text: Danio rerio

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: SC

text: public

text: CH1073_858K8-sc-2013-07-05T13:37:22Z-1660380

text: zebrafish

text: Danio rerio

characteristic: organism

text: Danio rerio


status: PUBLIC

text: Danio rerio

tag: attribute

characteristic: ArrayExpress-Species

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_115H8-sc-2013-07-05T13:37:30Z-1660390

characteristic: Submitter Id

text: zebrafish

characteristic: common name

text: Danio rerio

text: Danio rerio


characteristic: ENA-CHECKLIST

text: SRA-Webin

characteristic: ENA-SUBMISSION-TOOL

text: ISB-USA

text: public

text: baker's yeast

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

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

characteristic: title

type: has member


text: public

tag: Namespace:Max Planck Institute, Department of Genetics

text: ArrayExpress

characteristic: broker name

text: house mouse

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

characteristic: description

text: adult

characteristic: developmental stage

text: domestic animal house

characteristic: environmental history

text: Mus musculus

text: Mus musculus

text: liver

characteristic: organism part

text: Mus musculus

text: fresh specimen

characteristic: specimen with known storage state

characteristic: strain


text: Plasmodium falciparum

characteristic: ArrayExpress-Species

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: SC

characteristic: INSDC center name

text: public

text: malaria parasite P. falciparum

text: Plasmodium falciparum

characteristic: organism

text: Plasmodium falciparum


text: Danio rerio

text: SC

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: CH1073_21H6-sc-2013-07-05T13:37:24Z-1660383

characteristic: Submitter Id

text: zebrafish

characteristic: common name

text: Danio rerio

text: Danio rerio


text: male

characteristic: ArrayExpress-Sex

text: Mus musculus

text: SC

text: public

text: house mouse

text: Mus musculus

text: PCR products

characteristic: sample description

text: Mus musculus


text: Danio rerio

text: SC

text: public

text: CH73_322P19-sc-2013-07-05T13:38:35Z-1660464

text: zebrafish

text: Danio rerio

text: Danio rerio


text: GSC

text: public

text: fungi

text: Samples were pooled in this way (tag gradient site altitude plot type) : ACAT Vosges Guebviller 1180 A soil ACGA Vosges Guebviller 1180 B soil AGAC Vosges Guebviller 1180 C soil AGCT Vosges St_Nicolas 550 A soil ATAT Vosges St_Nicolas 550 B soil ATCA Vosges St_Nicolas 550 C soil ATGC Vosges Ligneville 380 A soil CAGC Vosges Ligneville 380 B soil CATA Vosges Ligneville 380 C soil CGAC Pyrenees Lienz 1533 A soil CGCA Pyrenees Lienz 1533 B soil CGTC Pyrenees Lienz 1533 C soil CTGA Pyrenees Haugarou 1190 A soil TACA Pyrenees Haugarou 1190 B soil TACT Pyrenees Haugarou 1190 C soil TAGC Pyrenees Arras-Sireix 833 A soil TCAC Pyrenees Arras-Sireix 833 B soil TCGT Pyrenees Arras-Sireix 833 C soil TGAT Pyrenees Lourdes 488 A soil TGTC Pyrenees Lourdes 488 B soil ACGT Pyrenees Lourdes 488 C soil ACTA Pyrenees Laveyron 131 A soil AGCA Pyrenees Laveyron 131 B soil AGTC Pyrenees Laveyron 131 C soil ATGA Alpes pic_de_l'oeilly 1450 A soil CACT Alpes pic_de_l'oeilly 1450 B soil CAGA Alpes pic_de_l'oeilly 1450 C soil CATC Alpes Montsec 1100 A soil CGCT Alpes Montsec 1100 B soil CGTA Alpes Montsec 1100 C soil CTAC Alpes Vizille 750 A soil CTCA Alpes Vizille 750 B soil CTGT Alpes Vizille 750 C soil

characteristic: description

text: Fungi

text: Fungi


characteristic: ENA-CHECKLIST

text: public

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

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

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

text: Dracunculus medinensis

characteristic: ArrayExpress-Species

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: SC

characteristic: INSDC center name

text: public

text: Dracunculus_medinensis-sc-2013-07-15T15:11:18Z-1667994

text: Guinea worm

text: Dracunculus medinensis

characteristic: organism

text: section of adult female worm

text: Dracunculus medinensis


characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

tag: Namespace:Systems Biology Ireland, University College Dublin

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

text: Homo sapiens

text: Homo sapiens


text: Max Planck Institute, Department of Genetics

text: public

text: ArrayExpress

characteristic: broker name

text: house mouse

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


text: Danio rerio

characteristic: ArrayExpress-Species

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: SC

characteristic: INSDC center name

text: public

text: CH1073_417M2-sc-2013-07-05T13:37:33Z-1660393

text: zebrafish

text: Danio rerio

text: Danio rerio


text: Mus Musculus

characteristic: ENA-CHECKLIST

text: SC

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: mES_lif_s1_cell28-sc-2013-07-11T08:56:49Z-1661125

