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characteristic: Submitter Id

text: urban biome (ENVO:01000249)

characteristic: broad-scale environmental context

characteristic: collection date

text: Stool sample Infant #I461 collected at 24 months of age

text: fecal material (ENVO:00002003)

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characteristic: title


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text: Finland

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characteristic: geographic location (longitude)

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text: Finland

characteristic: geographic location (country and/or sea)

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text: Finland

characteristic: geographic location (country and/or sea)

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text: Finland

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characteristic: description

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characteristic: environmental medium

text: Finland

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

text: feces (UBERON:0001988)

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characteristic: ENA-CHECKLIST

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text: University of Helsinki

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text: fecal material (ENVO:00002003)

text: Finland

characteristic: geographic location (longitude)

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text: feces (UBERON:0001988)

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characteristic: ENA-CHECKLIST

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text: University of Helsinki

characteristic: INSDC center name

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text: public

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characteristic: delivery mode

text: Stool sample Infant #I650 collected at 24 months of age

characteristic: description

text: fecal material (ENVO:00002003)

characteristic: environmental medium

text: Finland

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

text: feces (UBERON:0001988)

text: female

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text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

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characteristic: broad-scale environmental context

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text: Stool sample Infant #I636 collected at 24 months of age

text: fecal material (ENVO:00002003)

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text: University of Helsinki

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: urban biome (ENVO:01000249)

text: Stool sample Infant #I668 collected at 24 months of age

text: fecal material (ENVO:00002003)

text: Finland

characteristic: geographic location (longitude)

characteristic: host age

text: feces (UBERON:0001988)

characteristic: host body product

text: female

characteristic: host sex

characteristic: host subject id

text: fecal environment (ENVO:01001029)

text: human feces metagenome

text: human feces metagenome

text: Illumina

text: infant stool sample


text: University of Basel

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

tag: Namespace:University of Basel

characteristic: Submitter Id

text: resequencing of microbial1, microbial8 and microbial11

characteristic: description

text: soil metagenome

text: soil metagenome


text: Sanger Institute

characteristic: GAL

text: NOT PROVIDED

text: Tree of Life Programme

text: public

tag: Namespace:Tree of Life Programme

text: Nick Davison

text: Scottish Marine Animal Stranding Scheme University of Glasgow

characteristic: collecting institution

characteristic: collection date

text: saddleback dolphin

characteristic: common name

text: United Kingdom

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

text: Scotland | Highland | Scrabster

characteristic: geographic location (region and locality)

text: Beach

characteristic: habitat

text: Nick Davison

text: juvenile

characteristic: lifestage

text: Delphinus delphis

characteristic: organism

text: WHOLE ORGANISM

characteristic: organism part

text: DTOL

characteristic: project name

text: Delphinus delphis

text: MALE

characteristic: sex

text: NOT PROVIDED

text: N

characteristic: symbiont

characteristic: title

characteristic: tolid

type: derived from


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Sanger Institute

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: Nick Davison

text: white-beaked dolphin

text: United Kingdom

characteristic: geographic location (longitude)

text: Scotland | East Lothian | Morrisons Haven

text: Beach

text: Nick Davison

text: juvenile

text: Lagenorhynchus albirostris

text: WHOLE ORGANISM

text: DTOL

text: Lagenorhynchus albirostris

text: FEMALE

text: NOT PROVIDED

text: N


text: Sanger Institute

characteristic: GAL

text: NOT PROVIDED

text: Tree of Life Programme

text: public

text: Nick Davison

characteristic: collecting institution

characteristic: collection date

text: striped dolphin

characteristic: common name

text: United Kingdom

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

text: Scotland | Highland | Ardmair

characteristic: geographic location (region and locality)

