text: Plasmodium falciparum

characteristic: ArrayExpress-Species

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: SC

text: public

text: malaria parasite P. falciparum

text: Plasmodium falciparum

text: Plasmodium falciparum


status: PUBLIC

text: Danio rerio

tag: attribute

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_120J11-sc-2013-07-05T13:36:15Z-1660311

characteristic: Submitter Id

text: zebrafish

characteristic: common name

text: Danio rerio

characteristic: organism

text: Danio rerio


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

characteristic: title

type: has member


text: Mus Musculus

text: SC

text: public

text: mES_lif_s1_cell78-sc-2013-07-11T08:57:37Z-1661175

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: CH73_336P8-sc-2013-07-05T13:37:47Z-1660409

text: zebrafish

text: Danio rerio

text: Danio rerio


text: Danio rerio

text: SC

text: public

text: CH73_86P10-sc-2013-07-05T13:38:25Z-1660452

text: zebrafish

text: Danio rerio

text: Danio rerio


text: public

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

text: ArrayExpress

characteristic: broker name

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.).

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: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

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

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

text: adult

characteristic: individual

text: Homo sapiens

text: Homo sapiens

text: thyroid

text: Homo sapiens

text: frozen specimen


text: Danio rerio

characteristic: ArrayExpress-Species

text: SC

text: public

characteristic: INSDC status

characteristic: SRA accession

text: CH1073_37P10-sc-2013-07-05T13:36:49Z-1660345

characteristic: Submitter Id

text: zebrafish

characteristic: common name

text: Danio rerio

characteristic: organism

text: Danio rerio


text: Mus Musculus

text: SC

text: public

text: mES_lif_s1_cell39-sc-2013-07-11T08:56:58Z-1661136

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_816D6-sc-2013-07-05T13:36:52Z-1660348

text: zebrafish

text: Danio rerio

text: Danio rerio


text: public

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

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


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: University College London

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

tag: Namespace:University College London

text: ArrayExpress

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).

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens

text: fresh specimen


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

characteristic: Submitter Id

text: ArrayExpress

text: bread wheat

characteristic: common name

text: anthesis

text: mock inoculation

text: Triticum aestivum

characteristic: organism

text: Triticum aestivum

text: Triticum aestivum

text: frozen specimen


characteristic: ENA-CHECKLIST

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: lung

text: Homo sapiens

text: frozen specimen


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: public

text: ArrayExpress

text: human

text: adult

text: Homo sapiens

text: Homo sapiens

text: bladder

characteristic: organism part

text: Homo sapiens

text: frozen specimen

characteristic: specimen with known storage state

characteristic: title


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: mock inoculation

characteristic: infect

text: Malus domestica

text: Malus domestica

text: leaf

text: Malus domestica

text: fresh specimen

text: 17 +/- 2 degree celsius

characteristic: temperature

text: 96 hour

characteristic: time post inoculation


text: Plasmodium falciparum

characteristic: ArrayExpress-Species

characteristic: ENA-CHECKLIST

text: SC

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: malaria parasite P. falciparum

characteristic: common name

text: Plasmodium falciparum

characteristic: organism

text: Plasmodium falciparum


text: Mus musculus

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: SC

text: public

text: house mouse

text: Mus musculus

text: Mus musculus


text: Danio rerio

text: SC

text: public

text: CH1073_155H1-sc-2013-07-05T13:37:59Z-1660422

text: zebrafish

text: Danio rerio

text: Danio rerio


text: public

text: ArrayExpress

characteristic: broker name

text: bread wheat

characteristic: cultivar

characteristic: description

text: anthesis

characteristic: developmental stage

text: Fusarium graminearum inoculation

text: Triticum aestivum

text: Triticum aestivum

characteristic: organism part

text: Triticum aestivum

text: frozen specimen

characteristic: specimen with known storage state

characteristic: title


text: SRA-Webin

characteristic: ENA-SUBMISSION-TOOL

characteristic: External Id

text: ISB-USA

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

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: public

characteristic: INSDC status

characteristic: SRA accession

tag: Namespace:Max Planck Institute, Department of Genetics

characteristic: Submitter Id

text: ArrayExpress

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.

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: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: public

text: ArrayExpress

characteristic: broker name

text: apple

characteristic: common name

text: inoculated with Venturia inaequalis

characteristic: infect

text: Malus domestica

characteristic: organism

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: Mus Musculus

characteristic: ArrayExpress-Species

characteristic: External Id

text: SC

characteristic: INSDC center name

text: public

text: mES_lif_s1_cell12-sc-2013-07-11T08:56:32Z-1661109

text: house mouse

text: Mus musculus

text: mRNA-seq Nextera library

characteristic: sample description

text: Mus musculus


text: Mus Musculus

text: SC

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: mES_lif_s1_cell73-sc-2013-07-11T08:57:32Z-1661170

