ly5.1 (B6.SJL-Ptprca Pepcb/BoyJ; Charles River Laboratory) recipients with a total of 2.5 x 105 cells per recipient. Peripheral blood engraftment was assessed by flow cytometry 6 weeks post transplantation. Six weeks after reconstitution of the bone marrow, myocardial infarction was induced by permanent ligation of the left anterior descending artery in transplanted recipients. In brief, anesthesia was induced with isoflurane (4%/800 ml O2/min) and maintained by endotracheal ventilation (2–3%/800 ml O2/min). Thoracotomy was performed in the fourth left intercostal space. The left ventricle was exposed, and the left coronary artery was permanently occluded. Chest and skin were closed, and anesthesia was terminated. Animals were extubated when breathing was restored. Initial myocardial injury was evaluated by measuring cardiac Troponin T levels in plasma 24 h after induction of myocardial infarction. For mouse single-cell nuclei (sn) and single-cell (sc) RNA sequencing we used a transplantation model with tamoxifen-inducible Rosa26CreERT2:DNMT3A-R882H (Cre recombinase - estrogen receptor T2; known as R26-CreERT2 strain) intercross mice as donors. These mice do not require pI:pC treatment and are independent of intrinsic inflammatory IFN-response to induce DNMT3A-R882H expression within the hematopoietic compartment34. We generated complete “chimeras” mice by transplanting of non-induced Rosa26CreERT2:DNMT3A-R882H (Ly5.1+) hematopoietic cells (either (+/+) or (+/m)) into Ly5.1/2 recipients. 6 weeks after BM cells transplantation, recipients were subjected to myocardial infarction as described above. Dissolved tamoxifen (Sigma-Aldrich) in corn oil was administered via intraperitoneal injection (1mg/mouse/day) once every 24 hours for a total of 10 consecutive days. The injections started 28 days after the induction of the myocardial infarction. The mice were used at day 74-76 post LAD. Cardiac tissues were thawed on ice and cut into small pieces. Minced tissue was pre-digested with a 5-ml enzyme solution of collagenase (2,500 U, Thermo Fisher Scientific) in HBSS+/+ (Gibco) for 10 min at 37 °C in a water bath. After centrifugation at 500g and 4 °C for 5 min, the supernatant was discarded, and nuclei were isolated after cell disruption with a glass dounce homogenizer (five strokes with a loose pestle and ten strokes with a tight pestle). After filtering (20-µm strainer, pluriSelect), the suspension was centrifuged at 1,000g and 4 °C for 6 min and resuspended in 500 µl staining buffer containing 1% BSA (Sigma-Aldrich), 5 nM MgCl2 (Sigma-Aldrich), 1 mM EDTA (Gibco), 1 mM EGTA (Gibco), 0.2 U µl−1 RNasin Plus Inhibitor (Promega) and 0.1 µg ml−1 Hoechst (Life Technologies) in Dulbecco´s phosphaste buffered saline (DPBS). Hoechst-positive nuclei were separated from cell debris by using the FACSAria Fusion instrument (BD Biosciences) and sorted into staining buffer without Hoechst at 4 °C. Cellular suspensions were loaded on a 10X Chromium Controller (10X Genomics) according to manufacturer’s protocol based on the 10X Genomics proprietary technology. Single-cell RNA-Seq libraries were prepared using Chromium Single Cell 3′ Reagent Kit, v3 (10X Genomics) according to manufacturer’s protocol. Briefly, the initial step consisted in performing an emulsion capture where individual cells were isolated into droplets together with gel beads coated with unique primers bearing 10X cell barcodes, UMI (unique molecular identifiers) and poly(dT) sequences. Reverse transcription reactions were engaged to generate barcoded full-length cDNA followed by the disruption of emulsions using the recovery agent and cDNA clean up with DynaBeads MyOne Silane Beads (ThermoFisher). Bulk cDNA was amplified using a Biometra Thermocycler TProfessional Basic Gradient with 96-Well Sample Block (98°C for 3 minutes; cycled 14×: 98°C for 15s, 67°C for 20s, and 72°C for 1 minute; 72°C for 1 minute; held at 4°C). Amplified cDNA product was cleaned with the SPRIselect Reagent Kit (Beckman Coulter). Indexed sequencing libraries were constructed using the reagents from the Chromium Single Cell 3′ v3 Reagent Kit, as follows: fragmentation, end repair and A-tailing; size selection with SPRIselect; adaptor ligation; post-ligation cleanup with SPRIselect; sample index PCR and cleanup with SPRI select beads. Library quantification and quality assessment was performed using Bioanalyzer Agilent 2100 using a High Sensitivity DNA chip (Agilent Genomics). Indexed libraries were equimolarly pooled and sequenced on an Illumina NovaSeq 6000.

text: adult

characteristic: developmental stage

text: Ly5.1/2 + WT (Ly5.1)

characteristic: genotype

text: not collected

characteristic: individual

text: not applicable

characteristic: isolate

text: Mus musculus

characteristic: organism

text: Mus musculus

text: heart

characteristic: organism part

text: Mus musculus

text: female

characteristic: sex

characteristic: strain

text: Sample 1


E-MTAB-13384:Sample 2

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Institute of Cardiovascular Regeneration Centre of Molecular Medicine Goethe-University Frankfurt

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-13384:Sample 2

characteristic: Submitter Id

text: ArrayExpress

text: cardiac muscle cell

text: not collected

characteristic: collection date

text: house mouse

characteristic: description

text: adult

text: Ly5.1/2 + WT (Ly5.1)

text: not collected

characteristic: geographic location (country and/or sea)

text: not applicable

text: Mus musculus

text: Mus musculus

text: heart

text: Mus musculus

text: female

text: Sample 2


E-MTAB-13384:Sample 3

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: public

text: E-MTAB-13384:Sample 3

characteristic: age

text: ArrayExpress

characteristic: broker name

text: cardiac muscle cell

text: not collected

text: house mouse

characteristic: common name

text: adult

characteristic: developmental stage

text: Ly5.1/2 + WT (Ly5.1)

characteristic: genotype

text: not collected

characteristic: individual

text: not applicable

text: Mus musculus

text: Mus musculus

text: heart

text: Mus musculus

text: female

text: Sample 3

characteristic: title


E-MTAB-13384:Sample 4

characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: E-MTAB-13384:Sample 4

text: ArrayExpress

text: cardiac muscle cell

text: not collected

text: house mouse

text: adult

text: Ly5.1/2 + RosaCre-D3A-KI (Ly5.1)

text: not collected

text: not applicable

characteristic: isolate

text: Mus musculus

characteristic: organism

text: Mus musculus

text: heart

characteristic: organism part

text: Mus musculus

text: female

characteristic: sex

characteristic: strain

text: Sample 4


E-MTAB-13384:Sample 5

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-13384:Sample 5

characteristic: Submitter Id

text: ArrayExpress

text: cardiac muscle cell

text: not collected

characteristic: collection date

text: house mouse

characteristic: description

text: adult

text: Ly5.1/2 + RosaCre-D3A-KI (Ly5.1)