text: house mouse

text: Mus musculus

characteristic: organism

text: mRNA-seq Nextera library

characteristic: sample description

text: Mus musculus


text: public

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

characteristic: Submitter Id

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

characteristic: developmental stage

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: 72 hour

characteristic: time post inoculation

characteristic: title


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

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

text: house mouse

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

text: adult

characteristic: genotype

characteristic: individual

text: Mus musculus

text: Mus musculus

text: muscle

characteristic: organism part

text: Mus musculus

text: male

characteristic: sex


text: Systems Biology Ireland, University College Dublin

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: ArrayExpress

characteristic: broker name

characteristic: cell line

text: neuroblast

characteristic: cell type

text: human

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: Homo sapiens


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

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

text: public

text: ArrayExpress

text: apple

characteristic: common name

characteristic: description

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

characteristic: developmental stage

text: mock inoculation

characteristic: infect

text: Malus domestica

text: Malus domestica

text: leaf

text: Malus domestica

text: fresh specimen

characteristic: specimen with known storage state

text: 17 +/- 2 degree celsius

characteristic: temperature

text: 96 hour

characteristic: time post inoculation

characteristic: title


text: Mus Musculus

characteristic: ArrayExpress-Species

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: mES_lif_s1_cell85-sc-2013-07-11T08:57:43Z-1661182

text: house mouse

text: Mus musculus

text: mRNA-seq Nextera library

characteristic: sample description

text: Mus musculus


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: Science for Life Laboratory, Stockholm, Sweden

text: public

characteristic: Submitter Id

text: ArrayExpress

characteristic: broker name

text: human

text: adult

characteristic: individual

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: lung

characteristic: organism part

text: Homo sapiens

text: frozen specimen


text: Plasmodium falciparum

text: SC

text: public

text: malaria parasite P. falciparum

characteristic: common name

text: Plasmodium falciparum

text: Plasmodium falciparum


text: male

characteristic: ArrayExpress-Sex

text: Mus musculus

characteristic: ArrayExpress-Species

text: SC

text: public

text: gPool_3_2-sc-2013-06-26T16:17:30Z-1654033

text: house mouse

text: Mus musculus

text: PCR products

text: Mus musculus


characteristic: External Id

characteristic: INSDC center name

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

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)

text: Triticum aestivum

text: frozen specimen

characteristic: specimen with known storage state

characteristic: title


text: adult

characteristic: ArrayExpress-DevelopmentalStage

text: female

text: Dracunculus medinensis

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: SC

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: Dracunculus_medinensis-sc-2013-07-15T15:11:19Z-1667995

text: Guinea worm

text: Dracunculus medinensis

text: section of adult female worm

characteristic: sample description

text: Dracunculus medinensis


text: SRA-Webin

characteristic: ENA-SUBMISSION-TOOL

characteristic: External Id

text: ISB-USA

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


characteristic: INSDC center name

text: public

text: ArrayExpress

characteristic: broker name

text: human

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

characteristic: description

text: adult

characteristic: developmental stage

characteristic: individual

text: Homo sapiens

text: Homo sapiens

text: esophagus

characteristic: organism part

text: Homo sapiens

text: frozen specimen


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

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

text: public

text: 56 year

characteristic: age

text: ArrayExpress

text: human

text: adult

text: wild type

characteristic: genotype

text: Homo sapiens

text: Homo sapiens

text: brain

text: Homo sapiens

text: male

characteristic: sex

characteristic: title


text: adult

characteristic: ArrayExpress-DevelopmentalStage

text: female

characteristic: ArrayExpress-Sex

text: Dracunculus medinensis

characteristic: ArrayExpress-Species

characteristic: External Id

text: SC

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: Dracunculus_medinensis-sc-2013-07-15T15:11:25Z-1668000

text: Guinea worm

text: Dracunculus medinensis

text: section of adult female worm

characteristic: sample description

text: Dracunculus medinensis


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

characteristic: broker name

text: bread wheat

characteristic: common name

characteristic: cultivar

characteristic: description

text: anthesis

characteristic: developmental stage

text: Fusarium graminearum inoculation

characteristic: infect

text: Triticum aestivum

characteristic: organism

text: Triticum aestivum

characteristic: organism part

text: Triticum aestivum

text: frozen specimen

characteristic: specimen with known storage state


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Institut Pasteur de Montevideo