text: house mouse

text: Mus musculus

text: mRNA-seq Nextera library

text: Mus musculus


text: Danio rerio

text: SC

text: public

text: DKEY_115C21-sc-2013-07-05T13:39:02Z-1660492

characteristic: Submitter Id

text: zebrafish

text: Danio rerio

text: Danio rerio


text: Mouse

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: SC

text: public

text: SC_HUWE5569744-sc-2013-07-16T08:26:41Z-1667122

text: house mouse

text: Mus musculus

text: Mus musculus


characteristic: ENA-LAST-UPDATE

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: duodenum

characteristic: organism part

text: Homo sapiens

text: frozen specimen

characteristic: specimen with known storage state

characteristic: title


text: Mouse

characteristic: ArrayExpress-Species

characteristic: External Id

text: SC

characteristic: INSDC center name

text: public

text: SC_HUWE5569727-sc-2013-07-16T08:26:21Z-1667105

text: house mouse

characteristic: common name

text: Mus musculus

characteristic: organism

text: Mus musculus


text: Danio rerio

text: SC

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: zFOS_1367D7-sc-2013-07-05T13:36:30Z-1660325

text: zebrafish

text: Danio rerio

text: Danio rerio


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: public

tag: Namespace:Systems Biology Ireland, University College Dublin

characteristic: Submitter Id

text: ArrayExpress

characteristic: cell line

text: neuroblast

characteristic: cell type

text: human

text: Protocols: Cells were cultured in RPMI 1640 (Gibco), supplemented with 10% fetal bovine serum (FBS) (Gibco), 2mM L-glutamine (Gibco) and 1% Penicillin-Streptomycin solution (Gibco). IMR32 cells were treated as follows; untreated control, 24h 1uM azakenpaullone, 24h 1uM BIO or 24h 28mM LiCl with biological duplicates. Total mRNA was extracted using TRI Reagent (Sigma-Aldrich) according to manufacturers protocol and DNA was digested with DNA-free Kit (Applied Biosystems). RNA quality was checked by RT-qPCR (as above) and on a 2100 Bioanalyser (Agilent) using a Eukaryote Total RNA Nano Chip (version 2.6). All samples had a RIN value in the range of 9.8-10. Sequencing libraries were generated from 2ug of total RNA per sample with TruSeq RNA sample preparation Kit v2 (Illumina) according to manufacturers protocol. Size and purity of the libraries were analysed on a Bioanalyser High Sensitivity DNA chip (Agilent). Libraries were clustered using TruSeq Paired-End Cluster Kit v5-CS-GA (Illumina).

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens


text: Danio rerio

text: SC

text: public

text: CH1073_100G5-sc-2013-07-05T13:38:19Z-1660445

text: zebrafish

text: Danio rerio

text: Danio rerio


text: Mus Musculus

characteristic: ENA-CHECKLIST

text: SC

text: public

text: mES_lif_s1_cell92-sc-2013-07-11T08:57:49Z-1661189

text: house mouse

text: Mus musculus

text: mRNA-seq Nextera library

characteristic: sample description

text: Mus musculus


text: Plasmodium falciparum

text: SC

text: public

text: malaria parasite P. falciparum

text: Plasmodium falciparum

text: Plasmodium falciparum


text: Danio rerio

text: SC

text: public

text: CH1073_873G21-sc-2013-07-05T13:37:35Z-1660396

text: zebrafish

text: Danio rerio

text: Danio rerio


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: liver

characteristic: organism part

text: Homo sapiens

text: frozen specimen

characteristic: specimen with known storage state

characteristic: title


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_31L10-sc-2013-07-05T13:38:21Z-1660448

text: zebrafish

characteristic: common name

text: Danio rerio

characteristic: organism

text: Danio rerio


text: Mus Musculus

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: SC

text: public

characteristic: INSDC status

characteristic: SRA accession

text: mES_lif_s1_cell82-sc-2013-07-11T08:57:40Z-1661179

characteristic: Submitter Id

text: house mouse

text: Mus musculus

text: mRNA-seq Nextera library

text: Mus musculus


text: Mus Musculus

characteristic: ENA-CHECKLIST

text: SC

text: public

text: mES_lif_s1_cell33-sc-2013-07-11T08:56:53Z-1661130

text: house mouse

text: Mus musculus

text: mRNA-seq Nextera library

characteristic: sample description

text: Mus musculus


text: SRA-Webin

characteristic: ENA-SUBMISSION-TOOL

text: ISB-USA

text: public

text: baker's yeast

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae


text: Danio rerio

text: SC

text: public

text: CH1073_584H11-sc-2013-07-05T13:37:34Z-1660394

text: zebrafish

text: Danio rerio

text: Danio rerio


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: thyroid

characteristic: organism part

text: Homo sapiens

text: frozen specimen

characteristic: specimen with known storage state


characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: ArrayExpress

text: human

text: adult

text: Homo sapiens

text: Homo sapiens

text: animal ovary

text: Homo sapiens

text: frozen specimen

characteristic: title


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: Institut Pasteur de Montevideo

