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text: Protocols: Sampling of healthy and botrytized Vitis vinifera cv. Furmint berry samples was performed in Mád (Tokaj wine region), Hungary in vineyard Betsek, 48°11'16\N 21°19'03\E, on October 25 and November 3, 2016. Four different types of berry samples were collected starting with healthy berries followed by 3 consecutive stages of noble rot. Stage I. was characterized by partly botrytized epidermis and no shrivelling, stage II. berries showed fully colored epidermis and mild shrivelling while stage III. exhibited all features of mature noble rot berries (fully shrivelled with only limited presence of B. cinerea material on surface). Both sampling times five biological replicates were collected in 50 ml centrifuge tubes for all four stages of noble rot, one sample comprising 5 (healthy) to 15 (stage III.) berries. Samples were frozen immediately in liquid nitrogen, transported in dry ice and stored at -70 °C in an ultra low temperature laboratory freezer. RNA-Seq data were generated from samples collected within the frame of a field experiment. Description of the vineyard and viticultural practices have been described by Hegyi-Kaló et al. (2020). Reference: Hegyi-Kaló J., Hegyi Á.I., Geml J., Zsófi Z., Pálfi X., Váczy, K. Z. (2020) Physico-chemical characteristics and culturable microbial communities of grape berries change strongly during noble rot development. Plants 9: 1809. Berries were ground to a fine powder in liquid nitrogen by a Retsch laboratory ball mill. Considering the uneven dry weight of the berry samples varying amounts of frozen plant powder were weighed into new 50 ml centrifuge tubes, 800 mg for healthy and stage I. berries, 500 mg for stage II. berries and 250 mg for stage III. berries. Total RNA extraction was carried out according to Reid et al. (2006). Twenty milliliter extraction buffer [300 mM Tris HCl (pH 8.0), 25 mM EDTA, 2 M NaCl, 2% CTAB, 2% PVPP, 0.05% spermidine trihydrochloride, 2% β-mercaptoethanol (administered immediately before use)] was added to powdered samples incubated at 65 °C for 10 minutes and vortexed every 2 minutes. After that, mixtures were extracted twice with equal volumes of chloroform:isoamyl alcohol (24:1), thoroughly vortexed and centrifuged at 4800 x g for 10 minutes at 4 °C. The supernatant (10 ml) was transferred to a new 50 ml centrifuge tube and combined with 0.1 vol 3M NaOAc (pH 5.2) and 0.6 vol ice-cold isopropanol, mixed and kept for 30 minutes at -70 °C. The nucleic acid pellets were recovered by centrifugation at 4800 x g for 30 minutes at 4 °C. The supernatant was removed and the remaining pellet was washed with 5 ml of 70 % EtOH, then centrifuged at 4800 x g for 15 minutes at 4 °C. The liquid was discarded and the precipitate was dried with a lyophilizer.The nucleic acid pellets were dissolved in 1 ml TE (pH 7.0) and transferred to new 2 ml microcentrifuge tubes. Selective RNA precipitation was achieved by adding 0.3 vol of 8M LiCl and a subsequent overnight incubation at 4 °C. Total grapevine and fungal RNA were harvested by centrifugation at 21000 x g for 30 minutes at 4 °C followed by a washing step with 500 l 70 % ice-cold EtOH and finally drying by a lyophilizer. Isolated RNA pellets were dissolved in 42 microliter nuclease-free ultrapure water and RNA quality was first evaluated by using a nanodrop 1000 instrument. After the extraction was finished all samples were subjected to DNase treatment (Invitrogen, Thermo Fisher Scientific, Waltham, MA, USA, DNA-free™ DNA Removal Kit). Total RNA sample quality was analyzed more precisely on an Agilent BioAnalyzer using Eukaryotic Total RNA Nano and Pico Kit according to the manufacturer’s protocol. Samples with RNA integrity number (RIN) value >7 were accepted for library preparation process.Cited literature: Reid K.E., Olsson N., Schlosser J., Peng F., Lund S.T. (2006) An optimized grapevineRNA isolation procedure and statistical determination of reference genes for real-timeRT-PCR during berry development. BMC Plant Biology 6:27. RNA-Seq libraries were prepared from total RNA using TruSeq RNA Sample preparation kit (Illumina) according to the manufacturer’s instructions. Shortly, poly-A RNAs were captured by oligo-dT conjugated magnetic beads then the eluted mRNAs were fragmented at 94 °C. First strand cDNA was synthesized by random priming reverse transcription and after second strand synthesis step double stranded cDNA were produced. Following repairing ends, A-tailing and adapter ligation steps adapter ligated fragments were amplified in enrichment PCR and lastly double stranded mRNA sequencing library was generated.

