text: public

tag: Namespace:Aarhus University, Department of Molecular Biology and Genetics

text: ArrayExpress

characteristic: broker name

text: pig

text: Protocols: At an average weight of approximately 30 kg the offspring was transferred to the finishing unit. Slaughtering was done when the largest pig in the pen reached 110 kg. Blood samples were collected from the sows and muscle, lung and liver tissue from the boar and offspring were sampled at slaughter. The RNA fragments were then copied into first strand cDNA using reverse transcriptase and random hexamer primers followed by second strand cDNA synthesis using DNA Polymerase I and RNaseH. The short cDNA fragments were finally prepared for sequencing on the Illumina Genome Analyzer using reagents provided in the Illumina Genomic DNA Sequencing Sample Prep Kit. The cDNA fragments were end-repaired using T4 DNA polymerase and Klenow DNA polymerase and a single adenine nucleotide base was added to the cDNA fragments by using 3prime to 5prime exonuclease. This was followed by ligation of Illumina adaptors, gel purification of fragments of approximately 200 bases in size and finally PCR enrichment for 15 cycles. The concentrations of the libraries were measured using Invitrogen Qubit fluorometer and the size and purity were determined using the Agilent DNA 1000 Kit on Agilent 2100 Bioanalyzer. The 89 libraries were diluted in buffer EB from QIAGEN to 10 nM, denaturated with 2 N NaOH to a final DNA concentration of 1.0 nM, diluted to 4 pM with pre-chilled hybridization buffer from Illumina and loaded in individual lanes into a 1.0 mm flowcell together with a single lane of a 2 pM PhiX control library from Illumina.

characteristic: description

text: Single boar founder family

characteristic: family history

characteristic: individual

text: Sus scrofa

text: Sus scrofa

text: longissimus dorsi

text: Sus scrofa

characteristic: title


status: PUBLIC

text: Danio rerio

tag: attribute

characteristic: ArrayExpress-Species

text: TL

characteristic: ArrayExpress-StrainOrLine

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: SC

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: SL3_07_D4b-sc-2011-10-31T09:31:33Z-1281621

characteristic: Submitter Id

text: zebrafish

characteristic: common name

text: Danio rerio

characteristic: organism

text: Exome

characteristic: sample description

text: Danio rerio

text: TL

characteristic: strain


text: male

characteristic: ArrayExpress-Sex

text: Homo Sapien

text: SC

text: public

text: SC_GMJOL5309923-sc-2012-08-24T13:41:49Z-1376472

text: human

text: Homo sapiens

text: Homo sapiens


text: male

text: Homo Sapien

text: SC

text: public

text: SC_GMJOL5309971-sc-2012-07-20T12:41:50Z-1376570

text: human

text: Homo sapiens

text: Homo sapiens


text: Mus Musculus

text: SC

text: public

text: mES_i2m_s1_cell8-sc-2013-06-06T21:57:15Z-1643322

text: house mouse

text: Mus musculus

text: mRNA-seq Nextera library

text: Mus musculus


text: Mus Musculus

text: SC

text: public

text: 2042STDY5252514-sc-2012-02-22T11:51:01Z-1309835

text: house mouse

text: Mus musculus

text: Mus musculus


text: Haemonchus contortus

text: SC

text: public

text: barber pole worm

text: Haemonchus contortus

text: bacterial artificial chromosome (BAC)

text: Haemonchus contortus


text: Danio rerio

text: SC

text: public

text: CH73_352N13-sc-2012-02-29T12:11:52Z-1371847

text: zebrafish

text: Danio rerio

text: Danio rerio


text: Mus Musculus

text: SC

text: public

text: house mouse

text: Mus musculus

text: Mus musculus


text: Mus Musculus

text: SC

text: public

text: 2042STDY5305534-sc-2012-03-05T08:24:20Z-1370541

text: house mouse

text: Mus musculus

text: Mus musculus


text: male

text: Haemonchus contortus

text: inbred ISE

text: SC

text: public

text: Haemonchus_contortus-sc-2012-02-06T13:16:52Z-1289860

text: barber pole worm

text: Haemonchus contortus

text: Haemonchus contortus

text: inbred ISE


text: male

text: Mus Musculus

text: SC

text: public

text: 2042STDY5251969-sc-2011-11-30T14:48:32Z-1309336

text: house mouse

text: Mus musculus

text: Mus musculus


text: ES Cells

characteristic: ArrayExpress-CellType

text: NanogGFP

characteristic: ArrayExpress-Genotype

text: male

text: Mus Musculus

text: SC

text: public

text: house mouse

text: Mus musculus

text: BSSeq from ESCs

text: Mus musculus


text: Aedes aegypti

characteristic: ArrayExpress-Species

text: SC

text: public

text: Aedes_aegypti_MD_RNA-sc-2012-02-06T12:56:13Z-2958

text: yellow fever mosquito

text: Aedes aegypti

text: Aedes aegypti


text: Mus Musculus

characteristic: ENA-FIRST-PUBLIC

text: SC

text: public

text: mES_i2m_s1_cell84-sc-2013-06-06T21:59:32Z-1643398

text: house mouse

text: Mus musculus

text: mRNA-seq Nextera library

text: Mus musculus


text: Mus Musculus

characteristic: ENA-LAST-UPDATE

text: SC

text: public

text: SC_GCIGC5375938-sc-2012-08-02T09:01:22Z-1457623

text: house mouse

text: Mus musculus

text: Mus musculus


characteristic: External Id

text: Aarhus University, Department of Molecular Biology and Genetics

text: public

text: ArrayExpress

characteristic: broker name

text: pig

text: Protocols: Ten different tissues from two unrelated one year old Landrace boars were included in the study. Hence, total RNA was extracted from heart, spleen, liver, kidney, lung, musculus longissimus dorsi, occipital cortex, hypothalamus, frontal cortex, and cerebellum employing the mirVanaTM RNA extraction kit (Ambion) according to manufacturers protocol, yielding a total of 20 samples. RNA integrity was assessed by manual inspection of the individual RNA samples on a 2% agarose gel. The RNA fragments were then copied into first strand cDNA using reverse transcriptase and random hexamer primers followed by second strand cDNA synthesis using DNA Polymerase I and RNaseH. The short cDNA fragments were finally prepared for sequencing on the Illumina Genome Analyzer using reagents provided in the Illumina Genomic DNA Sequencing Sample Prep Kit. The cDNA fragments were end-repaired using T4 DNA polymerase and Klenow DNA polymerase and a single adenine nucleotide base was added to the cDNA fragments by using 3 prime to 5 prime exonuclease. This was followed by ligation of Illumina adaptors, gel purification of fragments of approximately 200 bases in size and finally PCR enrichment for 15 cycles. The concentrations of the libraries were measured using Invitrogen Qubit fluorometer and the size and purity were determined using the Agilent DNA 1000 Kit on Agilent 2100 Bioanalyzer. The 89 libraries were diluted in buffer EB from QIAGEN to 10 nM, denaturated with 2 N NaOH to a final DNA concentration of 1.0 nM, diluted to 4 pM with pre-chilled hybridization buffer from Illumina and loaded in individual lanes into a 1.0 mm flowcell together with a single lane of a 2 pM PhiX control library from Illumina.

