text: Institute for Biotechnology in Plant Production, IFA-Tulln, University of Natural Resources and Life Sciences, A-3430 Tulln, Austria

text: public

text: ArrayExpress

characteristic: broker name

text: bread wheat

characteristic: cultivar

text: Protocols: We utilized four early isogenic lines (NILs) previously generated from a cross of the resistant spring wheat line CM-82036 and Remus, a susceptible Austrian spring wheat cultivar. The NILs have Remus as the recurrent parent (5 backcrosses) and contain the resistance alleles from CM-82036 of both Fhb1 and Qfhs.ifa-5A (NIL1), or either Fhb1 (NIL2) or Qfhs.ifa-5A (NIL3) or none (NIL4). Additionally, CM-82036 was used in the subsequent experiments. In preparation for fungal innoculation, F. graminearum spores required for inoculation were produced on defined SNA medium under UV-light at 25 degrees C. After two weeks conidia were harvested and diluted to 50.000 conidia/mL in water. Aliquots were stored at -80 degrees C. Single seeds were sown and put at 4 C for one week. After vernalization, seeds were germinated at 20 degrees C for two weeks and each two plants were potted into 3 L pots. The plants were initially kept in a 18 degrees C/12 degrees C day/night cycle (12 hours light), which was gradually changed until anthesis to 21 degrees C/18 degrees C at 55 % relative humidity (16 hours light). At least 12 heads per experimental condition (three replications, F. graminearum/mock treatment, two time points) were subjected to further experiments. At anthesis, the plants were inoculated either with a F. graminearum spore suspensions or water: 10 ? of the respective inoculum was pipetted into one floret between palea and lemma, directly onto the generative part. Per head two outer floret of six spikelets in three central rows were treated in this way, while the central florets were not inoculated (in total 12 florets). The inoculated heads were moistened with distilled water and bagged into a plastic bag for 24 hours to provide favourable conditions for disease development. Tissues comprising only the initially inoculated spikelets were sampled 30 or 50 hours after inoculation (hai) and from these the generative parts (stigma, anthers, ovary) as well as the glumes and the central floret were discarded. Only palea, lemma and rachis were frozen immediately in liquid nitrogen and stored at -80 degrees C until use. Single seeds were sown and put at 4 degrees C for one week. After vernalization, seeds were germinated at 20 degrees C for two weeks and each two plants were potted into 3 L pots. The plants were initially kept in a 18 degrees C/12 degrees C day/night cycle (12 hours light), which was gradually changed until anthesis to 21 degrees C/18 degrees C at 55 % relative humidity (16 hours light). At least 12 heads per experimental condition (three replications, F. graminearum/mock treatment, two time points) were subjected to further experiments. At anthesis, the plants were inoculated either with a F. graminearum spore suspensions or water: 10 ? of the respective inoculum was pipetted into one floret between palea and lemma, directly onto the generative part. Per head two outer floret of six spikelets in three central rows were treated in this way, while the central florets were not inoculated (in total 12 florets). The inoculated heads were moistened with distilled water and bagged into a plastic bag for 24 hours to provide favourable conditions for disease development. Tissues comprising only the initially inoculated spikelets were sampled 30 or 50 hours after inoculation (hai) and from these the generative parts (stigma, anthers, ovary) as well as the glumes and the central floret were discarded. Only palea, lemma and rachis were frozen immediately in liquid nitrogen and stored at -80 degrees C until use. To eliminate RNases, metal jars with inherent metal spheres for Retsch-mill (MM 301, Haan, Germany) were sterilized at 180 degrees C for 3 h and then stored at -80 degrees C. All tissue belonging to one sample was pooled in one precooled jar and clamped in Retsch-mill. Grinding was performed for 30 s at full speed to obtain a fine tissue powder and immediately put back at -80 degrees C. Total-RNA was extracted from 100 ? of frozen tissue powder using the RNeasy Plant Mini Kit (#74903, Qiagen, Venlo, Netherlands) according to manufacturers instructions. The extracted RNA was checked for quality and quantity on an automated electrophoresis-system (Experion, #701-7000, Bio-Rad, Hercules, CA, US). Sequencing was performed on an Illumina HiSeq2000 machine using 8x multiplexing, theoretically generating 22 M reads per sample by an external sequencing-provider ?ATC?(Konstanz, Germany). Each sample represents one experimental condition (pathogen/mock; time points; genotype) and comprises pools of 12 treated wheat heads. Each experimental condition has been replicated 3x. cDNA was sent to a service provider (GATC konstanz germany) who have performed the library construction following the Illumina TruSeq RNA sample preparation guide (version 2, http://support.illumina.com/sequencing/sequencing_kits/truseq_rna_sample_prep_kit_v2/documentation.ilmn)

characteristic: description

text: anthesis

characteristic: developmental stage

text: mock inoculation

characteristic: infect

text: Triticum aestivum

text: Triticum aestivum

text: spikelets (only using palea, lemma and rachis)

characteristic: organism part

text: Triticum aestivum

text: frozen specimen

characteristic: specimen with known storage state

characteristic: title


status: PUBLIC

text: Danio rerio

tag: attribute

characteristic: ArrayExpress-Species

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: SC

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: CH1073_200E16-sc-2013-07-05T13:37:10Z-1660367

characteristic: Submitter Id

text: zebrafish

characteristic: common name

text: Danio rerio

characteristic: organism

text: Danio rerio


characteristic: ENA-CHECKLIST

text: SRA-Webin

characteristic: ENA-SUBMISSION-TOOL

text: ISB-USA

text: public

text: baker's yeast

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

text: RAD-seq reduced-genome sequencing of yeast strain for phylogenetic analysis

type: has member


text: Danio rerio

text: SC

text: public

text: CH73_377M23-sc-2013-07-05T13:38:10Z-1660435

text: zebrafish

text: Danio rerio

text: Danio rerio


text: University College London

text: public

tag: Namespace:University College London

text: ArrayExpress

characteristic: broker name

text: HEKn

characteristic: cell line

text: keratinocyte

characteristic: cell type

text: human

text: Protocols: Neonatal primary human epidermal keratinocytes (HEKn, Life technologies, Paisley, UK) were cultured on mouse collagen IV (0.67ug/cm2 BD Biosciences, Oxford, UK) coated surfaces in keratinocyte defined media containing epithelial growth factor (KDM and EpiLife, Life technologies). Differentiation was induced by shifting the cells to a high calcium media containing [1.2mM] Calcium Chloride. Viral infections for transcriptome experiments were carried out using VZV pOka cultured and used at less than 20 passages. Infected cell preparations were first treated with Mitomycin C (0.05mg/ml for 3hrs) prior to freezing and subsequently titered on Mewo cells. Cell-free VZV was generated by a rapid freeze (liquid N2) and thaw (37C), followed by removal of cellular debris by low speed centrifugation. For UV inactivated VZV, cell-free VZV supernatants were treated for 20 min at 150,000J/Cm2 using a Stratalinker UV Crosslinker (Stratagene). 1x105 HEKn cells per well of a 6 well dish were inoculated with 3x104 infectious units of virus. All VZV cultures were carried out at 34C, 5% CO2. This method involves several steps that are designed to convert total RNA into a library of template molecules suitable for high throughput DNA sequencing. The first step involves purifying the poly-A containing mRNA molecules using poly-T oligo-attached magnetic beads. Following purification, the mRNA is fragmented into small pieces using divalent cations under elevated temperature. Then, the cleaved mRNA fragments are copied into first strand cDNA using reverse transcriptase and a high concentration of random hexamer primers. Unique adaptors were ligated to the cDNA and 200bp fragments were size selected by agarose gel purification. Libraries were validated by using a DNA high sensitivity chip (Agilent, Cheshire, UK) and quantified by Qubit analysis using the Quant-iT dsDNA HS Assay (Life technologies).

characteristic: description

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens

text: fresh specimen


text: Plasmodium falciparum

characteristic: ArrayExpress-Species

characteristic: ENA-FIRST-PUBLIC

text: SC

text: public

text: malaria parasite P. falciparum

text: Plasmodium falciparum

text: Plasmodium falciparum


text: Mus Musculus

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: SC

text: public

text: mES_lif_s1_cell14-sc-2013-07-11T08:56:35Z-1661111

text: house mouse

text: Mus musculus

text: mRNA-seq Nextera library

characteristic: sample description

text: Mus musculus


text: Danio rerio

text: SC

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: CH1073_315F19-sc-2013-07-05T13:38:34Z-1660463

text: zebrafish

text: Danio rerio

text: Danio rerio


text: public

characteristic: INSDC status

characteristic: SRA accession

tag: Namespace:Plant Pathology Group, Integrative Biology Zurich (IBZ), ETH Zurich

characteristic: Submitter Id

text: ArrayExpress

text: apple

text: Protocols: Plant material comprised young Malus x domestica (Borkh.) cv. Golden Delicious saplings grafted on M9T337 rootstock. Plants were kept in active growth with a 16h/8h (day/night) photoperiod and a minimum of 65.5 umol m-2 s-1 light intensity provided with white fluorescent lamps (Philips Master TL-D 36W/830) and fertilized once with Obstdunger 12:8:16:2:0.2 (N:P:K:Mg:B; OBA-Lanze, Hauert AG, Switzerland) one week prior the start of the experiment. Plants were grown under greenhouse condition at 20 +/- degrees C and 70% RH until 10 to 15 leaves stadium. Rape-seed oil (Maag AG, Switzerland) mixed with Alaxon 50 (Maag AG, Switzerland) and two weeks later Vertimec (Maag AG, Switzerland) have been used as chemical treatment before starting the experiment to keep plants free of pest-insects. For inoculation, conidia of Venturia inaequalis (Cooke) single spore isolate no. 1639 were used.Inoculation, with a spore suspension of 5 x 105 spores ml-1, was performed at 17 +/- 2 degrees C and >98% RH. . Half of the plants were challenged with the apple scab pathogen and half were mock inoculated. After the treatment (scab or mock inoculation), plants were grown at 17 +/- 2 degrees C and 70% RH until sampling. The first sets of samples have been collected 72 hours post inoculation (hpi). The second sets of samples have been collected at 96 hpi. Samples have been collected from leaf 1 (L1) and leaf 7 (L7) by removing the leaf tip (< 100 mg) of each leaf in three biological replicates for inoculated and not inoculated shoots, 12 samples for each time points (72 and 96 hpi), 24 in total. Total RNA was extracted using SV Total RNA Isolation System (Promega Corporation, USA) with column purification Complementary DNA (cDNA) libraries were constructed, starting from 1 ug of total RNA, at the Functional Genomic Center Zurich (FGCZ) following the TruSeq RNA Sample preparation protocol v. 2 instructions (Low Throughput protocol, Illumina, Inc.).