text: public

characteristic: INSDC status

tag: Namespace:Institut Pasteur de Montevideo

text: ArrayExpress

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: differentiating

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: Homo sapiens

text: 3 day

characteristic: time

text: induction of adipocyte differentiation

characteristic: treatment


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

text: public

characteristic: SRA accession

characteristic: Submitter Id

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)

text: Triticum aestivum

text: frozen specimen


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-CHECKLIST

characteristic: External Id

text: SC

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: m_ChIP_GFP_high_N1-sc-2013-07-18T13:26:48Z-1669280

text: house mouse

text: Mus musculus

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

characteristic: sample description

text: Mus musculus

text: Bl6 MeCP2 GFP

characteristic: strain


text: Danio rerio

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: SC

text: public

characteristic: INSDC status

characteristic: SRA accession

text: CH73_365C21-sc-2013-07-05T13:38:43Z-1660474

characteristic: Submitter Id

text: zebrafish

characteristic: common name

text: Danio rerio

characteristic: organism

text: Danio rerio


text: Danio rerio

text: SC

text: public

text: CH1073_381D7-sc-2013-07-05T13:36:56Z-1660353

text: zebrafish

text: Danio rerio

text: Danio rerio


text: Mouse

text: SC

text: public

text: SC_HUWE5569737-sc-2013-07-16T08:26:34Z-1667115

text: house mouse

text: Mus musculus

text: Mus musculus


text: European Molecular Biology Laboratory

text: public

tag: Namespace:European Molecular Biology Laboratory

text: ArrayExpress

characteristic: broker name

text: fruit fly

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: ArrayExpress-Species

characteristic: External Id

text: SC

text: public

text: CH73_309L10-sc-2013-07-05T13:38:01Z-1660424

text: zebrafish

text: Danio rerio

text: Danio rerio


characteristic: ENA-CHECKLIST

characteristic: INSDC center name

characteristic: INSDC first public

text: public

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

text: adult

characteristic: individual

text: Homo sapiens

text: Homo sapiens

text: adrenal gland

characteristic: organism part

text: Homo sapiens

text: frozen specimen

characteristic: specimen with known storage state


text: Plasmodium falciparum

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: SC

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: malaria parasite P. falciparum

text: Plasmodium falciparum

text: Plasmodium falciparum


text: Systems Biology Ireland, University College Dublin

text: public

characteristic: SRA accession

characteristic: Submitter Id

text: ArrayExpress

characteristic: cell line

text: neuroblast

characteristic: cell type

text: human

characteristic: common name

text: Protocols: Cells were cultured in RPMI 1640 (Gibco), supplemented with 10% fetal bovine serum (FBS) (Gibco), 2mM L-glutamine (Gibco) and 1% Penicillin-Streptomycin solution (Gibco). IMR32 cells were treated as follows; untreated control, 24h 1uM azakenpaullone, 24h 1uM BIO or 24h 28mM LiCl with biological duplicates. Total mRNA was extracted using TRI Reagent (Sigma-Aldrich) according to manufacturers protocol and DNA was digested with DNA-free Kit (Applied Biosystems). RNA quality was checked by RT-qPCR (as above) and on a 2100 Bioanalyser (Agilent) using a Eukaryote Total RNA Nano Chip (version 2.6). All samples had a RIN value in the range of 9.8-10. Sequencing libraries were generated from 2ug of total RNA per sample with TruSeq RNA sample preparation Kit v2 (Illumina) according to manufacturers protocol. Size and purity of the libraries were analysed on a Bioanalyser High Sensitivity DNA chip (Agilent). Libraries were clustered using TruSeq Paired-End Cluster Kit v5-CS-GA (Illumina).

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: Homo sapiens


text: Danio rerio

characteristic: ArrayExpress-Species

characteristic: External Id

text: SC

text: public

text: CH73_369J2-sc-2013-07-05T13:39:07Z-1660498

text: zebrafish

text: Danio rerio

text: Danio rerio


characteristic: ENA-CHECKLIST

characteristic: INSDC center name

text: public

text: ArrayExpress

characteristic: broker name

text: human

characteristic: description

text: adult

characteristic: developmental stage

text: Homo sapiens

text: Homo sapiens

text: cerebral cortex

text: Homo sapiens

text: frozen specimen

characteristic: title


text: Danio rerio

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: SC

characteristic: INSDC first public

text: public

text: CH1073_264D3-sc-2013-07-05T13:36:56Z-1660352

text: zebrafish

text: Danio rerio

text: Danio rerio


E-MTAB-1746:Control 1

text: University of Dublin, Trinity College

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-1746:Control 1

tag: Namespace:University of Dublin, Trinity College

text: ArrayExpress

text: house mouse

text: Protocols: Heterozygous matings of Splotch-delayed mice were harvested at E14.5 (TS23) Splotch-delayed homozogous mutant and control (homozygous wild-type and heterozygote) embryos were dissected and Humerus forelimb tissue was dissected at embronic day 14.5 (Theiler Stage 23) RNA was extracted following manufacturers guidlines ( SV. Total RNA Isolation system, Promega, UK) The DNase-treated RNA (3ug) was used to prepare RNA-Seq libraries with the TruSeq RNA Sample Prep kit. A total of six cDNA libraries were constructed, representing triplicate biological replicates for each group.