text: public

tag: Namespace:Institut Pasteur de Montevideo

text: ArrayExpress

text: mesenchymal stem cell

characteristic: cell type

text: human

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

text: undifferentiated

characteristic: individual

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens

text: 3 day

characteristic: time

characteristic: title

text: no adipocyte differentiation induction

characteristic: treatment


characteristic: ENA-CHECKLIST

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: ArrayExpress

characteristic: broker name

text: human

text: adult

text: Homo sapiens

text: Homo sapiens

text: kidney

text: Homo sapiens

text: frozen specimen


text: public

text: ArrayExpress

text: bread wheat

characteristic: common name

characteristic: cultivar

characteristic: description

text: anthesis

characteristic: developmental stage

text: mock inoculation

characteristic: infect

text: Triticum aestivum

characteristic: organism

text: Triticum aestivum

characteristic: organism part

text: Triticum aestivum

text: frozen specimen

characteristic: specimen with known storage state


text: cultured human neurons

characteristic: ArrayExpress-CellType

text: MeCP2 overexpression

characteristic: ArrayExpress-Genotype

text: Brain

characteristic: ArrayExpress-OrganismPart

text: female

characteristic: ArrayExpress-Sex

text: Homo sapiens

characteristic: ArrayExpress-Species

text: day 9

characteristic: ArrayExpress-TimePoint

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: SC

text: public

text: JCW_24142_120713_3-sc-2013-07-18T13:11:21Z-1669273

text: human

text: Homo sapiens

text: Total cDNA from human neurons

characteristic: sample description

text: Homo sapiens


text: Mus musculus

characteristic: ENA-CHECKLIST

text: SC

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: house mouse

characteristic: common name

text: Mus musculus

text: Mus musculus


text: Danio rerio

text: SC

text: public

text: zFOS_1858G7-sc-2013-07-05T13:36:53Z-1660349

text: zebrafish

text: Danio rerio

characteristic: organism

text: Danio rerio


text: University College London

text: public

tag: Namespace:University College London

text: ArrayExpress

characteristic: broker name

text: HEKn

characteristic: cell line

text: keratinocyte

characteristic: cell type

text: human

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

characteristic: description

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens

text: fresh specimen

characteristic: specimen with known storage state

characteristic: title


text: male

characteristic: ArrayExpress-Sex

text: Mus musculus

characteristic: ArrayExpress-Species

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: SC

text: public

text: 6TGR_3_4-sc-2013-06-26T16:21:05Z-1654039

text: house mouse

text: Mus musculus

text: PCR products

text: Mus musculus


text: Plasmodium falciparum

characteristic: ENA-CHECKLIST

text: SC

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: malaria parasite P. falciparum

text: Plasmodium falciparum

text: Plasmodium falciparum


text: Max Planck Institute, Department of Genetics

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: ArrayExpress

text: house mouse

characteristic: common name

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

text: adult

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: strain


text: Science for Life Laboratory, Stockholm, Sweden

text: public

text: ArrayExpress

characteristic: broker name

text: human

characteristic: description

text: adult

characteristic: individual

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: prostate

text: Homo sapiens

text: frozen specimen

characteristic: specimen with known storage state

characteristic: title


text: Danio rerio

characteristic: ArrayExpress-Species

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: SC

characteristic: INSDC center name

text: public

text: CH1073_251J1-sc-2013-07-05T13:36:33Z-1660328

text: zebrafish

text: Danio rerio

text: Danio rerio


text: Danio rerio

text: SC

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: CH1073_329G6-sc-2013-07-05T13:37:39Z-1660400

characteristic: Submitter Id

text: zebrafish

text: Danio rerio

text: Danio rerio


text: Mus Musculus

characteristic: ENA-CHECKLIST

text: SC

text: public

text: mES_lif_s1_cell60-sc-2013-07-11T08:57:20Z-1661157

text: house mouse

characteristic: common name

text: Mus musculus

text: mRNA-seq Nextera library

characteristic: sample description

text: Mus musculus


text: Danio rerio

text: SC

text: public

text: CH73_323I2-sc-2013-07-05T13:38:42Z-1660472

text: zebrafish

text: Danio rerio

text: Danio rerio


text: European Molecular Biology Laboratory

text: public

tag: Namespace:European Molecular Biology Laboratory

text: ArrayExpress

characteristic: broker name

characteristic: cell line

text: hepatocyte

characteristic: cell type

text: human

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

characteristic: description

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens


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: developmental stage

characteristic: individual

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: heart

characteristic: organism part

text: Homo sapiens

text: frozen specimen

characteristic: specimen with known storage state

characteristic: title


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

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: JCW_4243_120713_4-sc-2013-07-18T13:11:22Z-1669274

text: human

text: Homo sapiens

text: Total cDNA from human neurons

text: Homo sapiens


text: Mus Musculus

characteristic: ENA-CHECKLIST

text: SC

text: public

characteristic: INSDC status

characteristic: SRA accession

text: mES_lif_s1_cell53-sc-2013-07-11T08:57:13Z-1661150

characteristic: Submitter Id

text: house mouse

characteristic: common name

text: Mus musculus

text: mRNA-seq Nextera library

characteristic: sample description

text: Mus musculus


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

text: public

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 (less than 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

