characteristic: Contains RNA extracts (sample codes)

characteristic: Cq (N1)

characteristic: Cq (N2)

characteristic: Date of amplification (ARTIC)

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: TNIB-WW0058-21-AR1_S97_L001_R1_001.fastq.gz

text: National Institute of Biology

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: TNIB-WW0058-21-AR1_S97_L001_R2_001.fastq.gz

characteristic: SRA accession

text: INEXTVIR -20

characteristic: Submitter Id

text: Sequenced wastewater sample from Central WWTP Ljubljana 1

characteristic: description

text: wastewater treatment plant influent

text: wastewater treatment plant

text: wastewater treatment plant influent

text: Slovenia

text: virus

characteristic: organism

text: Illumina

characteristic: title

text: wastewater/sludge


status: PUBLIC

tag: attribute

characteristic: Contains RNA extracts (sample codes)

characteristic: DNA concentration (Qubit)

text: PNIB-WW0058-21-AR2_S49_L001_R1_001.fastq.gz

characteristic: Forward file name

text: National Institute of Biology

text: public

characteristic: No. replicate

text: PNIB-WW0058-21-AR2_S49_L001_R2_001.fastq.gz

characteristic: Reverse file name

text: Institute of Microbiology and Immunology, Faculty of Medicine, University of Ljubljana

characteristic: Sequenced where/how

text: INEXTVIR -20

characteristic: Storage location at NIB

tag: Namespace:National Institute of Biology

text: Sequenced wastewater sample from Central WWTP Ljubljana 2

text: wastewater treatment plant influent

characteristic: environment (biome)

text: wastewater treatment plant

characteristic: environment (feature)

text: wastewater treatment plant influent

characteristic: environment (material)

text: Slovenia

characteristic: geographic location (country and/or sea)

unit: DD

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: virus

characteristic: investigation type

text: Severe acute respiratory syndrome coronavirus 2

text: Sequencing of Slovenian WW samples for SARS-CoV-2 variant detection

characteristic: project name

text: Illumina

characteristic: sequencing method

text: wastewater/sludge

characteristic: wastewater/sludge environmental package


characteristic: Contains RNA extracts (sample codes)

characteristic: Cq (N1)

characteristic: Cq (N2)

characteristic: Date of amplification (ARTIC)

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: TNIB-WW0058-21-AR2_S98_L001_R1_001.fastq.gz

text: National Institute of Biology

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: TNIB-WW0058-21-AR2_S98_L001_R2_001.fastq.gz

characteristic: SRA accession

text: INEXTVIR -20

characteristic: Submitter Id

characteristic: description

text: wastewater treatment plant influent

text: wastewater treatment plant

text: wastewater treatment plant influent

text: Slovenia

text: virus

characteristic: organism

text: Illumina

characteristic: title

text: wastewater/sludge


characteristic: Contains RNA extracts (sample codes)

characteristic: DNA concentration (Qubit)

text: PNIB-WW0082-21-IMI1_S49_L001 (paired)_R1.fastq.gz

characteristic: Forward file name

text: National Institute of Biology

text: public

characteristic: No. replicate

text: PNIB-WW0082-21-IMI1_S49_L001 (paired)_R2.fastq.gz

characteristic: Reverse file name

characteristic: Sequenced where/how

text: INEXTVIR -20

characteristic: Storage location at NIB

text: wastewater treatment plant influent

characteristic: environment (biome)

text: wastewater treatment plant

characteristic: environment (feature)

text: wastewater treatment plant influent

characteristic: environment (material)

text: Slovenia

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: virus

characteristic: investigation type

characteristic: project name

text: Illumina

characteristic: sequencing method

text: wastewater/sludge

characteristic: wastewater/sludge environmental package


characteristic: Contains RNA extracts (sample codes)

characteristic: Cq (N1)

characteristic: Cq (N2)

characteristic: Date of amplification (ARTIC)

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: TNIB-WW0082-21-IMI1_S102_L001 (paired)_R1.fastq.gz

text: National Institute of Biology

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: TNIB-WW0082-21-IMI1_S102_L001 (paired)_R2.fastq.gz

characteristic: SRA accession

text: INEXTVIR -20

characteristic: Submitter Id

characteristic: description

text: wastewater treatment plant influent

text: wastewater treatment plant

text: wastewater treatment plant influent

text: Slovenia

text: virus

characteristic: organism

text: Illumina

characteristic: title

text: wastewater/sludge


characteristic: Contains RNA extracts (sample codes)

characteristic: DNA concentration (Qubit)

text: PNIB-WW0082-21-IMI2_S50_L001 (paired)_R1.fastq.gz

characteristic: Forward file name

text: National Institute of Biology

text: public

characteristic: No. replicate

text: PNIB-WW0082-21-IMI2_S50_L001 (paired)_R2.fastq.gz

characteristic: Reverse file name

characteristic: Sequenced where/how

text: INEXTVIR -20

characteristic: Storage location at NIB

text: wastewater treatment plant influent

characteristic: environment (biome)

text: wastewater treatment plant

characteristic: environment (feature)

text: wastewater treatment plant influent

characteristic: environment (material)

text: Slovenia

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: virus

characteristic: investigation type

characteristic: project name

text: Illumina

characteristic: sequencing method

text: wastewater/sludge

characteristic: wastewater/sludge environmental package


characteristic: Contains RNA extracts (sample codes)

characteristic: Cq (N1)

characteristic: Cq (N2)

characteristic: Date of amplification (ARTIC)

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: TNIB-WW0082-21-IMI2_S103_L001 (paired)_R1.fastq.gz

text: National Institute of Biology

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: TNIB-WW0082-21-IMI2_S103_L001 (paired)_R2.fastq.gz

characteristic: SRA accession

text: INEXTVIR -20

characteristic: Submitter Id

characteristic: description

text: wastewater treatment plant influent

text: wastewater treatment plant

text: wastewater treatment plant influent

text: Slovenia

text: virus

characteristic: organism

text: Illumina

characteristic: title

text: wastewater/sludge


characteristic: Contains RNA extracts (sample codes)

characteristic: DNA concentration (Qubit)

text: PNIB-WW00-94-21-AR1_S48_L001 (paired)_R1.fastq.gz

characteristic: Forward file name

text: National Institute of Biology

text: public

characteristic: No. replicate

text: PNIB-WW00-94-21-AR1_S48_L001 (paired)_R2.fastq.gz

characteristic: Reverse file name

characteristic: Sequenced where/how

text: INEXTVIR -20

characteristic: Storage location at NIB

text: Sequenced wastewater sample from Central WWTP Ljubljana 1

text: wastewater treatment plant influent

characteristic: environment (biome)

text: wastewater treatment plant

characteristic: environment (feature)

text: wastewater treatment plant influent

characteristic: environment (material)

text: Slovenia

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: virus

characteristic: investigation type

characteristic: project name

text: Illumina

characteristic: sequencing method

text: wastewater/sludge

characteristic: wastewater/sludge environmental package


characteristic: Contains RNA extracts (sample codes)

characteristic: Cq (N1)

characteristic: Cq (N2)

characteristic: Date of amplification (ARTIC)

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: TNIB-WW00-94-21-AR1_S104_L001 (paired)_R1.fastq.gz

text: National Institute of Biology

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: TNIB-WW00-94-21-AR1_S104_L001 (paired)_R2.fastq.gz

characteristic: SRA accession

text: Institute of Microbiology and Immunology, Faculty of Medicine, University of Ljubljana

text: INEXTVIR -20

characteristic: Submitter Id

characteristic: description

text: wastewater treatment plant influent

text: wastewater treatment plant

text: wastewater treatment plant influent

text: Slovenia

text: virus

characteristic: organism

text: Illumina

characteristic: title

text: wastewater/sludge


characteristic: Contains RNA extracts (sample codes)

characteristic: DNA concentration (Qubit)

text: PNIB-WW00-94-21-AR2_S49_L001 (paired)_R1.fastq.gz

characteristic: Forward file name

text: National Institute of Biology

text: public

characteristic: No. replicate

text: PNIB-WW00-94-21-AR2_S49_L001 (paired)_R2.fastq.gz

characteristic: Reverse file name

characteristic: Sequenced where/how

text: INEXTVIR -20

characteristic: Storage location at NIB

text: Sequenced wastewater sample from Central WWTP Ljubljana 2

text: wastewater treatment plant influent

characteristic: environment (biome)

text: wastewater treatment plant

characteristic: environment (feature)

text: wastewater treatment plant influent

characteristic: environment (material)

text: Slovenia

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: virus

characteristic: investigation type

text: Severe acute respiratory syndrome coronavirus 2

text: Sequencing of Slovenian WW samples for SARS-CoV-2 variant detection

characteristic: project name

text: Illumina

characteristic: sequencing method

text: wastewater/sludge

characteristic: wastewater/sludge environmental package


characteristic: Contains RNA extracts (sample codes)

characteristic: Cq (N1)

characteristic: Cq (N2)

characteristic: Date of amplification (ARTIC)

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: TNIB-WW00-94-21-AR2_S105_L001 (paired)_R1.fastq.gz

text: National Institute of Biology

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: TNIB-WW00-94-21-AR2_S105_L001 (paired)_R2.fastq.gz

characteristic: SRA accession

text: INEXTVIR -20

characteristic: Submitter Id

characteristic: description

text: wastewater treatment plant influent

text: wastewater treatment plant

text: wastewater treatment plant influent

text: Slovenia

text: virus

characteristic: organism

text: Illumina

characteristic: title

text: wastewater/sludge


text: MD Anderson

text: public

tag: Namespace:MD Anderson

text: 13.5 to 16.5

unit: day

characteristic: age

text: ArrayExpress

characteristic: broker name

text: fetal liver hematopoietic progenitor cell

text: house mouse

characteristic: common name

text: Protocols: Fetal liver cells (FLCs) were isolated from pregnant wildtype CD45.2+ C57Bl/6 females between days 13.5 – 16.5 of gestation. The FLCs were transduced with either empty GFP vector or hnRNP K GFP plasmid. The transduced cells were then sorted for GFP positivity using flow cytometry. RNA was extracted and purified from GFP+ sorted FLCs using Zymo Quick-RNA columns (Zymo Research, Irvine, CA). Barcoded, Illumina-stranded total RNA libraries were prepared using the TruSeq Stranded Total RNA Sample Preparation Kit (Illumina, San Diego, CA). Briefly, 250 ng of DNase I-treated total RNA was depleted of cytoplasmic and mitochondrial ribosomal RNA (rRNA) using Ribo-Zero Gold (Illumina, San Diego, CA). After purification, RNA was fragmented using divalent cations and double stranded cDNA was synthesized using random primers. The ends of the resulting double stranded cDNA fragments were repaired, 5′-phosphorylated, 3’-A tailed and Illumina-specific indexed adapters are were ligated. The products were purified and enriched by 12 cycles of PCR to create the final cDNA library. The libraries were quantified by qPCR and assessed for size distribution using the 4200 TapeStation High Sensitivity D1000 ScreenTape (Agilent Technologies, Santa Clara, CA).

