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characteristic: sampling time point

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text: Triticum aestivum

text: Whole aerial organ

text: two hours after dusk (23:00)

text: Triticum aestivum


text: Earlham Institute

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: bread wheat

text: ROB

text: Triticum aestivum ROB 3 leaf stage (GS13) Whole aerial organ sampled two hours after dusk (23:00), biological replicate no. 3

text: 3 leaf stage (GS13)

text: Triticum aestivum

text: Whole aerial organ

text: two hours after dusk (23:00)

text: Triticum aestivum


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Earlham Institute

text: public

text: bread wheat

text: CDC Stanley

text: Triticum aestivum CDC Stanley 3 leaf stage (GS13) Whole aerial organ sampled four hours after dawn (09:00), biological replicate no. 1

text: 3 leaf stage (GS13)

text: Triticum aestivum

text: Whole aerial organ

text: four hours after dawn (09:00)

text: Triticum aestivum


text: Earlham Institute

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: bread wheat

text: CDC Stanley

text: Triticum aestivum CDC Stanley 3 leaf stage (GS13) Whole aerial organ sampled four hours after dawn (09:00), biological replicate no. 2

text: 3 leaf stage (GS13)

text: Triticum aestivum

text: Whole aerial organ

text: four hours after dawn (09:00)

text: Triticum aestivum


text: Earlham Institute

text: public

characteristic: SRA accession

characteristic: Submitter Id

text: bread wheat

text: CDC Stanley

text: Triticum aestivum CDC Stanley 3 leaf stage (GS13) Whole aerial organ sampled four hours after dawn (09:00), biological replicate no. 3

text: 3 leaf stage (GS13)

text: Triticum aestivum

text: Whole aerial organ

text: four hours after dawn (09:00)

text: Triticum aestivum


text: Earlham Institute

text: public

text: bread wheat

characteristic: common name

text: CDC Stanley

characteristic: cultivar

text: Triticum aestivum CDC Stanley 7 days post anthesis (GS71) Flag leaf sampled four hours after dawn (09:00), biological replicate no. 1

text: 7 days post anthesis (GS71)

text: Triticum aestivum

text: Flag leaf

text: four hours after dawn (09:00)

text: Triticum aestivum


text: Earlham Institute

text: public

text: bread wheat

text: CDC Stanley

text: Triticum aestivum CDC Stanley 7 days post anthesis (GS71) Flag leaf sampled four hours after dawn (09:00), biological replicate no. 2

characteristic: description

text: 7 days post anthesis (GS71)

text: Triticum aestivum

characteristic: organism

text: Flag leaf

text: four hours after dawn (09:00)

text: Triticum aestivum


text: Earlham Institute

text: public

text: bread wheat

text: CDC Stanley

text: Triticum aestivum CDC Stanley 3 leaf stage (GS13) Whole Root sampled four hours after dawn (09:00), biological replicate no. 1

text: 3 leaf stage (GS13)

text: Triticum aestivum

text: Whole Root

characteristic: organism part

characteristic: replicate

text: four hours after dawn (09:00)

text: Triticum aestivum


text: Earlham Institute

text: public

text: bread wheat

text: CDC Stanley

text: Triticum aestivum CDC Stanley 3 leaf stage (GS13) Whole Root sampled four hours after dawn (09:00), biological replicate no. 2

text: 3 leaf stage (GS13)

text: Triticum aestivum

text: Whole Root

text: four hours after dawn (09:00)

characteristic: sampling time point

text: Triticum aestivum

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: Earlham Institute

text: public

text: bread wheat

text: CDC Stanley

text: Triticum aestivum CDC Stanley 3 leaf stage (GS13) Whole Root sampled four hours after dawn (09:00), biological replicate no. 3

text: 3 leaf stage (GS13)

text: Triticum aestivum

text: Whole Root

text: four hours after dawn (09:00)

text: Triticum aestivum


text: Earlham Institute

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: bread wheat

text: CDC Stanley

text: Triticum aestivum CDC Stanley Heading (GS59) Whole spikelet sampled four hours after dawn (09:00), biological replicate no. 1

text: Heading (GS59)

text: Triticum aestivum

text: Whole spikelet

text: four hours after dawn (09:00)