text: not collected

characteristic: geographic location (country and/or sea)

text: not applicable

text: Mus musculus

text: Mus musculus

text: heart

text: Mus musculus

text: female

text: Sample 5


E-MTAB-13384:Sample 6

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: public

text: E-MTAB-13384:Sample 6

characteristic: age

text: ArrayExpress

characteristic: broker name

text: cardiac muscle cell

text: not collected

text: house mouse

characteristic: common name

text: adult

characteristic: developmental stage

text: Ly5.1/2 + RosaCre-D3A-KI (Ly5.1)

characteristic: genotype

text: not collected

characteristic: individual

text: not applicable

text: Mus musculus

text: Mus musculus

text: heart

text: Mus musculus

text: female

text: Sample 6

characteristic: title


E-MTAB-13386:Control 1

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: CARDIFF

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: E-MTAB-13386:Control 1

text: 19 to 82

unit: year

text: ArrayExpress

text: not collected

text: human

text: Protocols: Punch skin biopsies of the local area were performed under aseptic conditions and under local anaesthetic (Lidocaine Hydrochloride Injection BP 2%, w/v), using a 6-mm sterile disposable biopsy punch. Following the biopsy, samples were divided with half immediately placed in 10% formalin and transported to the laboratory and the other half placed in RNA laterTM (Fisher Scientific, Loughborough, UK) for bulk RNA sequencing. Control skin samples were obtained from female patients aged 19–82 years, following mastectomy or breast reduction after informed consent. Skin without obvious pathological findings, which was surplus to diagnostic histopathology requirements, was used in the experiments. Control punch biopsy samples were treated in the same manner as described above. After cutting skin samples into small pieces, samples were homogenised and lysed by using Tissue Raptor II and QIAzol® Lysis protocol (QIAzol® Handbook 2021, QIAgen, Crawley, UK). The quality of RNA was routinely assessed by determining the A260:A280 ratio using NanoDrop2000 (Thermo Scientific, UK). RNA libraries were created using TruSeq stranded Total RNA with ribozero GOLD (illumina, UK)

text: adult

text: normal

characteristic: disease

text: not collected

text: Control 1

text: not applicable

characteristic: isolate

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: skin

characteristic: organism part

text: Homo sapiens

text: female

characteristic: sex

text: Control 1


E-MTAB-13386:Control 2

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: CARDIFF

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-13386:Control 2

characteristic: Submitter Id

text: 19 to 82

text: ArrayExpress

text: not collected

characteristic: collection date

text: human

characteristic: description

text: adult

text: normal

text: not collected

characteristic: geographic location (country and/or sea)

text: Control 2

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: skin

text: Homo sapiens

text: female

text: Control 2


E-MTAB-13386:Control 3

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: CARDIFF

text: public

text: E-MTAB-13386:Control 3

text: 19 to 82

characteristic: age

text: ArrayExpress

characteristic: broker name

text: not collected

text: human

characteristic: common name

text: adult

characteristic: developmental stage

text: normal

text: not collected

text: Control 3

characteristic: individual

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: skin

text: Homo sapiens

text: female

text: Control 3

characteristic: title


characteristic: ENA-LAST-UPDATE

text: CARDIFF

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: ArrayExpress

text: not collected

text: human

text: adult

text: autoimmune type 1 diabetes

characteristic: disease

text: not collected

text: EEASI-A

text: not applicable

characteristic: isolate

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: skin

characteristic: organism part

text: Homo sapiens

text: male

characteristic: sex

text: EEASI-A


characteristic: External Id

text: CARDIFF

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: ArrayExpress

text: not collected

characteristic: collection date

text: human

characteristic: description

text: adult

text: autoimmune type 1 diabetes

text: not collected

characteristic: geographic location (country and/or sea)

text: EEASI-B

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: skin

text: Homo sapiens

text: female

text: EEASI-B


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: public

tag: Namespace:Respiratory Virus Unit, Microbiology Services Colindale, Public Health England

text: COVID-19 Genomics UK Consortium

characteristic: broker name

characteristic: collecting institution

text: not provided

characteristic: collector name

text: not provided

characteristic: definition for seropositive sample

text: United Kingdom

text: England

characteristic: geographic location (region and locality)

text: not provided

characteristic: host common name

text: not provided

characteristic: host health state

text: Human

characteristic: host scientific name

text: not provided

characteristic: host sex

text: not provided

characteristic: host subject id

text: not provided

text: Severe acute respiratory syndrome coronavirus 2

characteristic: receipt date

text: active surveillance in response to outbreak

characteristic: sample capture status

text: not provided

characteristic: serotype (required for a seropositive sample)

characteristic: title

text: not provided

characteristic: virus identifier


characteristic: ENA-CHECKLIST

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Respiratory Virus Unit, Microbiology Services Colindale, Public Health England

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

characteristic: collection date

text: not provided

text: not provided

text: United Kingdom

characteristic: geographic location (country and/or sea)

text: England

text: not provided

text: not provided

text: Human

text: not provided

text: not provided

text: not provided

characteristic: isolate

characteristic: organism

text: not provided

text: not provided


characteristic: ENA-FIRST-PUBLIC

text: QUADRAM INSTITUTE

text: public

tag: Namespace:QUADRAM INSTITUTE

characteristic: broker name

characteristic: description

text: United Kingdom

text: Not applicable

text: Campylobacter jejuni

text: Campylobacter jejuni


text: QUADRAM INSTITUTE

text: public

text: United Kingdom

text: Not applicable

text: Campylobacter coli

text: Campylobacter coli

characteristic: title


characteristic: ENA-CHECKLIST

text: QUADRAM INSTITUTE

text: public

text: United Kingdom

text: Not applicable

text: Escherichia coli

text: Escherichia coli


characteristic: ENA-LAST-UPDATE

text: QUADRAM INSTITUTE

text: public

text: United Kingdom

text: Not applicable

text: Phocaeicola dorei

text: Phocaeicola dorei


characteristic: External Id

text: QUADRAM INSTITUTE

text: public

text: United Kingdom

text: Not applicable

text: Pseudomonas aeruginosa

text: Pseudomonas aeruginosa


text: QUADRAM INSTITUTE

characteristic: INSDC center name

text: public

text: United Kingdom

text: Not applicable

text: Enterococcus faecalis

text: Enterococcus faecalis


text: QUADRAM INSTITUTE

characteristic: INSDC first public

text: public

text: United Kingdom

text: Not applicable

text: Enterococcus faecium

text: Enterococcus faecium


text: QUADRAM INSTITUTE

characteristic: INSDC last update

text: public

text: United Kingdom

text: Not applicable

text: Enterococcus hirae

text: Enterococcus hirae


text: public

characteristic: INSDC status

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

text: COVID-19 Genomics UK Consortium

characteristic: collecting institution

text: not provided

characteristic: collector name

text: not provided

characteristic: definition for seropositive sample

text: United Kingdom

text: Wales

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

text: public

characteristic: SRA accession

characteristic: Submitter Id

text: COVID-19 Genomics UK Consortium

characteristic: broker name

characteristic: collection date

text: not provided

text: not provided

text: United Kingdom

characteristic: geographic location (country and/or sea)