text: Leaf 1 (youngest leaf on the top of the shoot)

characteristic: developmental stage

text: mock inoculation

characteristic: infect

text: Malus domestica

text: Malus domestica

text: leaf

characteristic: organism part

text: Malus domestica

text: fresh specimen

characteristic: specimen with known storage state

text: 17 +/- 2 degree celsius

characteristic: temperature

text: 96 hour

characteristic: time post inoculation

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: public

tag: Namespace:Science for Life Laboratory, Stockholm, Sweden

text: ArrayExpress

characteristic: broker name

text: human

characteristic: common name

text: Protocols: The use of human tissue samples was approved by the Uppsala Ethical Review Board (Reference #2011/473). Tissues samples, collected within the infrastructure of an established biobank, were embedded in Optimal Cutting Temperature (O.C.T.) compound and stored at -80C. A hematoxylin-eosin (HE) stained frozen section (4um) was prepared from each sample using a cryostat and the CryoJane Tape-Transfer System (Instrumedics, St. Louis, MO, USA). Each slide was examined by a pathologist to ensure proper tissue morphology. Three sections (10um) were cut from each frozen tissue block and collected into a tube for subsequent RNA extraction. The tissue was homogenized mechanically using a 3 mm steel grinding ball (VWR). Total RNA was extracted from cell lines and tissue samples using the RNeasy Mini Kit (Qiagen, Hilden, Germany) according to the manufacturers instructions. The extracted RNA samples were analyzed using either an Experion automated electrophoresis system (Bio-Rad Laboratories, Hercules, CA, USA) with the standard-sensitivity RNA chip or an Agilent 2100 Bioanalyzer system(Agilent Biotechnologies, Palo Alto, USA) with the RNA 6000 Nano Labchip Kit. Only samples of high-quality RNA (RNA Integrity Number 7.5) were used in the following mRNA sample preparation for sequencing. Illumina Truseq RNA v2

characteristic: description

text: adult

characteristic: individual

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: testis

text: Homo sapiens

text: frozen specimen


text: Danio rerio

characteristic: ArrayExpress-Species

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: SC

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: CH1073_200J5-sc-2013-07-05T13:38:33Z-1660462

text: zebrafish

text: Danio rerio

text: Danio rerio


text: European Molecular Biology Laboratory

text: public

characteristic: SRA accession

tag: Namespace:European Molecular Biology Laboratory

characteristic: Submitter Id

text: ArrayExpress

characteristic: cell line

text: erythroleukemia

characteristic: cell type

text: human

text: Protocols: Cells were cultured in RPMI supplemented with 10% FBS. Trizol Illumina mRNA-seq library construction protocol

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens


text: Mus Musculus

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: SC

text: public

text: mES_lif_s1_cell71-sc-2013-07-11T08:57:30Z-1661168

text: house mouse

text: Mus musculus

text: mRNA-seq Nextera library

characteristic: sample description

text: Mus musculus


text: Mus Musculus

text: SC

text: public

text: mES_lif_s1_cell36-sc-2013-07-11T08:56:56Z-1661133

text: house mouse

characteristic: common name

text: Mus musculus

text: mRNA-seq Nextera library

text: Mus musculus


text: Science for Life Laboratory, Stockholm, Sweden

text: public

text: ArrayExpress

characteristic: broker name

text: human

characteristic: description

text: adult

characteristic: developmental stage

characteristic: individual

text: Homo sapiens

text: Homo sapiens

text: bone marrow

characteristic: organism part

text: Homo sapiens

text: frozen specimen

characteristic: specimen with known storage state

characteristic: title


text: Neurons

characteristic: ArrayExpress-CellType

text: Adult

characteristic: ArrayExpress-DevelopmentalStage

text: MeCP2 GFP tagged

characteristic: ArrayExpress-Genotype

text: Chromotek GFP trap Agarose

characteristic: ArrayExpress-Immunoprecipitate

text: Brain

characteristic: ArrayExpress-OrganismPart

text: wildtype

characteristic: ArrayExpress-Phenotype

text: male

characteristic: ArrayExpress-Sex

text: Mus musculus

characteristic: ArrayExpress-Species

text: Bl6 MeCP2 GFP

characteristic: ArrayExpress-StrainOrLine

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: SC

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: m_ChIP_GFP_high_N3-sc-2013-07-18T13:26:50Z-1669282

text: house mouse

text: Mus musculus

characteristic: organism

text: ChIP DNA from GFP high neurons (MeCP2 GFP from 15 BL 6 male)

text: Mus musculus

text: Bl6 MeCP2 GFP

characteristic: strain


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: Plant Pathology Group, Integrative Biology Zurich (IBZ), ETH Zurich

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: ArrayExpress

characteristic: broker name

text: apple

characteristic: common name

characteristic: description

text: Leaf 7 (old leaf: seventh leaf position starting from the top of the shoot)

characteristic: developmental stage

text: inoculated with Venturia inaequalis

characteristic: infect

text: Malus domestica

text: Malus domestica

text: leaf

characteristic: organism part

text: Malus domestica

text: fresh specimen

characteristic: specimen with known storage state

text: 17 +/- 2 degree celsius

characteristic: temperature

text: 96 hour

characteristic: time post inoculation

characteristic: title


characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

tag: Namespace:College of Life Science, Sun Yat-Sen University

text: 40 year

characteristic: age

text: ArrayExpress

text: Indo-pacific humpbacked dolphin

text: Protocols: The blood sample of the Indo-Pacific humpback dolphin was obtained from a wild male adult individual The fresh blood were collected into EDTA-containing tubes, and then centrifuged for 5 min at 400-500g. The red supernatant was discarded and then 18 ml of Red Blood Cell Lysis Buffer (Beyotime Institute of Biotechnology) were added, mixed gently by flicking the tubes and lasted for 10 min. The tubes were then centrifuged at 1000g for 5 minutes at 4 degrees C to collect the leukocyte pellet. Total RNA was extracted from the leucocytes of Indo-Pacific humpback dolphin using TRIzol reagent (Invitrogen) according to the manufacturer's protocol. Illumina sequencing was performed at Beijing Genomics Institute (BGI)-Shenzhen, China. mRNA with poly(A) tail was isolated from 20ug total RNA treated with DNase I using Magnetic Oligo (dT) Beads (Illumina). The mRNA was fragmented into small pieces (200-700 bp) by treatment with divalent cations at 94 degrees C for 5 minutes. With random hex-amer primers (Illumina), the double-stranded cDNA was synthesized using the SuperScript double-stranded cDNA synthesis kit (Invitrogen) and was further subjected to end-repair using T4 DNA polymerase, the Klenow fragment, and T4 polynucleotide kinase followed by a single A base addition using Klenow 3' to 5' exo-polymerase, then ligated with an adapter or index adapter using T4 DNA ligase. To select the proper templates for downstream enrichment, the products of ligation reaction were purified on 2% agarose gel. The cDNA fragments (about 200 bp) were excised from the gel. Fifteen rounds of PCR amplification were carried out to enrich the purified cDNA template using PCR primer PE 1.0 and 2.0 (Illumina) with phusion DNA polymerase. Finally, the cDNA library was constructed with 200 bp insertion fragment.

text: adult

text: Sousa chinensis

characteristic: organism

text: Sousa chinensis

text: Leucocyte

text: Sousa chinensis

text: male

characteristic: sex

text: fresh specimen

text: leucocyte


characteristic: ENA-FIRST-PUBLIC

text: public

characteristic: INSDC status

characteristic: SRA accession

tag: Namespace:Institute for Biotechnology in Plant Production, IFA-Tulln, University of Natural Resources and Life Sciences, A-3430 Tulln, Austria

characteristic: Submitter Id

text: ArrayExpress

characteristic: broker name

text: bread wheat

characteristic: common name

characteristic: cultivar

text: Protocols: We utilized four early isogenic lines (NILs) previously generated from a cross of the resistant spring wheat line CM-82036 and Remus, a susceptible Austrian spring wheat cultivar. The NILs have Remus as the recurrent parent (5 backcrosses) and contain the resistance alleles from CM-82036 of both Fhb1 and Qfhs.ifa-5A (NIL1), or either Fhb1 (NIL2) or Qfhs.ifa-5A (NIL3) or none (NIL4). Additionally, CM-82036 was used in the subsequent experiments. In preparation for fungal innoculation, F. graminearum spores required for inoculation were produced on defined SNA medium under UV-light at 25 degrees C. After two weeks conidia were harvested and diluted to 50.000 conidia/mL in water. Aliquots were stored at -80 degrees C. Single seeds were sown and put at 4 C for one week. After vernalization, seeds were germinated at 20 degrees C for two weeks and each two plants were potted into 3 L pots. The plants were initially kept in a 18 degrees C/12 degrees C day/night cycle (12 hours light), which was gradually changed until anthesis to 21 degrees C/18 degrees C at 55 % relative humidity (16 hours light). At least 12 heads per experimental condition (three replications, F. graminearum/mock treatment, two time points) were subjected to further experiments. At anthesis, the plants were inoculated either with a F. graminearum spore suspensions or water: 10 ? of the respective inoculum was pipetted into one floret between palea and lemma, directly onto the generative part. Per head two outer floret of six spikelets in three central rows were treated in this way, while the central florets were not inoculated (in total 12 florets). The inoculated heads were moistened with distilled water and bagged into a plastic bag for 24 hours to provide favourable conditions for disease development. Tissues comprising only the initially inoculated spikelets were sampled 30 or 50 hours after inoculation (hai) and from these the generative parts (stigma, anthers, ovary) as well as the glumes and the central floret were discarded. Only palea, lemma and rachis were frozen immediately in liquid nitrogen and stored at -80 degrees C until use. Single seeds were sown and put at 4 degrees C for one week. After vernalization, seeds were germinated at 20 degrees C for two weeks and each two plants were potted into 3 L pots. The plants were initially kept in a 18 degrees C/12 degrees C day/night cycle (12 hours light), which was gradually changed until anthesis to 21 degrees C/18 degrees C at 55 % relative humidity (16 hours light). At least 12 heads per experimental condition (three replications, F. graminearum/mock treatment, two time points) were subjected to further experiments. At anthesis, the plants were inoculated either with a F. graminearum spore suspensions or water: 10 ? of the respective inoculum was pipetted into one floret between palea and lemma, directly onto the generative part. Per head two outer floret of six spikelets in three central rows were treated in this way, while the central florets were not inoculated (in total 12 florets). The inoculated heads were moistened with distilled water and bagged into a plastic bag for 24 hours to provide favourable conditions for disease development. Tissues comprising only the initially inoculated spikelets were sampled 30 or 50 hours after inoculation (hai) and from these the generative parts (stigma, anthers, ovary) as well as the glumes and the central floret were discarded. Only palea, lemma and rachis were frozen immediately in liquid nitrogen and stored at -80 degrees C until use. To eliminate RNases, metal jars with inherent metal spheres for Retsch-mill (MM 301, Haan, Germany) were sterilized at 180 degrees C for 3 h and then stored at -80 degrees C. All tissue belonging to one sample was pooled in one precooled jar and clamped in Retsch-mill. Grinding was performed for 30 s at full speed to obtain a fine tissue powder and immediately put back at -80 degrees C. Total-RNA was extracted from 100 ? of frozen tissue powder using the RNeasy Plant Mini Kit (#74903, Qiagen, Venlo, Netherlands) according to manufacturers instructions. The extracted RNA was checked for quality and quantity on an automated electrophoresis-system (Experion, #701-7000, Bio-Rad, Hercules, CA, US). Sequencing was performed on an Illumina HiSeq2000 machine using 8x multiplexing, theoretically generating 22 M reads per sample by an external sequencing-provider ?ATC?(Konstanz, Germany). Each sample represents one experimental condition (pathogen/mock; time points; genotype) and comprises pools of 12 treated wheat heads. Each experimental condition has been replicated 3x. cDNA was sent to a service provider (GATC konstanz germany) who have performed the library construction following the Illumina TruSeq RNA sample preparation guide (version 2, http://support.illumina.com/sequencing/sequencing_kits/truseq_rna_sample_prep_kit_v2/documentation.ilmn)

text: anthesis

text: mock inoculation

text: Triticum aestivum

text: Triticum aestivum

text: spikelets (only using palea, lemma and rachis)

text: Triticum aestivum

text: frozen specimen


characteristic: ENA-CHECKLIST

text: SRA-Webin

characteristic: ENA-SUBMISSION-TOOL

text: ISB-USA

text: public

text: baker's yeast

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

text: RAD-seq reduced-genome sequencing of yeast strain for phylogenetic analysis