characteristic: description

characteristic: individual

text: Sus scrofa

text: Sus scrofa

text: kidney

characteristic: organism part

text: Sus scrofa

text: male

characteristic: sex

characteristic: title

type: has member


text: EBI

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: arak

text: khomein

text: Asiatic mouflon

characteristic: common name

text: Asiatic Mouflon IROO-M12-9997 from NextGen project

text: Iran

characteristic: geographic location (country and/or sea)

text: 34.178 degrees

characteristic: latitude

text: 50.344 degrees

characteristic: longitude

text: Ovis orientalis

characteristic: sampling date

text: Ovis orientalis

text: male

text: Ovis orientalis


text: Mus Musculus

characteristic: ArrayExpress-Species

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: SC

text: public

text: 2042STDY5252898-sc-2012-02-22T11:54:44Z-1310206

text: house mouse

text: Mus musculus

characteristic: organism

text: Mus musculus


text: Danio rerio

text: SC

text: public

text: ZFOS_429H6-sc-2012-02-29T12:45:20Z-1372580

text: zebrafish

text: Danio rerio

text: Danio rerio


text: Neurons

characteristic: ArrayExpress-CellType

text: Adult

characteristic: ArrayExpress-DevelopmentalStage

text: Wildtype

characteristic: ArrayExpress-Genotype

text: Brain

characteristic: ArrayExpress-OrganismPart

text: wildtype

characteristic: ArrayExpress-Phenotype

text: male

characteristic: ArrayExpress-Sex

text: Mus musculus

characteristic: ArrayExpress-StrainOrLine

text: SC

text: public

text: m_5mC_Neuron_2-sc-2013-03-19T13:56:08Z-1599115

text: house mouse

text: Mus musculus

text: gDNA from FACS sorted neurons

characteristic: sample description

text: Mus musculus

characteristic: strain


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

text: mES_lif_s1_cell49-sc-2013-07-11T08:57:08Z-1661146

characteristic: Submitter Id

text: house mouse

characteristic: common name

text: Mus musculus

text: mRNA-seq Nextera library

text: Mus musculus


text: Danio rerio

characteristic: ArrayExpress-Species

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: SC

text: public

text: CH1073_595E10-sc-2013-07-05T13:36:20Z-1660315

text: zebrafish

text: Danio rerio

characteristic: organism

text: Danio rerio


text: Mus Musculus

text: SC

text: public

text: mES_i2m_s1_cell65-sc-2013-06-06T21:58:53Z-1643379

text: house mouse

text: Mus musculus

text: mRNA-seq Nextera library

text: Mus musculus


text: Human

text: Promega

text: SC

text: public

text: Homo_sapiens-sc-2013-04-03T15:16:58Z-1606966

text: human

text: Homo sapiens

text: genomic DNA

text: Homo sapiens

text: Promega


text: male

characteristic: ArrayExpress-Sex

text: Homo Sapien

text: SC

text: public

text: SC_GMJOL5309902-sc-2012-07-20T12:40:49Z-1376423

text: human

text: Homo sapiens

text: Homo sapiens


text: public

text: ArrayExpress

characteristic: broker name

text: pig

text: Protocols: At an average weight of approximately 30 kg the offspring was transferred to the finishing unit. Slaughtering was done when the largest pig in the pen reached 110 kg. Blood samples were collected from the sows and muscle, lung and liver tissue from the boar and offspring were sampled at slaughter. The RNA fragments were then copied into first strand cDNA using reverse transcriptase and random hexamer primers followed by second strand cDNA synthesis using DNA Polymerase I and RNaseH. The short cDNA fragments were finally prepared for sequencing on the Illumina Genome Analyzer using reagents provided in the Illumina Genomic DNA Sequencing Sample Prep Kit. The cDNA fragments were end-repaired using T4 DNA polymerase and Klenow DNA polymerase and a single adenine nucleotide base was added to the cDNA fragments by using 3prime to 5prime exonuclease. This was followed by ligation of Illumina adaptors, gel purification of fragments of approximately 200 bases in size and finally PCR enrichment for 15 cycles. The concentrations of the libraries were measured using Invitrogen Qubit fluorometer and the size and purity were determined using the Agilent DNA 1000 Kit on Agilent 2100 Bioanalyzer. The 89 libraries were diluted in buffer EB from QIAGEN to 10 nM, denaturated with 2 N NaOH to a final DNA concentration of 1.0 nM, diluted to 4 pM with pre-chilled hybridization buffer from Illumina and loaded in individual lanes into a 1.0 mm flowcell together with a single lane of a 2 pM PhiX control library from Illumina.

characteristic: description

text: Single boar founder family

characteristic: family history

characteristic: individual

text: Sus scrofa

text: Sus scrofa

text: longissimus dorsi

characteristic: organism part

text: Sus scrofa

characteristic: title


text: diseased

characteristic: ArrayExpress-DiseaseState

text: cancer

characteristic: ArrayExpress-Phenotype

text: Mus Musculus

text: cancer

characteristic: EGA-Disease

text: SC

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: 3__SB_induced_tumour_37-sc-2011-11-07T15:37:30Z-1297095

text: house mouse

text: Mus musculus

text: transposon-induced tumour

characteristic: sample description

text: Mus musculus


text: Mus musculus

characteristic: ArrayExpress-Species

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: SC

text: public

characteristic: INSDC status

characteristic: SRA accession

text: 2042STDY5261034-sc-2011-12-15T14:31:36Z-1319264

characteristic: Submitter Id

text: house mouse

characteristic: common name

text: Mus musculus

text: Mus musculus


text: Mus musculus

characteristic: External Id

text: SC

text: public

text: SC_GCIGC5274853-sc-2012-01-23T14:01:37Z-1335097

text: house mouse

text: Mus musculus

characteristic: organism

text: Mus musculus


text: Mus Musculus

text: SC

text: public

text: SC_GCIGC5375917-sc-2012-08-02T09:00:58Z-1457602

text: house mouse

text: Mus musculus

text: Mus musculus


text: Plasmodium falciparum

characteristic: ENA-CHECKLIST

text: SC

text: public

text: malaria parasite P. falciparum

text: Plasmodium falciparum

text: Plasmodium falciparum


text: diseased

characteristic: ArrayExpress-DiseaseState

text: cancer

text: Mus Musculus

text: cancer

text: SC

text: public

text: 5__SB_induced_tumour_72-sc-2011-11-07T15:37:02Z-1297057

text: house mouse

text: Mus musculus

text: transposon-induced tumour

text: Mus musculus


text: diseased

text: cancer

characteristic: ArrayExpress-Phenotype

text: Mus Musculus

text: cancer

text: SC

text: public

text: 3__SB_induced_tumour_38-sc-2011-11-07T15:37:31Z-1297096

text: house mouse

text: Mus musculus

text: transposon-induced tumour

text: Mus musculus


text: Mus Musculus

text: SC

text: public

text: mES_lif_s1_cell67-sc-2013-07-11T08:57:26Z-1661164

text: house mouse

text: Mus musculus

text: mRNA-seq Nextera library

text: Mus musculus


text: Danio rerio

text: SC

text: public

text: CH73_26J14-sc-2013-05-28T14:22:49Z-1633986

text: zebrafish

text: Danio rerio

text: Danio rerio


text: cercariae

characteristic: ArrayExpress-DevelopmentalStage

text: whole

characteristic: ArrayExpress-OrganismPart

text: Schistosoma mansoni

text: Puerto Rican

characteristic: ArrayExpress-StrainOrLine

text: SC

text: public

text: S__mansoni_CF1_Line-sc-2013-04-30T12:02:52Z-1619914

text: Schistosoma mansoni

text: cercariae

text: Schistosoma mansoni

text: Puerto Rican

characteristic: strain


text: Mus Musculus

text: SC

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: SC_MOG5351613-sc-2012-05-31T09:00:16Z-1426161