text: embryo stage

characteristic: developmental stage

text: empty GFP vector

characteristic: genotype

text: GFP+

characteristic: immunophenotype

text: not applicable

characteristic: isolate

text: Mus musculus

text: Mus musculus

text: liver

characteristic: organism part

text: Mus musculus

characteristic: strain


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: MD Anderson

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: 13.5 to 16.5

text: ArrayExpress

text: house mouse

text: embryo stage

text: hnRNP K GFP overexpression

text: GFP+

text: not applicable

text: Mus musculus

text: Mus musculus

text: liver

text: Mus musculus


characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

tag: Namespace:WAGENINGEN UNIVERSITY, LABORATORY OF MICROBIOLOGY

characteristic: Submitter Id

text: SPAdes

characteristic: assembly software

text: default

characteristic: binning parameters

text: MetaWRAP

characteristic: binning software

text: ocean floor

characteristic: broad-scale environmental context

characteristic: collection date

characteristic: completeness score

text: CheckM

characteristic: completeness software

characteristic: contamination score

text: binned metagenome Gb4_35

characteristic: description

text: marine sponge tissue

characteristic: environmental medium

text: Norway

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: metagenome-assembled genome

characteristic: investigation type

text: marine sponge metagenome

characteristic: isolation source

text: marine sponge

characteristic: local environmental context

text: sponge metagenome

characteristic: metagenomic source

text: Candidatus Tectomicrobia bacterium AG-2022

characteristic: organism

text: SponGES

characteristic: project name

characteristic: sample derived from

text: Illumina

characteristic: sequencing method

text: multi-marker approach

characteristic: taxonomic identity marker


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:Key Laboratory of Environmental and Applied Microbiology, CAS

characteristic: Submitter Id

characteristic: collection date

text: water

characteristic: environment (biome)

text: water

characteristic: environment (feature)

text: water

characteristic: environment (material)

text: China

unit: m

characteristic: geographic location (depth)

text: metagenome

text: gut metagenome

text: temperature

text: gut metagenome

text: water

characteristic: title

text: water

characteristic: water environmental package


characteristic: ENA-CHECKLIST

text: Key Laboratory of Environmental and Applied Microbiology, CAS

text: public

text: water

text: water

text: water

text: China

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: metagenome

characteristic: investigation type

text: gut metagenome

characteristic: organism

text: temperature

characteristic: project name

text: gut metagenome

characteristic: sequencing method

text: water

text: water


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Rouen university

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

tag: Namespace:Rouen university

text: aquatic

characteristic: broad-scale environmental context

characteristic: depth

text: sediment microbial community

characteristic: description

characteristic: elevation

text: sediment�permeated�by�freshwater

characteristic: environmental medium

text: France

text: metagenome

text: freshwater

characteristic: local environmental context

text: sediment metagenome

text: AVANTSEINE

text: sediment metagenome

text: sediment

characteristic: sediment environmental package

text: Illumina MiSeq


characteristic: ENA-CHECKLIST

text: Hebrew University, Genetics department

text: public

tag: Namespace:Hebrew University, Genetics department

characteristic: Submitter Id

text: ArrayExpress

characteristic: broker name

text: neuron

text: human

characteristic: common name

text: Protocols: Cells were washed with PBS and trypsinized Qiagen RNeasy Kit KAPA Stranded mRNA-Seq Kit

text: embryo

characteristic: developmental stage

text: wild type genotype

characteristic: genotype

text: not applicable

characteristic: isolate

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: embryonic stem cell

characteristic: progenitor cell type

text: Homo sapiens

characteristic: title


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Hebrew University, Genetics department

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: ArrayExpress

text: neuron

text: human

text: embryo

text: HOXA6 mutant

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: embryonic stem cell

text: Homo sapiens


characteristic: ENA-CHECKLIST

text: Hebrew University, Genetics department

text: public

characteristic: Submitter Id

text: ArrayExpress

text: neuron

text: human

characteristic: description

text: embryo

text: HOXB6 mutant

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: embryonic stem cell

text: Homo sapiens


text: Hebrew University, Genetics department

text: public

text: ArrayExpress

characteristic: broker name

text: neuron

text: human

characteristic: common name

text: embryo

characteristic: developmental stage

text: pooledLibrary

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: embryonic stem cell

text: Homo sapiens

text: pooledLibrary


text: Sanger Institute

characteristic: GAL

text: NOT PROVIDED

text: Tree of Life Programme

text: public

tag: Namespace:Tree of Life Programme

text: Akito Kawahara

characteristic: collected by

text: Florida Museum of Natural History, University of Florida

characteristic: collecting institution

characteristic: collection date

text: ~50 m

characteristic: elevation

text: USA

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: Florida | Alachua County | 9424 SW 1st Place, Gainesville, Florida

characteristic: geographic location (region and locality)

text: Secondary forest

characteristic: habitat

text: Akito Y. Kawahara

characteristic: identified by

text: adult

characteristic: lifestage

text: Amorpha juglandis

characteristic: organism

text: WHOLE ORGANISM

characteristic: organism part

text: ToL

characteristic: project name

text: DTOL

text: Amorpha juglandis

text: MALE

characteristic: sex

characteristic: specimen id

text: NOT COLLECTED

characteristic: specimen voucher

text: N

characteristic: symbiont

characteristic: tolid


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Sanger Institute

characteristic: GAL

text: NOT PROVIDED

text: Tree of Life Programme

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: Akito Kawahara

characteristic: collected by

characteristic: collecting institution

characteristic: collection date

text: southern pine sphinx

characteristic: common name

text: ~50 m

text: USA

text: Secondary forest

text: Akito Y. Kawahara

text: adult

text: Lapara coniferarum

text: WHOLE ORGANISM

text: ToL

text: DTOL

text: Lapara coniferarum

text: MALE

text: NOT COLLECTED

text: N

characteristic: title


text: Sanger Institute

text: NOT PROVIDED

text: Tree of Life Programme

text: public

text: Akito Kawahara

text: ~50 m

characteristic: elevation

text: USA

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: Florida | Alachua County | University of Florida, Natural Area Teaching Laboratory

characteristic: geographic location (region and locality)

text: Grassy Field

characteristic: habitat

text: Akito Y. Kawahara

characteristic: identified by

text: adult

characteristic: lifestage

text: Hypercompe scribonia

characteristic: organism

text: WHOLE ORGANISM

characteristic: organism part

text: ToL

characteristic: project name

text: DTOL

text: Hypercompe scribonia

text: MALE

characteristic: sex

characteristic: specimen id

text: NOT COLLECTED

characteristic: specimen voucher

text: N

characteristic: symbiont

characteristic: tolid


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Hebrew university, Genetics Department

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

tag: Namespace:Hebrew university, Genetics Department

characteristic: Submitter Id

text: ArrayExpress

characteristic: broker name

text: differentiated ESCs

text: human

characteristic: common name

text: Protocols: Harvested using Trypsin gSYNC DNA extraction kit (Geneaid) PCR with Nextera overhangs

characteristic: description

text: pooled libraryR1

characteristic: genotype

text: Neuronal differentiation

characteristic: growth condition

text: not applicable

characteristic: isolate

text: Homo sapiens

text: Homo sapiens

text: embryonic stem cell

characteristic: progenitor cell type

text: Homo sapiens

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: Hebrew university, Genetics Department

text: public

text: ArrayExpress

text: differentiated ESCs

text: human

text: pooled libraryR2

text: Neuronal differentiation

text: not applicable

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: embryonic stem cell

text: Homo sapiens


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Hebrew university, Genetics Department

characteristic: INSDC center name

text: public

text: ArrayExpress

text: differentiated ESCs

text: human

text: pooled libraryR3

text: Neuronal differentiation

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: embryonic stem cell

text: Homo sapiens


text: Hebrew University, Genetics Department

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

tag: Namespace:Hebrew University, Genetics Department

text: ArrayExpress

text: hPSCs

text: human

text: infected ZIKA-MR

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens


text: Hebrew University, Genetics Department

text: public

characteristic: SRA accession

characteristic: Submitter Id

text: ArrayExpress

characteristic: broker name

text: hPSCs

text: human

text: infected ZIKA-PR

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens


E-MTAB-11970:Sample 1

text: public

text: E-MTAB-11970:Sample 1

tag: Namespace:Institut de Genetique et de Biologie Moleculaire et Cellulaire, Illkirch, France Centre National de la Recherche Scientifique, UMR7104, Illkirch, France Institut National de la Sante et de la Recherche Medicale, U1258, Illkirch, France Universite de Strasbourg, Illkirch, France

text: 108 to 117 hours after egg laying

characteristic: age

text: ArrayExpress

text: hemocyte

text: fruit fly

characteristic: common name

text: Protocols: For each replicate, the hemocytes were bled from 100 wandering 3rd instar larvae of the following genotypes: (1) gcm26/+ issued from the cross gcm26/CyOGFP x w1118, (2) Toll10b/+ issued from the cross Toll10b/Ser,TM3 x w1118 and (3) gcm26/+;Toll10b/+ issued from the cross gcm26/CyOGFP x Toll10b/Ser,TM3. The RNA were extracted using Tri reagent (Sigma) following the manufacturer’s instruction. Library preparation and sequencing were carried out by the genomeast facility (https://www.igbmc.fr/plateformes-technologiques/genomeast) at the IGBMC. Stranded mRNA libraries were prepared with Directional mRNA-Seq (SamplePrep).