text: Wales

text: not provided

text: not provided

text: Human

text: not provided

text: not provided

text: not provided

characteristic: isolate

characteristic: organism

text: not provided

characteristic: title

text: not provided


characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

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

text: COVID-19 Genomics UK Consortium

characteristic: collecting institution

text: not provided

characteristic: collector name

text: not provided

characteristic: definition for seropositive sample

text: United Kingdom

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

text: not provided

text: not provided

text: not provided


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

text: public

characteristic: SRA accession

characteristic: Submitter Id

text: COVID-19 Genomics UK Consortium

characteristic: broker name

characteristic: collection date

text: not provided

text: not provided

text: United Kingdom

text: Scotland

text: not provided

text: not provided

text: Human

text: not provided

text: not provided

characteristic: host subject id

text: not provided

characteristic: sample capture status

text: not provided

characteristic: serotype (required for a seropositive sample)

text: not provided

characteristic: virus identifier


text: Cell Line

characteristic: ArrayExpress-Phenotype

text: unknown

characteristic: ArrayExpress-Sex

text: Homo sapiens

characteristic: ArrayExpress-Species

text: SC

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: not provided

text: human

characteristic: common name

text: not provided

characteristic: geographic location (country and/or sea)

text: Homo sapiens

characteristic: organism

text: Sanger Tag 79

text: Homo sapiens

characteristic: strain

characteristic: title


text: Cell Line

text: unknown

text: Homo sapiens

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: SC

text: public

characteristic: SRA accession

characteristic: Submitter Id

text: not provided

characteristic: collection date

text: human

text: not provided

text: Homo sapiens

text: Sanger Tag 57

text: Homo sapiens


text: Cell Line

characteristic: ArrayExpress-Phenotype

text: unknown

characteristic: ArrayExpress-Sex

text: Homo sapiens

characteristic: ArrayExpress-Species

text: SC

text: public

text: not provided

text: human

text: not provided

text: Homo sapiens

text: Sanger Tag 58

text: Homo sapiens


text: Cell Line

text: unknown

text: Homo sapiens

text: SC

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: not provided

text: human

text: not provided

text: Homo sapiens

text: Sanger Tag 76

text: Homo sapiens


text: Cell Line

characteristic: ArrayExpress-PHENOTYPE

text: unknown

characteristic: ArrayExpress-SEX

text: Homo sapiens

characteristic: ArrayExpress-SPECIES

text: Unknown

characteristic: GENDER

text: SC

text: public

characteristic: INSDC status

text: Cell Line

characteristic: PHENOTYPE

text: not provided

text: human

characteristic: common name

text: not provided

characteristic: geographic location (country and/or sea)

text: Homo sapiens

text: Homo sapiens


text: Cell Line

text: unknown

text: Homo sapiens

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: SC

text: public

characteristic: SRA accession

text: not provided

text: human

text: not provided

text: Homo sapiens

characteristic: organism

text: Sanger Tag 6

text: Homo sapiens

characteristic: strain

characteristic: title


text: Cell Line

characteristic: ArrayExpress-Phenotype

text: unknown

characteristic: ArrayExpress-Sex

text: Homo sapiens

characteristic: ArrayExpress-Species

text: SC

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: Submitter Id

text: not provided

characteristic: collection date

text: human

text: not provided

text: Homo sapiens

text: Sanger Tag 7

text: Homo sapiens


text: Cell Line

text: unknown

text: Homo sapiens

text: SC

text: public

characteristic: INSDC status

text: not provided

text: human

characteristic: common name

text: not provided

characteristic: geographic location (country and/or sea)

text: Homo sapiens

text: Sanger Tag 59

text: Homo sapiens


text: Cell Line

text: unknown

text: Homo sapiens

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: SC

text: public

text: not provided

text: human

text: not provided

text: Homo sapiens

text: Sanger Tag 1

text: Homo sapiens


text: Cell Line

text: unknown

text: Homo sapiens

characteristic: External Id

text: SC

text: public

characteristic: SRA accession

text: not provided

text: human

text: not provided

text: Homo sapiens

characteristic: organism

text: Sanger Tag 2

text: Homo sapiens


E-MTAB-13388:EEASI-A GEX

text: CARDIFF

text: public

text: E-MTAB-13388:EEASI-A GEX

characteristic: age

text: ArrayExpress

characteristic: broker name

text: lymphocyte

text: not collected

text: human

text: Protocols: Skin suction blisters were raised: Suction cups were applied to the deltoid region of participants’ arms, at the site of previous injection. Skin suction blisters were performed by gradually applying negative pressure (up to 60 kPa) from a suction pump machine VP25 (Eschmann, Lancing, UK) through a suction blister cup with a 15-mm hole in the base (UHBristol NHS Foundation Trust Medical Engineering Department, Bristol, UK) for 2–4 hr until a unilocular blister had formed within the cup. The cup was left in place for a further 30-60 minutes to encourage migration of lymphocytes into the blister fluid. The cup was then removed, and the blister fluid aspirated using a needle and syringe. Blister fluid was immediately suspended in 10ml heparinised RPMI (Gibco)+ 5% foetal calf serum Cells were counted then washed once and resuspended in an appropriate volume for scRNAseq. Samples were used fresh on the day of the collection. Samples were processed using a 10xGenomics V1 human 5’GEX kit libraries were constructed following standard 10xGenomics protocols.

characteristic: description

text: adult

characteristic: developmental stage

text: autoimmune type 1 diabetes

characteristic: disease

text: not collected

text: yes

characteristic: individual

text: not applicable

characteristic: isolate

text: Homo sapiens

text: Homo sapiens

text: zone of skin

characteristic: organism part

text: GEX

characteristic: protocol

text: Homo sapiens

text: male

characteristic: sex

text: EEASI-A GEX

characteristic: title


E-MTAB-13388:EEASI-A VDJ

characteristic: ENA-CHECKLIST

text: CARDIFF

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: E-MTAB-13388:EEASI-A VDJ

characteristic: Submitter Id

text: ArrayExpress

text: lymphocyte

text: not collected

characteristic: collection date

text: human

characteristic: common name

text: adult

text: autoimmune type 1 diabetes

text: not collected

characteristic: geographic location (country and/or sea)