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text: Vitis vinifera

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text: fully colored epidermis, mild shrivelling

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text: October 25, 2016

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text: Agricultural Institute, Centre for Agricultural Research, ELKH

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text: Center for Laboratory Medicine, St. Gallen, Switzerland

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characteristic: ENA-CHECKLIST

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characteristic: title


characteristic: GISAID Accession ID

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text: hCoV-19/Switzerland/SG-CLM-11117102/2021

characteristic: isolate

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text: active surveillance in response to outbreak

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characteristic: ENA-CHECKLIST

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text: Center for Laboratory Medicine St. Gallen

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text: hCoV-19/Switzerland/SG-CLM-11126203/2021


characteristic: GISAID Accession ID

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text: public

text: SIB

text: Yannick Gerth

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text: hCoV-19/Switzerland/SG-CLM-11127096/2021

characteristic: title


characteristic: ENA-CHECKLIST

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text: public

text: SIB

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text: restricted access

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text: restricted access

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text: hCoV-19/Switzerland/SG-CLM-11126699/2021

characteristic: isolate

text: Severe acute respiratory syndrome coronavirus 2

characteristic: organism

characteristic: sample capture status


text: Sanger Institute

characteristic: GAL

text: NOT PROVIDED

text: EarlhamInstitute

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: COPO

characteristic: broker name

text: RICHARD PITMAN

characteristic: collected by

text: Environment Agency

characteristic: collecting institution

characteristic: collection date

text: crucian carp

characteristic: common name

text: United Kingdom

unit: DD

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: Nottingham | Calverton | Moor Ln | Lake Side View | Calverton Fish Farm

text: Hatchery pond

characteristic: habitat

text: BERND HÄNFLING

characteristic: identified by

text: University of Hull

text: juvenile

characteristic: lifestage

text: Carassius carassius

text: WHOLE ORGANISM

characteristic: organism part

text: DTOL

characteristic: project name

text: Carassius carassius

text: FEMALE

characteristic: sex

characteristic: specimen id

text: NOT COLLECTED

characteristic: specimen voucher

text: 17fd5f4b-74d0-4416-95b8-e856892b078c-DTOL-specimen

characteristic: tolid

type: derived from


characteristic: ENA-CHECKLIST

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characteristic: External Id

text: Sanger Institute

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text: NOT PROVIDED

text: EarlhamInstitute

characteristic: INSDC center name

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characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: COPO

text: RICHARD PITMAN

text: Environment Agency

text: barbel

text: United Kingdom

characteristic: geographic location (country and/or sea)

characteristic: geographic location (region and locality)

text: Hatchery pond

text: BERND HÄNFLING

text: University of Hull

text: juvenile

text: Barbus barbus

characteristic: organism

text: WHOLE ORGANISM

text: DTOL

text: Barbus barbus

text: MALE

text: NOT COLLECTED

text: 4a9f3b59-86c1-4ca0-b724-b27526b46795-DTOL-specimen

characteristic: title


text: Sanger Institute

text: NOT PROVIDED

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text: public

text: COPO

characteristic: broker name

text: RICHARD PITMAN

characteristic: collected by

text: Environment Agency

characteristic: collecting institution

characteristic: collection date

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text: juvenile

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text: Abramis brama

text: WHOLE ORGANISM

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text: Abramis brama

text: NOT PROVIDED

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text: 0b4e2bfc-44ae-42d3-acc7-1d910aa04ab6-DTOL-specimen


characteristic: ENA-CHECKLIST

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text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: COPO

text: ANDY NUNN| PAOLO MOCCETTI

text: University of Hull

text: river trout

text: United Kingdom

characteristic: geographic location (country and/or sea)

text: Collingham | Collingham Beck

characteristic: geographic location (region and locality)