text: Triticum aestivum


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Earlham Institute

text: public

text: bread wheat

text: CDC Stanley

text: Triticum aestivum CDC Stanley Heading (GS59) Whole spikelet sampled four hours after dawn (09:00), biological replicate no. 2

text: Heading (GS59)

text: Triticum aestivum

text: Whole spikelet

text: four hours after dawn (09:00)

text: Triticum aestivum


text: Earlham Institute

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: bread wheat

text: CDC Stanley

text: Triticum aestivum CDC Stanley Heading (GS59) Whole spikelet sampled four hours after dawn (09:00), biological replicate no. 3

text: Heading (GS59)

text: Triticum aestivum

text: Whole spikelet

text: four hours after dawn (09:00)

text: Triticum aestivum


text: Earlham Institute

text: public

characteristic: SRA accession

characteristic: Submitter Id

text: bread wheat

text: CDC Stanley

text: Triticum aestivum CDC Stanley 3 leaf stage (GS13) Whole aerial organ sampled two hours after dusk (23:00), biological replicate no. 1

text: 3 leaf stage (GS13)

text: Triticum aestivum

text: Whole aerial organ

text: two hours after dusk (23:00)

text: Triticum aestivum


text: Earlham Institute

text: public

text: bread wheat

characteristic: common name

text: CDC Stanley

characteristic: cultivar

text: Triticum aestivum CDC Stanley 3 leaf stage (GS13) Whole aerial organ sampled two hours after dusk (23:00), biological replicate no. 2

text: 3 leaf stage (GS13)

text: Triticum aestivum

text: Whole aerial organ

text: two hours after dusk (23:00)

text: Triticum aestivum


text: Earlham Institute

text: public

text: bread wheat

text: CIMMYT-Weebil

text: Triticum aestivum CIMMYT-Weebil 3 leaf stage (GS13) Whole aerial organ sampled four hours after dawn (09:00), biological replicate no. 1

characteristic: description

text: 3 leaf stage (GS13)

text: Triticum aestivum

characteristic: organism

text: Whole aerial organ

text: four hours after dawn (09:00)

text: Triticum aestivum


text: Earlham Institute

text: public

text: bread wheat

text: CIMMYT-Weebil

text: Triticum aestivum CIMMYT-Weebil 3 leaf stage (GS13) Whole aerial organ sampled four hours after dawn (09:00), biological replicate no. 2

text: 3 leaf stage (GS13)

text: Triticum aestivum

text: Whole aerial organ

characteristic: organism part

characteristic: replicate

text: four hours after dawn (09:00)

text: Triticum aestivum


text: Earlham Institute

text: public

text: bread wheat

text: CIMMYT-Weebil

text: Triticum aestivum CIMMYT-Weebil 3 leaf stage (GS13) Whole aerial organ sampled four hours after dawn (09:00), biological replicate no. 3

text: 3 leaf stage (GS13)

text: Triticum aestivum

text: Whole aerial organ

text: four hours after dawn (09:00)

characteristic: sampling time point

text: Triticum aestivum

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: Earlham Institute

text: public

text: bread wheat

text: CIMMYT-Weebil

text: Triticum aestivum CIMMYT-Weebil 7 days post anthesis (GS71) Flag leaf sampled four hours after dawn (09:00), biological replicate no. 1

text: 7 days post anthesis (GS71)

text: Triticum aestivum

text: Flag leaf

text: four hours after dawn (09:00)

text: Triticum aestivum


text: Earlham Institute

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: bread wheat

text: CIMMYT-Weebil

text: Triticum aestivum CIMMYT-Weebil 7 days post anthesis (GS71) Flag leaf sampled four hours after dawn (09:00), biological replicate no. 2

text: 7 days post anthesis (GS71)

text: Triticum aestivum

text: Flag leaf

text: four hours after dawn (09:00)

text: Triticum aestivum


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Earlham Institute

text: public

text: bread wheat

text: CIMMYT-Weebil

text: Triticum aestivum CIMMYT-Weebil 7 days post anthesis (GS71) Flag leaf sampled four hours after dawn (09:00), biological replicate no. 3

text: 7 days post anthesis (GS71)