text: Beach

characteristic: habitat

text: Nick Davison

text: juvenile

characteristic: lifestage

text: Stenella coeruleoalba

characteristic: organism

text: WHOLE ORGANISM

characteristic: organism part

text: DTOL

text: Stenella coeruleoalba

text: MALE

text: NOT PROVIDED

text: N


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Sanger Institute

text: NOT PROVIDED

text: Tree of Life Programme

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: Andrew Brownlow

text: minke whale

text: United Kingdom

text: Scotland | FIfe | Dalgety Bay

text: Beach

text: Nick Davison

text: juvenile

text: Balaenoptera acutorostrata

text: WHOLE ORGANISM

text: DTOL

characteristic: project name

text: Balaenoptera acutorostrata

text: FEMALE

characteristic: sex

text: NOT PROVIDED

text: N

characteristic: symbiont

characteristic: title

characteristic: tolid


characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

tag: Namespace:CENTER FOR BIOTECHNOLOGY, BIELEFELD UNIVERSITY

characteristic: Submitter Id

text: sugar beet

characteristic: common name

text: Beta vulgaris subsp. vulgaris

text: Beta vulgaris subsp. vulgaris

text: sample ID: KWS2320


text: CENTER FOR BIOTECHNOLOGY, BIELEFELD UNIVERSITY

text: public

text: sugar beet

text: Beta vulgaris subsp. vulgaris

characteristic: organism

text: Beta vulgaris subsp. vulgaris

text: sample ID: U2Bv


characteristic: ENA-CHECKLIST

text: BIMSB

text: public

text: ArrayExpress

characteristic: broker name

text: human

text: Protocols: In vitro transcribed synthetic spike-in RNA was prepared as described66. 1 µL ERCC RNA Spike-in Mix (Invitrogen) were reverse transcribed using Protoscript II reverse transcriptase (New England Biolabs). cDNA was diluted 1:4 in H2O and used as a template for PCR amplification of ERCC spike-ins 00043, 00170, 00136, 00145, 00092 and 00002. PCR products were purified and verified by agarose gel electrophoresis and Sanger sequencing. 0.5 µg PCR product were used as an input for in vitro transcription using the MEGAscript T7 transcription kit (Invitrogen) according to the manufacturer’s instructions. For spike-ins 00043, 00136 and 00092 10% UTP were substituted with 4-Thio-UTP. RNA spike-ins were purified using AMPure XP beads (Beckman Coulter), quantified using Qubit HS RNA Assay kit (Invitrogen) and mixed at a final concentration of 1 ng/µL of each spike-in RNA. The final spike-in mix was quantified again using Qubit HS RNA Assay kit (Invitrogen) and stored at -80 °C in single-use aliquots. For preparation of 4TU-labeled yeast RNA, an ON culture of S. cerevisiae BY4741 was diluted to OD600=0.1 in 50 mL YPD + 2% (w/v) glucose at grown at 30°C, 180 rpm until OD600=0.8. 4TU was added to a final concentration of 5 mM and cells were labeled for 5 min. Labeled cells were pelleted, resuspended in 250 µL 0.8 M sorbitol, 0.1 M EDTA, 0.1% β-mercaptoethanol, 200 U/mL lyticase and incubated at 30 °C for 30 min. Lysate was mixed with 750 µL TRI Reagent LS (Sigma), 200 µL Chloroform (Applichem) were added, samples were mixed and centrifuged at 4°C, max. speed for 15 min. The aqueous phase was subjected to isopropanol precipitation. RNA was treated with DNase I (Roche) at 37°C for 30 min and purified by phenol-chloroform extraction and Ethanol precipitation. Sequencing libraries were prepared using the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (New England Biolabs) according to the manufacturer’s instructions.