characteristic: description

text: wandering third instar larval stage

characteristic: developmental stage

characteristic: genotype

text: pool of 100 larvae

characteristic: individual

text: not applicable

text: Drosophila melanogaster

text: Drosophila melanogaster

text: hematopoietic system

characteristic: organism part

text: Drosophila melanogaster

text: mixed

characteristic: sex

characteristic: strain

text: Sample 1


E-MTAB-11970:Sample 2

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Institut de Genetique et de Biologie Moleculaire et Cellulaire, Illkirch, France Centre National de la Recherche Scientifique, UMR7104, Illkirch, France Institut National de la Sante et de la Recherche Medicale, U1258, Illkirch, France Universite de Strasbourg, Illkirch, France

text: public

text: E-MTAB-11970:Sample 2

text: 108 to 117 hours after egg laying

text: ArrayExpress

text: hemocyte

text: fruit fly

text: wandering third instar larval stage

text: pool of 100 larvae

text: not applicable

characteristic: isolate

text: Drosophila melanogaster

characteristic: organism

text: Drosophila melanogaster

text: hematopoietic system

text: Drosophila melanogaster

text: mixed

text: Sample 2

characteristic: title


E-MTAB-11970:Sample 3

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-11970:Sample 3

characteristic: Submitter Id

text: 108 to 117 hours after egg laying

text: ArrayExpress

characteristic: broker name

text: hemocyte

text: fruit fly

text: wandering third instar larval stage

text: pool of 100 larvae

text: not applicable

text: Drosophila melanogaster

text: Drosophila melanogaster

text: hematopoietic system

text: Drosophila melanogaster

text: mixed

text: Sample 3


E-MTAB-11970:Sample 4

text: public

text: E-MTAB-11970:Sample 4

text: 108 to 117 hours after egg laying

characteristic: age

text: ArrayExpress

text: hemocyte

text: fruit fly

characteristic: common name

characteristic: description

text: wandering third instar larval stage

characteristic: developmental stage

characteristic: genotype

text: pool of 100 larvae

characteristic: individual

text: not applicable

text: Drosophila melanogaster

text: Drosophila melanogaster

text: hematopoietic system

characteristic: organism part

text: Drosophila melanogaster

text: mixed

text: Sample 4


E-MTAB-11970:Sample 5

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: public

text: E-MTAB-11970:Sample 5

text: 108 to 117 hours after egg laying

text: ArrayExpress

text: hemocyte

text: fruit fly

text: wandering third instar larval stage

text: pool of 100 larvae

text: not applicable

characteristic: isolate

text: Drosophila melanogaster

text: Drosophila melanogaster

text: hematopoietic system

text: Drosophila melanogaster

text: mixed

characteristic: sex

characteristic: strain

text: Sample 5


E-MTAB-11970:Sample 6

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-11970:Sample 6

text: 108 to 117 hours after egg laying

text: ArrayExpress

text: hemocyte

text: fruit fly

text: wandering third instar larval stage

text: pool of 100 larvae

text: not applicable

text: Drosophila melanogaster

characteristic: organism

text: Drosophila melanogaster

text: hematopoietic system

text: Drosophila melanogaster

text: mixed

text: Sample 6

characteristic: title


E-MTAB-11970:Sample 7

text: public

text: E-MTAB-11970:Sample 7

characteristic: Submitter Id

text: 108 to 117 hours after egg laying

characteristic: age

text: ArrayExpress

characteristic: broker name

text: hemocyte

text: fruit fly

characteristic: common name

characteristic: description

text: wandering third instar larval stage

characteristic: developmental stage

characteristic: genotype

text: pool of 100 larvae

text: not applicable

text: Drosophila melanogaster

text: Drosophila melanogaster

text: hematopoietic system

text: Drosophila melanogaster

text: mixed

text: Sample 7


E-MTAB-11970:Sample 8

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: public

text: E-MTAB-11970:Sample 8

text: 108 to 117 hours after egg laying

text: ArrayExpress

text: hemocyte

text: fruit fly

text: wandering third instar larval stage

text: pool of 100 larvae

characteristic: individual

text: not applicable

characteristic: isolate

text: Drosophila melanogaster

text: Drosophila melanogaster

text: hematopoietic system

characteristic: organism part

text: Drosophila melanogaster

text: mixed

text: Sample 8


E-MTAB-11970:Sample 9

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-11970:Sample 9

text: 108 to 117 hours after egg laying

text: ArrayExpress

text: hemocyte

text: fruit fly

text: wandering third instar larval stage

text: pool of 100 larvae

text: not applicable

text: Drosophila melanogaster

text: Drosophila melanogaster

text: hematopoietic system

text: Drosophila melanogaster

text: mixed

characteristic: sex

characteristic: strain

text: Sample 9


text: Rouen university

text: public

characteristic: Submitter Id

text: aquatic biome

characteristic: broad-scale environmental context

characteristic: collection date

text: Cu-exposed males (n=25)

characteristic: description

text: whole copepod

characteristic: environmental medium

text: France

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: copepod

characteristic: local environmental context

text: crustacean metagenome

characteristic: organism

text: LITOTES

characteristic: project name

text: crustacean metagenome

text: Illumina MiSeq

characteristic: sequencing method

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Rouen university

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: aquatic biome

text: Cu-exposed females (n=25)

text: whole copepod

text: France

text: copepod

text: crustacean metagenome

text: LITOTES

text: crustacean metagenome

text: Illumina MiSeq


text: Rouen university

text: public

characteristic: SRA accession

characteristic: Submitter Id

text: aquatic biome

characteristic: broad-scale environmental context

characteristic: collection date

text: controls males (n=25)

characteristic: description

text: whole copepod

characteristic: environmental medium

text: France

text: copepod

text: crustacean metagenome

text: LITOTES

text: crustacean metagenome

text: Illumina MiSeq


text: Rouen university

text: public

text: aquatic biome

text: controls females (n=25)

text: whole copepod

text: France

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: copepod

characteristic: local environmental context

text: crustacean metagenome

characteristic: organism

text: LITOTES

characteristic: project name

text: crustacean metagenome

text: Illumina MiSeq


text: Control

characteristic: ArrayExpress-PHENOTYPE

text: female

characteristic: ArrayExpress-SEX

text: Homo Sapiens

characteristic: ArrayExpress-SPECIES

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Female

characteristic: GENDER

text: SC

text: public

text: Control

characteristic: PHENOTYPE

text: human

characteristic: common name

text: Homo sapiens

text: Homo sapiens

characteristic: title


text: Control

text: female

text: Homo sapiens

text: Female

text: SC

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: Control

characteristic: SRA accession

characteristic: Submitter Id

text: human

text: Homo sapiens

text: Homo sapiens


text: public

tag: Namespace:Lecturer in Computational Cancer Biology, University of Southampton

text: ArrayExpress

characteristic: broker name

text: unmuted B cell

characteristic: clinical information

text: human

text: Protocols: Thirty-eight basal tumour samples were obtained from CLL patients diagnosed using the International Workshop on Chronic Lymphocytic Leukemia (iwCLL) guidelines and managed at Southampton General Hospital (Southampton, UK). Informed consent was obtained in accordance with the declaration of Helsinki and the study was approved by our regional research ethics committee. RNA was extracted using miRNeasy kits (Qiagen) from 1x10^6 cells as per manufacturer instructions mRNA libraries were prepared using TruSeq small RNA Library Prep kit (Illumina, Hayward, CA, USA).

characteristic: description

text: adult

characteristic: developmental stage

text: chronic lymphocytic leukemia

characteristic: disease

characteristic: individual

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: blood

characteristic: organism part

text: Homo sapiens

text: female

characteristic: sex


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Lecturer in Computational Cancer Biology, University of Southampton

text: public

text: ArrayExpress

text: unmuted B cell

text: human

characteristic: common name

text: adult

text: chronic lymphocytic leukemia

text: Homo sapiens

text: Homo sapiens

text: blood

text: Homo sapiens

text: female


characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: ArrayExpress

text: unmuted B cell

text: human

text: adult

text: chronic lymphocytic leukemia

text: Homo sapiens

text: Homo sapiens

text: blood

text: Homo sapiens

text: male

characteristic: title


text: public

characteristic: SRA accession

characteristic: Submitter Id

text: ArrayExpress

characteristic: broker name

text: muted B cell

characteristic: clinical information

text: human

characteristic: description

text: adult

text: chronic lymphocytic leukemia

text: Homo sapiens

text: Homo sapiens

text: blood

text: Homo sapiens

text: female


text: public

text: ArrayExpress

text: muted B cell

text: human

text: adult

characteristic: developmental stage

text: chronic lymphocytic leukemia

characteristic: disease

characteristic: individual

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: blood

characteristic: organism part

text: Homo sapiens

text: male


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: public

text: ArrayExpress

text: unmuted B cell

text: human

text: Protocols: Thirty-eight basal tumour samples were obtained from CLL patients diagnosed using the International Workshop on Chronic Lymphocytic Leukemia (iwCLL) guidelines and managed at Southampton General Hospital (Southampton, UK). Informed consent was obtained in accordance with the declaration of Helsinki and the study was approved by our regional research ethics committee. RNA was extracted using miRNeasy kits (Qiagen) from 1x10^6 cells as per manufacturer instructions mRNA libraries were prepared using TruSeq RNA Library Prep kit (Illumina, Hayward, CA, USA)

text: adult

text: chronic lymphocytic leukemia

text: Homo sapiens

text: Homo sapiens

text: blood

text: Homo sapiens

text: female

characteristic: sex


characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: ArrayExpress

text: unmuted B cell

text: human

characteristic: common name

text: adult

text: chronic lymphocytic leukemia

text: Homo sapiens

text: Homo sapiens

text: blood

text: Homo sapiens

text: male


text: public

characteristic: SRA accession

characteristic: Submitter Id

text: ArrayExpress

characteristic: broker name

text: muted B cell

characteristic: clinical information

text: human

text: adult

text: chronic lymphocytic leukemia

text: Homo sapiens

text: Homo sapiens

text: blood

text: Homo sapiens

text: female

characteristic: title


text: public

text: ArrayExpress

text: muted B cell

text: human

characteristic: description

text: adult

characteristic: developmental stage

text: chronic lymphocytic leukemia

characteristic: disease

characteristic: individual

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: blood

text: Homo sapiens

text: male


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Aala Abulfaraj

text: public

text: ena-SAMPLE-TAB-01-08-2022-23:22:51:851-11709

tag: Namespace:Aala Abulfaraj

text: Desert Soil

characteristic: broad-scale environmental context

text: horseradish tree

text: Plant Rhizosphere

text: soil

characteristic: environmental medium

text: Saudi Arabia

characteristic: geographic location (country and/or sea)

text: 21.4858 N

characteristic: geographic location (latitude)

text: 39.1925 E

characteristic: geographic location (longitude)

text: rhizosphere environment [ENVO:01000999]

characteristic: local environmental context

text: Moringa oleifera

text: soil metagenomics

characteristic: project name

text: Moringa oleifera

text: NovaSeq 6000

characteristic: sequencing method


text: Aala Abulfaraj

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: ena-SAMPLE-TAB-01-08-2022-23:22:51:851-11710

characteristic: Submitter Id

text: Desert Soil

text: horseradish tree

characteristic: common name

text: Plant Rhizosphere

characteristic: description

text: soil

text: Saudi Arabia

text: 21.4858 N

text: 39.1925 E

text: rhizosphere environment [ENVO:01000999]