text: Theiler stage 23

text: Splotch-delayed (Pax3Spd/+)

characteristic: genotype

text: Mus musculus

text: Mus musculus

text: humerus

characteristic: organism part

text: Mus musculus

text: Control 1


text: public

characteristic: Submitter Id

text: ArrayExpress

text: bread wheat

characteristic: common name

characteristic: cultivar

text: anthesis

text: Fusarium graminearum inoculation

characteristic: infect

text: Triticum aestivum

characteristic: organism

text: Triticum aestivum

text: Triticum aestivum

text: frozen specimen

characteristic: specimen with known storage state


characteristic: ENA-CHECKLIST

characteristic: External Id

text: Science for Life Laboratory, Stockholm, Sweden

characteristic: INSDC center name

text: public

text: ArrayExpress

characteristic: broker name

text: human

characteristic: description

text: adult

characteristic: individual

text: Homo sapiens

text: Homo sapiens

text: kidney

text: Homo sapiens

text: frozen specimen


text: cultured human neurons

characteristic: ArrayExpress-CellType

text: scrambled shRNA

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: ENA-LAST-UPDATE

text: SC

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: JCW_1143_120713_5-sc-2013-07-18T13:11:23Z-1669275

text: human

text: Homo sapiens

text: Total cDNA from human neurons

characteristic: sample description

text: Homo sapiens


text: Mouse

characteristic: ENA-CHECKLIST

text: SC

text: public

characteristic: INSDC status

characteristic: SRA accession

text: SC_HUWE5569729-sc-2013-07-16T08:26:24Z-1667107

characteristic: Submitter Id

text: house mouse

characteristic: common name

text: Mus musculus

characteristic: organism

text: Mus musculus


text: SRA-Webin

characteristic: ENA-SUBMISSION-TOOL

characteristic: External Id

text: ISB-USA

characteristic: INSDC center name

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: Institut Pasteur de Montevideo

text: public

text: ArrayExpress

characteristic: broker name

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).

characteristic: description

text: undifferentiated

characteristic: developmental stage

characteristic: individual

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens

text: 3 day

characteristic: time

text: induction of adipocyte differentiation

characteristic: treatment


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: ArrayExpress

text: human

text: adult

text: Homo sapiens

text: Homo sapiens

text: skin

characteristic: organism part

text: Homo sapiens

text: frozen specimen

characteristic: specimen with known storage state


text: male

characteristic: ArrayExpress-Sex

text: Mus musculus

characteristic: ArrayExpress-Species

characteristic: External Id

text: SC

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: house mouse

characteristic: common name

text: Mus musculus

characteristic: organism

text: PCR products

characteristic: sample description

text: Mus musculus


text: University College London

characteristic: INSDC center name

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: title


text: male

text: Mus musculus

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: SC

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: 6TGR_3_1-sc-2013-06-26T16:19:09Z-1654036

text: house mouse

text: Mus musculus

text: PCR products

text: Mus musculus


text: Mus Musculus

characteristic: ArrayExpress-Species

characteristic: ENA-CHECKLIST

characteristic: External Id

text: SC

text: public

text: mES_lif_s1_cell7-sc-2013-07-11T08:56:27Z-1661104

text: house mouse

text: Mus musculus

text: mRNA-seq Nextera library

text: Mus musculus


text: Plasmodium falciparum

text: SC

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: malaria parasite P. falciparum

text: Plasmodium falciparum

text: Plasmodium falciparum


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

text: public

text: ArrayExpress

text: apple

characteristic: common name

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: inoculated with Venturia inaequalis

characteristic: infect

text: Malus domestica

characteristic: organism

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


text: cultured human neurons

characteristic: ArrayExpress-CellType

text: scrambled shRNA

characteristic: ArrayExpress-Genotype

text: Brain

characteristic: ArrayExpress-OrganismPart

text: female

characteristic: ArrayExpress-Sex

text: Homo sapiens

text: day 9

characteristic: ArrayExpress-TimePoint

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: SC

characteristic: INSDC center name

text: public

text: JCW_240613_1143_5-sc-2013-07-01T15:01:09Z-1656029

text: human

text: Homo sapiens

text: Total cDNA from human neurons

characteristic: sample description

text: Homo sapiens


text: Mus Musculus

characteristic: ArrayExpress-Species

characteristic: ENA-CHECKLIST

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_cell8-sc-2013-07-11T08:56:28Z-1661105