characteristic: description

text: embryo stage

characteristic: developmental stage

text: normal

characteristic: disease

text: DIDO SPOC domain deletion

characteristic: genotype

text: not applicable

characteristic: isolate

text: Homo sapiens

text: Homo sapiens

text: kidney

characteristic: organism part

text: Homo sapiens


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: BIMSB

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: ArrayExpress

text: human

text: embryo stage

text: normal

text: DIDO knockout

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: kidney

text: Homo sapiens


text: BIMSB

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: ArrayExpress

text: human

text: embryo stage

text: normal

text: DIDO wild type

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: kidney

text: Homo sapiens

characteristic: title


characteristic: ENA-CHECKLIST

text: BIMSB

text: public

characteristic: Submitter Id

text: ArrayExpress

text: human

characteristic: common name

text: embryo stage

text: normal

text: PHF3 SPOC domain deletion

text: not applicable

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: kidney

text: Homo sapiens


text: BIMSB

text: public

text: ArrayExpress

characteristic: broker name

text: human

characteristic: description

text: embryo stage

characteristic: developmental stage

text: normal

characteristic: disease

text: PHF3 knockout

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: kidney

text: Homo sapiens


characteristic: ENA-FIRST-PUBLIC

text: BIMSB

text: public

text: ArrayExpress

text: human

text: embryo stage

text: normal

text: PHF3 wild type

characteristic: genotype

text: not applicable

characteristic: isolate

text: Homo sapiens

text: Homo sapiens

text: kidney

characteristic: organism part

text: Homo sapiens


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: BIMSB

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: ArrayExpress

text: human

text: embryo stage

text: normal

text: RBM15 SPOC domain deletion

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: kidney

text: Homo sapiens


text: BIMSB

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: ArrayExpress

text: human

text: embryo stage

text: normal

text: RBM15 knockout

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: kidney

text: Homo sapiens

characteristic: title


characteristic: ENA-CHECKLIST

text: BIMSB

text: public

characteristic: Submitter Id

text: ArrayExpress

text: human

characteristic: common name

text: embryo stage

text: normal

text: RBM15 wild type

text: not applicable

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: kidney

text: Homo sapiens


text: BIMSB

text: public

text: ArrayExpress

characteristic: broker name

text: human

characteristic: description

text: embryo stage

characteristic: developmental stage

text: normal

characteristic: disease

text: SHARP SPOC domain deletion

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: kidney

text: Homo sapiens


characteristic: ENA-FIRST-PUBLIC

text: BIMSB

text: public

text: ArrayExpress

text: human

text: embryo stage

text: normal

text: SHARP wild type

characteristic: genotype

text: not applicable

characteristic: isolate

text: Homo sapiens

text: Homo sapiens

text: kidney

characteristic: organism part

text: Homo sapiens


characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC first public

text: public

tag: Namespace:Institute of Natural Resources and Agrobiology of Salamanca (IRNASA-CSIC)

text: liver fluke

text: Fasciola control 1

text: Fasciola hepatica

text: Fasciola hepatica


text: Institute of Natural Resources and Agrobiology of Salamanca (IRNASA-CSIC)

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: liver fluke

text: Fasciola control 2

text: Fasciola hepatica

text: Fasciola hepatica

characteristic: title


characteristic: ENA-CHECKLIST

text: public

characteristic: Submitter Id

text: liver fluke

characteristic: common name

text: Fasciola control 3

text: Fasciola hepatica

characteristic: organism

text: Fasciola hepatica


text: public

text: liver fluke

text: Fasciola treated 1

characteristic: description

text: Fasciola hepatica

text: Fasciola hepatica


characteristic: ENA-FIRST-PUBLIC

text: public

text: liver fluke

text: Fasciola treated 2

text: Fasciola hepatica

text: Fasciola hepatica


text: public

text: liver fluke

text: Fasciola treated 3

text: Fasciola hepatica

text: Fasciola hepatica


text: public

text: house mouse

text: Mouse control 1

text: Mus musculus

text: Mus musculus


text: public

text: house mouse

text: Mouse control 2

text: Mus musculus

text: Mus musculus


text: public

text: house mouse

text: Mouse control 3

text: Mus musculus

text: Mus musculus


text: public

text: house mouse

text: Mouse treated 1

text: Mus musculus

text: Mus musculus


text: public

text: house mouse

text: Mouse treated 2

text: Mus musculus

text: Mus musculus


text: public

text: house mouse

text: Mouse treated 3

text: Mus musculus

text: Mus musculus


text: ArrayExpress

text: public

unit: year

characteristic: age

text: ArrayExpress

characteristic: broker name

text: promyeloblast

text: human

text: Protocols: HL-60 cells were grown in RPMI 1640 media with 10% heat-inactivated FBS (#10500-064, Gibco) and 1% Penicillin-Streptomycin (#15140-122, Gibco) in a humidified incubator at 37°C with 5% CO2. Cells were differentiated by adding 1.5% DMSO (#D2438, Sigma Aldrich). Each independently-differentiated batch was treated as a biological replicate. Cells were harvested before and at 24, 48, 72, 96 and 120 hours after differentiation with medium supplementation of 1.5% DMSO (#D2438, Sigma Aldrich). CRISPR/Cas9 generation in HL-60 cells was performed as described previously (Graziano et al. PLoS Biol 2019). Cloning of the target guide sequence to target Snx33 was performed using CRISPR/Cas9 technology. (Forward: CACCGctgggacgacGGATGCACAG; Reverse: aaacCTGTGCATCCgtcgtcccagC). Cells expressing BFP-tagged Cas9 were single-cell sorted in 96-well plate on BD FACSAria™ Fusion at EMBL Flow Cytometry Core Facility. Single-cell clones were verified by genomic DNA amplification by Touchdown PCR and sequencing, followed by Western blot of selected clonal lines. Total RNA samples obtained from 3 biological replicates were purified using RNeasy Mini Kit (#74104, Qiagen) according the manufacturer instructions with a DNase digestion step (#79254, Qiagen) using 10 mln of cells for each sample preparation Total RNA samples obtained from 3 biological replicates were purified using RNeasy Mini Kit (#74104, Qiagen) according the manufacturer instructions with a DNase digestion step (#79254, Qiagen) using 10 mln of cells for each sample preparation. To ensure high quality, samples were analyzed on an Agilent 2100 Bioanalyzer (Agilent Technologies).