text: female

characteristic: ArrayExpress-Sex

text: Haemonchus contortus

characteristic: ArrayExpress-Species

characteristic: ArrayExpress-StrainOrLine

characteristic: ENA-LAST-UPDATE

text: SC

text: public

text: Haemonchus_contortus_MHco3_4_BC4_S3_0_2IVM_2313-sc-2013-07-09T16:18:46Z-1660681

text: barber pole worm

text: Haemonchus contortus

text: 60 female worms, strain identity was checked using a panel of 4 microsatellite loci that discriminate Haemonchus contortus strains

characteristic: sample description

text: Haemonchus contortus

characteristic: strain


characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: ArrayExpress

text: human

characteristic: description

text: adult

characteristic: developmental stage

characteristic: individual

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: testis

characteristic: organism part

text: Homo sapiens

text: frozen specimen

characteristic: specimen with known storage state

characteristic: title


characteristic: ENA-FIRST-PUBLIC

text: Institut Pasteur de Montevideo

text: public

characteristic: INSDC status

characteristic: SRA accession

tag: Namespace:Institut Pasteur de Montevideo

characteristic: Submitter Id

text: ArrayExpress

characteristic: broker name

text: mesenchymal stem cell

characteristic: cell type

text: human

characteristic: common name

text: Protocols: Stem cells were obtained from adipose tissue from obese human donors ( two males and one female, ages: 41, 52, 23) . All samples were isolated, collected after informed consent had been obtained. hASCs were isolated, cultured and characterized as following. Briefly, 100 ml of adipose tissue was washed with sterile phosphate-buffered saline (PBS) (Gibco Invitrogen). A one-step digestion by 1 mg/ml collagenase type I (Invitrogen) was performed for 30 mins at 37 degrees C during permanent shaking and was followed by filtration through first a 100- and then 40-um mesh filter (BD FALCON, BD Biosciences Discovery Labware, Bedford, MA, USA).

text: undifferentiated

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens

text: 3 day

characteristic: time

text: no adipocyte differentiation induction

characteristic: treatment


text: Danio rerio

characteristic: ArrayExpress-Species

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: SC

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: CH73_308C16-sc-2013-07-05T13:37:54Z-1660416

text: zebrafish

text: Danio rerio

text: Danio rerio


text: Danio rerio

text: SC

text: public

text: CH1073_34F24-sc-2013-07-05T13:38:54Z-1660487

text: zebrafish

text: Danio rerio

characteristic: organism

text: Danio rerio


text: adult

characteristic: ArrayExpress-DevelopmentalStage

text: female

characteristic: ArrayExpress-Sex

text: Dracunculus medinensis

characteristic: ENA-CHECKLIST

text: SC

text: public

text: Dracunculus_medinensis-sc-2013-07-15T15:11:16Z-1667992

text: Guinea worm

text: Dracunculus medinensis

text: section of adult female worm

characteristic: sample description

text: Dracunculus medinensis


text: Mus Musculus

characteristic: ENA-FIRST-PUBLIC

text: SC

text: public

characteristic: INSDC status

characteristic: SRA accession

text: mES_lif_s1_cell51-sc-2013-07-11T08:57:11Z-1661148

characteristic: Submitter Id

text: house mouse

text: Mus musculus

text: mRNA-seq Nextera library

text: Mus musculus


text: Danio rerio

text: SC

text: public

text: zFOS_354B9-sc-2013-07-05T13:37:36Z-1660397

text: zebrafish

characteristic: common name

text: Danio rerio

text: Danio rerio


text: Mus Musculus

text: SC

text: public

text: mES_lif_s1_cell9-sc-2013-07-11T08:56:29Z-1661106

text: house mouse

text: Mus musculus

text: mRNA-seq Nextera library

text: Mus musculus


text: Danio rerio

text: SC

text: public

text: CH73_384J22-sc-2013-07-05T13:38:31Z-1660459

text: zebrafish

text: Danio rerio

text: Danio rerio


text: Danio rerio

text: SC

text: public

text: CH1073_700J1-sc-2013-07-05T13:37:28Z-1660387

text: zebrafish

text: Danio rerio

text: Danio rerio


text: Science for Life Laboratory, Stockholm, Sweden

text: public

text: ArrayExpress

characteristic: broker name

text: human

text: Protocols: The use of human tissue samples was approved by the Uppsala Ethical Review Board (Reference #2011/473). Tissues samples, collected within the infrastructure of an established biobank, were embedded in Optimal Cutting Temperature (O.C.T.) compound and stored at -80C. A hematoxylin-eosin (HE) stained frozen section (4um) was prepared from each sample using a cryostat and the CryoJane Tape-Transfer System (Instrumedics, St. Louis, MO, USA). Each slide was examined by a pathologist to ensure proper tissue morphology. Three sections (10um) were cut from each frozen tissue block and collected into a tube for subsequent RNA extraction. The tissue was homogenized mechanically using a 3 mm steel grinding ball (VWR). Total RNA was extracted from cell lines and tissue samples using the RNeasy Mini Kit (Qiagen, Hilden, Germany) according to the manufacturers instructions. The extracted RNA samples were analyzed using either an Experion automated electrophoresis system (Bio-Rad Laboratories, Hercules, CA, USA) with the standard-sensitivity RNA chip or an Agilent 2100 Bioanalyzer system(Agilent Biotechnologies, Palo Alto, USA) with the RNA 6000 Nano Labchip Kit. Only samples of high-quality RNA (RNA Integrity Number 7.5) were used in the following mRNA sample preparation for sequencing. Illumina Truseq RNA v2

characteristic: description

text: adult

characteristic: developmental stage

characteristic: individual

text: Homo sapiens

text: Homo sapiens

text: placenta

characteristic: organism part

text: Homo sapiens

text: frozen specimen

characteristic: specimen with known storage state

characteristic: title


text: Plasmodium falciparum

characteristic: ArrayExpress-Species

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: SC

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: malaria parasite P. falciparum

text: Plasmodium falciparum

characteristic: organism

text: Plasmodium falciparum


characteristic: ENA-FIRST-PUBLIC

text: Institute for Biotechnology in Plant Production, IFA-Tulln, University of Natural Resources and Life Sciences, A-3430 Tulln, Austria

text: public

characteristic: INSDC status

characteristic: SRA accession

text: ArrayExpress

text: bread wheat

characteristic: cultivar

text: anthesis

text: Fusarium graminearum inoculation

characteristic: infect

text: Triticum aestivum

text: Triticum aestivum

text: Triticum aestivum

text: frozen specimen


text: Danio rerio

text: SC

text: public

text: zFOS_896D6-sc-2013-07-05T13:38:12Z-1660437

characteristic: Submitter Id

text: zebrafish

characteristic: common name

text: Danio rerio

text: Danio rerio


text: Danio rerio

text: SC

text: public

text: CH1073_112A5-sc-2013-07-05T13:38:46Z-1660477

text: zebrafish

text: Danio rerio

text: Danio rerio


text: Danio rerio

text: SC

text: public

text: CH1073_303P16-sc-2013-07-05T13:38:27Z-1660455

text: zebrafish

text: Danio rerio

text: Danio rerio


text: public

text: ArrayExpress

characteristic: broker name

text: bread wheat

text: Protocols: We utilized four early isogenic lines (NILs) previously generated from a cross of the resistant spring wheat line CM-82036 and Remus, a susceptible Austrian spring wheat cultivar. The NILs have Remus as the recurrent parent (5 backcrosses) and contain the resistance alleles from CM-82036 of both Fhb1 and Qfhs.ifa-5A (NIL1), or either Fhb1 (NIL2) or Qfhs.ifa-5A (NIL3) or none (NIL4). Additionally, CM-82036 was used in the subsequent experiments. In preparation for fungal innoculation, F. graminearum spores required for inoculation were produced on defined SNA medium under UV-light at 25 degrees C. After two weeks conidia were harvested and diluted to 50.000 conidia/mL in water. Aliquots were stored at -80 degrees C. Single seeds were sown and put at 4 C for one week. After vernalization, seeds were germinated at 20 degrees C for two weeks and each two plants were potted into 3 L pots. The plants were initially kept in a 18 degrees C/12 degrees C day/night cycle (12 hours light), which was gradually changed until anthesis to 21 degrees C/18 degrees C at 55 % relative humidity (16 hours light). At least 12 heads per experimental condition (three replications, F. graminearum/mock treatment, two time points) were subjected to further experiments. At anthesis, the plants were inoculated either with a F. graminearum spore suspensions or water: 10 ? of the respective inoculum was pipetted into one floret between palea and lemma, directly onto the generative part. Per head two outer floret of six spikelets in three central rows were treated in this way, while the central florets were not inoculated (in total 12 florets). The inoculated heads were moistened with distilled water and bagged into a plastic bag for 24 hours to provide favourable conditions for disease development. Tissues comprising only the initially inoculated spikelets were sampled 30 or 50 hours after inoculation (hai) and from these the generative parts (stigma, anthers, ovary) as well as the glumes and the central floret were discarded. Only palea, lemma and rachis were frozen immediately in liquid nitrogen and stored at -80 degrees C until use. Single seeds were sown and put at 4 degrees C for one week. After vernalization, seeds were germinated at 20 degrees C for two weeks and each two plants were potted into 3 L pots. The plants were initially kept in a 18 degrees C/12 degrees C day/night cycle (12 hours light), which was gradually changed until anthesis to 21 degrees C/18 degrees C at 55 % relative humidity (16 hours light). At least 12 heads per experimental condition (three replications, F. graminearum/mock treatment, two time points) were subjected to further experiments. At anthesis, the plants were inoculated either with a F. graminearum spore suspensions or water: 10 ? of the respective inoculum was pipetted into one floret between palea and lemma, directly onto the generative part. Per head two outer floret of six spikelets in three central rows were treated in this way, while the central florets were not inoculated (in total 12 florets). The inoculated heads were moistened with distilled water and bagged into a plastic bag for 24 hours to provide favourable conditions for disease development. Tissues comprising only the initially inoculated spikelets were sampled 30 or 50 hours after inoculation (hai) and from these the generative parts (stigma, anthers, ovary) as well as the glumes and the central floret were discarded. Only palea, lemma and rachis were frozen immediately in liquid nitrogen and stored at -80 degrees C until use. To eliminate RNases, metal jars with inherent metal spheres for Retsch-mill (MM 301, Haan, Germany) were sterilized at 180 degrees C for 3 h and then stored at -80 degrees C. All tissue belonging to one sample was pooled in one precooled jar and clamped in Retsch-mill. Grinding was performed for 30 s at full speed to obtain a fine tissue powder and immediately put back at -80 degrees C. Total-RNA was extracted from 100 ? of frozen tissue powder using the RNeasy Plant Mini Kit (#74903, Qiagen, Venlo, Netherlands) according to manufacturers instructions. The extracted RNA was checked for quality and quantity on an automated electrophoresis-system (Experion, #701-7000, Bio-Rad, Hercules, CA, US). Sequencing was performed on an Illumina HiSeq2000 machine using 8x multiplexing, theoretically generating 22 M reads per sample by an external sequencing-provider ?ATC?(Konstanz, Germany). Each sample represents one experimental condition (pathogen/mock; time points; genotype) and comprises pools of 12 treated wheat heads. Each experimental condition has been replicated 3x. cDNA was sent to a service provider (GATC konstanz germany) who have performed the library construction following the Illumina TruSeq RNA sample preparation guide (version 2, http://support.illumina.com/sequencing/sequencing_kits/truseq_rna_sample_prep_kit_v2/documentation.ilmn)