text: Moringa oleifera

text: soil metagenomics

text: Moringa oleifera

text: NovaSeq 6000

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Aala Abulfaraj

text: public

text: ena-SAMPLE-TAB-01-08-2022-23:22:51:852-11712

text: Desert Soil

characteristic: broad-scale environmental context

text: horseradish tree

text: Bulk soil

text: soil

text: Saudi Arabia

text: 21.4858 N

text: 39.1925 E

text: rhizosphere environment [ENVO:01000999]

text: Moringa oleifera

characteristic: organism

text: soil metagenomics

text: Moringa oleifera

text: NovaSeq 6000


text: Aala Abulfaraj

text: public

text: ena-SAMPLE-TAB-01-08-2022-23:22:51:852-11713

text: Desert Soil

text: horseradish tree

text: Bulk soil

text: soil

characteristic: environmental medium

text: Saudi Arabia

characteristic: geographic location (country and/or sea)

text: 21.4858 N

characteristic: geographic location (latitude)

text: 39.1925 E

characteristic: geographic location (longitude)

text: rhizosphere environment [ENVO:01000999]

characteristic: local environmental context

text: Moringa oleifera

text: soil metagenomics

characteristic: project name

text: Moringa oleifera

text: NovaSeq 6000


text: EMBL

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: 2 to 4

unit: hour

characteristic: age

text: ArrayExpress

characteristic: broker name

text: fruit fly

text: Protocols: Wildtype Drosophila melanogaster flies were grown in population cages at 25 degr. Staged 2 hr populations of embryos were collected and aged at 25 degr till the required stage of development. Two independent collections were performed for each timepoint. The collected embryos were dechorionated using 50% bleach and formaldehyde fixed in 10 ml cross-linking solution (50 mM Hepes, 1 mM EDTA, 0.5 mM EGTA, 100 mM NaCl, 1.8 % formaldehyde, pH 8.0) and 30ml n-heptane on a shaker table at RT for 15 minutes. The reaction was terminated with 125 mM glycine, 0.1% Triton X-100 in PBS. After washing out the fix, the embryos were blotted dry and frozen in liquid nitrogen. 1g of frozen embryos were dounce-homogenized, 20 times with a loose pestle and 10 times with a tight pestle, in 10 ml of chilled HB buffer (15 mM Tris-HCl (pH 7.4), 0.34 M sucrose, 15 mM NaCl, 60 mM KCl, 0.2 mM EDTA and 0.2 mM EGTA) on ice. The lysate was filtered through 2 layers of Miracloth and spun at 3,500g for 10 min to pellet the nuclei. The nuclei were then washed in 10 ml of chilled HB buffer, spun at 3,500g for 10 min and resuspended in 3 ml of PBTB buffer (5% (wt/vol) BSA, 0.1% (vol/vol) Triton X-100 in PBS). The nuclei were dissociated by passing them ten times through a 20-G needle and then ten times through a 22-G needle using a 5-ml syringe, and filtered through a 20-�uem Sefar Nitex membrane. The total number of nuclei was estimated by microscopy, and 30 million nuclei aliquots were frozen in liquid nitrogen. Three aliquots of 30x106 nuclei in 2 biological replicates were used for each 3C template preparation. The Hi-C libraries were prepared as previously described (Sexton et al. 2012), using DpnII as restriction enzyme. The final library was prepared using the NEBNext Ultra DNA Library Prep Kit for Illumina (NEB) according to the manufacturer's instructions from at least 1 �g of DNA.

text: stage 5-8

characteristic: developmental stage

text: egg laying

characteristic: initial time point

text: Drosophila melanogaster

text: Drosophila melanogaster

text: whole embryo

characteristic: organism part

text: Drosophila melanogaster

text: mixed sex

characteristic: sex

text: OregonR

characteristic: strain


E-MTAB-12022:PT52 Tumor

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: public

text: E-MTAB-12022:PT52 Tumor

tag: Namespace:Department of General, Visceral and Pediatric Surgery, University Medical Center Gottingen

characteristic: Submitter Id

unit: year

text: ArrayExpress

text: desmoplastic histopathological growth pattern

characteristic: clinical information

text: human

characteristic: common name

text: Protocols: CRCLM and normal, non-transformed hepatic tissue located as distant to the metastases as possible from 6 patients with CRCLM (3 dHGP vs 3 rHGP) (Supplementary Table 1) was used for scRNA-seq. The HGP was determined retrospectively in H&E slides covering the tumor-liver interface at the margin of sample collection. Specimens underwent single-cell dissociation with the gentleMACs Octo Dissociator (Miltenyi Biotec,130-095-937), cryopreservation at -80°C and magnetic-activated cell sorting (MACS) with Basic MicroBeads (Miltenyi Biotec, 130-048-001) for depletion of dead cells. Nucleic acid extraction was performed using the 10xGenomics Chromium Next GEMSingle Cell 3ʹ Reagent Kits v3.1 following the given protocol (CG000204) Nucleic acid library construction was performed using the 10xGenomics Chromium Next GEMSingle Cell 3ʹ Reagent Kits v3.1 following the given protocol (CG000204 Rev D)

characteristic: description

text: adult

text: metastatic colorectal cancer

characteristic: disease

characteristic: individual

text: not applicable

characteristic: isolate

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: liver

text: neoplasm

characteristic: sampling site

text: Homo sapiens

text: male

text: PT52 Tumor

characteristic: title


E-MTAB-12022:PT52 Healthy

text: Department of General, Visceral and Pediatric Surgery, University Medical Center Gottingen

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-12022:PT52 Healthy

characteristic: age

text: ArrayExpress

characteristic: broker name

text: human

text: adult

characteristic: developmental stage

text: metastatic colorectal cancer

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: liver

characteristic: organism part

text: normal tissue

text: Homo sapiens

text: male

text: PT52 Healthy


E-MTAB-12022:PT55 Tumor

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: public

text: E-MTAB-12022:PT55 Tumor

characteristic: Submitter Id

text: ArrayExpress

characteristic: clinical information

text: human

characteristic: common name

text: adult

text: metastatic colorectal cancer

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: liver

text: neoplasm

text: Homo sapiens

text: female

characteristic: sex

text: PT55 Tumor


E-MTAB-12022:PT55 Healthy

characteristic: INSDC center name

text: public

text: E-MTAB-12022:PT55 Healthy

text: ArrayExpress

text: human

characteristic: description

text: adult

text: metastatic colorectal cancer

characteristic: disease

characteristic: individual

text: not applicable

characteristic: isolate

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: liver

text: normal tissue

characteristic: sampling site

text: Homo sapiens

text: female

text: PT55 Healthy

characteristic: title


E-MTAB-12022:PT61 Tumor

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-12022:PT61 Tumor

characteristic: age

text: ArrayExpress

characteristic: broker name

text: human

text: adult

characteristic: developmental stage

text: metastatic colorectal cancer

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: liver

characteristic: organism part

text: neoplasm

text: Homo sapiens

text: male

text: PT61 Tumor


E-MTAB-12022:PT61 Healthy

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: public

text: E-MTAB-12022:PT61 Healthy

characteristic: Submitter Id

text: ArrayExpress

characteristic: clinical information

text: human

characteristic: common name

text: adult

text: metastatic colorectal cancer

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: liver

text: normal tissue

text: Homo sapiens

text: male

characteristic: sex

text: PT61 Healthy


E-MTAB-12022:PT44 Tumor

characteristic: INSDC center name

text: public

text: E-MTAB-12022:PT44 Tumor

text: ArrayExpress

text: replacement histopathological growth pattern

text: human

characteristic: description

text: adult

text: metastatic colorectal cancer

characteristic: disease

characteristic: individual

text: not applicable

characteristic: isolate

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: liver

text: neoplasm

characteristic: sampling site

text: Homo sapiens

text: female

text: PT44 Tumor

characteristic: title


E-MTAB-12022:PT44 Healthy

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-12022:PT44 Healthy

characteristic: age

text: ArrayExpress

characteristic: broker name

text: human

text: adult

characteristic: developmental stage

text: metastatic colorectal cancer

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: liver

characteristic: organism part

text: normal tissue

text: Homo sapiens

text: female

text: PT44 Healthy


E-MTAB-12022:PT54 Tumor

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: public

text: E-MTAB-12022:PT54 Tumor

characteristic: Submitter Id

text: ArrayExpress

characteristic: clinical information

text: human

characteristic: common name

text: adult

text: metastatic colorectal cancer

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: liver

text: neoplasm

text: Homo sapiens

text: female

characteristic: sex

text: PT54 Tumor


E-MTAB-12022:PT54 Healthy

characteristic: INSDC center name

text: public

text: E-MTAB-12022:PT54 Healthy

text: ArrayExpress

text: human

characteristic: description

text: adult

text: metastatic colorectal cancer

characteristic: disease

characteristic: individual

text: not applicable

characteristic: isolate

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: liver

text: normal tissue

characteristic: sampling site

text: Homo sapiens

text: female

text: PT54 Healthy

characteristic: title


E-MTAB-12022:PT59 Tumor

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-12022:PT59 Tumor

characteristic: age

text: ArrayExpress

characteristic: broker name

text: human

text: adult

characteristic: developmental stage

text: metastatic colorectal cancer

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: liver

characteristic: organism part

text: neoplasm

text: Homo sapiens

text: male

text: PT59 Tumor


E-MTAB-12022:PT59 Healthy

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: public

text: E-MTAB-12022:PT59 Healthy

characteristic: Submitter Id

text: ArrayExpress

characteristic: clinical information

text: human

characteristic: common name

text: adult

text: metastatic colorectal cancer

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: liver

text: normal tissue

text: Homo sapiens

text: male

characteristic: sex

text: PT59 Healthy


E-MTAB-12021:Sample 10

characteristic: INSDC center name

text: public

text: E-MTAB-12021:Sample 10

tag: Namespace:Department of Pediatrics and Adolescent Medicine, Medical University of Vienna, Austria

text: ArrayExpress

text: HCMEC

text: microvascular endothelial cell

text: human

text: Protocols: Human endothelial umbilical vein cells (HUVEC), human cardiac microvascular endothelial cells (HCMEC) and the immortalized mesothelial cell line (MeT-5A) were purchased from established vendors (HUVEC and HCMEC from Promocell, Heidelberg, Germany; MeT-5A (ATCC® CRL-9444™) from LGC Standards, Wesel, Germany). Endothelial cells were grown in endothelial cell growth medium (Promocell, Heidelberg, Germany) with supplements and antibiotics according to manufacturer´s instructions. MeT-5A were cultured in Medium 199 (M199, 31150022, Gibco, Thermo Fisher Scientific, Waltham, MA, USA) supplemented with 10% (v/v) fetal bovine serum (FBS, Gibco, Thermo Fisher Scientific, Waltham, MA, USA), 1% (v/v) penicillin/streptomycin (P/S, Gibco, Thermo Fisher Scientific, Waltham, MA, USA). Human peritoneal mesothelial cells (HPMC) were isolated from four non-uremic patients and cultured as previously described [Stylianou et al. Kidney Int. 1990], as approved by the Ethic committee of the Medical Faculty, Heidelberg University (S-501/2018). Informed written consent was signed by the patients. The cells were grown in M199 medium supplemented with 10% FBS, 1% penicillin/streptomycin, 0.5 μg/ml insulin, 0.5 μg/ml transferrin, 0.4 μg/ml hydrocortisone and 2 mM L-glutamine (all from Merck, Darmstadt, Germany). Cells were seeded at a density of 2x 105 cells per well on polyester mesh (24 mm Transwell®, 0.4 µm pore size, 6-well type; Corning, MA, USA) under normal culture condition in 3 technical replicates per group. HCMEC and HPMC were pooled (4 donors) before seeding while HUVEC were bought pooled. The insert and outer chamber were filled with 1.5 and 3 mL of cell culture medium, respectively. Cell pellets were collected after reaching plateau. Total RNA isolation was performed using RLT buffer with 1% ß-mercaptoethanol and purified using Micro RNAeasy Kit with on column DNA digestion (Qiagen, Hilden, Germany) following the manufacturer´s procedure. The RNA concentration was measured using Qubit kit (Invitrogen). RNA integrity quantification was performed using RNA screen tape (Agilent, Santa Clara, USA). Detected RNA integrity number (RIN) values of samples were over 9.0 and 500 ng/sample were used for sequencing. The library was prepared using TruSeq Stranded mRNA Library Prep Kit (Illumina, San Diego, USA).