text: house mouse

text: Mus musculus

text: Mus musculus


text: Mus Musculus

characteristic: ArrayExpress-Species

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: SC

text: public

text: house mouse

text: Mus musculus

text: Mus musculus


text: Primary macrophages

characteristic: ArrayExpress-CellType

text: 100 nM

characteristic: ArrayExpress-Dose

characteristic: ArrayExpress-Genotype

text: Bone marrow

text: KO

text: male

characteristic: ArrayExpress-Sex

text: Mus musculus

text: Mus musculus

text: 24 hours

characteristic: ArrayExpress-TimePoint

text: SC

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: house mouse

text: Mus musculus

text: RNA from BMDM

characteristic: sample description

text: Mus musculus

text: Mus musculus


text: Danio rerio

characteristic: External Id

text: SC

text: public

text: ZFOS_505G6-sc-2012-02-29T12:45:26Z-1372586

text: zebrafish

characteristic: common name

text: Danio rerio

characteristic: organism

text: Danio rerio


text: Human

text: Promega

characteristic: ArrayExpress-StrainOrLine

text: SC

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: Homo_sapiens-sc-2012-03-12T16:26:44Z-1378718

text: human

text: Homo sapiens

text: genomic DNA

text: Homo sapiens

text: Promega

characteristic: strain


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: Humanitas Clinical and Research Center

characteristic: INSDC last update

text: public

tag: Namespace:Humanitas Clinical and Research Center

text: ArrayExpress

characteristic: broker name

text: cardiac myocyte

characteristic: cell type

text: house mouse

text: Protocols: 2-month-old male C57BL/6J mice were subjected under anesthesia to transverse aortic constriction for 1 week. Cardiomyocytes were isolated from the hearts at the end of perfusion with collagenase(collagenase type II). Immunoprecipitate DNA from Chromatin Immunoprecipitaion assay (ChIP) using antibody to H3K9ac,H3K27ac,H3K4me3, H3K79me2, H3K9me2, H3K9me3 and H3K27me3.

characteristic: description

text: Mus musculus

text: Mus musculus

text: Mus musculus

text: male

characteristic: sex

characteristic: strain or line

characteristic: title


text: Mus musculus

characteristic: ArrayExpress-Species

text: SC

text: public

characteristic: INSDC status

characteristic: SRA accession

text: nr2adc_f_rnaseq-sc-2012-02-06T13:08:28Z-1001789

characteristic: Submitter Id

text: house mouse

text: Mus musculus

text: Mus musculus


text: Yeast

characteristic: External Id

text: SC

text: public

text: SC_MFY5287908-sc-2012-02-02T14:10:25Z-1349328

text: baker's yeast

characteristic: common name

text: Saccharomyces cerevisiae

characteristic: organism

text: Saccharomyces cerevisiae


text: SC

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: RolandsMouseTumoursFeb2011-sc-2011-03-23-1101558

text: western European house mouse

text: Mus musculus domesticus

text: Mus musculus domesticus

characteristic: strain


text: Human

text: Promega

characteristic: ArrayExpress-StrainOrLine

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: SC

characteristic: INSDC last update

text: public

text: Homo_sapiens-sc-2013-04-03T15:18:38Z-1607036

text: human

text: Homo sapiens

text: genomic DNA

characteristic: sample description

text: Homo sapiens

text: Promega


text: Danio rerio

text: SC

text: public

text: CH1073_184F13-sc-2011-10-27T10:26:31Z-1289986

text: zebrafish

text: Danio rerio

text: Danio rerio


status: KILLED

text: HeLa Kyoto H2B-mRFP/mEGFP-alpha-tubulin

characteristic: CellLine

text: cervical carcinoma

characteristic: CellType

text: EMBL Heidelberg

text: killed

text: Homo sapiens

characteristic: Organism

characteristic: Replicate

text: female

characteristic: Sex

tag: Namespace:EMBL Heidelberg

text: ArrayExpress

characteristic: broker name

text: human

text: Protocols: Cells were cultured in DMEM containing 4.5 g/l glucose, 10 % heatinactivated foetal bovine serum, 2 mM glutamine, 100 U/ml penicillin and 100ug/ml streptomycin and incubated at 37 degrees C and 5% CO2 RNA free genomic DNA was prepared using Qiagen DNeasy Blood and Tissue kit (Qiagen)

characteristic: description

text: Homo sapiens

text: Homo sapiens


E-MTAB-1628:ST-HSC dH19/dIgf1r

characteristic: External Id

text: Stowers Institute for Medical Research

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-1628:ST-HSC dH19/dIgf1r

tag: Namespace:Stowers Institute for Medical Research

characteristic: Submitter Id

text: 6 week

characteristic: age

text: ArrayExpress

text: ST-HSC (Lin- Sca1+ cKit+ CD34+ Flk2-)

characteristic: cell type

text: house mouse

characteristic: common name

text: Protocols: All mice used in this study were housed in the animal facility at the Stowers Institute for Medical Research (SIMR) and handled according to SIMR and National Institutes of Health (NIH) guidelines. All procedures were approved by the Institutional Animal Care and Use Committee (IACUC) of SIMR. H19-DMR flDMR/flDMR mice on B6 background were kindly provided by Dr. Marisa S. Bartolomei (University of Pennsylvania Perelman School of Medicine). Conditional mutant Igf1rfl/+ was kindly provided by Thomas L Clemens (Center for Musculoskeletal Research, Johns Hopkins Medicine, 601 North Caroline Street, Baltimore, MD 21287). Interferon inducible Mx1-Cre or tamoxifen inducible Scl-Cre mouse strains were used to delete the floxed H19-DMR and Igf1r. For Mx1-Cre activation, 250ug of pIpC was injected intraperitoneal every other day for 14 days at 5 weeks of age. For Scl-CreER activation, 2mg tamoxifen dissolved in 0.1 ml of corn oil was injected intraperitoneal every day for 5 days. Illumina TruSeq RNA Sample Prep Kit (Catalog #: FC-122-1001) The RNA-sequencing library was prepared from approximately 200 ng of total RNA (mH19dDMR/+ Igf1r-/- , mH19dDMR/+Igf1rf-/- and mH19flDMR/+) for each sample. The fragment size in the generated library ranged from 220 to 500 bps with a peak at 280 bps.