characteristic: description

text: anthesis

characteristic: developmental stage

text: mock inoculation

text: Triticum aestivum

text: Triticum aestivum

text: spikelets (only using palea, lemma and rachis)

characteristic: organism part

text: Triticum aestivum

text: frozen specimen


characteristic: ENA-CHECKLIST

characteristic: ENA-LAST-UPDATE

text: public

text: ArrayExpress

text: human

text: adult

characteristic: individual

text: Homo sapiens

text: Homo sapiens

text: lymph node

text: Homo sapiens

text: frozen specimen

characteristic: specimen with known storage state

characteristic: title


characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: E-MTAB-1104_furthernewsamples:tc152038_spleen

tag: Namespace:Cancer Research UK, Cambridge Research Institute, Robinson Way, Cambridge, UK

text: 2 to 6 month

characteristic: age

text: ArrayExpress

text: house mouse

text: Protocols: doi:10.1016/j.ymeth.2009.03.001; Shortly, liver material was crosslinked in 1% formaldehyde for 20 minutes followed by a 10 minute incubation in 500 mM glycine buffer to neutralize the formaldehyde. Samples were rinsed with PBS and frozen until use. Human material was obtained from Addenbrooke's Hospital, Cambridge licence (08/H0308/117) and the Liver Tissue Distribution Program at the University of Pittsburgh (NIDDK Contract # N01-DK-9-2310). Formaldehyde-crosslinked/flash frozen tissue was stored at -80 C at the CRI. Tc1 mice (annotated as Tc1_with_hschr21) were generated as described in (O'Doherty et al., 2005). Mice were initially obtained from Victor Tybulewic and Elizabeth Fisher and subsequently housed and bred within the Biological Resources Unit at CRI. Tc0 mice (annotated as Tc1_without_hschr21) are Tc1 sibling mice (ie the same genetic background) that have not inherited a copy of HsChr21.

text: adult

characteristic: genotype

text: Mus musculus

characteristic: organism

text: Mus musculus

text: spleen

text: Mus musculus

text: male

characteristic: sex


characteristic: ENA-FIRST-PUBLIC

text: SRA-Webin

characteristic: ENA-SUBMISSION-TOOL

text: ISB-USA

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: baker's yeast

characteristic: common name

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

text: RAD-seq reduced-genome sequencing of yeast strain for phylogenetic analysis


E-MTAB-1712:SW1015 sample

characteristic: ENA-LAST-UPDATE

text: SLU Alnarp

text: public

text: E-MTAB-1712:SW1015 sample

tag: Namespace:SLU Alnarp

text: ArrayExpress

characteristic: broker name

text: potato

characteristic: cultivar

text: Protocols: Leaves from 4 week-old plants were harvested 24 hours after whole-plant infection with Phytopthora infestans RNA was isolated by RNeasy Plant Mini Kit (Qiagen) Beads with oligo(dT) were used to isolate poly(A) mRNA. Fragmentation buffer was added for interrupting mRNA to short fragments. Taking these short fragments as templates, Random hexamerprimer were used to synthesize the first-strand cDNA. The second-strand cDNA was synthesized using buffer, dNTPs, RNase H and DNA polymerase I, respectively. Short fragments were purified with QiaQuick PCR extraction kit and resolved with EB buffer for end reparation and adding poly(A). After that, the short fragments were connected with sequencing adaptors. And, for amplification with PCR, we selected suitable fragments, as templates, with respect to the result of agarose gel electrophoresis.

characteristic: description

text: fully expanded leaves

characteristic: developmental stage

text: Phytopthora infestans

characteristic: infect

text: Solanum tuberosum

text: Solanum tuberosum

text: leaf

characteristic: organism part

text: Solanum tuberosum

text: frozen specimen

text: SW1015 sample


text: Danio rerio

characteristic: ArrayExpress-Species

characteristic: External Id

text: SC

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: CH73_370K12-sc-2013-07-05T13:37:49Z-1660411

text: zebrafish

text: Danio rerio

text: Danio rerio


text: Danio rerio

characteristic: ENA-FIRST-PUBLIC

text: SC

text: public

text: zFOS_553C10-sc-2013-07-05T13:36:39Z-1660334

text: zebrafish

text: Danio rerio

characteristic: organism

text: Danio rerio


text: Danio rerio

text: SC

text: public

characteristic: INSDC status

characteristic: SRA accession

text: zFOS_857B4-sc-2013-07-05T13:36:54Z-1660350

text: zebrafish

text: Danio rerio

text: Danio rerio


text: Danio rerio

text: SC

text: public

text: CH1073_203M5-sc-2013-07-05T13:37:17Z-1660375

characteristic: Submitter Id

text: zebrafish

characteristic: common name

text: Danio rerio

text: Danio rerio


text: Danio rerio

characteristic: ENA-LAST-UPDATE

text: SC

text: public

text: CH1073_835H3-sc-2013-07-05T13:37:14Z-1660372

text: zebrafish

text: Danio rerio

text: Danio rerio


text: adult

characteristic: ArrayExpress-DevelopmentalStage

text: female

characteristic: ArrayExpress-Sex

text: Dracunculus medinensis

characteristic: ENA-CHECKLIST

text: SC

text: public

text: Dracunculus_medinensis-sc-2013-07-15T15:11:26Z-1668001

text: Guinea worm

text: Dracunculus medinensis

text: section of adult female worm

characteristic: sample description

text: Dracunculus medinensis


text: Mus Musculus

text: SC

text: public

text: mES_lif_s1_cell3-sc-2013-07-11T08:56:23Z-1661100

text: house mouse

text: Mus musculus

text: mRNA-seq Nextera library

text: Mus musculus


text: Mus Musculus

text: SC

text: public

text: mES_lif_s1_cell17-sc-2013-07-11T08:56:38Z-1661114

text: house mouse

text: Mus musculus

text: mRNA-seq Nextera library

text: Mus musculus


text: Danio rerio

text: SC

text: public

text: CH1073_325P11-sc-2013-07-05T13:38:41Z-1660471

text: zebrafish

text: Danio rerio

text: Danio rerio


text: Mus Musculus

text: SC

text: public

text: mES_lif_s1_cell48-sc-2013-07-11T08:57:07Z-1661145

text: house mouse

text: Mus musculus

text: mRNA-seq Nextera library

text: Mus musculus


text: University College London

text: public

text: ArrayExpress

characteristic: broker name

text: HEKn

characteristic: cell line

text: keratinocyte

characteristic: cell type

text: human

text: Protocols: Neonatal primary human epidermal keratinocytes (HEKn, Life technologies, Paisley, UK) were cultured on mouse collagen IV (0.67ug/cm2 BD Biosciences, Oxford, UK) coated surfaces in keratinocyte defined media containing epithelial growth factor (KDM and EpiLife, Life technologies). Differentiation was induced by shifting the cells to a high calcium media containing [1.2mM] Calcium Chloride. Viral infections for transcriptome experiments were carried out using VZV pOka cultured and used at less than 20 passages. Infected cell preparations were first treated with Mitomycin C (0.05mg/ml for 3hrs) prior to freezing and subsequently titered on Mewo cells. Cell-free VZV was generated by a rapid freeze (liquid N2) and thaw (37C), followed by removal of cellular debris by low speed centrifugation. For UV inactivated VZV, cell-free VZV supernatants were treated for 20 min at 150,000J/Cm2 using a Stratalinker UV Crosslinker (Stratagene). 1x105 HEKn cells per well of a 6 well dish were inoculated with 3x104 infectious units of virus. All VZV cultures were carried out at 34C, 5% CO2. This method involves several steps that are designed to convert total RNA into a library of template molecules suitable for high throughput DNA sequencing. The first step involves purifying the poly-A containing mRNA molecules using poly-T oligo-attached magnetic beads. Following purification, the mRNA is fragmented into small pieces using divalent cations under elevated temperature. Then, the cleaved mRNA fragments are copied into first strand cDNA using reverse transcriptase and a high concentration of random hexamer primers. Unique adaptors were ligated to the cDNA and 200bp fragments were size selected by agarose gel purification. Libraries were validated by using a DNA high sensitivity chip (Agilent, Cheshire, UK) and quantified by Qubit analysis using the Quant-iT dsDNA HS Assay (Life technologies).

characteristic: description

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens

text: fresh specimen

characteristic: specimen with known storage state

characteristic: title


characteristic: ENA-FIRST-PUBLIC

characteristic: External Id

text: Plant Pathology Group, Integrative Biology Zurich (IBZ), ETH Zurich

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: ArrayExpress

text: apple

text: Protocols: Plant material comprised young Malus x domestica (Borkh.) cv. Golden Delicious saplings grafted on M9T337 rootstock. Plants were kept in active growth with a 16h/8h (day/night) photoperiod and a minimum of 65.5 umol m-2 s-1 light intensity provided with white fluorescent lamps (Philips Master TL-D 36W/830) and fertilized once with Obstdunger 12:8:16:2:0.2 (N:P:K:Mg:B; OBA-Lanze, Hauert AG, Switzerland) one week prior the start of the experiment. Plants were grown under greenhouse condition at 20 +/- degrees C and 70% RH until 10 to 15 leaves stadium. Rape-seed oil (Maag AG, Switzerland) mixed with Alaxon 50 (Maag AG, Switzerland) and two weeks later Vertimec (Maag AG, Switzerland) have been used as chemical treatment before starting the experiment to keep plants free of pest-insects. For inoculation, conidia of Venturia inaequalis (Cooke) single spore isolate no. 1639 were used.Inoculation, with a spore suspension of 5 x 105 spores ml-1, was performed at 17 +/- 2 degrees C and >98% RH. . Half of the plants were challenged with the apple scab pathogen and half were mock inoculated. After the treatment (scab or mock inoculation), plants were grown at 17 +/- 2 degrees C and 70% RH until sampling. The first sets of samples have been collected 72 hours post inoculation (hpi). The second sets of samples have been collected at 96 hpi. Samples have been collected from leaf 1 (L1) and leaf 7 (L7) by removing the leaf tip (< 100 mg) of each leaf in three biological replicates for inoculated and not inoculated shoots, 12 samples for each time points (72 and 96 hpi), 24 in total. Total RNA was extracted using SV Total RNA Isolation System (Promega Corporation, USA) with column purification Complementary DNA (cDNA) libraries were constructed, starting from 1 ug of total RNA, at the Functional Genomic Center Zurich (FGCZ) following the TruSeq RNA Sample preparation protocol v. 2 instructions (Low Throughput protocol, Illumina, Inc.).