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

characteristic: title


text: Mus Musculus

characteristic: ArrayExpress-Species

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: SC

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: mES_lif_s1_cell18-sc-2013-07-11T08:56:39Z-1661115

text: house mouse

text: Mus musculus

text: mRNA-seq Nextera library

text: Mus musculus


characteristic: ENA-CHECKLIST

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: ArrayExpress

characteristic: broker name

text: human

characteristic: common name

text: adult

characteristic: individual

text: Homo sapiens

text: Homo sapiens

text: spleen

text: Homo sapiens

text: frozen specimen


text: SRA-Webin

characteristic: ENA-SUBMISSION-TOOL

text: ISB-USA

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: Danio rerio

text: SC

text: public

text: CH73_358J19-sc-2013-07-05T13:38:03Z-1660426

text: zebrafish

text: Danio rerio

text: Danio rerio


text: Mouse

text: SC

text: public

text: SC_HUWE5569738-sc-2013-07-16T08:26:35Z-1667116

text: house mouse

text: Mus musculus

text: Mus musculus


E-MTAB-1746:Control 3

text: University of Dublin, Trinity College

text: public

text: E-MTAB-1746:Control 3

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.

characteristic: description

text: Theiler stage 23

characteristic: developmental stage

text: Splotch-delayed (Pax3Spd/+)

characteristic: genotype

text: Mus musculus

text: Mus musculus

text: humerus

characteristic: organism part

text: Mus musculus

text: Control 3

characteristic: title


text: L1 larvae

characteristic: ArrayExpress-DevelopmentalStage

text: mixed

characteristic: ArrayExpress-Sex

text: Dracunculus medinensis

characteristic: ArrayExpress-Species

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: SC

characteristic: INSDC center name

text: public

text: Dracunculus_medinensis-sc-2013-07-15T15:11:17Z-1667993

text: Guinea worm

text: Dracunculus medinensis

text: mixed sex L1 larvae

characteristic: sample description

text: Dracunculus medinensis


characteristic: ENA-CHECKLIST

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

characteristic: broker name

text: human

characteristic: common name

text: adult

text: Homo sapiens

text: Homo sapiens

text: gall bladder

text: Homo sapiens

text: frozen specimen

characteristic: specimen with known storage state


text: Danio rerio

text: SC

text: public

text: CH73_329O13-sc-2013-07-05T13:38:49Z-1660480

text: zebrafish

text: Danio rerio

characteristic: organism

text: Danio rerio


text: Mus Musculus

text: SC

text: public

text: mES_lif_s1_cell86-sc-2013-07-11T08:57:44Z-1661183

text: house mouse

text: Mus musculus

text: mRNA-seq Nextera library

text: Mus musculus


text: public

text: ArrayExpress

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: title


E-MTAB-1712:Desiree sample

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: SLU Alnarp

characteristic: INSDC center name

text: public

text: E-MTAB-1712:Desiree sample

tag: Namespace:SLU Alnarp

text: ArrayExpress

text: potato

text: Desiree

characteristic: cultivar

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

text: fully expanded leaves

text: Phytopthora infestans

characteristic: infect

text: Solanum tuberosum

text: Solanum tuberosum

text: leaf

text: Solanum tuberosum

text: frozen specimen

text: Desiree sample


text: L1 larvae

characteristic: ArrayExpress-DevelopmentalStage

text: mixed

characteristic: ArrayExpress-Sex

text: Dracunculus medinensis

characteristic: ArrayExpress-Species

characteristic: ENA-CHECKLIST

text: SC

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: Dracunculus_medinensis-sc-2013-07-15T15:11:30Z-1668004

text: Guinea worm

text: Dracunculus medinensis

text: mixed sex L1 larvae

characteristic: sample description

text: Dracunculus medinensis


text: Plasmodium falciparum

text: SC

text: public

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: mES_lif_s1_cell61-sc-2013-07-11T08:57:21Z-1661158