characteristic: Submitter Id

text: house mouse

characteristic: common name

text: Mus musculus

text: mRNA-seq Nextera library

text: Mus musculus


text: Danio rerio

text: SC

text: public

text: zFOS_323B12-sc-2013-07-05T13:37:22Z-1660381

text: zebrafish

text: Danio rerio

characteristic: organism

text: Danio rerio


text: Max Planck Institute, Department of Genetics

text: public

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: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: INSDC center name

text: public

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

text: adult

characteristic: individual

text: Homo sapiens

text: Homo sapiens

text: spleen

text: Homo sapiens

text: frozen specimen


characteristic: External Id

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

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: ArrayExpress

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: Fusarium graminearum inoculation

characteristic: infect

text: Triticum aestivum

text: Triticum aestivum

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

text: Triticum aestivum

text: frozen specimen


text: Danio rerio

characteristic: ArrayExpress-Species

text: SC

text: public

text: zFOS_261A2-sc-2013-07-05T13:37:08Z-1660365

characteristic: Submitter Id

text: zebrafish

characteristic: common name

text: Danio rerio

characteristic: organism

text: Danio rerio


text: Mus Musculus

text: SC

text: public

text: mES_lif_s1_cell96-sc-2013-07-11T08:57:53Z-1661193

text: house mouse

text: Mus musculus

text: mRNA-seq Nextera library

characteristic: sample description

text: Mus musculus


text: L1 larvae

characteristic: ArrayExpress-DevelopmentalStage

text: mixed

characteristic: ArrayExpress-Sex

text: Dracunculus medinensis

characteristic: ENA-CHECKLIST

text: SC

text: public

text: Dracunculus_medinensis-sc-2013-07-15T15:11:23Z-1667998

text: Guinea worm

text: Dracunculus medinensis

text: mixed sex L1 larvae

text: Dracunculus medinensis


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: INSDC center name

text: public

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

text: 2 to 6 month

characteristic: age

text: ArrayExpress

characteristic: broker name

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.

characteristic: description

text: adult

characteristic: developmental stage

characteristic: genotype

text: Mus musculus

text: Mus musculus

text: spleen

characteristic: organism part

text: Mus musculus

text: male

characteristic: sex

characteristic: title


characteristic: External Id

text: Science for Life Laboratory, Stockholm, Sweden

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: ArrayExpress

text: human

characteristic: common name

text: adult

characteristic: individual

text: Homo sapiens

text: Homo sapiens

text: adrenal gland

text: Homo sapiens

text: frozen specimen

characteristic: specimen with known storage state


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: SRA-Webin

characteristic: ENA-SUBMISSION-TOOL

text: ISB-USA

characteristic: INSDC center name

text: public

text: baker's yeast

text: Saccharomyces cerevisiae

characteristic: organism

text: Saccharomyces cerevisiae

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


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: External Id

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: ArrayExpress

text: bread wheat

characteristic: cultivar

text: anthesis

characteristic: developmental stage

text: mock inoculation

characteristic: infect

text: Triticum aestivum

text: Triticum aestivum

characteristic: organism part

text: Triticum aestivum

text: frozen specimen

characteristic: title


text: Mus Musculus

characteristic: ArrayExpress-Species

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: SC

text: public

characteristic: INSDC status

characteristic: SRA accession

text: mES_lif_s1_cell24-sc-2013-07-11T08:56:44Z-1661121

characteristic: Submitter Id

text: house mouse

characteristic: common name

text: Mus musculus

text: mRNA-seq Nextera library

characteristic: sample description

text: Mus musculus


text: Mus Musculus

characteristic: ENA-LAST-UPDATE

text: SC

characteristic: INSDC center name

text: public

text: mES_lif_s1_cell75-sc-2013-07-11T08:57:34Z-1661172

text: house mouse

text: Mus musculus

characteristic: organism

text: mRNA-seq Nextera library

text: Mus musculus


text: Danio rerio

characteristic: External Id

text: SC

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: CH73_382F1-sc-2013-07-05T13:38:24Z-1660451