text: Triticum aestivum

text: Flag leaf

text: four hours after dawn (09:00)

text: Triticum aestivum


text: Earlham Institute

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: bread wheat

text: CIMMYT-Weebil

text: Triticum aestivum CIMMYT-Weebil 15 days post anthesis (GS77) Whole grain sampled four hours after dawn (09:00), biological replicate no. 1

text: 15 days post anthesis (GS77)

text: Triticum aestivum

text: Whole grain

text: four hours after dawn (09:00)

text: Triticum aestivum


text: Earlham Institute

text: public

characteristic: SRA accession

characteristic: Submitter Id

text: bread wheat

text: CIMMYT-Weebil

text: Triticum aestivum CIMMYT-Weebil 15 days post anthesis (GS77) Whole grain sampled four hours after dawn (09:00), biological replicate no. 2

text: 15 days post anthesis (GS77)

text: Triticum aestivum

text: Whole grain

text: four hours after dawn (09:00)

text: Triticum aestivum


text: Earlham Institute

text: public

text: bread wheat

characteristic: common name

text: CIMMYT-Weebil

characteristic: cultivar

text: Triticum aestivum CIMMYT-Weebil 15 days post anthesis (GS77) Whole grain sampled four hours after dawn (09:00), biological replicate no. 3

text: 15 days post anthesis (GS77)

text: Triticum aestivum

text: Whole grain

text: four hours after dawn (09:00)

text: Triticum aestivum


text: Earlham Institute

text: public

text: bread wheat

text: CIMMYT-Weebil

text: Triticum aestivum CIMMYT-Weebil 3 leaf stage (GS13) Whole Root sampled four hours after dawn (09:00), biological replicate no. 1

characteristic: description

text: 3 leaf stage (GS13)

text: Triticum aestivum

characteristic: organism

text: Whole Root

text: four hours after dawn (09:00)

text: Triticum aestivum


text: Earlham Institute

text: public

text: bread wheat

text: CIMMYT-Weebil

text: Triticum aestivum CIMMYT-Weebil 3 leaf stage (GS13) Whole Root sampled four hours after dawn (09:00), biological replicate no. 2

text: 3 leaf stage (GS13)

text: Triticum aestivum

text: Whole Root

characteristic: organism part

characteristic: replicate

text: four hours after dawn (09:00)

text: Triticum aestivum


text: Earlham Institute

text: public

text: bread wheat

text: CIMMYT-Weebil

text: Triticum aestivum CIMMYT-Weebil 3 leaf stage (GS13) Whole Root sampled four hours after dawn (09:00), biological replicate no. 3

text: 3 leaf stage (GS13)

text: Triticum aestivum

text: Whole Root

text: four hours after dawn (09:00)

characteristic: sampling time point

text: Triticum aestivum

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: Earlham Institute

text: public

text: bread wheat

text: CIMMYT-Weebil

text: Triticum aestivum CIMMYT-Weebil Heading (GS59) Whole spikelet sampled four hours after dawn (09:00), biological replicate no. 1

text: Heading (GS59)

text: Triticum aestivum

text: Whole spikelet

text: four hours after dawn (09:00)

text: Triticum aestivum


text: Earlham Institute

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: bread wheat

text: CIMMYT-Weebil

text: Triticum aestivum CIMMYT-Weebil Heading (GS59) Whole spikelet sampled four hours after dawn (09:00), biological replicate no. 2

text: Heading (GS59)

text: Triticum aestivum

text: Whole spikelet

text: four hours after dawn (09:00)

text: Triticum aestivum


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Earlham Institute

text: public

text: bread wheat

text: CIMMYT-Weebil

text: Triticum aestivum CIMMYT-Weebil Heading (GS59) Whole spikelet sampled four hours after dawn (09:00), biological replicate no. 3

text: Heading (GS59)

text: Triticum aestivum

text: Whole spikelet

text: four hours after dawn (09:00)

text: Triticum aestivum


text: Earlham Institute

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: bread wheat

text: CIMMYT-Weebil

text: Triticum aestivum CIMMYT-Weebil 3 leaf stage (GS13) Whole aerial organ sampled two hours after dusk (23:00), biological replicate no. 1