characteristic: description

text: not available

text: normal

characteristic: disease

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: heart

text: Homo sapiens

text: Sample 10

characteristic: title


E-MTAB-12021:Sample 11

text: Department of Pediatrics and Adolescent Medicine, Medical University of Vienna, Austria

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-12021:Sample 11

text: ArrayExpress

text: HCMEC

text: microvascular endothelial cell

text: human

text: not available

text: normal

text: Homo sapiens

text: Homo sapiens

text: heart

text: Homo sapiens

text: Sample 11


E-MTAB-12021:Sample 12

characteristic: ENA-CHECKLIST

text: public

text: E-MTAB-12021:Sample 12

text: ArrayExpress

characteristic: broker name

text: HCMEC

text: microvascular endothelial cell

text: human

text: not available

characteristic: developmental stage

text: normal

text: Homo sapiens

text: Homo sapiens

text: heart

characteristic: organism part

text: Homo sapiens

text: Sample 12


E-MTAB-12021:Sample 7

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: public

text: E-MTAB-12021:Sample 7

characteristic: Submitter Id

text: ArrayExpress

text: HPMC

text: mesothelial cell

text: human

text: not available

text: not available

text: Homo sapiens

text: Homo sapiens

text: peritoneum

text: Homo sapiens

text: Sample 7


E-MTAB-12021:Sample 8

characteristic: INSDC center name

text: public

text: E-MTAB-12021:Sample 8

text: ArrayExpress

text: HPMC

text: mesothelial cell

text: human

characteristic: common name

text: not available

text: not available

text: Homo sapiens

text: Homo sapiens

text: peritoneum

text: Homo sapiens

text: Sample 8


E-MTAB-12021:Sample 9

text: public

text: E-MTAB-12021:Sample 9

text: ArrayExpress

text: HPMC

text: mesothelial cell

text: human

characteristic: description

text: not available

text: not available

characteristic: disease

text: Homo sapiens

text: Homo sapiens

text: peritoneum

text: Homo sapiens

text: Sample 9


E-MTAB-12021:Sample 4

text: public

text: E-MTAB-12021:Sample 4

text: ArrayExpress

text: HUVEC

text: endothelial cell

text: human

text: neonate

text: normal

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: umbilical vain

text: Homo sapiens

text: Sample 4

characteristic: title


E-MTAB-12021:Sample 5

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: E-MTAB-12021:Sample 5

text: ArrayExpress

text: HUVEC

text: endothelial cell

text: human

text: neonate

text: normal

text: Homo sapiens

text: Homo sapiens

text: umbilical vain

text: Homo sapiens

text: Sample 5


E-MTAB-12021:Sample 6

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-12021:Sample 6

text: ArrayExpress

text: HUVEC

text: endothelial cell

text: human

text: neonate

text: normal

text: Homo sapiens

text: Homo sapiens

text: umbilical vain

text: Homo sapiens

text: Sample 6


E-MTAB-12021:Sample 1

characteristic: ENA-CHECKLIST

text: public

text: E-MTAB-12021:Sample 1

text: ArrayExpress

characteristic: broker name

text: mesothelial cell

text: human

text: not available

text: normal

text: Homo sapiens

text: Homo sapiens

text: pleura

text: Homo sapiens

text: Sample 1


E-MTAB-12021:Sample 2

text: public

text: E-MTAB-12021:Sample 2

text: ArrayExpress

text: mesothelial cell

text: human

text: not available

characteristic: developmental stage

text: normal

text: Homo sapiens

text: Homo sapiens

text: pleura

characteristic: organism part

text: Homo sapiens

text: Sample 2


E-MTAB-12021:Sample 3

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: public

text: E-MTAB-12021:Sample 3

text: ArrayExpress

text: mesothelial cell

text: human

text: not available

text: normal

text: Homo sapiens

text: Homo sapiens

text: pleura

text: Homo sapiens

text: Sample 3


characteristic: External Id

text: public

text: No

characteristic: Is the sequenced pathogen host associated?

tag: Namespace:Institut d'Investigacio Sanitaria de Palma

characteristic: Submitter Id

text: Hospital de Galdakao. Servicio de Microbiolog�a

characteristic: collection date

text: No

text: Spain

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: diseased

characteristic: host health state

text: human

characteristic: host scientific name

text: Pseudomonas aeruginosa

characteristic: isolate

text: Pseudomonas aeruginosa

text: Pseudomonas aeruginosa


text: Institut d'Investigacio Sanitaria de Palma

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: No

characteristic: SRA accession

text: No

text: Spain

text: diseased

text: human

text: Pseudomonas aeruginosa

text: Pseudomonas aeruginosa

characteristic: organism

text: Pseudomonas aeruginosa

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: UNIVERSITY OF SANTIAGO DE COMPOSTELA

text: public

tag: Namespace:UNIVERSITY OF SANTIAGO DE COMPOSTELA

characteristic: description

text: Spain

text: Bos taurus

text: beef meat

text: Escherichia coli

text: Escherichia coli


tag: attribute

text: UNIVERSITY OF SANTIAGO DE COMPOSTELA

text: public

characteristic: Submitter Id

characteristic: collection date

text: Spain

characteristic: geographic location (country and/or sea)

text: Meleagris gallopavo

text: turkey meat

text: Escherichia coli

text: Escherichia coli


text: UNIVERSITY OF SANTIAGO DE COMPOSTELA

text: public

text: Spain

text: Gallus gallus domesticus

characteristic: host scientific name

text: chicken meat

text: Escherichia coli

text: Escherichia coli


text: UNIVERSITY OF SANTIAGO DE COMPOSTELA

text: public

text: Spain

text: Sus scrofa

characteristic: isolate

text: pork meat

text: Escherichia coli

text: Escherichia coli


text: UNIVERSITY OF SANTIAGO DE COMPOSTELA

characteristic: INSDC center name

text: public

text: Spain

text: diseased

characteristic: host health state

text: Homo sapiens

text: human UTI

text: Escherichia coli

text: Escherichia coli


text: Genoscope CEA

characteristic: INSDC first public

characteristic: INSDC last update

text: public

tag: Namespace:Genoscope CEA

characteristic: common name

text: Thermococcus nautili

text: Thermococcus nautili

characteristic: strain

text: Thermococcus nautili 33-3


text: Maastricht University

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-12078:thyroid_organoids_DMSO_1_ComboSeq

tag: Namespace:Maastricht University

characteristic: age

text: ArrayExpress

characteristic: broker name

text: house mouse

text: Protocols: The human epithelial follicular cell line Nthy-ori 3-1 was seeded at a density of 40,000 cells/cm^2 in a 6-well plate exposed for 24 hours in triplicate to 1 μM or 10 μM benzo[a]pyrene (BAP) (B-1760, Sigma) dissolved in DMSO (1029521000, Merck) (final concentration of DMSO 0.5%). Six 0.5% DMSO solvent controls were also included. The medium used for cell culture was RPMI 1640 Medium, GlutaMAX™ Supplement (61870036, Gibco) supplemented with 10% FBS and 100 U mL-1 Penicillin-Streptomycin (15140122, Gibco). Enriched thyroid follicles were exposed to DMSO 0.5% for 24 hours (5 biological replicates). The medium used was DMEM (31966021, Gibco) supplemented with 15% FBS, vitamin C (50 μg mL-1) (A4544, Sigma), nonessential amino acids (0.1 mM) (11140035, Gibco), sodium pyruvate (1 mM) (11360039, Gibco), penicillin and streptomycin (50 U mL-1) (15140122, Gibco), 2-mercaptoethanol (0.1 mM) (31350010, Gibco), 8-Br-cAMP (10 µM) and TGF-βRI inhibitor SB431542 (10 µM) (1614, Tocris). At the end of the exposure time, cells were collected in 1.5 mL Eppendorf tubes and washed once with PBS. They were then lysed in QIAzol Lysis Reagent (79306, Qiagen). Murine thyroid organoids were derived from recombinant embryonic stem cell line (A2LoxNkx2-1-Pax8). Total RNA was extracted using the Direct-zol RNA miniprep (R2051, Zymo Research) for Nthy-ori 3-1 cells. Total RNA was extracted using the miRNAeasy Micro Kit (217084, Qiagen) for the thyroid follicles. All prepared libraries were quantified on a Qubit 2.0 Fluorometer (ThermoFisher) and quality control checked on the 2200 TapeStation System (Agilent) or BioAnalyzer 2100 expert (Agilent). 50 ng of total RNA isolated from Nthy-ori 3-1 samples were used as input for the NEXTFLEX® Combo-Seq™ mRNA/miRNA Kit (NOVA-5139-53, PerkinElmer). All RIN (RNA Integrity Number) values were 8 or higher. To deplete tRNA fragments and Y RNA fragments during the library preparation, the NEXTFLEX® tRNA/YRNA Blocker was used following the manufacturer’s instruction. We performed 13 PCR cycles during library preparation. 20 ng of total RNA isolated from thyroid organoids samples were used as input for the NEXTFLEX® Combo-Seq™ mRNA/miRNA Kit (NOVA-5139-53, PerkinElmer). All RIN (RNA Integrity Number) values were 8 or higher. To deplete tRNA fragments and Y RNA fragments during the library preparation, the NEXTFLEX® tRNA/YRNA Blocker was used following the manufacturer’s instruction. We performed 16 PCR cycles during library preparation. Poly(A) libraries were prepared on an automated system (Zephyr G3® NGS) with the NEXTFLEX® Rapid Directional RNA-Seq Kit 2.0 (NOVA-5198-02, PerkinElmer) using 1 μg of total RNA extracted from Nthy-ori 3-1 samples and performing 10 PCR cycles. NEXTFLEX® Poly(A) Beads 2.0 (NOVA-512992, PerkinElmer) and NEXTFLEX® Unique Dual Index Barcodes (NOVA-512923, PerkinElmer) were used during the library preparation. Small RNA libraries were prepared manually with the NEXTFLEX® Small RNA-Seq Kit v3 (NOVA-5132, PerkinElmer) from 100 ng of total input Nthy-ori 3-1 RNA and performing 18 PCR cycles.