text: zebrafish

text: Danio rerio

text: Danio rerio


text: Plasmodium falciparum

text: SC

text: public

text: malaria parasite P. falciparum

text: Plasmodium falciparum

text: Plasmodium falciparum


text: Danio rerio

text: SC

text: public

text: zFOS_407F11-sc-2013-07-05T13:36:31Z-1660326

text: zebrafish

text: Danio rerio

text: Danio rerio


text: Danio rerio

text: SC

text: public

text: CH73_95G16-sc-2013-07-05T13:38:45Z-1660476

text: zebrafish

text: Danio rerio

text: Danio rerio


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: gall bladder

text: Homo sapiens

text: frozen specimen

characteristic: specimen with known storage state


text: Mus Musculus

characteristic: ArrayExpress-Species

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: SC

text: public

text: mES_lif_s1_cell62-sc-2013-07-11T08:57:22Z-1661159

text: house mouse

text: Mus musculus

text: mRNA-seq Nextera library

text: Mus musculus


text: Danio rerio

text: SC

text: public

characteristic: INSDC status

characteristic: SRA accession

text: CH73_73J20-sc-2013-07-05T13:37:58Z-1660420

characteristic: Submitter Id

text: zebrafish

text: Danio rerio

text: Danio rerio


text: Danio rerio

characteristic: ENA-LAST-UPDATE

text: SC

text: public

text: CH1073_193N16-sc-2013-07-05T13:38:20Z-1660446

text: zebrafish

characteristic: common name

text: Danio rerio

text: Danio rerio


text: Danio rerio

text: SC

characteristic: INSDC center name

text: public

text: CH1073_6J10-sc-2013-07-05T13:37:21Z-1660379

text: zebrafish

text: Danio rerio

characteristic: organism

text: Danio rerio


text: Danio rerio

characteristic: External Id

text: SC

characteristic: INSDC first public

text: public

text: CH1073_242M16-sc-2013-07-05T13:36:25Z-1660320

text: zebrafish

text: Danio rerio

text: Danio rerio


text: Mouse

text: SC

characteristic: INSDC last update

text: public

text: SC_HUWE5569726-sc-2013-07-16T08:26:18Z-1667104

text: house mouse

text: Mus musculus

text: Mus musculus


text: Mus Musculus

text: SC

text: public

text: mES_lif_s1_cell1-sc-2013-07-11T08:56:18Z-1661098

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_655O12-sc-2013-07-05T13:36:51Z-1660347

text: zebrafish

text: Danio rerio

text: Danio rerio


text: Institut Pasteur de Montevideo

text: public

text: ArrayExpress

characteristic: broker name

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).

characteristic: description

text: differentiating

characteristic: developmental stage

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens

text: 3 day

characteristic: time

characteristic: title

text: no adipocyte differentiation induction

characteristic: treatment


text: Mus Musculus

characteristic: ArrayExpress-Species

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: SC

text: public

characteristic: INSDC status

characteristic: SRA accession

text: mES_lif_s1_cell45-sc-2013-07-11T08:57:04Z-1661142

text: house mouse

text: Mus musculus

text: mRNA-seq Nextera library

text: Mus musculus


characteristic: ENA-LAST-UPDATE

text: SRA-Webin

characteristic: ENA-SUBMISSION-TOOL

text: ISB-USA

characteristic: INSDC center name

text: public

characteristic: Submitter Id

text: baker's yeast

characteristic: common name

text: Saccharomyces cerevisiae

characteristic: organism

text: Saccharomyces cerevisiae

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


text: Mus Musculus

characteristic: External Id

text: SC

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: mES_lif_s1_cell89-sc-2013-07-11T08:57:47Z-1661186

text: house mouse

text: Mus musculus

text: mRNA-seq Nextera library

characteristic: sample description

text: Mus musculus


text: Mouse

text: SC

text: public

text: SC_HUWE5569740-sc-2013-07-16T08:26:37Z-1667118

text: house mouse

text: Mus musculus

text: Mus musculus


text: Mus Musculus

text: SC

text: public

text: mES_lif_s1_cell40-sc-2013-07-11T08:56:59Z-1661137

text: house mouse

text: Mus musculus

text: mRNA-seq Nextera library

text: Mus musculus


text: Plasmodium falciparum

text: SC

text: public

text: malaria parasite P. falciparum

text: Plasmodium falciparum

text: Plasmodium falciparum


text: Danio rerio

text: SC

text: public

text: CH73_375O21-sc-2013-07-05T13:37:57Z-1660419

text: zebrafish

text: Danio rerio

text: Danio rerio


text: Systems Biology Ireland, University College Dublin

text: public

text: ArrayExpress

characteristic: broker name

characteristic: cell line

text: neuroblast

characteristic: cell type

text: human

text: Protocols: Cells were cultured in RPMI 1640 (Gibco), supplemented with 10% fetal bovine serum (FBS) (Gibco), 2mM L-glutamine (Gibco) and 1% Penicillin-Streptomycin solution (Gibco). IMR32 cells were treated as follows; untreated control, 24h 1uM azakenpaullone, 24h 1uM BIO or 24h 28mM LiCl with biological duplicates. Total mRNA was extracted using TRI Reagent (Sigma-Aldrich) according to manufacturers protocol and DNA was digested with DNA-free Kit (Applied Biosystems). RNA quality was checked by RT-qPCR (as above) and on a 2100 Bioanalyser (Agilent) using a Eukaryote Total RNA Nano Chip (version 2.6). All samples had a RIN value in the range of 9.8-10. Sequencing libraries were generated from 2ug of total RNA per sample with TruSeq RNA sample preparation Kit v2 (Illumina) according to manufacturers protocol. Size and purity of the libraries were analysed on a Bioanalyser High Sensitivity DNA chip (Agilent). Libraries were clustered using TruSeq Paired-End Cluster Kit v5-CS-GA (Illumina).