text: house mouse

text: Mus musculus

text: mRNA-seq Nextera library

text: Mus musculus


text: mixed

text: Haemonchus contortus

characteristic: ArrayExpress-StrainOrLine

characteristic: External Id

text: SC

characteristic: INSDC center name

text: public

text: Haemonchus_contortus_MHco3_10_BC4_P2__5779-sc-2013-07-09T16:18:37Z-1660680

text: barber pole worm

text: Haemonchus contortus

text: 25-30 mixed male and female worms, strain identity was checked using a panel of 4 microsatellite loci that discriminate Haemonchus contortus strains

text: Haemonchus contortus

characteristic: strain


text: Mouse

text: SC

text: public

text: SC_HUWE5569728-sc-2013-07-16T08:26:23Z-1667106

text: house mouse

text: Mus musculus

text: Mus musculus


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

text: day 9

characteristic: ArrayExpress-TimePoint

text: SC

text: public

text: JCW_240613_4243_4-sc-2013-07-01T15:01:07Z-1656028

text: human

text: Homo sapiens

text: Total cDNA from human neurons

text: Homo sapiens


text: Danio rerio

characteristic: ArrayExpress-Species

text: SC

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: CH1073_890K2-sc-2013-07-05T13:37:43Z-1660405

text: zebrafish

text: Danio rerio

text: Danio rerio


characteristic: ENA-CHECKLIST

text: SRA-Webin

characteristic: ENA-SUBMISSION-TOOL

text: ISB-USA

text: public

characteristic: SRA accession

characteristic: Submitter Id

text: baker's yeast

characteristic: common name

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

characteristic: title


text: Danio rerio

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: SC

characteristic: INSDC center name

text: public

text: CH73_86A21-sc-2013-07-05T13:38:18Z-1660444

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


text: Mus musculus

characteristic: ArrayExpress-Species

characteristic: ENA-CHECKLIST

text: SC

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: house mouse

text: Mus musculus

text: Mus musculus


characteristic: ENA-FIRST-PUBLIC

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

text: public

characteristic: SRA accession

characteristic: Submitter Id

text: ArrayExpress

text: bread wheat

characteristic: common name

characteristic: cultivar

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

text: anthesis

text: 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

characteristic: title


text: Danio rerio

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: SC

characteristic: INSDC center name

text: public

text: CH1073_502G12-sc-2013-07-05T13:36:57Z-1660354

text: zebrafish

text: Danio rerio

characteristic: organism

text: Danio rerio


text: Mus Musculus

text: SC

text: public

text: mES_lif_s1_cell77-sc-2013-07-11T08:57:36Z-1661174

text: house mouse

text: Mus musculus

text: mRNA-seq Nextera library

characteristic: sample description

text: Mus musculus


text: Danio rerio

characteristic: ArrayExpress-Species

text: SC

text: public

text: CH1073_111B24-sc-2013-07-05T13:37:23Z-1660382

text: zebrafish

text: Danio rerio

text: Danio rerio


text: Danio rerio

text: SC

text: public

text: CH1073_185A15-sc-2013-07-05T13:36:54Z-1660351

text: zebrafish

text: Danio rerio

text: Danio rerio


text: Danio rerio

text: SC

text: public

text: CH1073_622I5-sc-2013-07-05T13:36:28Z-1660323

text: zebrafish

text: Danio rerio

text: Danio rerio


text: public

text: ArrayExpress

characteristic: broker name

text: bread wheat

characteristic: description

text: anthesis

characteristic: developmental stage

text: mock inoculation

text: Triticum aestivum

text: Triticum aestivum

characteristic: organism part

text: Triticum aestivum

text: frozen specimen

characteristic: specimen with known storage state


text: Danio rerio

characteristic: ENA-FIRST-PUBLIC

text: SC

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: DKEY_100B10-sc-2013-07-05T13:38:52Z-1660484

text: zebrafish

text: Danio rerio

text: Danio rerio


text: Danio rerio

text: SC

text: public

text: CH1073_411E14-sc-2013-07-05T13:37:26Z-1660385

characteristic: Submitter Id

text: zebrafish

characteristic: common name

text: Danio rerio

text: Danio rerio


text: Plasmodium falciparum

characteristic: ENA-CHECKLIST

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: SC

text: public

text: malaria parasite P. falciparum

text: Plasmodium falciparum

text: Plasmodium falciparum


text: Danio rerio

text: SC

characteristic: INSDC center name

text: public

text: zFOS_2548D4-sc-2013-07-05T13:37:59Z-1660421

text: zebrafish

text: Danio rerio

characteristic: organism

text: Danio rerio


text: Danio rerio

characteristic: ArrayExpress-Species

text: SC

text: public

text: CH1073_269A11-sc-2013-07-05T13:37:11Z-1660368

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: Mus Musculus

characteristic: ENA-FIRST-PUBLIC

text: SC

characteristic: INSDC first public

text: public

text: mES_lif_s1_cell90-sc-2013-07-11T08:57:48Z-1661187

text: house mouse

text: Mus musculus

text: mRNA-seq Nextera library

characteristic: sample description

text: Mus musculus


text: Mus Musculus

text: SC

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: mES_lif_s1_cell32-sc-2013-07-11T08:56:52Z-1661129