text: mH19 dDMR/+ Igf1r -/-

characteristic: genotype

text: Mus musculus

text: Mus musculus

text: FACS-sorted bone marrow

characteristic: organism part

text: Mus musculus

text: fresh specimen

characteristic: specimen with known storage state

text: ST-HSC dH19/dIgf1r

characteristic: title


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: University of Helsinki

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

tag: Namespace:University of Helsinki

text: ArrayExpress

characteristic: cell line

text: fruit fly

text: Protocols: Chromatin immunoprecipitation (ChIP)-assays were done as in Tuupanen et al.Nature Genetics 41, 885, 2009. ChIP-seq was performed essentially as described in (Tuupanen et al.Nature Genetics 41, 885, 2009) with the following modifications. ChIP for Myc and Max: S2 cells were formaldehyde crosslinked, sonicated and immunoprecipitated with the following set of antibodies (Santa Cruz Biotechnology, Inc.): Myc: dN-20 and d1-717, sc-15832 and sc-28207. Max: d1-160, sc-28209. IgG controls sc-2027 and sc-2028. ChIP for E2f and Myb: S2 cells were transiently transfected with plasmids (backbone pRmHa-1) containing metallothionein promoter driven Cterminally His-streptavidin binding peptide-3xV5 tagged Drosophila open reading frames. Expression of the genes was induced 24 hr after transfection by 0.5 mM CuSO4, and the incubation continued for 48 hr until formaldehyde crosslinking was done. Immunoprecipitations were made with 7.5 mg of monoclonal anti-V5 antibody (46-1157; Invitrogen) or IgG control antibody (sc-2025; Santa Cruz Biotechnology, Inc.) Chromatin immunoprecipitation (ChIP)-seq libraries were prepaired as in Tuupanen et al.Nature Genetics 41, 885, 2009. Library preparations were done by repairing the immunoprecipitated DNA using Klenow and T4 DNA polymerase and T4 polynucleotide kinase (MBI Fermentas, Vilnius, Latvia), and ligating the Illumina sequencing adapters according to manufacturers instructions.

text: Drosophila melanogaster

characteristic: organism

text: Drosophila melanogaster

text: Drosophila melanogaster

text: fresh specimen


text: Haemonchus contortus

characteristic: ArrayExpress-Species

characteristic: External Id

text: SC

text: public

characteristic: INSDC status

text: barber pole worm

text: Haemonchus contortus

text: bacterial artificial chromosome (BAC)

characteristic: sample description

text: Haemonchus contortus


text: Danio rerio

text: SC

text: public

characteristic: SRA accession

text: ZFOS_2158C6-sc-2012-02-29T12:44:55Z-1372555

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_cell79-sc-2013-07-11T08:57:38Z-1661176

text: house mouse

characteristic: common name

text: Mus musculus

text: mRNA-seq Nextera library

text: Mus musculus


text: Aarhus University, Department of Molecular Biology and Genetics

text: public

text: ArrayExpress

characteristic: broker name

text: pig

text: Protocols: Ten different tissues from two unrelated one year old Landrace boars were included in the study. Hence, total RNA was extracted from heart, spleen, liver, kidney, lung, musculus longissimus dorsi, occipital cortex, hypothalamus, frontal cortex, and cerebellum employing the mirVanaTM RNA extraction kit (Ambion) according to manufacturers protocol, yielding a total of 20 samples. RNA integrity was assessed by manual inspection of the individual RNA samples on a 2% agarose gel. The RNA fragments were then copied into first strand cDNA using reverse transcriptase and random hexamer primers followed by second strand cDNA synthesis using DNA Polymerase I and RNaseH. The short cDNA fragments were finally prepared for sequencing on the Illumina Genome Analyzer using reagents provided in the Illumina Genomic DNA Sequencing Sample Prep Kit. The cDNA fragments were end-repaired using T4 DNA polymerase and Klenow DNA polymerase and a single adenine nucleotide base was added to the cDNA fragments by using 3 prime to 5 prime exonuclease. This was followed by ligation of Illumina adaptors, gel purification of fragments of approximately 200 bases in size and finally PCR enrichment for 15 cycles. The concentrations of the libraries were measured using Invitrogen Qubit fluorometer and the size and purity were determined using the Agilent DNA 1000 Kit on Agilent 2100 Bioanalyzer. The 89 libraries were diluted in buffer EB from QIAGEN to 10 nM, denaturated with 2 N NaOH to a final DNA concentration of 1.0 nM, diluted to 4 pM with pre-chilled hybridization buffer from Illumina and loaded in individual lanes into a 1.0 mm flowcell together with a single lane of a 2 pM PhiX control library from Illumina.

characteristic: description

characteristic: individual

text: Sus scrofa

text: Sus scrofa

text: spleen

characteristic: organism part

text: Sus scrofa

text: male

characteristic: sex


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: INSDC center name

characteristic: INSDC first public

text: public

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

text: ArrayExpress

text: human

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

text: adult

characteristic: developmental stage

text: Homo sapiens

text: Homo sapiens

text: lymph node

text: Homo sapiens

text: frozen specimen

characteristic: specimen with known storage state

characteristic: title


text: female

characteristic: ArrayExpress-Sex

text: Homo Sapien

characteristic: ArrayExpress-Species

characteristic: External Id

text: SC

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: SC_GMJOL5309868-sc-2012-07-19T11:01:55Z-1376530