text: yes

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: zone of skin

text: VDJ

text: Homo sapiens

text: male

text: EEASI-A VDJ


E-MTAB-13388:EEASI-B GEX

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: CARDIFF

text: public

characteristic: SRA accession

text: E-MTAB-13388:EEASI-B GEX

characteristic: age

text: ArrayExpress

characteristic: broker name

text: lymphocyte

text: not collected

text: human

characteristic: description

text: adult

characteristic: developmental stage

text: autoimmune type 1 diabetes

text: not collected

text: yes

text: not applicable

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: zone of skin

text: GEX

text: Homo sapiens

text: female

text: EEASI-B GEX


E-MTAB-13388:EEASI-B VDJ

characteristic: ENA-CHECKLIST

text: CARDIFF

characteristic: INSDC center name

text: public

text: E-MTAB-13388:EEASI-B VDJ

text: ArrayExpress

text: lymphocyte

text: not collected

text: human

text: adult

text: autoimmune type 1 diabetes

characteristic: disease

text: not collected

text: yes

characteristic: individual

text: not applicable

characteristic: isolate

text: Homo sapiens

text: Homo sapiens

text: zone of skin

characteristic: organism part

text: VDJ

characteristic: protocol

text: Homo sapiens

text: female

characteristic: sex

text: EEASI-B VDJ

characteristic: title


E-MTAB-13388:EEASI-C GEX

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: CARDIFF

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: E-MTAB-13388:EEASI-C GEX

characteristic: Submitter Id

text: ArrayExpress

text: lymphocyte

text: not collected

characteristic: collection date

text: human

characteristic: common name

text: adult

text: autoimmune type 1 diabetes

text: not collected

characteristic: geographic location (country and/or sea)

text: yes

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: zone of skin

text: GEX

text: Homo sapiens

text: male

text: EEASI-C GEX


E-MTAB-13388:EEASI-C VDJ

characteristic: ENA-CHECKLIST

characteristic: External Id

text: CARDIFF

characteristic: INSDC center name

text: public

characteristic: SRA accession

text: E-MTAB-13388:EEASI-C VDJ

characteristic: age

text: ArrayExpress

characteristic: broker name

text: lymphocyte

text: not collected

text: human

characteristic: description

text: adult

characteristic: developmental stage

text: autoimmune type 1 diabetes

text: not collected

text: yes

text: not applicable

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: zone of skin

text: VDJ

text: Homo sapiens

text: male

text: EEASI-C VDJ


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: Anthony Smith, NICD

text: public

tag: Namespace:Anthony Smith, NICD

text: EnteroBase

text: EnteroBase

text: A. Smith, National Institute for Communicable Diseases

text: Whole genome sequencing data uploaded by EnteroBase user

text: South Africa

text: North West

characteristic: geographic location (region and locality)

text: Human, Stool

text: Salmonella enterica

text: Salmonella enterica

text: Manhattan

characteristic: serovar

characteristic: strain

characteristic: title


text: Anthony Smith, NICD

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: Submitter Id

text: EnteroBase

text: EnteroBase

characteristic: collection date

text: South Africa

text: North West

text: Human, Stool

text: Salmonella enterica

text: Salmonella enterica

text: Irumu


characteristic: ENA-CHECKLIST

characteristic: External Id

text: Anthony Smith, NICD

characteristic: INSDC center name

text: public

characteristic: SRA accession

text: EnteroBase

text: EnteroBase

text: South Africa

characteristic: geographic location (country and/or sea)