text: adult

characteristic: developmental stage

text: normal

characteristic: disease

text: wild type genotype

characteristic: genotype

text: thyroid organoid culture

characteristic: growth condition

text: not applicable

text: Mus musculus

characteristic: organism

text: Mus musculus

text: thyroid gland

characteristic: organism part

text: embryonic stem cell

characteristic: progenitor cell type

characteristic: replicate

text: Mus musculus

characteristic: sex

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Maastricht University

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: E-MTAB-12078:thyroid_organoids_DMSO_2_ComboSeq

characteristic: Submitter Id

text: ArrayExpress

text: house mouse

characteristic: description

text: adult

text: normal

text: wild type genotype

text: thyroid organoid culture

text: not applicable

characteristic: isolate

text: Mus musculus

text: Mus musculus

text: thyroid gland

text: embryonic stem cell

text: Mus musculus


text: Maastricht University

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-12078:thyroid_organoids_DMSO_3_ComboSeq

characteristic: age

text: ArrayExpress

characteristic: broker name

text: house mouse

characteristic: common name

text: adult

characteristic: developmental stage

text: normal

characteristic: disease

text: wild type genotype

characteristic: genotype

text: thyroid organoid culture

characteristic: growth condition

text: not applicable

text: Mus musculus

text: Mus musculus

text: thyroid gland

text: embryonic stem cell

text: Mus musculus


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: Maastricht University

text: public

text: E-MTAB-12078:thyroid_organoids_DMSO_4_ComboSeq

text: ArrayExpress

text: house mouse

text: adult

text: normal

text: wild type genotype

text: thyroid organoid culture

text: not applicable

text: Mus musculus

characteristic: organism

text: Mus musculus

text: thyroid gland

characteristic: organism part

text: embryonic stem cell

characteristic: progenitor cell type

characteristic: replicate

text: Mus musculus

characteristic: sex

characteristic: title


characteristic: External Id

text: Maastricht University

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-12078:thyroid_organoids_DMSO_5_ComboSeq

characteristic: Submitter Id

text: ArrayExpress

text: house mouse

characteristic: description

text: adult

text: normal

text: wild type genotype

text: thyroid organoid culture

text: not applicable

characteristic: isolate

text: Mus musculus

text: Mus musculus

text: thyroid gland

text: embryonic stem cell

text: Mus musculus


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: Maastricht University

text: public

text: E-MTAB-12078:Nthyori_BAP_1_uM_1_ComboSeq

characteristic: age

text: ArrayExpress

characteristic: broker name

text: Nthy-ori 3-1

text: epithelial cell

text: human

characteristic: common name

text: adult

characteristic: developmental stage

text: normal

characteristic: disease

text: wild type genotype

characteristic: genotype

characteristic: growth condition

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: thyroid gland

text: Homo sapiens

text: female


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Maastricht University

characteristic: INSDC center name

text: public

text: E-MTAB-12078:Nthyori_BAP_1_uM_1_smallRNA

text: ArrayExpress

text: Nthy-ori 3-1

text: epithelial cell

text: human

text: adult

text: normal

text: wild type genotype

text: not applicable

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: thyroid gland

characteristic: organism part

characteristic: progenitor cell type

characteristic: replicate

text: Homo sapiens

text: female

characteristic: sex

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: Maastricht University

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: ArrayExpress

text: Nthy-ori 3-1

text: epithelial cell

text: human

characteristic: description

text: adult

text: normal

text: wild type genotype

text: not applicable

characteristic: isolate

text: Homo sapiens

text: Homo sapiens

text: thyroid gland

text: Homo sapiens

text: female


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Maastricht University

text: public

text: E-MTAB-12078:Nthyori_BAP_1_uM_2_ComboSeq

characteristic: age

text: ArrayExpress

characteristic: broker name

text: Nthy-ori 3-1

text: epithelial cell

text: human

characteristic: common name

text: adult

characteristic: developmental stage

text: normal

characteristic: disease

text: wild type genotype

characteristic: genotype

characteristic: growth condition

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: thyroid gland

text: Homo sapiens

text: female


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: Maastricht University

characteristic: INSDC center name

text: public

text: E-MTAB-12078:Nthyori_BAP_1_uM_2_smallRNA

text: ArrayExpress

text: Nthy-ori 3-1

text: epithelial cell

text: human

text: adult

text: normal

text: wild type genotype

text: not applicable

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: thyroid gland

characteristic: organism part

characteristic: progenitor cell type

characteristic: replicate

text: Homo sapiens

text: female

characteristic: sex

characteristic: title


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Maastricht University

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-12078:Nthyori_BAP_1_uM_3_ComboSeq

characteristic: Submitter Id

text: ArrayExpress

text: Nthy-ori 3-1

text: epithelial cell

text: human

characteristic: description

text: adult

text: normal

text: wild type genotype

text: not applicable

characteristic: isolate

text: Homo sapiens

text: Homo sapiens

text: thyroid gland

text: Homo sapiens

text: female


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: Maastricht University

text: public

text: E-MTAB-12078:Nthyori_BAP_1_uM_3_smallRNA

characteristic: age

text: ArrayExpress

characteristic: broker name

text: Nthy-ori 3-1

text: epithelial cell

text: human

characteristic: common name

text: adult

characteristic: developmental stage

text: normal

characteristic: disease

text: wild type genotype

characteristic: genotype

characteristic: growth condition

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: thyroid gland

text: Homo sapiens

text: female


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Maastricht University

characteristic: INSDC center name

text: public

text: E-MTAB-12078:Nthyori_BAP_10_uM_1_ComboSeq

text: ArrayExpress

text: Nthy-ori 3-1

text: epithelial cell

text: human

text: adult

text: normal

text: wild type genotype

text: not applicable

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: thyroid gland

characteristic: organism part

characteristic: progenitor cell type

characteristic: replicate

text: Homo sapiens

text: female

characteristic: sex

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: Maastricht University

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-12078:Nthyori_BAP_10_uM_1_smallRNA

characteristic: Submitter Id

text: ArrayExpress

text: Nthy-ori 3-1

text: epithelial cell

text: human

characteristic: description

text: adult

text: normal

text: wild type genotype

text: not applicable

characteristic: isolate

text: Homo sapiens

text: Homo sapiens

text: thyroid gland

text: Homo sapiens

text: female


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Maastricht University

text: public

text: E-MTAB-12078:Nthyori_BAP_10_uM_1_poly(A)

characteristic: age

text: ArrayExpress

characteristic: broker name

text: Nthy-ori 3-1

text: epithelial cell

text: human

characteristic: common name

text: adult

characteristic: developmental stage

text: normal

characteristic: disease

text: wild type genotype

characteristic: genotype

characteristic: growth condition

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: thyroid gland

text: Homo sapiens

text: female


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: Maastricht University

characteristic: INSDC center name

text: public

text: E-MTAB-12078:Nthyori_BAP_10_uM_2_ComboSeq

text: ArrayExpress

text: Nthy-ori 3-1

text: epithelial cell

text: human

text: adult

text: normal

text: wild type genotype

text: not applicable

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: thyroid gland

characteristic: organism part

characteristic: progenitor cell type

characteristic: replicate

text: Homo sapiens

text: female

characteristic: sex

characteristic: title


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Maastricht University

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-12078:Nthyori_BAP_10_uM_2_smallRNA

characteristic: Submitter Id

text: ArrayExpress

text: Nthy-ori 3-1

text: epithelial cell

text: human

characteristic: description

text: adult

text: normal

text: wild type genotype

text: not applicable

characteristic: isolate

text: Homo sapiens

text: Homo sapiens

text: thyroid gland

text: Homo sapiens

text: female


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: Maastricht University

text: public

text: E-MTAB-12078:Nthyori_BAP_10_uM_2_poly(A)