text: human

text: Homo sapiens

characteristic: organism

text: Homo sapiens


text: male

text: Mus Musculus

text: SC

text: public

characteristic: SRA accession

text: 2042STDY5252081-sc-2011-11-30T14:49:15Z-1309380

characteristic: Submitter Id

text: house mouse

characteristic: common name

text: Mus musculus

text: Mus musculus


text: Mouse

characteristic: ENA-CHECKLIST

text: SC

text: public

text: SC_HUWE5569746-sc-2013-07-16T08:26:43Z-1667124

text: house mouse

text: Mus musculus

text: Mus musculus


text: Plasmodium falciparum

characteristic: ENA-FIRST-PUBLIC

text: SC

text: public

text: malaria parasite P. falciparum

text: Plasmodium falciparum

text: Plasmodium falciparum


text: Danio rerio

text: TL/AB

characteristic: ArrayExpress-StrainOrLine

characteristic: ENA-LAST-UPDATE

text: SC

text: public

text: SL6_10_H5-sc-2013-02-21T15:17:16Z-1513925

text: zebrafish

text: Danio rerio

text: Exome

characteristic: sample description

text: Danio rerio

text: TL/AB

characteristic: strain


text: SC

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: house mouse

text: Mus musculus

text: Mus musculus

text: F1 cross


text: Homo Sapien

text: SC

text: public

text: ILBHuGRC5514802-sc-2013-04-09T14:46:03Z-1609532

text: human

text: Homo sapiens

text: Homo sapiens


text: Mus Musculus

text: SC

text: public

text: mES_lif_s1_cell13-sc-2013-07-11T08:56:34Z-1661110

text: house mouse

text: Mus musculus

text: mRNA-seq Nextera library

text: Mus musculus


text: Mus musculus

text: SC

text: public

text: SC_GCIGC5271299-sc-2012-01-18T12:40:34Z-1331053

text: house mouse

text: Mus musculus

text: Mus musculus


text: Mus Musculus

text: SC

text: public

text: 2042STDY5252693-sc-2012-02-22T11:52:05Z-1310001

text: house mouse

text: Mus musculus

text: Mus musculus


text: male

characteristic: ArrayExpress-Sex

text: Homo Sapien

text: SC

text: public

text: 2042STDY5251919-sc-2012-03-08T09:10:42Z-1309237

text: human

text: Homo sapiens

text: Homo sapiens


text: female

text: Homo Sapien

characteristic: ArrayExpress-Species

text: SC

text: public

text: SC_GMMAN5482215-sc-2013-03-07T10:02:13Z-1575215

text: human

text: Homo sapiens

text: Homo sapiens


text: Danio rerio

characteristic: External Id

text: SC

text: public

text: ZFOS_2210A7-sc-2012-02-29T12:44:57Z-1372557

text: zebrafish

text: Danio rerio

text: Danio rerio


text: male

text: Mus Musculus

text: SC

characteristic: INSDC last update

text: public

text: 2042STDY5252393-sc-2012-03-13T13:17:10Z-1309622

text: house mouse

text: Mus musculus

text: Mus musculus


text: Mus Musculus

text: SC

text: public

characteristic: INSDC status

text: 2042STDY5305480-sc-2012-03-05T08:22:18Z-1370450

text: house mouse

text: Mus musculus

text: Mus musculus


text: Mouse

text: SC

text: public

text: SC_MTV5229158-sc-2011-10-12T11:48:22Z-1281391

text: house mouse

text: Mus musculus

characteristic: organism

text: Mus musculus


text: Danio rerio

text: TL

text: SC

text: public

characteristic: SRA accession

text: SL3_08_C10b-sc-2011-10-31T09:35:03Z-1281944

text: zebrafish

text: Danio rerio

text: Exome

text: Danio rerio

text: TL


text: Plasmodium falciparum

text: SC

text: public

text: HB3EXO0_cDNA-sc-2012-09-21T11:20:55Z-1483618

characteristic: Submitter Id

text: malaria parasite P. falciparum

text: Plasmodium falciparum

text: 0hr blood-stage exonuclease treated RNA

text: Plasmodium falciparum


text: Haemonchus contortus

text: SC

text: public

text: barber pole worm

characteristic: common name

text: Haemonchus contortus

text: bacterial artificial chromosome (BAC)

text: Haemonchus contortus


text: Danio rerio

text: TL/AB

text: SC

text: public

text: SL6_10_A6-sc-2013-02-21T15:17:17Z-1513926

text: zebrafish

text: Danio rerio

text: Exome

text: Danio rerio

text: TL/AB


text: Homo Sapien

text: SC

text: public

text: SC_CTRAC5375833-sc-2012-07-31T07:51:09Z-1457518

text: human

text: Homo sapiens

text: Homo sapiens


text: Mus musculus

text: SC

text: public

text: SC_GCIGC5274872-sc-2012-01-23T14:01:52Z-1335116

text: house mouse

text: Mus musculus

text: Mus musculus


text: Mouse

characteristic: ENA-CHECKLIST

text: SC

text: public

text: SC_HUWE5569730-sc-2013-07-16T08:26:25Z-1667108

text: house mouse

text: Mus musculus

text: Mus musculus


characteristic: ENA-FIRST-PUBLIC

text: Aarhus University, Department of Molecular Biology and Genetics

text: public

text: ArrayExpress

characteristic: broker name

text: pig

text: Protocols: Ten different tissues from two unrelated one year old Landrace boars were included in the study. Hence, total RNA was extracted from heart, spleen, liver, kidney, lung, musculus longissimus dorsi, occipital cortex, hypothalamus, frontal cortex, and cerebellum employing the mirVanaTM RNA extraction kit (Ambion) according to manufacturers protocol, yielding a total of 20 samples. RNA integrity was assessed by manual inspection of the individual RNA samples on a 2% agarose gel. The RNA fragments were then copied into first strand cDNA using reverse transcriptase and random hexamer primers followed by second strand cDNA synthesis using DNA Polymerase I and RNaseH. The short cDNA fragments were finally prepared for sequencing on the Illumina Genome Analyzer using reagents provided in the Illumina Genomic DNA Sequencing Sample Prep Kit. The cDNA fragments were end-repaired using T4 DNA polymerase and Klenow DNA polymerase and a single adenine nucleotide base was added to the cDNA fragments by using 3 prime to 5 prime exonuclease. This was followed by ligation of Illumina adaptors, gel purification of fragments of approximately 200 bases in size and finally PCR enrichment for 15 cycles. The concentrations of the libraries were measured using Invitrogen Qubit fluorometer and the size and purity were determined using the Agilent DNA 1000 Kit on Agilent 2100 Bioanalyzer. The 89 libraries were diluted in buffer EB from QIAGEN to 10 nM, denaturated with 2 N NaOH to a final DNA concentration of 1.0 nM, diluted to 4 pM with pre-chilled hybridization buffer from Illumina and loaded in individual lanes into a 1.0 mm flowcell together with a single lane of a 2 pM PhiX control library from Illumina.

characteristic: description

characteristic: individual

text: Sus scrofa

text: Sus scrofa

text: lung

characteristic: organism part

text: Sus scrofa

text: male

characteristic: sex

characteristic: title


text: Homo Sapien

characteristic: ENA-LAST-UPDATE

text: SC

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: ILBHuGRC5514804-sc-2013-04-09T14:46:07Z-1609534

text: human

text: Homo sapiens

text: Homo sapiens


characteristic: External Id

characteristic: INSDC last update

text: public

text: ArrayExpress

text: pig

text: Sus scrofa

text: Sus scrofa

text: heart

text: Sus scrofa

text: male


text: Danio rerio

characteristic: ArrayExpress-Species

text: TL

characteristic: ArrayExpress-StrainOrLine

text: SC

text: public

characteristic: INSDC status

text: SL3_07_E11b-sc-2011-10-31T09:32:42Z-1281730

text: zebrafish

text: Danio rerio

characteristic: organism

text: Exome

characteristic: sample description

text: Danio rerio

text: TL

characteristic: strain


text: Homo Sapien

characteristic: ENA-FIRST-PUBLIC

text: SC

text: public

characteristic: SRA accession

text: 2014STDY5345496-sc-2012-05-25T10:41:16Z-1419628

characteristic: Submitter Id

text: human

characteristic: common name

text: Homo sapiens

text: Homo sapiens


text: SC

text: public

text: house mouse

text: Mus musculus

text: Mus musculus


text: Human

text: Promega

text: SC

text: public

text: Homo_sapiens-sc-2013-04-03T15:17:04Z-1606972

text: human

text: Homo sapiens

text: genomic DNA

text: Homo sapiens

text: Promega


text: female

characteristic: ArrayExpress-Sex

text: Mus Musculus

text: SC

text: public

text: 2042STDY5252017-sc-2011-11-30T14:47:02Z-1309245

text: house mouse

text: Mus musculus

text: Mus musculus


text: Plasmodium falciparum

characteristic: ENA-CHECKLIST

text: SC

text: public

text: malaria parasite P. falciparum

text: Plasmodium falciparum

text: Plasmodium falciparum


text: diseased

characteristic: ArrayExpress-DiseaseState

text: cancer

characteristic: ArrayExpress-Phenotype

text: Mus Musculus

text: cancer

characteristic: EGA-Disease

characteristic: ENA-LAST-UPDATE

text: SC

text: public

text: 5__SB_induced_tumour_32-sc-2011-11-07T15:36:34Z-1297017

text: house mouse

text: Mus musculus

text: transposon-induced tumour

text: Mus musculus


text: diseased

text: cancer

text: Mus Musculus

text: cancer

characteristic: External Id

text: SC

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: 5__SB_induced_tumour_61-sc-2011-11-07T15:36:54Z-1297046