text: North West

text: Human, Blood culture

text: Salmonella enterica

text: Salmonella enterica

text: Bovismorbificans


text: public

tag: Namespace:UNIVERSITY OF COLORADO DENVER, SCHOOL OF MEDICINE

text: IS-Seq of B. fragilis Colony 1

characteristic: description

text: USA

text: Bacteroides fragilis

characteristic: organism

text: Bacteroides fragilis

text: B. fragilis Colony 1


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: UNIVERSITY OF COLORADO DENVER, SCHOOL OF MEDICINE

text: public

text: IS-Seq of B. fragilis Colony 2

text: USA

text: Bacteroides fragilis

text: Bacteroides fragilis

text: B. fragilis Colony 2


text: public

text: IS-Seq of B. fragilis Colony 3

text: USA

text: Bacteroides fragilis

text: Bacteroides fragilis

text: B. fragilis Colony 3


text: public

text: IS-Seq of B. fragilis Colony 4

text: USA

text: Bacteroides fragilis

text: Bacteroides fragilis

text: B. fragilis Colony 4


text: public

text: IS-Seq of B. fragilis Colony 5

text: USA

text: Bacteroides fragilis

text: Bacteroides fragilis

text: B. fragilis Colony 5


text: public

text: IS-Seq of B. thetaiotamicron Colony 1

text: USA

text: Bacteroides thetaiotaomicron

text: Bacteroides thetaiotaomicron

text: B. thetaiotamicron Colony 1


text: public

text: IS-Seq of B. thetaiotamicron Colony 2

text: USA

text: Bacteroides thetaiotaomicron

text: Bacteroides thetaiotaomicron

text: B. thetaiotamicron Colony 2


text: public

text: IS-Seq of B. thetaiotamicron Colony 3

text: USA

text: Bacteroides thetaiotaomicron

text: Bacteroides thetaiotaomicron

text: B. thetaiotamicron Colony 3


text: public

text: IS-Seq of B. thetaiotamicron Colony 4

text: USA

text: Bacteroides thetaiotaomicron

text: Bacteroides thetaiotaomicron

text: B. thetaiotamicron Colony 4


text: public

text: IS-Seq of B. thetaiotamicron Colony 5

text: USA

text: Bacteroides thetaiotaomicron

text: Bacteroides thetaiotaomicron

text: B. thetaiotamicron Colony 5


Bt BHIS-1

text: public

text: Bt BHIS-1

text: IS-Seq of B. thetaiotamicron Colony 3 passaged in BHIS

text: USA

text: Bacteroides thetaiotaomicron

text: Bacteroides thetaiotaomicron

text: B. thetaiotamicron Colony 1 BHIS


Bt BHIS-2

text: public

text: Bt BHIS-2

text: IS-Seq of B. thetaiotamicron Colony 4 passaged in BHIS

text: USA

text: Bacteroides thetaiotaomicron

text: Bacteroides thetaiotaomicron

text: B. thetaiotamicron Colony 1 BHIS


Bt BHIS-3

text: public

text: Bt BHIS-3

text: IS-Seq of B. thetaiotamicron Colony 5 passaged in BHIS

text: USA

text: Bacteroides thetaiotaomicron

text: Bacteroides thetaiotaomicron

text: B. thetaiotamicron Colony 1 BHIS


Bt MM-1

text: public

text: Bt MM-1

text: IS-Seq of B. thetaiotamicron Colony 3 passaged in MM

text: USA

text: Bacteroides thetaiotaomicron

text: Bacteroides thetaiotaomicron

text: B. thetaiotamicron Colony 1 BHIS


Bt MM-2

text: public

text: Bt MM-2

text: IS-Seq of B. thetaiotamicron Colony 4 passaged in MM

text: USA

text: Bacteroides thetaiotaomicron

text: Bacteroides thetaiotaomicron

text: B. thetaiotamicron Colony 1 BHIS


Bt MM-3

text: public

text: Bt MM-3

text: IS-Seq of B. thetaiotamicron Colony 5 passaged in MM

text: USA

text: Bacteroides thetaiotaomicron

text: Bacteroides thetaiotaomicron

text: B. thetaiotamicron Colony 1 BHIS


Bt CPS3 WT-1

text: public

text: Bt CPS3 WT-1

text: IS-Seq of B. thetaiotamicron CPS3 Colony 1 Untreated

text: USA

text: Bacteroides thetaiotaomicron

text: Bacteroides thetaiotaomicron

text: B. thetaiotamicron CPS3 Colony 1 WT


Bt CPS3 WT-2

text: public

text: Bt CPS3 WT-2

text: IS-Seq of B. thetaiotamicron CPS3 Colony 2 Untreated

text: USA

text: Bacteroides thetaiotaomicron

text: Bacteroides thetaiotaomicron

text: B. thetaiotamicron CPS3 Colony 2 WT


Bt CPS3 WT-3

text: public

text: Bt CPS3 WT-3

text: IS-Seq of B. thetaiotamicron CPS3 Colony 3 Untreated

text: USA

text: Bacteroides thetaiotaomicron

text: Bacteroides thetaiotaomicron

text: B. thetaiotamicron CPS3 Colony 3 WT


Bt CPS3 DAC15-1

text: public

text: Bt CPS3 DAC15-1

text: IS-Seq of B. thetaiotamicron CPS3 Colony 1 DAC15

text: USA

text: Bacteroides thetaiotaomicron

text: Bacteroides thetaiotaomicron

text: B. thetaiotamicron CPS3 Colony 1 DAC15


Bt CPS3 DAC15-2

text: public

text: Bt CPS3 DAC15-2

text: IS-Seq of B. thetaiotamicron CPS3 Colony 2 DAC15

text: USA

text: Bacteroides thetaiotaomicron

text: Bacteroides thetaiotaomicron

text: B. thetaiotamicron CPS3 Colony 2 DAC15


Bt CPS3 DAC15-3

text: public

text: Bt CPS3 DAC15-3

text: IS-Seq of B. thetaiotamicron CPS3 Colony 3 DAC15

text: USA

text: Bacteroides thetaiotaomicron

text: Bacteroides thetaiotaomicron

text: B. thetaiotamicron CPS3 Colony 3 DAC15


Bt CPS3 DAC17-1

text: public

text: Bt CPS3 DAC17-1

text: IS-Seq of B. thetaiotamicron CPS3 Colony 1 DAC17

text: USA

text: Bacteroides thetaiotaomicron

text: Bacteroides thetaiotaomicron

text: B. thetaiotamicron CPS3 Colony 1 DAC17


Bt CPS3 DAC17-2

text: public

text: Bt CPS3 DAC17-2

text: IS-Seq of B. thetaiotamicron CPS3 Colony 2 DAC17

text: USA

text: Bacteroides thetaiotaomicron

text: Bacteroides thetaiotaomicron

text: B. thetaiotamicron CPS3 Colony 2 DAC17


Bt CPS3 DAC17-3

text: public

text: Bt CPS3 DAC17-3

text: IS-Seq of B. thetaiotamicron CPS3 Colony 3 DAC17

text: USA

text: Bacteroides thetaiotaomicron

text: Bacteroides thetaiotaomicron

text: B. thetaiotamicron CPS3 Colony 3 DAC17


text: public

text: E-MTAB-13389:Primary tumor 2x0.5Gy+anti-PD-L1

tag: Namespace:Team INSERM U1030 \"Molecular radiotherapy and Therapeutic Innovations\"

unit: week

characteristic: age

text: ArrayExpress

characteristic: broker name

text: not collected

text: house mouse

characteristic: common name

text: Protocols: MC38 tumors harvested from immunocompetent C57BL/6 mice treated with different conditions Mechanic and enzymatic dissociation, and then CD45 positive sorting to obtain CD45+ single-cell suspensions to be sequenced CD45+ single-cell suspensions were stored at a concentration of 106 cells/mL and kept on ice until use. Single-cell suspensions were loaded onto a chromium single-cell chip (10X Genomics™) according to the manufacturer’s instructions for coencapsulation with barcoded gel beads at a target capture rate of ~10,000 individual cells per sample. Captured mRNAs were barcoded during cDNA synthesis using the Chromium Next GEM Single-Cell 3’ gel beads-in emulsion (GEM), Library and Gel Bead Kit v3.1 (10X Genomics™) according to the manufacturer’s instructions. The resulting libraries were prepared in parallel in one single batch for each condition.

text: not collected

text: MC-38 tumorigenic cells grown in mice

characteristic: growth condition

text: not applicable

characteristic: isolate

text: Mus musculus

text: Mus musculus

text: primary tumor

characteristic: organism part

text: Mus musculus

text: Primary tumor 2x0.5Gy+anti-PD-L1

text: MC-38 cell line

characteristic: xenograft


E-MTAB-13389:Primary tumor 2x0.5Gy+IgG

text: Team INSERM U1030 \"Molecular radiotherapy and Therapeutic Innovations\"

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: E-MTAB-13389:Primary tumor 2x0.5Gy+IgG

characteristic: Submitter Id

text: ArrayExpress

text: not collected

characteristic: collection date

text: house mouse

text: not collected

text: MC-38 tumorigenic cells grown in mice

text: not applicable

text: Mus musculus

text: Mus musculus

text: primary tumor

text: Mus musculus

characteristic: strain

text: Primary tumor 2x0.5Gy+IgG

characteristic: title

text: MC-38 cell line


characteristic: ENA-CHECKLIST

characteristic: External Id

characteristic: INSDC center name

text: public

characteristic: SRA accession

text: E-MTAB-13389:Primary tumor 2x2Gy+anti-PD-L1

text: ArrayExpress

text: not collected

text: house mouse

characteristic: description

text: not collected

characteristic: geographic location (country and/or sea)

text: MC-38 tumorigenic cells grown in mice

text: not applicable

text: Mus musculus

characteristic: organism

text: Mus musculus

text: primary tumor

text: Mus musculus

text: Primary tumor 2x2Gy+anti-PD-L1

text: MC-38 cell line


E-MTAB-13389:Primary tumor 2x2Gy+IgG

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: public

text: E-MTAB-13389:Primary tumor 2x2Gy+IgG

characteristic: age

text: ArrayExpress

characteristic: broker name

text: not collected

text: house mouse

characteristic: common name

text: not collected

text: MC-38 tumorigenic cells grown in mice

characteristic: growth condition

text: not applicable

characteristic: isolate

text: Mus musculus

text: Mus musculus

text: primary tumor

text: Mus musculus

text: Primary tumor 2x2Gy+IgG

text: MC-38 cell line


E-MTAB-13389:Primary tumor 2x8Gy+IgG

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: E-MTAB-13389:Primary tumor 2x8Gy+IgG