characteristic: age

text: ArrayExpress

characteristic: broker name

text: Nthy-ori 3-1

text: epithelial cell

text: human

characteristic: common name

text: adult

characteristic: developmental stage

text: normal

characteristic: disease

text: wild type genotype

characteristic: genotype

characteristic: growth condition

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: thyroid gland

text: Homo sapiens

text: female


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Maastricht University

characteristic: INSDC center name

text: public

text: E-MTAB-12078:Nthyori_BAP_10_uM_3_ComboSeq

text: ArrayExpress

text: Nthy-ori 3-1

text: epithelial cell

text: human

text: Protocols: The human epithelial follicular cell line Nthy-ori 3-1 was seeded at a density of 40,000 cells/cm^2 in a 6-well plate exposed for 24 hours in triplicate to 1 μM or 10 μM benzo[a]pyrene (BAP) (B-1760, Sigma) dissolved in DMSO (1029521000, Merck) (final concentration of DMSO 0.5%). Six 0.5% DMSO solvent controls were also included. The medium used for cell culture was RPMI 1640 Medium, GlutaMAX™ Supplement (61870036, Gibco) supplemented with 10% FBS and 100 U mL-1 Penicillin-Streptomycin (15140122, Gibco). Enriched thyroid follicles were exposed to DMSO 0.5% for 24 hours (5 biological replicates). The medium used was DMEM (31966021, Gibco) supplemented with 15% FBS, vitamin C (50 μg mL-1) (A4544, Sigma), nonessential amino acids (0.1 mM) (11140035, Gibco), sodium pyruvate (1 mM) (11360039, Gibco), penicillin and streptomycin (50 U mL-1) (15140122, Gibco), 2-mercaptoethanol (0.1 mM) (31350010, Gibco), 8-Br-cAMP (10 µM) and TGF-βRI inhibitor SB431542 (10 µM) (1614, Tocris). At the end of the exposure time, cells were collected in 1.5 mL Eppendorf tubes and washed once with PBS. They were then lysed in QIAzol Lysis Reagent (79306, Qiagen). Murine thyroid organoids were derived from recombinant embryonic stem cell line (A2LoxNkx2-1-Pax8). Total RNA was extracted using the Direct-zol RNA miniprep (R2051, Zymo Research) for Nthy-ori 3-1 cells. Total RNA was extracted using the miRNAeasy Micro Kit (217084, Qiagen) for the thyroid follicles. All prepared libraries were quantified on a Qubit 2.0 Fluorometer (ThermoFisher) and quality control checked on the 2200 TapeStation System (Agilent) or BioAnalyzer 2100 expert (Agilent). 50 ng of total RNA isolated from Nthy-ori 3-1 samples were used as input for the NEXTFLEX® Combo-Seq™ mRNA/miRNA Kit (NOVA-5139-53, PerkinElmer). All RIN (RNA Integrity Number) values were 8 or higher. To deplete tRNA fragments and Y RNA fragments during the library preparation, the NEXTFLEX® tRNA/YRNA Blocker was used following the manufacturer’s instruction. We performed 13 PCR cycles during library preparation. 20 ng of total RNA isolated from thyroid organoids samples were used as input for the NEXTFLEX® Combo-Seq™ mRNA/miRNA Kit (NOVA-5139-53, PerkinElmer). All RIN (RNA Integrity Number) values were 8 or higher. To deplete tRNA fragments and Y RNA fragments during the library preparation, the NEXTFLEX® tRNA/YRNA Blocker was used following the manufacturer’s instruction. We performed 16 PCR cycles during library preparation. Poly(A) libraries were prepared on an automated system (Zephyr G3® NGS) with the NEXTFLEX® Rapid Directional RNA-Seq Kit 2.0 (NOVA-5198-02, PerkinElmer) using 1 μg of total RNA extracted from Nthy-ori 3-1 samples and performing 10 PCR cycles. NEXTFLEX® Poly(A) Beads 2.0 (NOVA-512992, PerkinElmer) and NEXTFLEX® Unique Dual Index Barcodes (NOVA-512923, PerkinElmer) were used during the library preparation. Small RNA libraries were prepared manually with the NEXTFLEX® Small RNA-Seq Kit v3 (NOVA-5132, PerkinElmer) from 100 ng of total input Nthy-ori 3-1 RNA and performing 18 PCR cycles.

text: adult

text: normal

text: wild type genotype

text: not applicable

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: thyroid gland

characteristic: organism part

characteristic: progenitor cell type

characteristic: replicate

text: Homo sapiens

text: female

characteristic: sex

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: Maastricht University

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-12078:Nthyori_BAP_10_uM_3_smallRNA

characteristic: Submitter Id

text: ArrayExpress

text: Nthy-ori 3-1

text: epithelial cell

text: human

characteristic: description

text: adult

text: normal

text: wild type genotype

text: not applicable

characteristic: isolate

text: Homo sapiens

text: Homo sapiens

text: thyroid gland

text: Homo sapiens

text: female


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Maastricht University

text: public

text: E-MTAB-12078:Nthyori_BAP_10_uM_3_poly(A)

characteristic: age

text: ArrayExpress

characteristic: broker name

text: Nthy-ori 3-1

text: epithelial cell

text: human

characteristic: common name

text: adult

characteristic: developmental stage

text: normal

characteristic: disease

text: wild type genotype

characteristic: genotype

characteristic: growth condition

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: thyroid gland

text: Homo sapiens

text: female


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: Royal Botanic Gardens, Kew

characteristic: INSDC center name

text: public

tag: Namespace:Royal Botanic Gardens, Kew

text: Chase, M.W.

characteristic: collectorNo

text: Chile

characteristic: geographic location (country and/or sea)

text: Gilliesia graminea

characteristic: organism

text: Gilliesia graminea

text: Chase, M.W. 450 (K)

text: Gilliesia graminea

characteristic: title


text: Royal Botanic Gardens, Kew

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: Chase, M.W.

characteristic: collected by

text: South Africa

characteristic: isolation source

text: Amaryllis belladonna

text: Amaryllis belladonna

text: Chase, M.W. 612 (K)

text: Amaryllis belladonna


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Royal Botanic Gardens, Kew

text: public

text: Chase, M.W.

text: Brazil

text: spermatophyte root

text: spermatophyte root

text: Chase, M.W. 962 (K)

text: Urceolina korsakoffii


text: Royal Botanic Gardens, Kew

text: public

text: Chase, M.W.

text: Syria

text: spermatophyte root

text: spermatophyte root

text: Chase, M.W. 1066 (K)

text: Vagaria sp. - Chase, M.W. 1066 (K)


text: Royal Botanic Gardens, Kew

text: public

text: Chase, M.W.

text: Australia

text: Calostemma luteum

text: Calostemma luteum

text: Chase, M.W. 1505 (K)

text: Calostemma luteum


text: Royal Botanic Gardens, Kew

text: public

text: Chase, M.W.

text: Morocco

text: Acis tingitana

text: Acis tingitana

text: Chase, M.W. 1525 (K)

text: Acis tingitana


text: Royal Botanic Gardens, Kew

text: public

text: Chase, M.W.

text: Peru

text: Rauhia decora

text: Rauhia decora

text: Chase, M.W. 1573 (K)

text: Rauhia decora


text: Royal Botanic Gardens, Kew

text: public

text: Chase, M.W.

text: Paramongaia weberbaueri

text: Paramongaia weberbaueri

text: Chase, M.W. 1594 (K)

text: Paramongaia weberbaueri


text: Royal Botanic Gardens, Kew

text: public

text: Chase, M.W.

text: Romania

text: Leucojum vernum

text: Leucojum vernum

text: Chase, M.W. 1651 (K)

text: Leucojum vernum


text: Royal Botanic Gardens, Kew

text: public

text: Chase, M.W.

text: Peru

text: Nothoscordum andicola

text: Nothoscordum andicola

text: Chase, M.W. 1818 (K)

text: Nothoscordum andicola


text: Royal Botanic Gardens, Kew

text: public

text: Chase, M.W.

text: South Africa

text: Tulbaghia capensis

text: Tulbaghia capensis

text: Chase, M.W. 1832 (K)

characteristic: specimen voucher

text: Tulbaghia capensis


characteristic: ENA-CHECKLIST

text: Royal Botanic Gardens, Kew

text: public

text: Chase, M.W.

text: Ecuador

text: Phaedranassa cinerea

text: Phaedranassa cinerea

text: Chase, M.W. 1834 (K)

text: Phaedranassa cinerea


characteristic: ENA-FIRST-PUBLIC

text: Royal Botanic Gardens, Kew

text: public

text: Chase, M.W.

text: South Africa

text: Hessea breviflora

text: Hessea breviflora

text: Chase, M.W. 2238 (K)

text: Hessea breviflora


text: Royal Botanic Gardens, Kew

characteristic: INSDC center name

text: public

text: Chase, M.W.

text: Tanzania

text: Boophone disticha

text: Boophone disticha

text: Chase, M.W. 2246 (K)

text: Boophone disticha


text: Royal Botanic Gardens, Kew

text: public

text: Chase, M.W.

characteristic: collectorNo

text: USA

text: Tristagma nivale

text: Tristagma nivale

text: Chase, M.W. 2757 (K)

text: Tristagma nivale


text: Royal Botanic Gardens, Kew

text: public

text: Chase, M.W.

text: Ismene longipetala

text: Ismene longipetala

text: Chase, M.W. 3583 (K)

text: Ismene longipetala


text: Royal Botanic Gardens, Kew

text: public

text: Chase, M.W.

text: Iran

characteristic: geographic location (country and/or sea)

text: Ungernia flava

text: Ungernia flava

text: Chase, M.W. 3640 (K)

text: Ungernia flava


text: Royal Botanic Gardens, Kew

text: public

text: Snijman, D.

text: South Africa

text: Strumaria truncata

characteristic: organism

text: Strumaria truncata

text: Snijman, D. 281 (NBG)

text: Strumaria truncata


text: Royal Botanic Gardens, Kew

text: public

text: Chase, M.W.

text: Argentina

text: Hieronymiella argentina

text: Hieronymiella argentina

text: Chase, M.W. 14076 (K)

text: Hieronymiella argentina

characteristic: title


text: Royal Botanic Gardens, Kew

characteristic: INSDC first public

text: public

text: Chase, M.W.

text: Brazil

text: Hippeastrum psittacinum

text: Hippeastrum psittacinum

text: Chase, M.W. 14823 (K)

text: Hippeastrum psittacinum


text: Royal Botanic Gardens, Kew

characteristic: INSDC last update

text: public

text: Chase, M.W.

text: Peru

text: Stenomesson miniatum

text: Stenomesson miniatum

text: Chase, M.W. 16481 (K)

text: Stenomesson miniatum


text: Royal Botanic Gardens, Kew

text: public

characteristic: INSDC status

text: Chase, M.W.

text: South Africa

text: Nerine undulata

text: Nerine undulata

text: Chase, M.W. 18199 (K)

text: Nerine undulata


text: Royal Botanic Gardens, Kew

text: public

characteristic: SRA accession

text: Chase, M.W.

text: Miersia chilensis

text: Miersia chilensis

text: Chase, M.W. 18891 (K)

text: Miersia chilensis


text: Royal Botanic Gardens, Kew

text: public

characteristic: Submitter Id

text: South Africa

text: Haemanthus coccineus

text: Haemanthus coccineus

text: RBG Kew DNA Bank 26846

text: Haemanthus coccineus


text: Royal Botanic Gardens, Kew

text: public

text: South Africa

text: Apodolirion cedarbergense

text: Apodolirion cedarbergense

text: RBG Kew DNA Bank 26879

text: Apodolirion cedarbergense


text: Royal Botanic Gardens, Kew

text: public

text: South Africa

text: Gethyllis afra

text: Gethyllis afra

text: RBG Kew DNA Bank 26989

text: Gethyllis afra


text: Royal Botanic Gardens, Kew

text: public

text: South Africa

text: Cyrtanthus spiralis

text: Cyrtanthus spiralis

text: RBG Kew DNA Bank 27798

text: Cyrtanthus spiralis


text: Royal Botanic Gardens, Kew

text: public

text: South Africa

text: Crossyne guttata

text: Crossyne guttata

text: RBG Kew DNA Bank 27801

text: Crossyne guttata


text: Royal Botanic Gardens, Kew

text: public

text: Snijman, D.

text: South Africa

text: Scadoxus multiflorus

text: Scadoxus multiflorus

text: Snijman, D. s.n.; 28302 (K)

text: Scadoxus multiflorus


text: Royal Botanic Gardens, Kew

text: public

text: Duncan, G.