text: house mouse

text: Mus musculus

text: transposon-induced tumour

text: Mus musculus


text: Danio rerio

characteristic: ArrayExpress-Species

text: TL

characteristic: ArrayExpress-StrainOrLine

text: SC

text: public

characteristic: INSDC status

text: SL3_07_C11b-sc-2011-10-31T09:32:38Z-1281725

text: zebrafish

text: Danio rerio

characteristic: organism

text: Exome

text: Danio rerio

text: TL


text: Homo Sapien

characteristic: ENA-FIRST-PUBLIC

text: SC

text: public

characteristic: SRA accession

text: SC_CTRAC5324876-sc-2012-04-04T13:26:23Z-1393233

text: human

text: Homo sapiens

text: Homo sapiens


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: title


text: Signaling and Functional Genomics, DKFZ

text: public

tag: Namespace:Signaling and Functional Genomics, DKFZ

text: 21 day

characteristic: age

text: ArrayExpress

characteristic: broker name

text: house mouse

text: Protocols: Evi floxed mice were crossed with K14-Cre mice to delete Evi gene in epithelial cells. Skin of 21 day old mice was collected from mutants and wildtype animals. After tissue digestion RNA from epidermal sheets was prepared. Three fully independent biological replicates where sampled. RNA was extracted from epidermal sheets of three wildtype and Evi-LOF mice. The poly(A)+ fraction was isolated from each of the six samples with the Dynabeads mRNA Purification Kit (Invitrogen). For each sample, a library for sequencing with a SOLiD4 sequencer was prepared. random primers with a hexamer adapter sequence were annealed to the 3' end of the mRNA and the first DNA strand synthesized. Following RNA digestion, the DNA was purified using Agencourt RNAClean XP Beads. Random primers were annealed to the DNA for second strand synthesis. Agencourt Ampure XP Bead selection was used to purify and size select the double stranded DNA. The library was amplified and barcoded.

characteristic: description

text: adult

characteristic: developmental stage

text: wild type

characteristic: genotype

text: Mus musculus

text: Mus musculus

text: epidermis

characteristic: organism part

text: Mus musculus


text: Mus Musculus

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: SC

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: 2042STDY5252818-sc-2012-02-22T11:53:27Z-1310106

text: house mouse

text: Mus musculus

text: Mus musculus


text: male

characteristic: ArrayExpress-Sex

text: Mus Musculus

characteristic: ArrayExpress-Species

characteristic: ENA-FIRST-PUBLIC

text: SC

text: public

characteristic: INSDC status

text: 2042STDY5252251-sc-2011-11-30T14:51:40Z-1309530

text: house mouse

text: Mus musculus

characteristic: organism

text: Mus musculus


text: Danio rerio

text: SC

text: public

characteristic: SRA accession

text: CH73_278J10-sc-2012-02-29T12:12:00Z-1371854

characteristic: Submitter Id

text: zebrafish

characteristic: common name

text: Danio rerio

text: Danio rerio


text: diseased

characteristic: ArrayExpress-DiseaseState

text: cancer

characteristic: ArrayExpress-Phenotype

text: Mus Musculus

text: cancer

characteristic: EGA-Disease

text: SC

text: public

text: 3__SB_induced_tumour_59-sc-2011-11-07T15:37:45Z-1297117

text: house mouse

text: Mus musculus

text: transposon-induced tumour

characteristic: sample description

text: Mus musculus


text: Mus Musculus

characteristic: ENA-LAST-UPDATE

text: SC

text: public

text: 2042STDY5252917-sc-2012-02-22T11:55:00Z-1310225

text: house mouse

text: Mus musculus

text: Mus musculus


text: female

text: Mus Musculus

characteristic: External Id

text: SC

text: public

text: 2042STDY5252331-sc-2011-11-30T14:53:52Z-1309672

text: house mouse

text: Mus musculus

text: Mus musculus


text: Aarhus University, Department of Molecular Biology and Genetics

characteristic: INSDC center name

text: public

text: ArrayExpress

characteristic: broker name

text: pig

text: Protocols: At an average weight of approximately 30 kg the offspring was transferred to the finishing unit. Slaughtering was done when the largest pig in the pen reached 110 kg. Blood samples were collected from the sows and muscle, lung and liver tissue from the boar and offspring were sampled at slaughter. The RNA fragments were then copied into first strand cDNA using reverse transcriptase and random hexamer primers followed by second strand cDNA synthesis using DNA Polymerase I and RNaseH. The short cDNA fragments were finally prepared for sequencing on the Illumina Genome Analyzer using reagents provided in the Illumina Genomic DNA Sequencing Sample Prep Kit. The cDNA fragments were end-repaired using T4 DNA polymerase and Klenow DNA polymerase and a single adenine nucleotide base was added to the cDNA fragments by using 3prime to 5prime exonuclease. This was followed by ligation of Illumina adaptors, gel purification of fragments of approximately 200 bases in size and finally PCR enrichment for 15 cycles. The concentrations of the libraries were measured using Invitrogen Qubit fluorometer and the size and purity were determined using the Agilent DNA 1000 Kit on Agilent 2100 Bioanalyzer. The 89 libraries were diluted in buffer EB from QIAGEN to 10 nM, denaturated with 2 N NaOH to a final DNA concentration of 1.0 nM, diluted to 4 pM with pre-chilled hybridization buffer from Illumina and loaded in individual lanes into a 1.0 mm flowcell together with a single lane of a 2 pM PhiX control library from Illumina.

characteristic: description

text: Single boar founder family

characteristic: family history

characteristic: individual

text: Sus scrofa

text: Sus scrofa

text: longissimus dorsi

characteristic: organism part

text: Sus scrofa

characteristic: title


text: male

characteristic: ArrayExpress-Sex

text: Homo Sapien

characteristic: ArrayExpress-Species

characteristic: ENA-FIRST-PUBLIC

text: SC

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: KUU25220247-sc-2011-09-30T11:06:35Z-1270495

text: human

text: Homo sapiens

characteristic: organism

text: Homo sapiens


text: Mus musculus

characteristic: ENA-CHECKLIST

text: SC

text: public

characteristic: SRA accession

characteristic: Submitter Id

text: house mouse

characteristic: common name

text: Mus musculus

text: Mus musculus


text: Xenopus tropicalis

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: SC

characteristic: INSDC center name

text: public

text: SC_XTEP5232351-sc-2011-10-04T11:18:19Z-1284630

text: western clawed frog

text: Xenopus (Silurana) tropicalis

text: toe clip DNA prep

characteristic: sample description

text: Xenopus (Silurana) tropicalis


text: Mus musculus

text: PWK/PhJ

characteristic: ArrayExpress-StrainOrLine

text: SC

text: public

text: house mouse

text: Mus musculus

text: Mus musculus

text: PWK/PhJ

characteristic: strain


text: Mus musculus

text: SC

text: public

text: RP23_283L5_-sc-2011-10-17T17:51:22Z-1289889

text: house mouse

text: Mus musculus

text: Mus musculus


text: Mus musculus

text: BALB/cJ

text: SC

text: public

text: house mouse

text: Mus musculus

text: Mus musculus

text: BALB/cJ


text: female

characteristic: ArrayExpress-Sex

text: Homo Sapien

text: SC

text: public

text: SC_GMJOL5309914-sc-2012-08-22T15:41:34Z-1376450

text: human

text: Homo sapiens

text: Homo sapiens


characteristic: ArrayExpress-CellType

characteristic: ArrayExpress-Compound

characteristic: ArrayExpress-DevelopmentalStage

characteristic: ArrayExpress-DiseaseState

characteristic: ArrayExpress-Dose

characteristic: ArrayExpress-Genotype

characteristic: ArrayExpress-GrowthCondition

characteristic: ArrayExpress-Immunoprecipitate

characteristic: ArrayExpress-OrganismPart

characteristic: ArrayExpress-Phenotype

text: not applicable

text: Homo sapiens

characteristic: ArrayExpress-Species

characteristic: ArrayExpress-TimePoint

characteristic: EGA-Disease

characteristic: EGA-Treatment

text: SC

text: killed

text: Nugen Liver

characteristic: Sample Description

characteristic: Strain

text: THKREC188-sc-2012-02-06T13:18:35Z-1305584

text: human

text: Homo sapiens

text: Homo sapiens


text: Mus musculus

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: SC

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: RP23_320O23_-sc-2011-10-17T17:51:24Z-1289891