characteristic: Submitter Id

text: ArrayExpress

text: not collected

characteristic: collection date

text: house mouse

text: not collected

text: MC-38 tumorigenic cells grown in mice

text: not applicable

text: Mus musculus

text: Mus musculus

text: primary tumor

characteristic: organism part

text: Mus musculus

text: Primary tumor 2x8Gy+IgG

text: MC-38 cell line

characteristic: xenograft


characteristic: ENA-CHECKLIST

characteristic: External Id

characteristic: INSDC center name

text: public

characteristic: SRA accession

text: E-MTAB-13389:Primary tumor NIR+anti-PD-L1

text: ArrayExpress

text: not collected

text: house mouse

characteristic: description

text: not collected

text: MC-38 tumorigenic cells grown in mice

text: not applicable

text: Mus musculus

text: Mus musculus

text: primary tumor

text: Mus musculus

characteristic: strain

text: Primary tumor NIR+anti-PD-L1

characteristic: title

text: MC-38 cell line


E-MTAB-13389:Primary tumor NIR+IgG

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: public

text: E-MTAB-13389:Primary tumor NIR+IgG

characteristic: age

text: ArrayExpress

characteristic: broker name

text: not collected

text: house mouse

characteristic: common name

text: not collected

characteristic: geographic location (country and/or sea)

text: MC-38 tumorigenic cells grown in mice

text: not applicable

text: Mus musculus

characteristic: organism

text: Mus musculus

text: primary tumor

text: Mus musculus

text: Primary tumor NIR+IgG

text: MC-38 cell line


characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: E-MTAB-13389:Secondary tumor 2x0.5Gy+anti-PD-L1

characteristic: Submitter Id

text: ArrayExpress

text: not collected

characteristic: collection date

text: house mouse

text: not collected

text: MC-38 tumorigenic cells grown in mice

characteristic: growth condition

text: not applicable

characteristic: isolate

text: Mus musculus

text: Mus musculus

text: secondary tumor

text: Mus musculus

text: Secondary tumor 2x0.5Gy+anti-PD-L1

text: MC-38 cell line


characteristic: ENA-CHECKLIST

characteristic: External Id

characteristic: INSDC center name

text: public

characteristic: SRA accession

text: E-MTAB-13389:Secondary tumor 2x0.5Gy+IgG

text: ArrayExpress

text: not collected

text: house mouse

characteristic: description

text: not collected

text: MC-38 tumorigenic cells grown in mice

text: not applicable

text: Mus musculus

text: Mus musculus

text: secondary tumor

characteristic: organism part

text: Mus musculus

text: Secondary tumor 2x0.5Gy+IgG

text: MC-38 cell line

characteristic: xenograft


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: public

text: E-MTAB-13389:Secondary tumor 2x2Gy+anti-PD-L1

characteristic: age

text: ArrayExpress

characteristic: broker name

text: not collected

text: house mouse

characteristic: common name

text: not collected

text: MC-38 tumorigenic cells grown in mice

text: not applicable

text: Mus musculus

text: Mus musculus

text: secondary tumor

text: Mus musculus

characteristic: strain

text: Secondary tumor 2x2Gy+anti-PD-L1

characteristic: title

text: MC-38 cell line


E-MTAB-13389:Secondary tumor 2x2Gy+IgG

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: E-MTAB-13389:Secondary tumor 2x2Gy+IgG

characteristic: Submitter Id

text: ArrayExpress

text: not collected

characteristic: collection date

text: house mouse

text: not collected

characteristic: geographic location (country and/or sea)

text: MC-38 tumorigenic cells grown in mice

text: not applicable

text: Mus musculus

characteristic: organism

text: Mus musculus

text: secondary tumor

text: Mus musculus

text: Secondary tumor 2x2Gy+IgG

text: MC-38 cell line


characteristic: ENA-CHECKLIST

characteristic: External Id

characteristic: INSDC center name

text: public

characteristic: SRA accession

text: E-MTAB-13389:Secondary tumor 2x8Gy+anti-PD-L1

text: ArrayExpress

text: not collected

text: house mouse

characteristic: description

text: not collected

text: MC-38 tumorigenic cells grown in mice

characteristic: growth condition

text: not applicable

characteristic: isolate

text: Mus musculus

text: Mus musculus

text: secondary tumor

text: Mus musculus

text: Secondary tumor 2x8Gy+anti-PD-L1

text: MC-38 cell line


E-MTAB-13389:Secondary tumor 2x8Gy+IgG

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: public

text: E-MTAB-13389:Secondary tumor 2x8Gy+IgG

characteristic: age

text: ArrayExpress

characteristic: broker name

text: not collected

text: house mouse

characteristic: common name

text: not collected

text: MC-38 tumorigenic cells grown in mice

text: not applicable

text: Mus musculus

text: Mus musculus

text: secondary tumor

characteristic: organism part

text: Mus musculus

text: Secondary tumor 2x8Gy+IgG

text: MC-38 cell line

characteristic: xenograft


characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: E-MTAB-13389:Secondary tumor NIR+anti-PD-L1

characteristic: Submitter Id

text: ArrayExpress

text: not collected

characteristic: collection date

text: house mouse

text: not collected

text: MC-38 tumorigenic cells grown in mice

text: not applicable

text: Mus musculus

text: Mus musculus

text: secondary tumor

text: Mus musculus

characteristic: strain

text: Secondary tumor NIR+anti-PD-L1

characteristic: title

text: MC-38 cell line


E-MTAB-13389:Secondary tumor NIR+IgG

characteristic: ENA-CHECKLIST

characteristic: External Id

characteristic: INSDC center name

text: public

characteristic: SRA accession

text: E-MTAB-13389:Secondary tumor NIR+IgG

text: ArrayExpress

text: not collected

text: house mouse

characteristic: description

text: not collected

characteristic: geographic location (country and/or sea)

text: MC-38 tumorigenic cells grown in mice

text: not applicable

text: Mus musculus

characteristic: organism

text: Mus musculus

text: secondary tumor

text: Mus musculus

text: Secondary tumor NIR+IgG

text: MC-38 cell line


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: public

tag: Namespace:Hopital du Valais, Institut Central des Hopitaux, Sion, Switzerland

text: SIB

characteristic: broker name

text: Valais Hospital, Central Institute; Sion, Switzerland

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text: Shanghai Normal University

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text: Streptococcus pneumoniae

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text: Streptococcus pneumoniae

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text: Streptococcus pneumoniae

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characteristic: collecting institution

text: Danish Covid-19 Genome Consortium

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characteristic: geographic location (country and/or sea)

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text: not provided

text: not provided

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text: University Hospital Basel