text: Leaf 1 (youngest leaf on the top of the shoot)

characteristic: developmental stage

text: mock inoculation

characteristic: infect

text: Malus domestica

text: Malus domestica

text: leaf

characteristic: organism part

text: Malus domestica

text: fresh specimen

text: 17 +/- 2 degree celsius

characteristic: temperature

text: 72 hour

characteristic: time post inoculation


text: Mus Musculus

characteristic: ArrayExpress-Species

characteristic: ENA-CHECKLIST

characteristic: ENA-LAST-UPDATE

text: SC

text: public

characteristic: INSDC status

characteristic: SRA accession

text: mES_lif_s1_cell52-sc-2013-07-11T08:57:12Z-1661149

characteristic: Submitter Id

text: house mouse

characteristic: common name

text: Mus musculus

characteristic: organism

text: mRNA-seq Nextera library

characteristic: sample description

text: Mus musculus


characteristic: ENA-FIRST-PUBLIC

characteristic: External Id

text: Science for Life Laboratory, Stockholm, Sweden

characteristic: INSDC center name

text: public

text: ArrayExpress

characteristic: broker name

text: human

text: Protocols: The use of human tissue samples was approved by the Uppsala Ethical Review Board (Reference #2011/473). Tissues samples, collected within the infrastructure of an established biobank, were embedded in Optimal Cutting Temperature (O.C.T.) compound and stored at -80C. A hematoxylin-eosin (HE) stained frozen section (4um) was prepared from each sample using a cryostat and the CryoJane Tape-Transfer System (Instrumedics, St. Louis, MO, USA). Each slide was examined by a pathologist to ensure proper tissue morphology. Three sections (10um) were cut from each frozen tissue block and collected into a tube for subsequent RNA extraction. The tissue was homogenized mechanically using a 3 mm steel grinding ball (VWR). Total RNA was extracted from cell lines and tissue samples using the RNeasy Mini Kit (Qiagen, Hilden, Germany) according to the manufacturers instructions. The extracted RNA samples were analyzed using either an Experion automated electrophoresis system (Bio-Rad Laboratories, Hercules, CA, USA) with the standard-sensitivity RNA chip or an Agilent 2100 Bioanalyzer system(Agilent Biotechnologies, Palo Alto, USA) with the RNA 6000 Nano Labchip Kit. Only samples of high-quality RNA (RNA Integrity Number 7.5) were used in the following mRNA sample preparation for sequencing. Illumina Truseq RNA v2

characteristic: description

text: adult

characteristic: individual

text: Homo sapiens

text: Homo sapiens

text: lymph node

text: Homo sapiens

text: frozen specimen

characteristic: specimen with known storage state

characteristic: title


text: European Molecular Biology Laboratory

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: ArrayExpress

characteristic: cell line

text: erythroleukemia

characteristic: cell type

text: human

text: Protocols: Cells were cultured in RPMI supplemented with 10% FBS. Trizol Illumina mRNA-seq library construction protocol

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens


characteristic: ENA-CHECKLIST

characteristic: ENA-LAST-UPDATE

text: Cancer Research UK, Cambridge Research Institute, Robinson Way, Cambridge, UK

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-1104:tc1_28.1_m9_AND_28.2_m10_liver

text: 2 to 6 month

characteristic: age

text: ArrayExpress

text: house mouse

text: Protocols: doi:10.1016/j.ymeth.2009.03.001; Shortly, liver material was crosslinked in 1% formaldehyde for 20 minutes followed by a 10 minute incubation in 500 mM glycine buffer to neutralize the formaldehyde. Samples were rinsed with PBS and frozen until use. Human material was obtained from Addenbrooke's Hospital, Cambridge licence (08/H0308/117) and the Liver Tissue Distribution Program at the University of Pittsburgh (NIDDK Contract # N01-DK-9-2310). Formaldehyde-crosslinked/flash frozen tissue was stored at -80 C at the CRI. Tc1 mice (annotated as Tc1_with_hschr21) were generated as described in (O'Doherty et al., 2005). Mice were initially obtained from Victor Tybulewic and Elizabeth Fisher and subsequently housed and bred within the Biological Resources Unit at CRI. Tc0 mice (annotated as Tc1_without_hschr21) are Tc1 sibling mice (ie the same genetic background) that have not inherited a copy of HsChr21.

text: adult

characteristic: developmental stage

characteristic: genotype

text: Mus musculus

text: Mus musculus

text: liver

characteristic: organism part

text: Mus musculus

text: male

characteristic: sex


text: cultured human neurons

characteristic: ArrayExpress-CellType

text: MeCP2 overexpression

characteristic: ArrayExpress-Genotype

text: Brain

characteristic: ArrayExpress-OrganismPart

text: female

characteristic: ArrayExpress-Sex

text: Homo sapiens

characteristic: ArrayExpress-Species

text: day 9

characteristic: ArrayExpress-TimePoint

characteristic: ENA-FIRST-PUBLIC

characteristic: External Id

text: SC

characteristic: INSDC center name

text: public

text: JCW_240613_24143_6-sc-2013-07-01T15:01:10Z-1656030

characteristic: Submitter Id

text: human

characteristic: common name

text: Homo sapiens

characteristic: organism

text: Total cDNA from human neurons

characteristic: sample description

text: Homo sapiens


text: Neurons

text: Adult

characteristic: ArrayExpress-DevelopmentalStage

text: MeCP2 GFP tagged

text: Chromotek GFP trap Agarose

characteristic: ArrayExpress-Immunoprecipitate

text: Brain

text: wildtype

characteristic: ArrayExpress-Phenotype

text: male

text: Mus musculus

text: Bl6 MeCP2 GFP

characteristic: ArrayExpress-StrainOrLine

characteristic: ENA-CHECKLIST

characteristic: ENA-LAST-UPDATE

text: SC

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: m_ChIP_GFP_high_N2-sc-2013-07-18T13:26:49Z-1669281

text: house mouse

text: Mus musculus

text: ChIP DNA from GFP high neurons (MeCP2 GFP from 15 BL 6 male)

text: Mus musculus

text: Bl6 MeCP2 GFP

characteristic: strain


characteristic: ENA-FIRST-PUBLIC

text: SRA-Webin

characteristic: ENA-SUBMISSION-TOOL

characteristic: External Id

text: ISB-USA

text: public

text: baker's yeast

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

text: RAD-seq reduced-genome sequencing of yeast strain for phylogenetic analysis

characteristic: title


text: Danio rerio

characteristic: ArrayExpress-Species

text: SC

characteristic: INSDC center name

text: public

text: CH1073_109I19-sc-2013-07-05T13:38:32Z-1660461

characteristic: Submitter Id

text: zebrafish

characteristic: common name

text: Danio rerio

characteristic: organism

text: Danio rerio


text: Plasmodium falciparum

text: SC

text: public

text: malaria parasite P. falciparum

text: Plasmodium falciparum

text: Plasmodium falciparum


text: public

text: ArrayExpress

characteristic: broker name

text: apple

characteristic: description

text: Leaf 7 (old leaf: seventh leaf position starting from the top of the shoot)

characteristic: developmental stage

text: inoculated with Venturia inaequalis

characteristic: infect

text: Malus domestica

text: Malus domestica

text: leaf

characteristic: organism part

text: Malus domestica

text: fresh specimen

characteristic: specimen with known storage state

text: 17 +/- 2 degree celsius

characteristic: temperature

text: 72 hour

characteristic: time post inoculation


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: Institut Pasteur de Montevideo

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: ArrayExpress

text: mesenchymal stem cell

characteristic: cell type

text: human

text: Protocols: Stem cells were obtained from adipose tissue from obese human donors ( two males and one female, ages: 41, 52, 23) . All samples were isolated, collected after informed consent had been obtained. hASCs were isolated, cultured and characterized as following. Briefly, 100 ml of adipose tissue was washed with sterile phosphate-buffered saline (PBS) (Gibco Invitrogen). A one-step digestion by 1 mg/ml collagenase type I (Invitrogen) was performed for 30 mins at 37 degrees C during permanent shaking and was followed by filtration through first a 100- and then 40-um mesh filter (BD FALCON, BD Biosciences Discovery Labware, Bedford, MA, USA).

text: undifferentiated

characteristic: individual

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens

text: 3 day

characteristic: time

text: no adipocyte differentiation induction

characteristic: treatment


text: Danio rerio

characteristic: ArrayExpress-Species

characteristic: External Id

text: SC

characteristic: INSDC center name

text: public

text: CH1073_218I20-sc-2013-07-05T13:38:54Z-1660486

characteristic: Submitter Id

text: zebrafish

characteristic: common name

text: Danio rerio

characteristic: organism

text: Danio rerio


text: Mus Musculus

characteristic: ENA-CHECKLIST

text: SC

text: public

text: mES_lif_s1_cell74-sc-2013-07-11T08:57:33Z-1661171

text: house mouse

text: Mus musculus

text: mRNA-seq Nextera library

characteristic: sample description

text: Mus musculus


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: Institute for Biotechnology in Plant Production, IFA-Tulln, University of Natural Resources and Life Sciences, A-3430 Tulln, Austria

text: public

text: ArrayExpress

characteristic: broker name

text: bread wheat

characteristic: cultivar

text: Protocols: We utilized four early isogenic lines (NILs) previously generated from a cross of the resistant spring wheat line CM-82036 and Remus, a susceptible Austrian spring wheat cultivar. The NILs have Remus as the recurrent parent (5 backcrosses) and contain the resistance alleles from CM-82036 of both Fhb1 and Qfhs.ifa-5A (NIL1), or either Fhb1 (NIL2) or Qfhs.ifa-5A (NIL3) or none (NIL4). Additionally, CM-82036 was used in the subsequent experiments. In preparation for fungal innoculation, F. graminearum spores required for inoculation were produced on defined SNA medium under UV-light at 25 degrees C. After two weeks conidia were harvested and diluted to 50.000 conidia/mL in water. Aliquots were stored at -80 degrees C. Single seeds were sown and put at 4 C for one week. After vernalization, seeds were germinated at 20 degrees C for two weeks and each two plants were potted into 3 L pots. The plants were initially kept in a 18 degrees C/12 degrees C day/night cycle (12 hours light), which was gradually changed until anthesis to 21 degrees C/18 degrees C at 55 % relative humidity (16 hours light). At least 12 heads per experimental condition (three replications, F. graminearum/mock treatment, two time points) were subjected to further experiments. At anthesis, the plants were inoculated either with a F. graminearum spore suspensions or water: 10 ? of the respective inoculum was pipetted into one floret between palea and lemma, directly onto the generative part. Per head two outer floret of six spikelets in three central rows were treated in this way, while the central florets were not inoculated (in total 12 florets). The inoculated heads were moistened with distilled water and bagged into a plastic bag for 24 hours to provide favourable conditions for disease development. Tissues comprising only the initially inoculated spikelets were sampled 30 or 50 hours after inoculation (hai) and from these the generative parts (stigma, anthers, ovary) as well as the glumes and the central floret were discarded. Only palea, lemma and rachis were frozen immediately in liquid nitrogen and stored at -80 degrees C until use. Single seeds were sown and put at 4 degrees C for one week. After vernalization, seeds were germinated at 20 degrees C for two weeks and each two plants were potted into 3 L pots. The plants were initially kept in a 18 degrees C/12 degrees C day/night cycle (12 hours light), which was gradually changed until anthesis to 21 degrees C/18 degrees C at 55 % relative humidity (16 hours light). At least 12 heads per experimental condition (three replications, F. graminearum/mock treatment, two time points) were subjected to further experiments. At anthesis, the plants were inoculated either with a F. graminearum spore suspensions or water: 10 ? of the respective inoculum was pipetted into one floret between palea and lemma, directly onto the generative part. Per head two outer floret of six spikelets in three central rows were treated in this way, while the central florets were not inoculated (in total 12 florets). The inoculated heads were moistened with distilled water and bagged into a plastic bag for 24 hours to provide favourable conditions for disease development. Tissues comprising only the initially inoculated spikelets were sampled 30 or 50 hours after inoculation (hai) and from these the generative parts (stigma, anthers, ovary) as well as the glumes and the central floret were discarded. Only palea, lemma and rachis were frozen immediately in liquid nitrogen and stored at -80 degrees C until use. To eliminate RNases, metal jars with inherent metal spheres for Retsch-mill (MM 301, Haan, Germany) were sterilized at 180 degrees C for 3 h and then stored at -80 degrees C. All tissue belonging to one sample was pooled in one precooled jar and clamped in Retsch-mill. Grinding was performed for 30 s at full speed to obtain a fine tissue powder and immediately put back at -80 degrees C. Total-RNA was extracted from 100 ? of frozen tissue powder using the RNeasy Plant Mini Kit (#74903, Qiagen, Venlo, Netherlands) according to manufacturers instructions. The extracted RNA was checked for quality and quantity on an automated electrophoresis-system (Experion, #701-7000, Bio-Rad, Hercules, CA, US). Sequencing was performed on an Illumina HiSeq2000 machine using 8x multiplexing, theoretically generating 22 M reads per sample by an external sequencing-provider ?ATC?(Konstanz, Germany). Each sample represents one experimental condition (pathogen/mock; time points; genotype) and comprises pools of 12 treated wheat heads. Each experimental condition has been replicated 3x. cDNA was sent to a service provider (GATC konstanz germany) who have performed the library construction following the Illumina TruSeq RNA sample preparation guide (version 2, http://support.illumina.com/sequencing/sequencing_kits/truseq_rna_sample_prep_kit_v2/documentation.ilmn)