characteristic: description

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens

characteristic: title


text: Danio rerio

characteristic: ArrayExpress-Species

characteristic: ENA-FIRST-PUBLIC

text: SC

text: public

characteristic: INSDC status

text: CH1073_451O12-sc-2013-07-05T13:36:35Z-1660330

text: zebrafish

text: Danio rerio

text: Danio rerio


text: Danio rerio

characteristic: ENA-LAST-UPDATE

text: SC

text: public

characteristic: SRA accession

text: zFOS_422C12-sc-2013-07-05T13:38:05Z-1660429

text: zebrafish

text: Danio rerio

text: Danio rerio


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

characteristic: INSDC center name

text: public

characteristic: Submitter Id

text: ArrayExpress

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

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: ENA-CHECKLIST

characteristic: External Id

text: Science for Life Laboratory, Stockholm, Sweden

characteristic: INSDC first public

characteristic: INSDC last update

text: public

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

text: adult

characteristic: individual

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: skin

text: Homo sapiens

text: frozen specimen


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: European Molecular Biology Laboratory

text: public

characteristic: INSDC status

text: ArrayExpress

text: house mouse

text: Protocols: Trizol Illumina mRNA-seq library construction protocol

characteristic: description

text: Mus musculus

text: Mus musculus

text: brain

text: Mus musculus

characteristic: strain

characteristic: title


text: Danio rerio

characteristic: ArrayExpress-Species

text: SC

characteristic: INSDC center name

text: public

characteristic: SRA accession

text: CH1073_280C5-sc-2013-07-05T13:38:21Z-1660447

characteristic: Submitter Id

text: zebrafish

text: Danio rerio

text: Danio rerio


text: Mus Musculus

characteristic: ENA-CHECKLIST

characteristic: External Id

text: SC

text: public

text: mES_lif_s1_cell94-sc-2013-07-11T08:57:51Z-1661191

text: house mouse

text: Mus musculus

text: mRNA-seq Nextera library

characteristic: sample description

text: Mus musculus


text: Danio rerio

text: SC

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: CH1073_792K11-sc-2013-07-05T13:36:37Z-1660332

text: zebrafish

text: Danio rerio

text: Danio rerio


E-MTAB-1746:Mutant 1

text: University of Dublin, Trinity College

text: public

text: E-MTAB-1746:Mutant 1

text: ArrayExpress

characteristic: broker name

text: house mouse

characteristic: common name

text: Protocols: Heterozygous matings of Splotch-delayed mice were harvested at E14.5 (TS23) Splotch-delayed homozogous mutant and control (homozygous wild-type and heterozygote) embryos were dissected and Humerus forelimb tissue was dissected at embronic day 14.5 (Theiler Stage 23) RNA was extracted following manufacturers guidlines ( SV. Total RNA Isolation system, Promega, UK) The DNase-treated RNA (3ug) was used to prepare RNA-Seq libraries with the TruSeq RNA Sample Prep kit. A total of six cDNA libraries were constructed, representing triplicate biological replicates for each group.

text: Theiler stage 23

characteristic: developmental stage

text: Splotch-delayed (Pax3Spd/Spd)

characteristic: genotype

text: Mus musculus

text: Mus musculus

text: humerus

characteristic: organism part

text: Mus musculus

text: Mutant 1


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: Max Planck Institute, Department of Genetics

text: public

characteristic: INSDC status

text: ArrayExpress

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

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: ENA-CHECKLIST

text: SRA-Webin

characteristic: ENA-SUBMISSION-TOOL

text: ISB-USA

characteristic: INSDC center name

text: public

characteristic: SRA accession

characteristic: Submitter Id

text: baker's yeast

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

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

characteristic: title


characteristic: External Id

text: European Molecular Biology Laboratory

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: ArrayExpress

characteristic: broker name

characteristic: cell line

text: erythroleukemia

characteristic: cell type

text: human

characteristic: common name

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: ArrayExpress-Species

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: SC

text: public

characteristic: INSDC status

text: mES_lif_s1_cell81-sc-2013-07-11T08:57:39Z-1661178

text: house mouse

text: Mus musculus

text: mRNA-seq Nextera library

characteristic: sample description

text: Mus musculus


characteristic: ENA-CHECKLIST

text: public

text: ArrayExpress

text: human

characteristic: description

text: adult

characteristic: developmental stage

characteristic: individual

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: lung

characteristic: organism part

text: Homo sapiens

text: frozen specimen

characteristic: specimen with known storage state


text: Danio rerio

characteristic: External Id

text: SC

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: SRA accession

text: CH1073_133E3-sc-2013-07-05T13:39:03Z-1660493

characteristic: Submitter Id

text: zebrafish

text: Danio rerio

text: Danio rerio


text: Mus Musculus

characteristic: ArrayExpress-Species

characteristic: ENA-FIRST-PUBLIC

text: SC

text: public

text: mES_lif_s1_cell46-sc-2013-07-11T08:57:05Z-1661143

text: house mouse

characteristic: common name

text: Mus musculus

text: mRNA-seq Nextera library

text: Mus musculus


characteristic: ENA-LAST-UPDATE

text: public

characteristic: INSDC status

text: ArrayExpress

characteristic: broker name

text: human

text: adult

text: Homo sapiens

text: Homo sapiens

text: esophagus

text: Homo sapiens

text: frozen specimen

characteristic: title


text: Glia

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

text: Bl6 MeCP2 GFP

characteristic: ArrayExpress-StrainOrLine

characteristic: ENA-CHECKLIST

text: SC

text: public

text: m_ChIP_GFP_low_G3-sc-2013-07-18T13:26:53Z-1669285

text: house mouse

text: Mus musculus

text: ChIP DNA from GFP low glia (MeCP2 GFP from 15 BL 6 male)