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text: Homo sapiens

characteristic: host scientific name

text: restricted access

characteristic: host sex

text: restricted access

characteristic: host subject id

text: hCoV-19/Switzerland/BS-UHB-USB_2023_08_13_ea9c59de/2023

characteristic: isolate

characteristic: sample capture status

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: University Hospital Basel

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: SIB

text: Switzerland

characteristic: geographic location (country and/or sea)

text: BS

text: Human

text: restricted access

text: Homo sapiens

text: restricted access

text: restricted access

text: hCoV-19/Switzerland/BS-UHB-USB_2023_08_13_5f1d8f1c/2023

characteristic: organism


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: University Hospital Basel

text: public

characteristic: Submitter Id

text: SIB

characteristic: broker name

characteristic: collecting institution

characteristic: collection date

characteristic: collector name

text: Switzerland

text: BS

characteristic: geographic location (region and locality)

text: Human

characteristic: host common name

text: restricted access

text: Homo sapiens

text: restricted access

text: restricted access

text: hCoV-19/Switzerland/BS-UHB-USB_2023_08_13_c0e1894f/2023


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: University Hospital Basel

text: public

text: SIB

text: Switzerland

text: BS

text: Human

text: restricted access

characteristic: host health state

text: Homo sapiens

characteristic: host scientific name

text: restricted access

characteristic: host sex

text: restricted access

characteristic: host subject id

text: hCoV-19/Switzerland/BS-UHB-USB_2023_08_13_42dbace9/2023

characteristic: isolate

characteristic: sample capture status

characteristic: title


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: University Hospital Basel

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: SIB

text: Switzerland

characteristic: geographic location (country and/or sea)

text: BE

text: Human

text: restricted access

text: Homo sapiens

text: restricted access

text: restricted access

text: hCoV-19/Switzerland/BE-UHB-USB_2023_08_13_a7a5227d/2023

characteristic: organism


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: University Hospital Basel

text: public

characteristic: Submitter Id

text: SIB

characteristic: broker name

characteristic: collecting institution

characteristic: collection date

characteristic: collector name

text: Switzerland

text: BL

characteristic: geographic location (region and locality)

text: Human

characteristic: host common name

text: restricted access

text: Homo sapiens

text: restricted access

text: restricted access

text: hCoV-19/Switzerland/BL-UHB-USB_2023_08_13_661d620c/2023


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: University Hospital Basel

text: public

text: SIB

text: Switzerland

text: JU

text: Human

text: restricted access

characteristic: host health state

text: Homo sapiens

characteristic: host scientific name

text: restricted access

characteristic: host sex

text: restricted access

characteristic: host subject id

text: hCoV-19/Switzerland/JU-UHB-USB_2023_08_13_9a7be80f/2023

characteristic: isolate

characteristic: sample capture status

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: University Hospital Basel

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: SIB

text: Switzerland

characteristic: geographic location (country and/or sea)

text: BL

text: Human

text: restricted access

text: Homo sapiens

text: restricted access

text: restricted access

text: hCoV-19/Switzerland/BL-UHB-USB_2023_08_13_af7a3a46/2023

text: Severe acute respiratory syndrome coronavirus 2

characteristic: organism


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: University Hospital Basel

text: public

characteristic: Submitter Id

text: SIB

characteristic: broker name

characteristic: collecting institution

characteristic: collection date

characteristic: collector name

text: Switzerland

text: BS

characteristic: geographic location (region and locality)

text: Human

characteristic: host common name

text: restricted access

text: Homo sapiens

text: restricted access

text: restricted access

text: hCoV-19/Switzerland/BS-UHB-USB_2023_08_13_b4ada8c4/2023


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: University Hospital Basel

text: public

text: SIB

text: Clinical Virology, University Hospital Basel, Basel, Switzerland

text: Switzerland

text: BL

text: Human

text: restricted access

characteristic: host health state

text: Homo sapiens

characteristic: host scientific name

text: restricted access

characteristic: host sex

text: restricted access

characteristic: host subject id

text: hCoV-19/Switzerland/BL-UHB-USB_2023_08_13_a421f745/2023

characteristic: isolate

characteristic: sample capture status

characteristic: title


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: University Hospital Basel

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: SIB

text: Yi-Wen Lim, Pascal Schläpfer, Rainer Gosert, Klaudia Nägele, Svenia Schmid, Karoline Leuzinger

text: Switzerland

characteristic: geographic location (country and/or sea)

text: BS

text: Human

text: restricted access

text: Homo sapiens

text: restricted access

text: restricted access

text: hCoV-19/Switzerland/BS-UHB-USB_2023_08_13_15cb101f/2023

characteristic: organism


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: University Hospital Basel

text: public

characteristic: Submitter Id

text: SIB

characteristic: broker name

characteristic: collecting institution

characteristic: collection date

characteristic: collector name

text: Switzerland

text: BL

characteristic: geographic location (region and locality)

text: Human

characteristic: host common name

text: restricted access

text: Homo sapiens

text: restricted access

text: restricted access

text: hCoV-19/Switzerland/BL-UHB-USB_2023_08_13_88778ee5/2023

text: active surveillance not initiated by an outbreak


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: University Hospital Basel

text: public

text: SIB

text: Switzerland

text: BS

text: Human

text: restricted access

characteristic: host health state

text: Homo sapiens

characteristic: host scientific name

text: restricted access

characteristic: host sex

text: restricted access

characteristic: host subject id

text: hCoV-19/Switzerland/BS-UHB-USB_2023_08_13_3803e352/2023

characteristic: isolate

characteristic: sample capture status

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: University Hospital Basel

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: SIB

text: Switzerland

characteristic: geographic location (country and/or sea)

text: BS

text: Human

text: restricted access

text: Homo sapiens

text: restricted access

text: restricted access

text: hCoV-19/Switzerland/BS-UHB-USB_2023_08_13_d96ebfca/2023

characteristic: organism


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: University Hospital Basel

text: public

characteristic: Submitter Id

text: SIB

characteristic: broker name

characteristic: collecting institution

characteristic: collection date

characteristic: collector name

text: Switzerland

text: BS

characteristic: geographic location (region and locality)

text: Human

characteristic: host common name

text: restricted access

text: Homo sapiens

text: restricted access

text: restricted access

text: hCoV-19/Switzerland/BS-UHB-USB_2023_08_13_6d354f90/2023


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: University Hospital Basel

text: public

text: SIB

text: Switzerland

text: BL

text: Human

text: restricted access

characteristic: host health state

text: Homo sapiens

characteristic: host scientific name

text: restricted access

characteristic: host sex

text: restricted access

characteristic: host subject id

text: hCoV-19/Switzerland/BL-UHB-USB_2023_08_13_59d40ff7/2023

characteristic: isolate

characteristic: sample capture status

characteristic: title


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Team INSERM U1030 \"Molecular radiotherapy and Therapeutic Innovations\"

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-13389_2:Primary tumor 2x0.5Gy+anti-PD-L1

characteristic: age

text: ArrayExpress

text: not collected

text: house mouse

characteristic: common name

text: Protocols: MC38 tumors harvested from immunocompetent C57BL/6 mice treated with different conditions Mechanic and enzymatic dissociation, and then CD45 positive sorting to obtain CD45+ single-cell suspensions to be sequenced CD45+ single-cell suspensions were stored at a concentration of 106 cells/mL and kept on ice until use. Single-cell suspensions were loaded onto a chromium single-cell chip (10X Genomics™) according to the manufacturer’s instructions for coencapsulation with barcoded gel beads at a target capture rate of ~10,000 individual cells per sample. Captured mRNAs were barcoded during cDNA synthesis using the Chromium Next GEM Single-Cell 3’ gel beads-in emulsion (GEM), Library and Gel Bead Kit v3.1 (10X Genomics™) according to the manufacturer’s instructions. The resulting libraries were prepared in parallel in one single batch for each condition.