text: adult

characteristic: developmental stage

text: acute promyelocytic leukemia

characteristic: disease

text: gene knock out

characteristic: genetic modification

text: Snx33 knockout

characteristic: genotype

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: blood

text: Homo sapiens

text: female

characteristic: sex


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: ArrayExpress

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: ArrayExpress

text: promyeloblast

text: human

text: adult

text: acute promyelocytic leukemia

text: wild type genotype

text: not applicable

characteristic: isolate

text: Homo sapiens

text: Homo sapiens

text: blood

characteristic: organism part

text: Homo sapiens

text: female


characteristic: ENA-CHECKLIST

text: public

characteristic: INSDC status

characteristic: SRA accession

tag: Namespace:Istituto di Ricerche Farmacologiche \"Mario Negri\" IRCCS

characteristic: Submitter Id

text: ArrayExpress

text: AGS

text: human

characteristic: common name

text: Protocols: Collection of 5-10 million cells in PDS, and resuspension of the pellet in a buffer. Protocol: miRNeasy Mini Kit TruSeq Stranded Total RNA Sample Preparation Guide

text: adult

text: gastric adenocarcinoma

text: wild type genotype

text: not applicable

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: stomach

text: neoplasm

characteristic: sampling site

text: Homo sapiens

characteristic: title


characteristic: ENA-FIRST-PUBLIC

text: Istituto di Ricerche Farmacologiche \"Mario Negri\" IRCCS

text: public

text: ArrayExpress

characteristic: broker name

text: AGS

text: human

characteristic: description

text: adult

characteristic: developmental stage

text: gastric adenocarcinoma

characteristic: disease

text: wild type genotype

characteristic: genotype

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: stomach

text: neoplasm

text: Homo sapiens


characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: ArrayExpress

text: GCIY

text: human

text: adult

text: gastric carcinoma

text: wild type genotype

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: stomach

text: ascitic fluid

text: Homo sapiens


characteristic: ENA-CHECKLIST

text: public

characteristic: INSDC status

characteristic: SRA accession

text: ArrayExpress

text: GSS

text: human

text: adult

text: gastric carcinoma

text: wild type genotype

text: not applicable

characteristic: isolate

text: Homo sapiens

text: Homo sapiens

text: stomach

characteristic: organism part

text: liver

text: Homo sapiens


text: public

characteristic: Submitter Id

text: ArrayExpress

text: GSU

text: human

characteristic: common name

text: adult

text: gastric carcinoma

text: wild type genotype

text: not applicable

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: stomach

text: ascitic fluid

characteristic: sampling site

text: Homo sapiens

characteristic: title


characteristic: ENA-FIRST-PUBLIC

text: public

text: ArrayExpress

characteristic: broker name

text: human

characteristic: description

text: adult

characteristic: developmental stage

text: gastric carcinoma

characteristic: disease

text: wild type genotype

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: stomach

text: lymph node

text: Homo sapiens


characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: ArrayExpress

text: Hs 746.T

text: human

text: adult

text: gastric adenocarcinoma

text: wild type genotype

characteristic: genotype

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: stomach

text: skeletal muscle

text: Homo sapiens


characteristic: ENA-CHECKLIST

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: ArrayExpress

text: human

text: adult

text: gastric tubular adenocarcinoma

text: wild type genotype

text: not applicable

characteristic: isolate

text: Homo sapiens

text: Homo sapiens

text: stomach

text: ascitic fluid

text: Homo sapiens


text: public

characteristic: Submitter Id

text: ArrayExpress

text: human

characteristic: common name

text: adult

text: gastric adenocarcinoma

text: wild type genotype

text: not applicable

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: stomach

characteristic: organism part

characteristic: sampling site

text: Homo sapiens


characteristic: ENA-FIRST-PUBLIC

text: public

text: ArrayExpress

characteristic: broker name

text: KATO III

text: human

characteristic: description

text: adult

characteristic: developmental stage

text: Signet Ring Cell Gastric Adenocarcinoma

text: wild type genotype

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: stomach

text: pleural effusion

text: Homo sapiens

characteristic: title