characteristic: description

text: anthesis

characteristic: developmental stage

text: Fusarium graminearum inoculation

characteristic: infect

text: Triticum aestivum

text: Triticum aestivum

text: spikelets (only using palea, lemma and rachis)

characteristic: organism part

text: Triticum aestivum

text: frozen specimen

characteristic: specimen with known storage state

characteristic: title


text: Mus Musculus

characteristic: ArrayExpress-Species

characteristic: External Id

text: SC

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: mES_lif_s1_cell87-sc-2013-07-11T08:57:44Z-1661184

text: house mouse

text: Mus musculus

text: mRNA-seq Nextera library

text: Mus musculus


characteristic: ENA-CHECKLIST

text: Science for Life Laboratory, Stockholm, Sweden

characteristic: INSDC center name

text: public

characteristic: Submitter Id

text: ArrayExpress

text: human

characteristic: common name

text: Protocols: The use of human tissue samples was approved by the Uppsala Ethical Review Board (Reference #2011/473). Tissues samples, collected within the infrastructure of an established biobank, were embedded in Optimal Cutting Temperature (O.C.T.) compound and stored at -80C. A hematoxylin-eosin (HE) stained frozen section (4um) was prepared from each sample using a cryostat and the CryoJane Tape-Transfer System (Instrumedics, St. Louis, MO, USA). Each slide was examined by a pathologist to ensure proper tissue morphology. Three sections (10um) were cut from each frozen tissue block and collected into a tube for subsequent RNA extraction. The tissue was homogenized mechanically using a 3 mm steel grinding ball (VWR). Total RNA was extracted from cell lines and tissue samples using the RNeasy Mini Kit (Qiagen, Hilden, Germany) according to the manufacturers instructions. The extracted RNA samples were analyzed using either an Experion automated electrophoresis system (Bio-Rad Laboratories, Hercules, CA, USA) with the standard-sensitivity RNA chip or an Agilent 2100 Bioanalyzer system(Agilent Biotechnologies, Palo Alto, USA) with the RNA 6000 Nano Labchip Kit. Only samples of high-quality RNA (RNA Integrity Number 7.5) were used in the following mRNA sample preparation for sequencing. Illumina Truseq RNA v2

text: adult

characteristic: individual

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: salivary gland

text: Homo sapiens

text: frozen specimen


text: Mus Musculus

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: SC

text: public

text: mES_lif_s1_cell22-sc-2013-07-11T08:56:42Z-1661119

text: house mouse

text: Mus musculus

text: mRNA-seq Nextera library

characteristic: sample description

text: Mus musculus


text: Mus Musculus

text: SC

text: public

text: mES_lif_s1_cell25-sc-2013-07-11T08:56:45Z-1661122

text: house mouse

text: Mus musculus

text: mRNA-seq Nextera library

text: Mus musculus


text: public

tag: Namespace:Max Planck Institute, Department of Genetics

text: ArrayExpress

characteristic: broker name

text: house mouse

text: Protocols: We were feeding mice tuber and meat which was then either cooked or raw. In addition the cooked food was then given either restricted to a certain amount of calories or calorie un-restricted. For the library preparation we created cDNA libraries based on an Illumina library preparation protocol.

characteristic: description

text: adult

characteristic: developmental stage

text: domestic animal house

characteristic: environmental history

text: Mus musculus

text: Mus musculus

text: liver

characteristic: organism part

text: Mus musculus

text: fresh specimen

characteristic: specimen with known storage state

characteristic: strain


characteristic: External Id

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: ArrayExpress

text: bread wheat

characteristic: cultivar

text: anthesis

text: mock inoculation

characteristic: infect

text: Triticum aestivum

text: Triticum aestivum

text: Triticum aestivum

text: frozen specimen

characteristic: title


text: Danio rerio

characteristic: ArrayExpress-Species

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: SC

characteristic: INSDC center name

text: public

text: CH1073_266I8-sc-2013-07-05T13:37:04Z-1660360

characteristic: Submitter Id

text: zebrafish

characteristic: common name

text: Danio rerio

characteristic: organism

text: Danio rerio


text: Mus Musculus

characteristic: ENA-CHECKLIST

text: SC

text: public

text: mES_lif_s1_cell47-sc-2013-07-11T08:57:06Z-1661144

text: house mouse

text: Mus musculus

text: mRNA-seq Nextera library

characteristic: sample description

text: Mus musculus


text: Mouse

characteristic: External Id

text: SC

text: public

text: SC_HUWE5569749-sc-2013-07-16T08:26:47Z-1667127

text: house mouse

text: Mus musculus

text: Mus musculus


text: SRA-Webin

characteristic: ENA-SUBMISSION-TOOL

text: ISB-USA

characteristic: INSDC first public

text: public

text: baker's yeast

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

text: RAD-seq reduced-genome sequencing of yeast strain for phylogenetic analysis


text: Danio rerio

text: SC

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: CH73_332E21-sc-2013-07-05T13:38:55Z-1660488

text: zebrafish

text: Danio rerio

text: Danio rerio


text: Plasmodium falciparum

text: SC

text: public

characteristic: SRA accession

text: malaria parasite P. falciparum

text: Plasmodium falciparum

text: Plasmodium falciparum


text: Mus musculus

text: SC

text: public

text: house mouse

text: Mus musculus

text: Mus musculus


text: public

text: ArrayExpress

characteristic: broker name

text: human

characteristic: description

text: adult

characteristic: developmental stage

characteristic: individual

text: Homo sapiens

text: Homo sapiens

text: testis

characteristic: organism part

text: Homo sapiens

text: frozen specimen

characteristic: specimen with known storage state


text: Mouse

characteristic: ArrayExpress-Species

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: SC

characteristic: INSDC center name

text: public

text: SC_HUWE5569745-sc-2013-07-16T08:26:42Z-1667123

characteristic: Submitter Id

text: house mouse

text: Mus musculus

text: Mus musculus


text: Danio rerio

characteristic: External Id

text: SC

text: public

text: CH73_365E14-sc-2013-07-05T13:38:51Z-1660482

text: zebrafish

characteristic: common name

text: Danio rerio

characteristic: organism

text: Danio rerio


text: Max Planck Institute, Department of Genetics

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: ArrayExpress

text: house mouse

text: adult

text: domestic animal house

characteristic: environmental history

text: Mus musculus

text: Mus musculus

text: liver

text: Mus musculus

text: fresh specimen

characteristic: strain

characteristic: title


text: Mus Musculus

characteristic: ENA-CHECKLIST

text: SC

text: public

characteristic: INSDC status

characteristic: SRA accession

text: mES_lif_s1_cell42-sc-2013-07-11T08:57:01Z-1661139

text: house mouse

text: Mus musculus

text: mRNA-seq Nextera library

characteristic: sample description

text: Mus musculus


text: Danio rerio

characteristic: ArrayExpress-Species

text: SC

text: public

text: CH1073_200C7-sc-2013-07-05T13:38:26Z-1660454

text: zebrafish

text: Danio rerio

text: Danio rerio


characteristic: ENA-FIRST-PUBLIC

text: public

text: ArrayExpress

characteristic: broker name

text: human

characteristic: description

text: adult

characteristic: developmental stage

characteristic: individual

text: Homo sapiens

text: Homo sapiens

text: appendix

characteristic: organism part

text: Homo sapiens

text: frozen specimen

characteristic: specimen with known storage state


characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC first public

text: public

characteristic: Submitter Id

text: ArrayExpress

text: human

characteristic: common name

text: adult

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: pancreas

text: Homo sapiens

text: frozen specimen


text: Mus Musculus

characteristic: ENA-CHECKLIST

text: SC

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: mES_lif_s1_cell88-sc-2013-07-11T08:57:45Z-1661185

text: house mouse

text: Mus musculus

text: mRNA-seq Nextera library

text: Mus musculus


characteristic: ENA-FIRST-PUBLIC

text: Institute for Biotechnology in Plant Production, IFA-Tulln, University of Natural Resources and Life Sciences, A-3430 Tulln, Austria

text: public

text: ArrayExpress

characteristic: broker name

text: bread wheat

characteristic: cultivar

text: Protocols: We utilized four early isogenic lines (NILs) previously generated from a cross of the resistant spring wheat line CM-82036 and Remus, a susceptible Austrian spring wheat cultivar. The NILs have Remus as the recurrent parent (5 backcrosses) and contain the resistance alleles from CM-82036 of both Fhb1 and Qfhs.ifa-5A (NIL1), or either Fhb1 (NIL2) or Qfhs.ifa-5A (NIL3) or none (NIL4). Additionally, CM-82036 was used in the subsequent experiments. In preparation for fungal innoculation, F. graminearum spores required for inoculation were produced on defined SNA medium under UV-light at 25 degrees C. After two weeks conidia were harvested and diluted to 50.000 conidia/mL in water. Aliquots were stored at -80 degrees C. Single seeds were sown and put at 4 C for one week. After vernalization, seeds were germinated at 20 degrees C for two weeks and each two plants were potted into 3 L pots. The plants were initially kept in a 18 degrees C/12 degrees C day/night cycle (12 hours light), which was gradually changed until anthesis to 21 degrees C/18 degrees C at 55 % relative humidity (16 hours light). At least 12 heads per experimental condition (three replications, F. graminearum/mock treatment, two time points) were subjected to further experiments. At anthesis, the plants were inoculated either with a F. graminearum spore suspensions or water: 10 ? of the respective inoculum was pipetted into one floret between palea and lemma, directly onto the generative part. Per head two outer floret of six spikelets in three central rows were treated in this way, while the central florets were not inoculated (in total 12 florets). The inoculated heads were moistened with distilled water and bagged into a plastic bag for 24 hours to provide favourable conditions for disease development. Tissues comprising only the initially inoculated spikelets were sampled 30 or 50 hours after inoculation (hai) and from these the generative parts (stigma, anthers, ovary) as well as the glumes and the central floret were discarded. Only palea, lemma and rachis were frozen immediately in liquid nitrogen and stored at -80 degrees C until use. Single seeds were sown and put at 4 degrees C for one week. After vernalization, seeds were germinated at 20 degrees C for two weeks and each two plants were potted into 3 L pots. The plants were initially kept in a 18 degrees C/12 degrees C day/night cycle (12 hours light), which was gradually changed until anthesis to 21 degrees C/18 degrees C at 55 % relative humidity (16 hours light). At least 12 heads per experimental condition (three replications, F. graminearum/mock treatment, two time points) were subjected to further experiments. At anthesis, the plants were inoculated either with a F. graminearum spore suspensions or water: 10 ? of the respective inoculum was pipetted into one floret between palea and lemma, directly onto the generative part. Per head two outer floret of six spikelets in three central rows were treated in this way, while the central florets were not inoculated (in total 12 florets). The inoculated heads were moistened with distilled water and bagged into a plastic bag for 24 hours to provide favourable conditions for disease development. Tissues comprising only the initially inoculated spikelets were sampled 30 or 50 hours after inoculation (hai) and from these the generative parts (stigma, anthers, ovary) as well as the glumes and the central floret were discarded. Only palea, lemma and rachis were frozen immediately in liquid nitrogen and stored at -80 degrees C until use. To eliminate RNases, metal jars with inherent metal spheres for Retsch-mill (MM 301, Haan, Germany) were sterilized at 180 degrees C for 3 h and then stored at -80 degrees C. All tissue belonging to one sample was pooled in one precooled jar and clamped in Retsch-mill. Grinding was performed for 30 s at full speed to obtain a fine tissue powder and immediately put back at -80 degrees C. Total-RNA was extracted from 100 ? of frozen tissue powder using the RNeasy Plant Mini Kit (#74903, Qiagen, Venlo, Netherlands) according to manufacturers instructions. The extracted RNA was checked for quality and quantity on an automated electrophoresis-system (Experion, #701-7000, Bio-Rad, Hercules, CA, US). Sequencing was performed on an Illumina HiSeq2000 machine using 8x multiplexing, theoretically generating 22 M reads per sample by an external sequencing-provider ?ATC?(Konstanz, Germany). Each sample represents one experimental condition (pathogen/mock; time points; genotype) and comprises pools of 12 treated wheat heads. Each experimental condition has been replicated 3x. cDNA was sent to a service provider (GATC konstanz germany) who have performed the library construction following the Illumina TruSeq RNA sample preparation guide (version 2, http://support.illumina.com/sequencing/sequencing_kits/truseq_rna_sample_prep_kit_v2/documentation.ilmn)