text: South Africa

text: Cryptostephanus vansonii

text: Cryptostephanus vansonii

text: Duncan, G. s.n.; 28548 (K)

text: Cryptostephanus vansonii


text: Royal Botanic Gardens, Kew

text: public

text: Ameka & De Graft-Johnson

text: Ghana

text: Crinum natans

text: Crinum natans

text: Ameka & De Graft-Johnson 114 (GC)

text: Crinum natans


text: Royal Botanic Gardens, Kew

text: public

text: Chile

text: spermatophyte root

text: spermatophyte root

text: RBG Kew Living Collection 2008-1227

text: Miersia humilis


text: Royal Botanic Gardens, Kew

text: public

text: Mashaly, I.; Boulos, L.

text: Egypt

text: Pancratium maritimum

text: Pancratium maritimum

text: Mashaly, I.; Boulos, L. 20245 (K)

text: Pancratium maritimum


text: Royal Botanic Gardens, Kew

text: public

text: common snowdrop

characteristic: common name

text: Italy

text: Galanthus nivalis

text: Galanthus nivalis

text: HEPF 4236 (K)

text: Galanthus nivalis


text: Royal Botanic Gardens, Kew

text: public

text: Jury, S.L., Tahiri, B.; Upson, T.M.

characteristic: collected by

characteristic: isolation source

text: Hannonia hesperidum

text: Hannonia hesperidum

text: Jury, S.L., Tahiri, B.; Upson, T.M. 14314 (K)

text: Hannonia hesperidum


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Royal Botanic Gardens, Kew

text: public

text: Newitt, J.

characteristic: collection date

text: Clinanthus incarnatus

text: Clinanthus incarnatus

text: Newitt, J. 1 (K)

text: Clinanthus incarnatus


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: Royal Botanic Gardens, Kew

text: public

text: Newitt, J.

text: Zephyranthes gracilifolia

text: Zephyranthes gracilifolia

text: Newitt, J. 2 (K)

characteristic: specimen voucher

text: Zephyranthes gracilifolia


text: Royal Botanic Gardens, Kew

characteristic: INSDC center name

text: public

text: Newitt, J.

characteristic: collectorNo

text: Eustephia coccinea

text: Eustephia coccinea

text: Newitt, J. 3 (K)

text: Eustephia coccinea


text: Royal Botanic Gardens, Kew

text: public

text: Newitt, J.

text: Scadoxus puniceus

characteristic: organism

text: Scadoxus puniceus

text: Newitt, J. 4 (K)

text: Scadoxus puniceus

characteristic: title


text: Royal Botanic Gardens, Kew

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: Newitt, J.

text: Worsleya procera

text: Worsleya procera

text: Newitt, J. 5 (K)

text: Worsleya procera


text: Royal Botanic Gardens, Kew

text: public

characteristic: INSDC status

characteristic: SRA accession

text: Maurin, O.

text: Leucocoryne odorata

text: Leucocoryne odorata

text: Maurin, O. 4401 (K)

text: Leucocoryne odorata


text: Royal Botanic Gardens, Kew

text: public

characteristic: Submitter Id

text: Maurin, O.

text: Gilliesia miersioides

text: Gilliesia miersioides

text: Maurin, O. 4404 (K)

text: Gilliesia miersioides


text: Royal Botanic Gardens, Kew

text: public

text: Maurin, O.

characteristic: collected by

text: Phycella ornata

text: Phycella ornata

text: Maurin, O. 4406 (K)

text: Phycella ornata


E-MTAB-12051:Sample 1

text: public

text: E-MTAB-12051:Sample 1

tag: Namespace:Onderzoeksgroep Nefrologie en Niertransplantatie

text: ArrayExpress

characteristic: broker name

text: kidney transplant

characteristic: clinical history

text: human

characteristic: common name

text: Protocols: Kidney biopsy samples were collected at indicated time at Leuven' university hospital, Belgium. Cells were isolated after mechanical and enzymatic dissociation and resuspended in PBS containing 0.04% UltraPure BSA (AM2616, ThermoFisher Scientific) and strained through a 40 µm cell strainer to further remove cell clumps and large fragments. Cell number and viability was measured using Luna Cell counter. Libraries for scRNASeq were generated using the Chromium Single Cell 5′ library and Gel Bead & Multiplex Kit from 10x Genomics. We aimed to profile 2000 cells per library if sufficient cells were retained during the process. All libraries were sequenced on Illumina NextSeq until sufficient saturation was reached.

characteristic: description

text: Non rejection DSA+

characteristic: disease

text: Homo sapiens

text: Homo sapiens

text: kidney

characteristic: organism part

text: kidney transplant biopsy

characteristic: sampling site

text: 37 days after transplantation

characteristic: sampling time point

text: Homo sapiens

text: male

characteristic: sex

text: Sample 1


E-MTAB-12051:Sample 2

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Onderzoeksgroep Nefrologie en Niertransplantatie

characteristic: INSDC center name

text: public

text: E-MTAB-12051:Sample 2

text: ArrayExpress

text: kidney transplant

text: human

text: Antibody-mediated rejection

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: kidney

text: kidney transplant biopsy

text: 61 days after transplantation

text: Homo sapiens

text: female

text: Sample 2


E-MTAB-12051:Sample 3

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-12051:Sample 3

characteristic: Submitter Id

text: ArrayExpress

text: kidney transplant

text: human

text: Non rejection DSA+

text: Homo sapiens

text: Homo sapiens

text: kidney

text: kidney transplant biopsy

text: 12 days after transplantation

text: Homo sapiens

text: male

text: Sample 3

characteristic: title


E-MTAB-12051:Sample 4

text: public

text: E-MTAB-12051:Sample 4

text: ArrayExpress

characteristic: broker name

text: kidney transplant

characteristic: clinical history

text: human

characteristic: common name

characteristic: description

text: Non rejection DSA+

characteristic: disease

text: Homo sapiens

text: Homo sapiens

text: kidney

text: kidney transplant biopsy

text: 91 days after transplantation

text: Homo sapiens

text: female

text: Sample 4


E-MTAB-12051:Sample 5

characteristic: ENA-CHECKLIST

text: public

text: E-MTAB-12051:Sample 5

text: ArrayExpress

text: kidney transplant

text: human

text: Non rejection DSA+

text: Homo sapiens

text: Homo sapiens

text: kidney

characteristic: organism part

text: kidney transplant biopsy

characteristic: sampling site

text: 9 days after transplantation

characteristic: sampling time point

text: Homo sapiens

text: male

characteristic: sex

text: Sample 5


E-MTAB-12051:Sample 6

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC center name

text: public

text: E-MTAB-12051:Sample 6

text: ArrayExpress

text: kidney transplant

text: human

text: Non rejection DSA-

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: kidney

text: kidney transplant biopsy

text: 7709 days after transplantation

text: Homo sapiens

text: male

text: Sample 6


E-MTAB-12051:Sample 7

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-12051:Sample 7

characteristic: Submitter Id

text: ArrayExpress

text: kidney transplant

text: human

text: Antibody-mediated rejection

text: Homo sapiens

text: Homo sapiens

text: kidney

text: kidney transplant biopsy

text: 6 days after transplantation

text: Homo sapiens

text: male

text: Sample 7


E-MTAB-12051:Sample 8

text: public

text: E-MTAB-12051:Sample 8

text: ArrayExpress

characteristic: broker name

text: kidney transplant

characteristic: clinical history

text: human

characteristic: common name

characteristic: description

text: T cell-mediated rejection

text: Homo sapiens

text: Homo sapiens

text: kidney

text: kidney transplant biopsy

text: 6 days after transplantation

text: Homo sapiens

text: female

text: Sample 8

characteristic: title


E-MTAB-12051:Sample 9

characteristic: ENA-CHECKLIST

text: public

text: E-MTAB-12051:Sample 9

text: ArrayExpress

text: kidney transplant

text: human

text: Non rejection DSA-

characteristic: disease

text: Homo sapiens

text: Homo sapiens

text: kidney

characteristic: organism part

text: kidney transplant biopsy

characteristic: sampling site

text: 91 days after transplantation

characteristic: sampling time point

text: Homo sapiens

text: male

text: Sample 9


E-MTAB-12051:Sample 10

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC center name

text: public

text: E-MTAB-12051:Sample 10

text: ArrayExpress

text: kidney transplant

text: human

text: Non rejection DSA-

text: Homo sapiens

text: Homo sapiens

text: kidney

text: kidney transplant biopsy

text: 44 days after transplantation

text: Homo sapiens

text: male

characteristic: sex

text: Sample 10


E-MTAB-12051:Sample 11

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-12051:Sample 11

text: ArrayExpress

text: kidney transplant

text: human

text: Non rejection DSA+

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: kidney

text: kidney transplant biopsy

text: 247 days after transplantation

text: Homo sapiens

text: female

text: Sample 11


E-MTAB-12051:Sample 12

text: public

text: E-MTAB-12051:Sample 12

characteristic: Submitter Id

text: ArrayExpress

characteristic: broker name

text: kidney transplant

characteristic: clinical history

text: human

characteristic: common name

characteristic: description

text: Non rejection DSA+

text: Homo sapiens

text: Homo sapiens

text: kidney

text: kidney transplant biopsy

text: 2104 days after transplantation

text: Homo sapiens

text: male

text: Sample 12


E-MTAB-12051:Sample 13

characteristic: ENA-CHECKLIST

text: public

text: E-MTAB-12051:Sample 13

text: ArrayExpress

text: kidney transplant

text: human

text: Non rejection DSA+

characteristic: disease

text: Homo sapiens

text: Homo sapiens

text: kidney

characteristic: organism part

text: kidney transplant biopsy

characteristic: sampling site

text: 118 days after transplantation

text: Homo sapiens

text: male

text: Sample 13

characteristic: title


E-MTAB-12051:Sample 14

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC center name

text: public

text: E-MTAB-12051:Sample 14

text: ArrayExpress

text: kidney transplant

text: human

text: Non rejection DSA-

text: Homo sapiens

text: Homo sapiens

text: kidney

text: kidney transplant biopsy

text: 6 days after transplantation

characteristic: sampling time point

text: Homo sapiens

text: male

text: Sample 14


E-MTAB-12051:Sample 15

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-12051:Sample 15

text: ArrayExpress

text: kidney transplant

text: human

text: Non rejection DSA+

text: Homo sapiens

text: Homo sapiens

text: kidney

text: kidney transplant biopsy

text: 361 days after transplantation

text: Homo sapiens

text: female

characteristic: sex

text: Sample 15


E-MTAB-12051:Sample 16

text: public

text: E-MTAB-12051:Sample 16

characteristic: Submitter Id

text: ArrayExpress

characteristic: broker name

text: kidney transplant

characteristic: clinical history

text: human

characteristic: common name

text: Antibody-mediated rejection

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: kidney

text: kidney transplant biopsy

text: 2002 days after transplantation

text: Homo sapiens

text: female

text: Sample 16