text: house mouse

text: Mus musculus

text: mRNA-seq Nextera library

text: Mus musculus


characteristic: ENA-CHECKLIST

text: SRA-Webin

characteristic: ENA-SUBMISSION-TOOL

text: ISB-USA

text: public

characteristic: Submitter Id

text: baker's yeast

characteristic: common name

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

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


characteristic: External Id

text: GSC

characteristic: INSDC center name

text: public

text: fungi

text: Samples were pooled in this way (tag gradient site altitude plot type) : GTATG Alpes Vizille 750 A beech_leaf GTACT Alpes Vizille 750 B beech_leaf TCGCA Alpes Vizille 750 C beech_leaf TGATC Alpes Montsec 1100 A beech_leaf ATGCG Alpes Montsec 1100 B beech_leaf GCTGT Alpes Montsec 1100 C beech_leaf CACTA Alpes pic_de_l'oeilly 1450 A beech_leaf CTAGC Alpes pic_de_l'oeilly 1450 B beech_leaf CGACG Alpes pic_de_l'oeilly 1450 C beech_leaf ACTAC Vosges Ligneville 380 A beech_leaf GCAGC Vosges Ligneville 380 B beech_leaf GCGAT Vosges Ligneville 380 C beech_leaf ACACA Vosges St_Nicolas 550 A beech_leaf AGAGT Vosges St_Nicolas 550 B beech_leaf CTATA Vosges St_Nicolas 550 C beech_leaf ACTGA Vosges Guebviller 1180 A beech_leaf GTAGA Vosges Guebviller 1180 B beech_leaf GAGTG Vosges Guebviller 1180 C beech_leaf

text: Fungi

characteristic: organism

text: Fungi


text: Danio rerio

characteristic: ArrayExpress-Species

characteristic: ENA-LAST-UPDATE

text: SC

text: public

text: CH1073_578D10-sc-2013-07-05T13:37:27Z-1660386

text: zebrafish

text: Danio rerio

text: Danio rerio


text: Danio rerio

text: SC

text: public

text: CH1073_895H19-sc-2013-07-05T13:37:51Z-1660413

text: zebrafish

text: Danio rerio

text: Danio rerio


text: Liver

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

text: SC

text: public

text: m_ChIP_Control_Liver-sc-2013-07-18T13:26:54Z-1669286

text: house mouse

text: Mus musculus

text: ChIP DNA from Liver control (MeCP2 GFP from 15 BL 6 male)

text: Mus musculus

text: Bl6 MeCP2 GFP

characteristic: strain


text: Danio rerio

characteristic: ENA-FIRST-PUBLIC

text: SC

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: CH73_361N5-sc-2013-07-05T13:38:23Z-1660450

text: zebrafish

text: Danio rerio

text: Danio rerio


text: Mus Musculus

characteristic: ENA-CHECKLIST

characteristic: External Id

text: SC

characteristic: INSDC center name

text: public

text: mES_lif_s1_cell4-sc-2013-07-11T08:56:24Z-1661101

characteristic: Submitter Id

text: house mouse

characteristic: common name

text: Mus musculus

characteristic: organism

text: mRNA-seq Nextera library

characteristic: sample description

text: Mus musculus


characteristic: ENA-LAST-UPDATE

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

text: public

text: ArrayExpress

characteristic: broker name

text: bread wheat

characteristic: cultivar

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

characteristic: description

text: anthesis

characteristic: developmental stage

text: Fusarium graminearum inoculation

characteristic: infect

text: Triticum aestivum

text: Triticum aestivum

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

characteristic: organism part

text: Triticum aestivum

text: frozen specimen

characteristic: specimen with known storage state

characteristic: title


text: Danio rerio

characteristic: ArrayExpress-Species

characteristic: ENA-FIRST-PUBLIC

text: SC

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: CH73_42N4-sc-2013-07-05T13:39:07Z-1660499

text: zebrafish

text: Danio rerio

text: Danio rerio


text: female

characteristic: ArrayExpress-Sex

text: Haemonchus contortus

characteristic: ArrayExpress-StrainOrLine

characteristic: External Id

text: SC

characteristic: INSDC center name

text: public

text: Haemonchus_contortus_MHco3_4_BC4_S4_0_2IVM_2903-sc-2013-07-09T16:19:02Z-1660683

characteristic: Submitter Id

text: barber pole worm

characteristic: common name

text: Haemonchus contortus

characteristic: organism

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


E-MTAB-1754:TS (XY)