characteristic: description

text: not collected

characteristic: geographic location (country and/or sea)

text: MC-38 tumorigenic cells grown in mice

characteristic: growth condition

text: not applicable

text: Mus musculus

characteristic: organism

text: Mus musculus

text: primary tumor

characteristic: organism part

text: Mus musculus

characteristic: strain

text: Primary tumor 2x0.5Gy+anti-PD-L1

text: MC-38 cell line

characteristic: xenograft


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: public

text: E-MTAB-13389_2:Primary tumor 2x0.5Gy+IgG

characteristic: Submitter Id

text: ArrayExpress

characteristic: broker name

text: not collected

characteristic: collection date

text: house mouse

text: not collected

text: MC-38 tumorigenic cells grown in mice

text: not applicable

characteristic: isolate

text: Mus musculus

text: Mus musculus

text: primary tumor

text: Mus musculus

text: Primary tumor 2x0.5Gy+IgG

characteristic: title

text: MC-38 cell line


characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-13389_2:Primary tumor 2x2Gy+anti-PD-L1

text: ArrayExpress

text: not collected

text: house mouse

text: not collected

text: MC-38 tumorigenic cells grown in mice

text: not applicable

text: Mus musculus

text: Mus musculus

text: primary tumor

text: Mus musculus

text: Primary tumor 2x2Gy+anti-PD-L1

text: MC-38 cell line


E-MTAB-13389_2:Primary tumor 2x2Gy+IgG

text: public

text: E-MTAB-13389_2:Primary tumor 2x2Gy+IgG

characteristic: age

text: ArrayExpress

text: not collected

text: house mouse

characteristic: common name

characteristic: description

text: not collected

characteristic: geographic location (country and/or sea)

text: MC-38 tumorigenic cells grown in mice

characteristic: growth condition

text: not applicable

text: Mus musculus

characteristic: organism

text: Mus musculus

text: primary tumor

characteristic: organism part

text: Mus musculus

text: Primary tumor 2x2Gy+IgG

text: MC-38 cell line


E-MTAB-13389_2:Primary tumor 2x8Gy+IgG

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: public

text: E-MTAB-13389_2:Primary tumor 2x8Gy+IgG

characteristic: Submitter Id

text: ArrayExpress

characteristic: broker name

text: not collected

characteristic: collection date

text: house mouse

text: not collected

text: MC-38 tumorigenic cells grown in mice

text: not applicable

text: Mus musculus

text: Mus musculus

text: primary tumor

text: Mus musculus

characteristic: strain

text: Primary tumor 2x8Gy+IgG

text: MC-38 cell line

characteristic: xenograft


characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: E-MTAB-13389_2:Primary tumor NIR+anti-PD-L1

text: ArrayExpress

text: not collected

text: house mouse

text: not collected

text: MC-38 tumorigenic cells grown in mice

text: not applicable

characteristic: isolate

text: Mus musculus

text: Mus musculus

text: primary tumor

text: Mus musculus

text: Primary tumor NIR+anti-PD-L1

characteristic: title

text: MC-38 cell line


E-MTAB-13389_2:Primary tumor NIR+IgG

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-13389_2:Primary tumor NIR+IgG

characteristic: age

text: ArrayExpress

text: not collected

text: house mouse

characteristic: common name

characteristic: description

text: not collected

characteristic: geographic location (country and/or sea)

text: MC-38 tumorigenic cells grown in mice

characteristic: growth condition

text: not applicable

text: Mus musculus

text: Mus musculus

text: primary tumor

text: Mus musculus

text: Primary tumor NIR+IgG

text: MC-38 cell line


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: public

text: E-MTAB-13389_2:Secondary tumor 2x0.5Gy+anti-PD-L1

characteristic: Submitter Id

text: ArrayExpress

characteristic: broker name

text: not collected

characteristic: collection date

text: house mouse

text: not collected

text: MC-38 tumorigenic cells grown in mice

text: not applicable

text: Mus musculus

characteristic: organism

text: Mus musculus

text: secondary tumor

characteristic: organism part

text: Mus musculus

text: Secondary tumor 2x0.5Gy+anti-PD-L1

text: MC-38 cell line


characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: E-MTAB-13389_2:Secondary tumor 2x0.5Gy+IgG

text: ArrayExpress

text: not collected

text: house mouse

text: not collected

text: MC-38 tumorigenic cells grown in mice

text: not applicable

text: Mus musculus

text: Mus musculus

text: secondary tumor

text: Mus musculus

characteristic: strain

text: Secondary tumor 2x0.5Gy+IgG

text: MC-38 cell line

characteristic: xenograft


text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-13389_2:Secondary tumor 2x2Gy+anti-PD-L1

characteristic: age

text: ArrayExpress

text: not collected

text: house mouse

characteristic: common name

characteristic: description

text: not collected

text: MC-38 tumorigenic cells grown in mice

text: not applicable

characteristic: isolate

text: Mus musculus

text: Mus musculus

text: secondary tumor

text: Mus musculus

text: Secondary tumor 2x2Gy+anti-PD-L1

characteristic: title

text: MC-38 cell line


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: public

text: E-MTAB-13389_2:Secondary tumor 2x2Gy+IgG

characteristic: Submitter Id

text: ArrayExpress

characteristic: broker name

text: not collected

characteristic: collection date

text: house mouse

text: not collected

characteristic: geographic location (country and/or sea)

text: MC-38 tumorigenic cells grown in mice

characteristic: growth condition

text: not applicable

text: Mus musculus

text: Mus musculus

text: secondary tumor

text: Mus musculus

text: Secondary tumor 2x2Gy+IgG

text: MC-38 cell line


characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: E-MTAB-13389_2:Secondary tumor 2x8Gy+anti-PD-L1

text: ArrayExpress

text: not collected

text: house mouse

text: not collected

text: MC-38 tumorigenic cells grown in mice

text: not applicable

text: Mus musculus

characteristic: organism

text: Mus musculus

text: secondary tumor

characteristic: organism part

text: Mus musculus

text: Secondary tumor 2x8Gy+anti-PD-L1

text: MC-38 cell line


text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-13389_2:Secondary tumor 2x8Gy+IgG

characteristic: age

text: ArrayExpress

text: not collected

text: house mouse

characteristic: common name

characteristic: description

text: not collected

text: MC-38 tumorigenic cells grown in mice

text: not applicable

text: Mus musculus

text: Mus musculus

text: secondary tumor

text: Mus musculus

characteristic: strain

text: Secondary tumor 2x8Gy+IgG

text: MC-38 cell line

characteristic: xenograft


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: public

text: E-MTAB-13389_2:Secondary tumor NIR+anti-PD-L1

characteristic: Submitter Id

text: ArrayExpress

characteristic: broker name

text: not collected

characteristic: collection date

text: house mouse

text: not collected

text: MC-38 tumorigenic cells grown in mice

text: not applicable

characteristic: isolate

text: Mus musculus

text: Mus musculus

text: secondary tumor

text: Mus musculus

text: Secondary tumor NIR+anti-PD-L1

characteristic: title

text: MC-38 cell line