text: 3 leaf stage (GS13)

text: Triticum aestivum

text: Whole aerial organ

text: two hours after dusk (23:00)

text: Triticum aestivum


text: Earlham Institute

text: public

characteristic: SRA accession

characteristic: Submitter Id

text: bread wheat

text: CIMMYT-Weebil

text: Triticum aestivum CIMMYT-Weebil 3 leaf stage (GS13) Whole aerial organ sampled two hours after dusk (23:00), biological replicate no. 2

text: 3 leaf stage (GS13)

text: Triticum aestivum

text: Whole aerial organ

text: two hours after dusk (23:00)

text: Triticum aestivum


text: Earlham Institute

text: public

text: bread wheat

characteristic: common name

text: CIMMYT-Weebil

characteristic: cultivar

text: Triticum aestivum CIMMYT-Weebil 3 leaf stage (GS13) Whole aerial organ sampled two hours after dusk (23:00), biological replicate no. 3

text: 3 leaf stage (GS13)

text: Triticum aestivum

text: Whole aerial organ

text: two hours after dusk (23:00)

text: Triticum aestivum


text: public

tag: Namespace:Department of Biosciences and Nutrition, Karolinska Institutet

characteristic: batch

text: ArrayExpress

characteristic: broker name

text: LUHMES

text: neuron

text: human

text: Protocols: A frozen vial of Lund human mesencephalic (LUHMES) cells, an immortalized dopaminergic neuronal precursor cell line, was purchased from the ATCC (https://www.atcc.org/products/crl-2927). LUHMES cells were cultured in a standard incubator (37°C, 5% CO2), following the same conditions previously described (Scholz et al., 2011; Lauter et al., 2020). LUHMES cells were grown in DMEM/F-12 Ham growth medium (Sigma-Aldrich D6421) supplemented with L-glutamine solution (Sigma-Aldrich G7513; 2.5 mM), N-2 supplement (Gibco 17502-048; 1×) and human heat stable basic Fibroblast Growth Factor (bFGF) (Thermo Fisher Scientific PHG0369; 20 ng/ml). For routinary maintenance, 2×106 cells were seeded in T75 flasks (Sarstedt 83.3911.002) pre-coated with poly-L-ornithine hydrobromide (Sigma-Aldrich P3655, 50 μg/ml) and fibronectin from human plasma (Sigma-Aldrich F1056; 1 μg/ml), in order to reach 80% confluency in three days and being then passaged using trypsin-EDTA (Gibco 25300054) diluted 1:1 in phosphate-buffered saline (PBS) (Sigma-Aldrich P4417) as cell dissociation reagent. For all the experiments, a higher concentration of ornithine (100 μg/ml), fibronectin (10 μg/ml) and bFGF (40 ng/ml) was used to improve cell adhesion and propagation. To differentiate LUHMES into postmitotic neurons, the bFGF in the growth medium was replaced with tetracycline hydrochloride (Sigma-Aldrich T7660; 1 μg/ml) in order to terminate the v-myc transgene expression. Total RNA was extracted from LUHMES cells and purified in a column using an RNeasy mini kit (Qiagen 74104) following the manufacturer's protocol. RNA integrity was checked on 1% agarose gel electrophoresis (Sigma-Aldrich A9539) and concentration and purity were assessed with a Nanodrop ND-100 (Thermo Fisher Scientific). For library preparation and transcriptome analysis, an additional DNase step (Qiagen 79254) was introduced during the total RNA isolation, the RNA integrity value was evaluated using an Agilent Tech 2200 Tape Station (RIN value >8. KI Bioinformatics and Expression Analysis core facility; https://ki.se/en/bionut/bea-core-facility) and the RNA concentration was measured with a Qubit 3.0 Fluorometer (Thermo Fisher Scientific). The samples were then diluted to 10 ng/μl (±0.5 ng/µl) in nuclease-free water before proceeding with the RNA-seq library preparation. We used 20 ng of RNA to generate two 48-plex RNA-seq libraries employing a modified STRT method with unique molecular identifiers (UMIs) (Islam et al. Genome Res. 2011, Islam et al. Nat Methods. 2014, Ezer et al. STAR Protoc. 2021). Briefly, RNA samples were placed in a 48-well plate, and a universal primer, template-switching oligonucleotides and a well-specific 6-bp barcode sequence (for sample identification) were added to each well of the plate (Krjutškov et al., 2016). The synthesized cDNAs from these samples were then pooled into one library and amplified by single-primer PCR using a universal primer sequence.