characteristic: ENA-LAST-UPDATE

text: The Babraham Institute

text: public

text: E-MTAB-1754:TS (XY)

tag: Namespace:The Babraham Institute

text: ArrayExpress

characteristic: broker name

text: trophoblast stem cell

characteristic: cell type

text: house mouse

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

characteristic: description

text: XY

characteristic: karyotype

text: Mus musculus

text: Mus musculus

text: Mus musculus

text: fresh specimen

text: TS (XY)


text: Mus Musculus

characteristic: ArrayExpress-Species

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: SC

characteristic: INSDC first public

text: public

text: mES_lif_s1_cell37-sc-2013-07-11T08:56:57Z-1661134

text: house mouse

text: Mus musculus

text: mRNA-seq Nextera library

characteristic: sample description

text: Mus musculus


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

text: day 9

characteristic: ArrayExpress-TimePoint

text: SC

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: JCW_240613_4242_1-sc-2013-07-01T15:01:01Z-1656025

text: human

text: Homo sapiens

text: Total cDNA from human neurons

text: Homo sapiens


text: Plasmodium falciparum

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: SC

characteristic: INSDC center name

text: public

characteristic: Submitter Id

text: malaria parasite P. falciparum

characteristic: common name

text: Plasmodium falciparum

characteristic: organism

text: Plasmodium falciparum


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

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

text: public

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: mock inoculation

characteristic: infect

text: Malus domestica

text: Malus domestica

text: leaf

characteristic: organism part

text: Malus domestica

text: fresh specimen

characteristic: specimen with known storage state

text: 17 +/- 2 degree celsius

characteristic: temperature

text: 96 hour

characteristic: time post inoculation

characteristic: title


text: Danio rerio

characteristic: ArrayExpress-Species

characteristic: ENA-LAST-UPDATE

text: SC

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: CH1073_241F1-sc-2013-07-05T13:37:54Z-1660415

text: zebrafish

text: Danio rerio

text: Danio rerio


characteristic: ENA-CHECKLIST

characteristic: External Id

text: Science for Life Laboratory, Stockholm, Sweden

characteristic: INSDC center name

text: public

characteristic: Submitter Id

text: ArrayExpress

text: human

characteristic: common name

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

text: adult

characteristic: individual

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: testis

text: Homo sapiens

text: frozen specimen


text: Danio rerio

characteristic: ENA-FIRST-PUBLIC

text: SC

text: public

text: CH1073_627D2-sc-2013-07-05T13:36:36Z-1660331

text: zebrafish

text: Danio rerio

text: Danio rerio


text: University College London

text: public

text: ArrayExpress

characteristic: broker name

text: HEKn

characteristic: cell line

text: keratinocyte

characteristic: cell type

text: human

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

characteristic: description

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens

text: fresh specimen

characteristic: specimen with known storage state


text: Danio rerio

characteristic: ArrayExpress-Species

characteristic: ENA-LAST-UPDATE

text: SC

characteristic: INSDC first public

text: public

text: CH1073_833H13-sc-2013-07-05T13:37:08Z-1660364

text: zebrafish

text: Danio rerio

text: Danio rerio


characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: ArrayExpress

text: human

text: adult

characteristic: developmental stage

text: Homo sapiens

text: Homo sapiens

text: small intestine

characteristic: organism part

text: Homo sapiens

text: frozen specimen

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: External Id

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

characteristic: INSDC center name

text: public

text: E-MTAB-1104_furthernewsamples:tc152038_brain

characteristic: Submitter Id

text: 2 to 6 month

characteristic: age

text: ArrayExpress

text: house mouse

characteristic: common name

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

text: adult

characteristic: genotype

characteristic: individual

text: Mus musculus

text: Mus musculus

text: brain

text: Mus musculus

text: male

characteristic: sex


text: Danio rerio

characteristic: ArrayExpress-Species

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: SC

text: public

text: CH73_343C18-sc-2013-07-05T13:38:22Z-1660449

text: zebrafish

text: Danio rerio

characteristic: organism

text: Danio rerio


text: Systems Biology Ireland, University College Dublin

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

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


text: female

characteristic: ArrayExpress-Sex

text: Haemonchus contortus

characteristic: ArrayExpress-StrainOrLine

characteristic: External Id

text: SC

characteristic: INSDC center name

text: public

text: Haemonchus_contortus_MHco3_10_BC4_S4_0_2IVM_2970-sc-2013-07-09T16:19:09Z-1660684