text: River

text: BERND HÄNFLING

text: University of Hull

text: adult

text: Salmo trutta

characteristic: organism

text: WHOLE ORGANISM

text: DTOL

text: Salmo trutta

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text: NOT COLLECTED

text: d775af28-aa0d-4114-9cbd-050f2d3debe0-DTOL-specimen

characteristic: tolid


text: Sanger Institute

text: NOT PROVIDED

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text: public

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characteristic: broker name

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text: University of Hull

characteristic: collecting institution

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text: gudgeon

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text: United Kingdom

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: River Wharfe | confluence Riffa Beck

text: River

characteristic: habitat

text: BERND HÄNFLING

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text: adult

characteristic: lifestage

text: Gobio gobio

text: WHOLE ORGANISM

characteristic: organism part

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text: 5534b14f-86f0-4714-a948-856c7bf08ccb-DTOL-specimen

characteristic: title


characteristic: ENA-CHECKLIST

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text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: COPO

text: ANDY NUNN| PAOLO MOCCETTI

text: University of Hull

text: Eurasian minnow

text: United Kingdom

characteristic: geographic location (country and/or sea)

text: River Wharfe | confluence Riffa Beck

characteristic: geographic location (region and locality)

text: River

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text: adult

text: Phoxinus phoxinus

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text: f7f7351b-fd70-4035-8d72-cd800d5d9aa7-DTOL-specimen


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characteristic: broker name

text: ANDY NUNN| PAOLO MOCCETTI

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text: University of Hull

characteristic: collecting institution

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text: United Kingdom

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text: River Wharfe | confluence Riffa Beck

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text: Barbatula barbatula

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characteristic: tolid


characteristic: ENA-CHECKLIST

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characteristic: External Id

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characteristic: INSDC center name

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text: public

characteristic: INSDC status

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text: COPO

text: RICHARD PITMAN

text: Environment Agency

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characteristic: geographic location (country and/or sea)

characteristic: geographic location (region and locality)

text: Hatchery pond

text: BERND HÄNFLING

text: University of Hull

text: juvenile

text: Scardinius erythrophthalmus

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text: DTOL

text: Scardinius erythrophthalmus

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text: NOT COLLECTED

text: 19354bea-8be0-42ef-8f25-608513c5d1ea-DTOL-specimen

characteristic: title


text: Sanger Institute

text: NOT PROVIDED

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text: public

text: COPO

characteristic: broker name

text: RICHARD PITMAN

characteristic: collected by

text: Environment Agency

characteristic: collecting institution

characteristic: collection date

text: tench

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text: United Kingdom

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text: Hatchery pond

characteristic: habitat

text: BERND HÄNFLING

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characteristic: lifestage

text: Tinca tinca

text: WHOLE ORGANISM

characteristic: organism part

text: DTOL

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text: Tinca tinca

text: MALE

characteristic: sex

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text: NOT COLLECTED

characteristic: specimen voucher

text: 148661c1-abea-4405-b9dc-dacee9427ab0-DTOL-specimen


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

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characteristic: External Id

text: Sanger Institute

characteristic: GAL

text: NOT PROVIDED

text: EarlhamInstitute

characteristic: INSDC center name

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characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: COPO

text: RICHARD PITMAN

text: Environment Agency

text: roach minnow

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characteristic: geographic location (country and/or sea)

characteristic: geographic location (region and locality)

text: Hatchery pond

text: BERND HÄNFLING

text: University of Hull

text: juvenile

text: Rutilus rutilus

characteristic: organism

text: WHOLE ORGANISM

text: DTOL

text: Rutilus rutilus

text: FEMALE

text: NOT COLLECTED

text: b4b2a6cd-f7b9-45de-95b3-71bdd1b8e950-DTOL-specimen

characteristic: tolid


text: Sanger Institute

text: NOT PROVIDED

text: EarlhamInstitute

text: public

text: COPO

characteristic: broker name

text: RICHARD PITMAN

characteristic: collected by

text: Environment Agency

characteristic: collecting institution

characteristic: collection date

text: common dace

characteristic: common name

text: United Kingdom

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: Hatchery pond

characteristic: habitat

text: BERND HÄNFLING

characteristic: identified by

text: University of Hull

text: juvenile

characteristic: lifestage

text: Leuciscus leuciscus

text: WHOLE ORGANISM

characteristic: organism part

text: DTOL

characteristic: project name

text: Leuciscus leuciscus

text: NOT PROVIDED

characteristic: sex

characteristic: specimen id

text: NOT COLLECTED

text: b07370d5-9610-4eba-b88b-a6164e352f2a-DTOL-specimen

characteristic: title