text: anthesis

text: mock inoculation

characteristic: infect

text: Triticum aestivum

text: Triticum aestivum

text: spikelets (only using palea, lemma and rachis)

text: Triticum aestivum

text: frozen specimen

characteristic: title


text: Danio rerio

characteristic: ArrayExpress-Species

text: SC

text: public

text: zFOS_2054G6-sc-2013-07-05T13:37:00Z-1660357

text: zebrafish

text: Danio rerio

text: Danio rerio


text: Danio rerio

characteristic: ENA-LAST-UPDATE

text: SC

text: public

text: CH1073_684N20-sc-2013-07-05T13:37:13Z-1660371

text: zebrafish

text: Danio rerio

text: Danio rerio


text: Mouse

characteristic: External Id

text: SC

text: public

text: SC_HUWE5569734-sc-2013-07-16T08:26:30Z-1667112

text: house mouse

text: Mus musculus

text: Mus musculus


text: SRA-Webin

characteristic: ENA-SUBMISSION-TOOL

text: ISB-USA

characteristic: INSDC center name

text: public

text: baker's yeast

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae


text: Science for Life Laboratory, Stockholm, Sweden

characteristic: INSDC first public

text: public

characteristic: Submitter Id

text: ArrayExpress

text: human

text: Protocols: The use of human tissue samples was approved by the Uppsala Ethical Review Board (Reference #2011/473). Tissues samples, collected within the infrastructure of an established biobank, were embedded in Optimal Cutting Temperature (O.C.T.) compound and stored at -80C. A hematoxylin-eosin (HE) stained frozen section (4um) was prepared from each sample using a cryostat and the CryoJane Tape-Transfer System (Instrumedics, St. Louis, MO, USA). Each slide was examined by a pathologist to ensure proper tissue morphology. Three sections (10um) were cut from each frozen tissue block and collected into a tube for subsequent RNA extraction. The tissue was homogenized mechanically using a 3 mm steel grinding ball (VWR). Total RNA was extracted from cell lines and tissue samples using the RNeasy Mini Kit (Qiagen, Hilden, Germany) according to the manufacturers instructions. The extracted RNA samples were analyzed using either an Experion automated electrophoresis system (Bio-Rad Laboratories, Hercules, CA, USA) with the standard-sensitivity RNA chip or an Agilent 2100 Bioanalyzer system(Agilent Biotechnologies, Palo Alto, USA) with the RNA 6000 Nano Labchip Kit. Only samples of high-quality RNA (RNA Integrity Number 7.5) were used in the following mRNA sample preparation for sequencing. Illumina Truseq RNA v2

characteristic: description

text: adult

characteristic: developmental stage

characteristic: individual

text: Homo sapiens

text: Homo sapiens

text: heart

characteristic: organism part

text: Homo sapiens

text: frozen specimen

characteristic: specimen with known storage state


text: Danio rerio

characteristic: ENA-FIRST-PUBLIC

text: SC

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: CH1073_223O18-sc-2013-07-05T13:37:45Z-1660407

text: zebrafish

characteristic: common name

text: Danio rerio

characteristic: organism

text: Danio rerio


text: Mus musculus

characteristic: ArrayExpress-Species

characteristic: ENA-CHECKLIST

characteristic: ENA-LAST-UPDATE

text: SC

text: public

text: house mouse

text: Mus musculus

text: Mus musculus


text: Plasmodium falciparum

characteristic: External Id

text: SC

characteristic: INSDC center name

text: public

text: malaria parasite P. falciparum

text: Plasmodium falciparum

text: Plasmodium falciparum


characteristic: INSDC first public

text: public

characteristic: Submitter Id

text: ArrayExpress

characteristic: broker name

text: human

text: adult

text: Homo sapiens

text: Homo sapiens

text: salivary gland

text: Homo sapiens

text: frozen specimen

characteristic: title


E-MTAB-1712:Sarpo Mira sample

text: SLU Alnarp

text: public

text: E-MTAB-1712:Sarpo Mira sample

text: ArrayExpress

text: potato

text: Sarpo Mira

characteristic: cultivar

text: Protocols: Leaves from 4 week-old plants were harvested 24 hours after whole-plant infection with Phytopthora infestans RNA was isolated by RNeasy Plant Mini Kit (Qiagen) Beads with oligo(dT) were used to isolate poly(A) mRNA. Fragmentation buffer was added for interrupting mRNA to short fragments. Taking these short fragments as templates, Random hexamerprimer were used to synthesize the first-strand cDNA. The second-strand cDNA was synthesized using buffer, dNTPs, RNase H and DNA polymerase I, respectively. Short fragments were purified with QiaQuick PCR extraction kit and resolved with EB buffer for end reparation and adding poly(A). After that, the short fragments were connected with sequencing adaptors. And, for amplification with PCR, we selected suitable fragments, as templates, with respect to the result of agarose gel electrophoresis.

characteristic: description

text: fully expanded leaves

characteristic: developmental stage

text: Phytopthora infestans

characteristic: infect

text: Solanum tuberosum

text: Solanum tuberosum

text: leaf

characteristic: organism part

text: Solanum tuberosum

text: frozen specimen

text: Sarpo Mira sample


text: Danio rerio

characteristic: ENA-FIRST-PUBLIC

text: SC

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: CH1073_651L5-sc-2013-07-05T13:36:44Z-1660339

text: zebrafish

text: Danio rerio

text: Danio rerio


text: public

text: ArrayExpress

text: house mouse

characteristic: common name

text: Protocols: We were feeding mice tuber and meat which was then either cooked or raw. In addition the cooked food was then given either restricted to a certain amount of calories or calorie un-restricted. For the library preparation we created cDNA libraries based on an Illumina library preparation protocol.

text: adult

text: domestic animal house

characteristic: environmental history

text: Mus musculus

characteristic: organism

text: Mus musculus

text: liver

text: Mus musculus

text: fresh specimen

characteristic: specimen with known storage state

characteristic: strain


characteristic: ENA-CHECKLIST

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Plant Pathology Group, Integrative Biology Zurich (IBZ), ETH Zurich

characteristic: INSDC center name

characteristic: INSDC first public

text: public

characteristic: Submitter Id

text: ArrayExpress

text: apple

text: Protocols: Plant material comprised young Malus x domestica (Borkh.) cv. Golden Delicious saplings grafted on M9T337 rootstock. Plants were kept in active growth with a 16h/8h (day/night) photoperiod and a minimum of 65.5 umol m-2 s-1 light intensity provided with white fluorescent lamps (Philips Master TL-D 36W/830) and fertilized once with Obstdunger 12:8:16:2:0.2 (N:P:K:Mg:B; OBA-Lanze, Hauert AG, Switzerland) one week prior the start of the experiment. Plants were grown under greenhouse condition at 20 +/- degrees C and 70% RH until 10 to 15 leaves stadium. Rape-seed oil (Maag AG, Switzerland) mixed with Alaxon 50 (Maag AG, Switzerland) and two weeks later Vertimec (Maag AG, Switzerland) have been used as chemical treatment before starting the experiment to keep plants free of pest-insects. For inoculation, conidia of Venturia inaequalis (Cooke) single spore isolate no. 1639 were used.Inoculation, with a spore suspension of 5 x 105 spores ml-1, was performed at 17 +/- 2 degrees C and >98% RH. . Half of the plants were challenged with the apple scab pathogen and half were mock inoculated. After the treatment (scab or mock inoculation), plants were grown at 17 +/- 2 degrees C and 70% RH until sampling. The first sets of samples have been collected 72 hours post inoculation (hpi). The second sets of samples have been collected at 96 hpi. Samples have been collected from leaf 1 (L1) and leaf 7 (L7) by removing the leaf tip (< 100 mg) of each leaf in three biological replicates for inoculated and not inoculated shoots, 12 samples for each time points (72 and 96 hpi), 24 in total. Total RNA was extracted using SV Total RNA Isolation System (Promega Corporation, USA) with column purification Complementary DNA (cDNA) libraries were constructed, starting from 1 ug of total RNA, at the Functional Genomic Center Zurich (FGCZ) following the TruSeq RNA Sample preparation protocol v. 2 instructions (Low Throughput protocol, Illumina, Inc.).

text: Leaf 1 (youngest leaf on the top of the shoot)

text: inoculated with Venturia inaequalis

text: Malus domestica

text: Malus domestica

text: leaf

text: Malus domestica

text: fresh specimen

text: 17 +/- 2 degree celsius

characteristic: temperature

text: 72 hour

characteristic: time post inoculation


text: Danio rerio

characteristic: ArrayExpress-Species

characteristic: ENA-FIRST-PUBLIC

text: SC

text: public

text: zFOS_379E6-sc-2013-07-05T13:36:14Z-1660310

text: zebrafish

text: Danio rerio

text: Danio rerio


text: Danio rerio

text: SC

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: zFOS_1462A6-sc-2013-07-05T13:36:45Z-1660341

text: zebrafish

text: Danio rerio

text: Danio rerio


text: European Molecular Biology Laboratory

text: public

characteristic: SRA accession

text: ArrayExpress

characteristic: broker name

text: fruit fly

characteristic: common name

text: Protocols: Isogenic (y1; cn bw1 sp1) embryos were cultured on standard Drosophila medium. Qiagen RNeasy Illumina mRNA-seq library construction protocol

characteristic: description

text: L3 larvae

characteristic: developmental stage

text: Drosophila melanogaster

text: Drosophila melanogaster

text: Drosophila melanogaster

text: y1; cn bw1 sp1

characteristic: title


text: Danio rerio

characteristic: ENA-LAST-UPDATE

text: SC

text: public

text: CH73_40J19-sc-2013-07-05T13:38:51Z-1660483

text: zebrafish

text: Danio rerio

characteristic: organism

text: Danio rerio


text: Danio rerio

characteristic: External Id

text: SC

characteristic: INSDC center name

text: public

text: CH1073_252J5-sc-2013-07-05T13:36:41Z-1660336

text: zebrafish

text: Danio rerio

text: Danio rerio


text: European Molecular Biology Laboratory

characteristic: INSDC first public

text: public

characteristic: Submitter Id

text: ArrayExpress

characteristic: cell line

text: hepatocyte

characteristic: cell type

text: human

text: Protocols: Cells were cultured in DMEM supplemented with 10% FBS and 1% penicillin/streptomycin. Qiagen RNeasy Illumina mRNA-seq library construction protocol