characteristic: Submitter Id

text: barber pole worm

text: Haemonchus contortus

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

characteristic: sample description

text: Haemonchus contortus

characteristic: strain


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

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

text: public

text: ArrayExpress

text: bread wheat

characteristic: common name

characteristic: cultivar

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

text: anthesis

characteristic: developmental stage

text: mock inoculation

characteristic: infect

text: Triticum aestivum

text: Triticum aestivum

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

characteristic: organism part

text: Triticum aestivum

text: frozen specimen

characteristic: specimen with known storage state

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: ArrayExpress

characteristic: broker name

text: human

characteristic: description

text: adult

characteristic: individual

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: bladder

text: Homo sapiens

text: frozen specimen


text: Mus Musculus

characteristic: ArrayExpress-Species

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: SC

characteristic: INSDC center name

text: public

text: mES_lif_s1_cell70-sc-2013-07-11T08:57:29Z-1661167

characteristic: Submitter Id

text: house mouse

text: Mus musculus

text: mRNA-seq Nextera library

characteristic: sample description

text: Mus musculus


text: Institut Pasteur de Montevideo

text: public

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: undifferentiated

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


characteristic: ENA-CHECKLIST

text: SRA-Webin

characteristic: ENA-SUBMISSION-TOOL

text: ISB-USA

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: baker's yeast

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

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


text: Danio rerio

characteristic: ArrayExpress-Species

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: SC

text: public

text: CH1073_168E7-sc-2013-07-05T13:38:13Z-1660438

text: zebrafish

text: Danio rerio

characteristic: organism

text: Danio rerio


text: Mus Musculus

characteristic: External Id

text: SC

characteristic: INSDC center name

text: public

text: mES_lif_s1_cell44-sc-2013-07-11T08:57:03Z-1661141

characteristic: Submitter Id

text: house mouse

text: Mus musculus

text: mRNA-seq Nextera library

characteristic: sample description

text: Mus musculus


E-MTAB-1241:H3K36me3 -4OHT ChIP

text: public

text: E-MTAB-1241:H3K36me3 -4OHT ChIP

tag: Namespace:1 Universite de Toulouse ; UPS ; LBCMCP ; 118 route de Narbonne, 31062, Toulouse, France

text: ArrayExpress

characteristic: broker name

characteristic: cell line

text: human

characteristic: common name

text: Protocols: U20S AsiSI-ER cells were cultured in Dulbeccos modified Eagles medium (DMEM) supplemented with antibiotics and 10% FCS (Invitrogen) at 37 C under a humidified atmosphere with 5% CO2. Cells were treated with 300 nM 4OHT for 4 hours ChIP assays were carried out according the protocol described in (Iacovoni et al, 2010). Briefly, 200 ug of chromatin was subjected to immunoprecipitation using 2 ug of a gammaH2AX antibody (Epitomics 2212-1), XRCC4 (Abcam), or Rad51 (Santa Cruz). For ChIP against PolII-S2P (Abcam) 50 ug of chromatin was used, instead of 200 ug. After the washes the beads/chromatin complexes were re-suspended in 200 uL of TE buffer (Tris 10mM pH8, EDTA 0,5mM pH8) and were directly subjected to crosslink reversal in presence of 0.5% SDS overnight at 70 C. Following crosslink reversion, all immunoprecipitated DNA and input DNA were purified by phenol/chloroform, followed by DNA precipitation. DNA amount was quantified using the Quant-iTTM kit from Invitrogen. 10ng of DNA was next used for sequencing.

characteristic: description

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens

text: H3K36me3 -4OHT ChIP


text: Plasmodium falciparum

characteristic: ENA-CHECKLIST

text: SC

text: public

text: malaria parasite P. falciparum

text: Plasmodium falciparum

text: Plasmodium falciparum


text: Danio rerio

text: SC

characteristic: INSDC first public

text: public

text: CH73_362B7-sc-2013-07-05T13:38:30Z-1660458

text: zebrafish

text: Danio rerio

text: Danio rerio


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

text: SC

characteristic: INSDC last update

text: public

text: m_ChIP_GFP_low_G1-sc-2013-07-18T13:26:51Z-1669283

text: house mouse

text: Mus musculus

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

text: Mus musculus

text: Bl6 MeCP2 GFP

characteristic: strain


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Science for Life Laboratory, Stockholm, Sweden

characteristic: INSDC center name

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: ArrayExpress

text: human

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

text: adult

characteristic: developmental stage

characteristic: individual

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: kidney

characteristic: organism part

text: Homo sapiens

text: frozen specimen

characteristic: specimen with known storage state

characteristic: title


text: Mouse

characteristic: ArrayExpress-Species

characteristic: ENA-CHECKLIST

text: SC

characteristic: INSDC first public

text: public

text: SC_HUWE5569742-sc-2013-07-16T08:26:39Z-1667120

text: house mouse

characteristic: common name

text: Mus musculus

text: Mus musculus