characteristic: Submitter Id

text: house mouse

characteristic: common name

text: Mus musculus

characteristic: organism

text: Mus musculus


text: Danio rerio

characteristic: ArrayExpress-Species

text: SC

text: public

text: CH1073_845O23-sc-2013-05-28T14:22:27Z-1633965

text: zebrafish

text: Danio rerio

text: Danio rerio


text: female

characteristic: ArrayExpress-Sex

text: Homo Sapien

text: SC

text: public

text: SC_GMJOL5309817-sc-2012-08-22T15:41:16Z-1376431

text: human

text: Homo sapiens

text: Homo sapiens


text: Danio rerio

text: Tuebingen

characteristic: ArrayExpress-StrainOrLine

text: SC

text: public

text: Zebrafish_embryo_2_dpf_2-sc-2012-02-06T13:02:27Z-118157

text: zebrafish

text: Danio rerio

text: Danio rerio

text: Tuebingen

characteristic: strain


text: SC

text: public

text: house mouse

text: Mus musculus

text: Mus musculus


text: male

text: Mus Musculus

text: SC

text: public

text: 2042STDY5251968-sc-2011-11-30T14:48:30Z-1309334

text: house mouse

text: Mus musculus

text: Mus musculus


text: Mus Musculus

text: SC

text: public

text: SC_GCIGC5375923-sc-2012-08-02T09:01:08Z-1457608

text: house mouse

text: Mus musculus

text: Mus musculus


characteristic: ENA-CHECKLIST

text: Science for Life Laboratory, Stockholm, Sweden

text: public

text: ArrayExpress

characteristic: broker name

text: human

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

characteristic: description

text: adult

characteristic: developmental stage

characteristic: individual

text: Homo sapiens

text: Homo sapiens

text: appendix

characteristic: organism part

text: Homo sapiens

text: frozen specimen

characteristic: specimen with known storage state

characteristic: title


text: male

text: Homo Sapien

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: SC

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: SC_GMFUL5360722-sc-2012-06-20T14:50:55Z-1438188

text: human

text: Homo sapiens

text: Homo sapiens


text: Streptococcus pneumoniae

characteristic: ArrayExpress-Species

characteristic: ArrayExpress-StrainOrLine

text: SC

text: public

characteristic: SRA accession

characteristic: Submitter Id

text: Streptococcus pneumoniae

characteristic: organism

text: Streptococcus pneumoniae


text: Signaling and Functional Genomics, DKFZ

text: public

text: 21 day

characteristic: age

text: ArrayExpress

characteristic: broker name

text: house mouse

characteristic: common name

text: Protocols: Evi floxed mice were crossed with K14-Cre mice to delete Evi gene in epithelial cells. Skin of 21 day old mice was collected from mutants and wildtype animals. After tissue digestion RNA from epidermal sheets was prepared. Three fully independent biological replicates where sampled. RNA was extracted from epidermal sheets of three wildtype and Evi-LOF mice. The poly(A)+ fraction was isolated from each of the six samples with the Dynabeads mRNA Purification Kit (Invitrogen). For each sample, a library for sequencing with a SOLiD4 sequencer was prepared. random primers with a hexamer adapter sequence were annealed to the 3' end of the mRNA and the first DNA strand synthesized. Following RNA digestion, the DNA was purified using Agencourt RNAClean XP Beads. Random primers were annealed to the DNA for second strand synthesis. Agencourt Ampure XP Bead selection was used to purify and size select the double stranded DNA. The library was amplified and barcoded.

characteristic: description

text: adult

characteristic: developmental stage

text: gene knock out

characteristic: genetic modification

text: Evi floxed knockout

characteristic: genotype

text: Mus musculus

text: Mus musculus

text: epidermis

text: Mus musculus


text: male

characteristic: ArrayExpress-Sex

text: Homo Sapien

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: SC

text: public

text: 2042STDY5251919-sc-2011-11-29T10:16:32Z-1309237

text: human

text: Homo sapiens

text: Homo sapiens


text: Yeast

text: SC

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: SC_MFY5287920-sc-2012-02-02T14:10:39Z-1349340

text: baker's yeast

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae


text: Homo sapiens

characteristic: ArrayExpress-Species

text: SC

text: public

characteristic: SRA accession

text: DA33_TotalR-sc-2012-05-23T10:41:20Z-1425515

characteristic: Submitter Id

text: human

text: Homo sapiens

text: Homo sapiens


text: Danio rerio

text: TL

characteristic: ArrayExpress-StrainOrLine

text: SC

text: public

text: SL3_09_A9b-sc-2011-10-31T09:34:49Z-1281924

text: zebrafish

text: Danio rerio

characteristic: organism

text: Exome

characteristic: sample description

text: Danio rerio

text: TL

characteristic: strain


text: Salmonella enterica subsp. enterica serovar Typhi

text: SC

text: public


text: EMBL-EBI

text: public

text: ArrayExpress

characteristic: broker name

text: human

characteristic: common name

text: Protocols: to be confirmed to be confirmed For each sample, one paired-end mRNA library with approximately 150bp insert size was prepared using the TruSeq RNA Sample Preparation Kit v2 (Illumina).

characteristic: description

text: allergic bronchopulmonary aspergillosis

characteristic: disease state

characteristic: individual

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens

characteristic: title


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC center name

text: public

tag: Namespace:Max Planck Institute, Department of Genetics

text: ArrayExpress

text: house mouse

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

text: adult

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


text: Homo Sapien

characteristic: ArrayExpress-Species

text: SC

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: 2014STDY5345489-sc-2012-05-25T10:41:12Z-1419621

characteristic: Submitter Id

text: human

text: Homo sapiens

characteristic: organism

text: Homo sapiens


characteristic: ENA-CHECKLIST

text: SRA-Webin

characteristic: ENA-SUBMISSION-TOOL

text: ISB-USA

text: public

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


text: Th1 cells

characteristic: ArrayExpress-CellType

text: Anti H3K27me3 Millipore 07-449 (lot 1662421)