characteristic: sample description

text: Mus musculus

text: Bl6 MeCP2 GFP

characteristic: strain


text: Neurons

text: Adult

text: MeCP2 GFP tagged

text: Chromotek GFP trap Agarose

text: Brain

text: wildtype

text: male

text: Mus musculus

characteristic: ArrayExpress-Species

text: Bl6 MeCP2 GFP

characteristic: ENA-FIRST-PUBLIC

characteristic: External Id

text: SC

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: SRA accession

text: m_Input_N1-sc-2013-07-18T13:26:45Z-1669277

characteristic: Submitter Id

text: house mouse

text: Mus musculus

characteristic: organism

text: crosslinked and sonicated chromatin= Input from GFP high sample (MeCP2 GFP from 15 BL 6 male)

text: Mus musculus

text: Bl6 MeCP2 GFP


characteristic: ENA-LAST-UPDATE

text: Science for Life Laboratory, Stockholm, Sweden

text: public

characteristic: INSDC status

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: 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

characteristic: title


text: adult

characteristic: ArrayExpress-DevelopmentalStage

text: female

characteristic: ArrayExpress-Sex

text: Dracunculus medinensis

characteristic: ArrayExpress-Species

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: External Id

text: SC

text: public

text: Dracunculus_medinensis-sc-2013-07-15T15:11:21Z-1667997

text: Guinea worm

text: Dracunculus medinensis

text: section of adult female worm

characteristic: sample description

text: Dracunculus medinensis


text: Danio rerio

characteristic: ENA-LAST-UPDATE

text: SC

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: SRA accession

text: CH1073_750O3-sc-2013-07-05T13:37:42Z-1660403

characteristic: Submitter Id

text: zebrafish

text: Danio rerio

characteristic: organism

text: Danio rerio


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

text: public

characteristic: INSDC status

text: ArrayExpress

characteristic: broker name

text: apple

characteristic: common name

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.).

characteristic: description

text: Leaf 1 (youngest leaf on 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

text: 17 +/- 2 degree celsius

characteristic: temperature

text: 72 hour

characteristic: time post inoculation


text: Plasmodium falciparum

characteristic: ArrayExpress-Species

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: External Id

text: SC

text: public

text: malaria parasite P. falciparum

text: Plasmodium falciparum

text: Plasmodium falciparum


characteristic: ENA-LAST-UPDATE

text: University College London

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: ArrayExpress

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).

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens

text: fresh specimen

characteristic: specimen with known storage state

characteristic: title


text: Danio rerio

text: SC

text: public

characteristic: INSDC status

characteristic: SRA accession

text: CH1073_393B9-sc-2013-07-05T13:37:19Z-1660377

characteristic: Submitter Id

text: zebrafish

characteristic: common name

text: Danio rerio

characteristic: organism

text: Danio rerio


text: cultured human neurons

characteristic: ArrayExpress-CellType

text: MeCP2 shRNA

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

text: SC

text: public

text: JCW_4242_120713_1-sc-2013-07-18T13:11:17Z-1669271

text: human

text: Homo sapiens

text: Total cDNA from human neurons

characteristic: sample description

text: Homo sapiens


text: Danio rerio

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

text: CH1073_208N4-sc-2013-07-05T13:38:40Z-1660470

text: zebrafish

text: Danio rerio

text: Danio rerio


text: cultured human neurons

text: MeCP2 overexpression

text: Brain

text: female

text: Homo sapiens

text: day 9

characteristic: ENA-CHECKLIST

text: SC

text: public

characteristic: INSDC status

characteristic: SRA accession

text: JCW_24143_120713_6-sc-2013-07-18T13:11:24Z-1669276

text: human

text: Homo sapiens

text: Total cDNA from human neurons

text: Homo sapiens


text: Danio rerio

text: SC

text: public

text: CH1073_800B23-sc-2013-07-05T13:36:45Z-1660340

characteristic: Submitter Id

text: zebrafish

characteristic: common name

text: Danio rerio

characteristic: organism

text: Danio rerio


text: female

text: Haemonchus contortus

characteristic: ArrayExpress-StrainOrLine

text: SC

text: public

text: Haemonchus_contortus_MHco3_10_BC4_S3_0_2IVM_2267-sc-2013-07-09T16:18:54Z-1660682

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

text: Haemonchus contortus

characteristic: strain