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens


text: Danio rerio

characteristic: ArrayExpress-Species

characteristic: ENA-FIRST-PUBLIC

text: SC

text: public

text: CH73_337O2-sc-2013-07-05T13:37:55Z-1660417

text: zebrafish

text: Danio rerio

text: Danio rerio


characteristic: ENA-CHECKLIST

text: SRA-Webin

characteristic: ENA-SUBMISSION-TOOL

text: ISB-USA

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: baker's yeast

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

text: RAD-seq reduced-genome sequencing of yeast strain for phylogenetic analysis


text: Danio rerio

text: SC

text: public

characteristic: SRA accession

text: CH73_333G9-sc-2013-07-05T13:39:05Z-1660496

text: zebrafish

characteristic: common name

text: Danio rerio

text: Danio rerio


text: Science for Life Laboratory, Stockholm, Sweden

text: public

text: ArrayExpress

characteristic: broker name

text: human

text: Protocols: The use of human tissue samples was approved by the Uppsala Ethical Review Board (Reference #2011/473). Tissues samples, collected within the infrastructure of an established biobank, were embedded in Optimal Cutting Temperature (O.C.T.) compound and stored at -80C. A hematoxylin-eosin (HE) stained frozen section (4um) was prepared from each sample using a cryostat and the CryoJane Tape-Transfer System (Instrumedics, St. Louis, MO, USA). Each slide was examined by a pathologist to ensure proper tissue morphology. Three sections (10um) were cut from each frozen tissue block and collected into a tube for subsequent RNA extraction. The tissue was homogenized mechanically using a 3 mm steel grinding ball (VWR). Total RNA was extracted from cell lines and tissue samples using the RNeasy Mini Kit (Qiagen, Hilden, Germany) according to the manufacturers instructions. The extracted RNA samples were analyzed using either an Experion automated electrophoresis system (Bio-Rad Laboratories, Hercules, CA, USA) with the standard-sensitivity RNA chip or an Agilent 2100 Bioanalyzer system(Agilent Biotechnologies, Palo Alto, USA) with the RNA 6000 Nano Labchip Kit. Only samples of high-quality RNA (RNA Integrity Number 7.5) were used in the following mRNA sample preparation for sequencing. Illumina Truseq RNA v2

characteristic: description

text: adult

characteristic: developmental stage

characteristic: individual

text: Homo sapiens

text: Homo sapiens

text: small intestine

characteristic: organism part

text: Homo sapiens

text: frozen specimen

characteristic: specimen with known storage state

characteristic: title


text: Danio rerio

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: SC

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: CH73_389K12-sc-2013-07-05T13:38:44Z-1660475

characteristic: Submitter Id

text: zebrafish

text: Danio rerio

characteristic: organism

text: Danio rerio


text: Danio rerio

characteristic: ArrayExpress-Species

characteristic: ENA-FIRST-PUBLIC

text: SC

characteristic: INSDC last update

text: public

text: CH73_320O3-sc-2013-07-05T13:38:28Z-1660456

text: zebrafish

text: Danio rerio

text: Danio rerio


text: Danio rerio

text: SC

text: public

characteristic: INSDC status

characteristic: SRA accession

text: CH73_353L3-sc-2013-07-05T13:38:59Z-1660489

text: zebrafish

characteristic: common name

text: Danio rerio

text: Danio rerio


characteristic: ENA-CHECKLIST

text: public

text: ArrayExpress

characteristic: broker name

text: human

characteristic: description

text: adult

characteristic: developmental stage

text: Homo sapiens

text: Homo sapiens

text: colon

text: Homo sapiens

text: frozen specimen


text: Danio rerio

text: SC

text: public

text: CH1073_789L6-sc-2013-07-05T13:36:29Z-1660324

text: zebrafish

text: Danio rerio

text: Danio rerio


text: Mus Musculus

text: SC

text: public

text: mES_lif_s1_cell55-sc-2013-07-11T08:57:14Z-1661152

text: house mouse

text: Mus musculus

text: mRNA-seq Nextera library

characteristic: sample description

text: Mus musculus


text: Plasmodium falciparum

characteristic: ENA-LAST-UPDATE

text: SC

text: public

text: malaria parasite P. falciparum

text: Plasmodium falciparum

text: Plasmodium falciparum


text: Danio rerio

characteristic: External Id

text: SC

text: public

text: CH73_341M24-sc-2013-07-05T13:38:09Z-1660433

text: zebrafish

text: Danio rerio

text: Danio rerio


characteristic: INSDC center name

text: public

text: ArrayExpress

text: human

text: adult

characteristic: individual

text: Homo sapiens

text: Homo sapiens

text: lymph node

characteristic: organism part

text: Homo sapiens

text: frozen specimen

characteristic: specimen with known storage state

characteristic: title


E-MTAB-1754:XEN (XX)

characteristic: ENA-FIRST-PUBLIC

text: The Babraham Institute

characteristic: INSDC first public

text: public

text: E-MTAB-1754:XEN (XX)

tag: Namespace:The Babraham Institute

characteristic: Submitter Id

text: ArrayExpress

text: extraembryonic endoderm cell

characteristic: cell type

text: house mouse

text: Protocols: ES, TS, XEN, and EpiSC stem cell lines were cultured under standard conditions (see Supporting Information in the publication). Cell lines used were: ES, lines J1, E14, KH2, and PGK12.1 (a kind gift of Prof. N. Brockdorff, University of Oxford, U.K.); EpiSC, lines #5 and #9 (both a kind gift of Dr. P. Tesar, Case Western Reserve University, OH) and line PRG (a kind gift of Dr. P. Rugg-Gunn, The Babraham Institute, Cambridge, U.K.); TS, lines Rs26, GFP, and B6 (kind gifts of Dr. J. Rossant, Hospital for Sick Children, Toronto, Canada and Dr. A. Erlebacher, NY University School of Medicine, New York, USA); and XEN, lines IM8A1 (Dr. J. Rossant), #16, and E4 (Dr. P. Rugg-Gunn). DNA was extracted using a standard phenol choroform procedure. MeDIP-Seq was carried out as described previously [21]. Briefly, purified genomic DNA was sonicated to yield 150-600 bp fragments, and adaptors for paired-end sequencing (Illumina, San Diego, CA, USA, http://www.illumina.com) were ligated using NEB Next DNA Sample Prep Reagent Set 1 (New England Biolabs Hitchin, UK, http://www.neb.com). Immunoprecipitations (IPs) were carried out in triplicate using 500 ng DNA per sample, 1.25ug anti-5-methylcytosine (anti-5mC) antibody (Eurogentec, Southhampton, UK, http://www.eurogentec.com), and 10 ul Dynabeads coupled with M-280 sheep anti-mouse IgG (Invitrogen, Carlsbad, CA, http://www.invitrogen.com). The three IPs were pooled and amplified for 12 cycles with adapter specific primers, run on a 1% agarose gel, and fragments ranging between 300 and 500 bp in size were cut out and purified using the Gel Elution Kit (Qiagen, Crawley, UK, http://www.qiagen.com) before cluster generation and sequencing.

text: XX

characteristic: karyotype

text: Mus musculus

characteristic: organism

text: Mus musculus

text: Mus musculus

text: fresh specimen

text: XEN (XX)


text: Mus Musculus

characteristic: ArrayExpress-Species

characteristic: ENA-CHECKLIST

text: SC

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: mES_lif_s1_cell93-sc-2013-07-11T08:57:50Z-1661190

text: house mouse

characteristic: common name

text: Mus musculus

text: mRNA-seq Nextera library

text: Mus musculus


text: Danio rerio

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: SC

characteristic: INSDC center name

text: public

text: CH1073_659K1-sc-2013-07-05T13:36:58Z-1660355

text: zebrafish

text: Danio rerio

text: Danio rerio


text: Mus Musculus

text: SC

text: public

text: mES_lif_s1_cell19-sc-2013-07-11T08:56:39Z-1661116

text: house mouse

text: Mus musculus

text: mRNA-seq Nextera library

characteristic: sample description

text: Mus musculus


text: Danio rerio

text: SC

text: public

text: CH1073_588K24-sc-2013-07-05T13:37:41Z-1660402

text: zebrafish

text: Danio rerio

text: Danio rerio


text: Mus musculus

text: SC

text: public

text: house mouse

text: Mus musculus

text: Mus musculus


text: Mus Musculus

text: SC

text: public

text: mES_lif_s1_cell41-sc-2013-07-11T08:57:00Z-1661138

text: house mouse

text: Mus musculus

text: mRNA-seq Nextera library

text: Mus musculus


text: public

text: ArrayExpress

characteristic: broker name

text: human

characteristic: description

text: adult

characteristic: developmental stage

characteristic: individual

text: Homo sapiens

text: Homo sapiens

text: spleen

characteristic: organism part

text: Homo sapiens

text: frozen specimen

characteristic: specimen with known storage state

characteristic: title


text: Mouse

characteristic: ArrayExpress-Species

characteristic: ENA-FIRST-PUBLIC

text: SC

characteristic: INSDC first public

text: public

text: SC_HUWE5569735-sc-2013-07-16T08:26:31Z-1667113

characteristic: Submitter Id

text: house mouse

text: Mus musculus

characteristic: organism

text: Mus musculus


text: University College London

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: ArrayExpress

text: HEKn

characteristic: cell line

text: keratinocyte

characteristic: cell type

text: human

characteristic: common name

text: Protocols: Neonatal primary human epidermal keratinocytes (HEKn, Life technologies, Paisley, UK) were cultured on mouse collagen IV (0.67ug/cm2 BD Biosciences, Oxford, UK) coated surfaces in keratinocyte defined media containing epithelial growth factor (KDM and EpiLife, Life technologies). Differentiation was induced by shifting the cells to a high calcium media containing [1.2mM] Calcium Chloride. Viral infections for transcriptome experiments were carried out using VZV pOka cultured and used at less than 20 passages. Infected cell preparations were first treated with Mitomycin C (0.05mg/ml for 3hrs) prior to freezing and subsequently titered on Mewo cells. Cell-free VZV was generated by a rapid freeze (liquid N2) and thaw (37C), followed by removal of cellular debris by low speed centrifugation. For UV inactivated VZV, cell-free VZV supernatants were treated for 20 min at 150,000J/Cm2 using a Stratalinker UV Crosslinker (Stratagene). 1x105 HEKn cells per well of a 6 well dish were inoculated with 3x104 infectious units of virus. All VZV cultures were carried out at 34C, 5% CO2. This method involves several steps that are designed to convert total RNA into a library of template molecules suitable for high throughput DNA sequencing. The first step involves purifying the poly-A containing mRNA molecules using poly-T oligo-attached magnetic beads. Following purification, the mRNA is fragmented into small pieces using divalent cations under elevated temperature. Then, the cleaved mRNA fragments are copied into first strand cDNA using reverse transcriptase and a high concentration of random hexamer primers. Unique adaptors were ligated to the cDNA and 200bp fragments were size selected by agarose gel purification. Libraries were validated by using a DNA high sensitivity chip (Agilent, Cheshire, UK) and quantified by Qubit analysis using the Quant-iT dsDNA HS Assay (Life technologies).

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens

text: fresh specimen