characteristic: description

text: embryo

characteristic: developmental stage

text: normal

characteristic: disease

text: RFX2 -/-

characteristic: genotype

text: not applicable

characteristic: isolate

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: midbrain

text: Homo sapiens


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: Department of Biosciences and Nutrition, Karolinska Institutet

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: ArrayExpress

text: LUHMES

text: neuron

text: human

text: embryo

text: normal

text: RFX2 -/-

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: midbrain

characteristic: organism part

text: Homo sapiens

characteristic: title


characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: ArrayExpress

text: LUHMES

text: neuron

text: human

text: embryo

text: normal

text: wild type genotype

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: midbrain

text: Homo sapiens


text: public

tag: Namespace:Valencian Region Foundation for the Promotion of Health and Biomedical Research (FISABIO)

text: metagenome

characteristic: common name

text: Fermentation with individual 1 inoculum of Water Water, replicate a

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text: terrestrial biome

characteristic: environment (biome)

text: human-associated habitat

characteristic: environment (feature)

text: human-associated habitat

characteristic: environment (material)

text: Spain

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

unit: DD

characteristic: geographic location (longitude)

text: human-associated

characteristic: human-associated environmental package

text: metagenome

characteristic: investigation type

text: metagenome

characteristic: project name

text: metagenome

text: Illumina MiSeq

characteristic: sequencing method

text: Amplicon (V3-V4) of 16S rRNA gene


characteristic: ENA-CHECKLIST

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text: Valencian Region Foundation for the Promotion of Health and Biomedical Research (FISABIO)

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characteristic: INSDC first public

text: public

text: metagenome

text: Fermentation with individual 1 inoculum of Water Water, replicate b

text: terrestrial biome

text: human-associated habitat

text: human-associated habitat

text: Spain

text: human-associated

text: metagenome

text: metagenome

characteristic: organism

text: metagenome

text: Illumina MiSeq

text: Amplicon (V3-V4) of 16S rRNA gene

characteristic: title


characteristic: INSDC last update

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text: metagenome

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text: Fermentation with individual 1 inoculum of Fried Nut mix, replicate a

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text: terrestrial biome

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text: Illumina MiSeq

text: Amplicon (V3-V4) of 16S rRNA gene


text: public

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text: Fermentation with individual 1 inoculum of Fried Nut mix, replicate b

text: terrestrial biome

text: human-associated habitat

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characteristic: environment (material)

text: Spain

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characteristic: human-associated environmental package

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text: Illumina MiSeq

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text: Amplicon (V3-V4) of 16S rRNA gene


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text: Illumina MiSeq

text: Amplicon (V3-V4) of 16S rRNA gene

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text: Fermentation with individual 1 inoculum of Raw Nut mix, replicate b

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text: Amplicon (V3-V4) of 16S rRNA gene


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text: Amplicon (V3-V4) of 16S rRNA gene


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text: Illumina MiSeq

text: Amplicon (V3-V4) of 16S rRNA gene

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text: Fermentation with individual 1 inoculum of Fried Bread, replicate a

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text: Amplicon (V3-V4) of 16S rRNA gene


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text: Amplicon (V3-V4) of 16S rRNA gene


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text: Illumina MiSeq

text: Amplicon (V3-V4) of 16S rRNA gene

characteristic: title


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text: Fermentation with individual 1 inoculum of Raw Bread, replicate b

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text: Illumina MiSeq

text: Amplicon (V3-V4) of 16S rRNA gene


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text: Fermentation with individual 1 inoculum of Toasted Bread, replicate a

text: terrestrial biome

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characteristic: sequencing method

text: Amplicon (V3-V4) of 16S rRNA gene


characteristic: ENA-CHECKLIST

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text: public

text: metagenome

text: Fermentation with individual 1 inoculum of Toasted Bread, replicate b

text: terrestrial biome

text: human-associated habitat

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