characteristic: ArrayExpress-Immunoprecipitate

text: Mus musculus

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: SC

text: public

text: m_Th1_H3K27me3_P-sc-2011-11-15T14:50:58Z-483700

text: house mouse

text: Mus musculus

text: DNA isolated from ChIP

characteristic: sample description

text: Mus musculus


text: Plasmodium falciparum

characteristic: External Id

text: SC

characteristic: INSDC center name

text: public

text: malaria parasite P. falciparum

text: Plasmodium falciparum

text: Plasmodium falciparum


text: EBI

text: public

text: Tabriz

text: Sahand

text: Asiatic mouflon

text: Asiatic Mouflon IROO-F5-5079 from NextGen project

characteristic: description

text: 108 months

characteristic: estimated age

text: Iran

characteristic: geographic location (country and/or sea)

text: 37.855 degrees

characteristic: latitude

text: 46.57 degrees

characteristic: longitude

text: Ovis orientalis

characteristic: sampling date

text: Ovis orientalis

text: male

characteristic: sex

text: Ovis orientalis

characteristic: title


text: female

characteristic: ArrayExpress-Sex

text: Mus Musculus

characteristic: ArrayExpress-Species

text: SC

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: 2042STDY5252345-sc-2011-11-30T14:54:28Z-1309701

characteristic: Submitter Id

text: house mouse

text: Mus musculus

characteristic: organism

text: Mus musculus


text: Mus musculus

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: SC

characteristic: INSDC center name

text: public

text: cinap_e_rnaseq-sc-2012-02-06T13:08:05Z-1001769

text: house mouse

characteristic: common name

text: Mus musculus

text: Mus musculus


text: Streptococcus pneumoniae

text: SC

text: public

text: Sample52-sc-2012-01-06T08:05:46Z-1330189

text: Streptococcus pneumoniae

text: Streptococcus pneumoniae


text: Haemonchus contortus

text: WRS

characteristic: ArrayExpress-StrainOrLine

text: SC

text: public

text: Haemonchus_contortus-sc-2012-02-06T13:19:15Z-1336155

text: barber pole worm

text: Haemonchus contortus

text: Haemonchus contortus

text: WRS

characteristic: strain


text: SRA-Webin

characteristic: ENA-SUBMISSION-TOOL

text: CME

text: public

text: eubacteria

text: mimarks-culture

characteristic: investigation type

text: Bacteria

text: Bacteria

text: pyrosequencing

characteristic: seq meth

text: but

characteristic: target gene

text: Roseburia intestinalis L1-82, R. inulinivorans DSM 16841, Faecalibacterium prausnitzii A2-165, Eubacterium hallii DSM 3353 and E. rectale DSM 17629

characteristic: target organism

text: but mock community 10252011


text: macrophages

characteristic: ArrayExpress-CellType

text: Wildtype

characteristic: ArrayExpress-Genotype

text: mus musculus

characteristic: ArrayExpress-Species

text: SC

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: 129_mice_bone_marrow_derived_macrophage_infected_3-sc-2013-03-11T09:26:29Z-1581619

text: house mouse

text: Mus musculus

text: RNA from macrophages derived from bone marrow of 129 mice infected with Salmonella Typhimurium

characteristic: sample description

text: Mus musculus


text: Danio rerio

text: TL/AB

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: SC

text: public

characteristic: INSDC status

characteristic: SRA accession

text: SL4_04_H11-sc-2012-04-25T15:02:44Z-1403922

characteristic: Submitter Id

text: zebrafish

text: Danio rerio

characteristic: organism

text: Exome

text: Danio rerio

text: TL/AB


text: Mus musculus

characteristic: External Id

text: SC

characteristic: INSDC center name

text: public

text: SC_GCIGC5274882-sc-2012-01-23T14:02:00Z-1335126

text: house mouse

characteristic: common name

text: Mus musculus

text: Mus musculus


text: Mus Musculus

text: SC

text: public

text: 2042STDY5305552-sc-2012-03-05T08:24:58Z-1370574

text: house mouse

text: Mus musculus

text: Mus musculus


text: male

characteristic: ArrayExpress-Sex

text: Mus Musculus

text: SC

text: public

text: 2042STDY5252033-sc-2011-11-30T14:47:36Z-1309283

text: house mouse

text: Mus musculus

text: Mus musculus


text: Danio rerio

text: TL/AB

characteristic: ArrayExpress-StrainOrLine

text: SC

text: public

text: SL6_08_A3-sc-2013-02-21T15:13:44Z-1513710

text: zebrafish

text: Danio rerio

text: Exome

text: Danio rerio

text: TL/AB

characteristic: strain


text: Queen's University Belfast

text: public

tag: Namespace:Queen's University Belfast

text: 14 day

characteristic: age

characteristic: block

text: ArrayExpress

characteristic: broker name

text: velvet grass

text: Protocols: Arsenate tolerant and non-tolerant Holcus lanatus L. Genovars were selected randomly from a screened population, the arsenic uncontaminated Cruickshank Botanic Garden (CBG) and tillers of the plants were grown hydroponically for 2 weeks in 50ml individual centrifuge tubes with base of the tubes covered in tin-foil to block out light, in heated glasshouse at around 18C under supplemental sodium lamps. Plant tillers from arsenic tolerant (T) and non-tolerant (N) plants were grown hydroponically for 2 weeks in 50ml complete Hogland solution (plusP treatment) or 50ml Hogland solution minus Phosphate (minusP treatment). The experiment therefore investigated 4 treatments (TplusP, TminusP, NplusP, NminusP) and was repeated 2 time. Experiment1 was conducted on 4 plants (n=1), Experiment2 was conducted on 16 plants (n=4). dry roots and shoots for each replicate were ground under liquid nitrogen and total RNA was extrected using the Plant Rneasy kit (Qiagen), with additional on-column Dnase treatment. Extracted RNA of each sample was stored at -80C until shipping on dry ice for sequencing Illumina TrueSeq RNA sample preparation

characteristic: description

text: Hogland solution phosphatelus phosphate

characteristic: growth condition

characteristic: individual

text: Holcus lanatus

text: Holcus lanatus L

text: Arsenic-non-tolerant

characteristic: phenotype

text: Holcus lanatus

text: fresh specimen

characteristic: specimen with known storage state

characteristic: title


text: male

text: Mus Musculus

characteristic: ArrayExpress-Species

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: 2042STDY5252089-sc-2011-11-30T14:49:34Z-1309397

characteristic: Submitter Id

text: house mouse

text: Mus musculus

text: Mus musculus


text: Danio rerio

characteristic: External Id

text: SC

characteristic: INSDC center name

text: public

text: ILBZfGRC5521621-sc-2013-04-26T15:11:39Z-1616798

text: zebrafish

characteristic: common name

text: Danio rerio

characteristic: organism

text: Danio rerio


text: Danio rerio

text: SC

text: public

text: ILBZfGRC5521697-sc-2013-04-26T15:13:18Z-1616874

text: zebrafish

text: Danio rerio

text: Danio rerio


text: Mus Musculus

text: SC

text: public

text: 2042STDY5252740-sc-2012-02-22T11:53:15Z-1310090

text: house mouse

text: Mus musculus

text: Mus musculus


text: Homo Sapien

text: SC

text: public

text: 2014STDY5345514-sc-2012-05-25T10:41:31Z-1419646

text: human

text: Homo sapiens

text: Homo sapiens


text: Homo Sapien

text: SC

text: public

text: 2014STDY5345482-sc-2012-05-25T10:41:06Z-1419614

text: human

text: Homo sapiens

text: Homo sapiens


text: Mus musculus

text: SC

text: public

text: sscam_4_rnaseq-sc-2012-02-06T13:06:41Z-1001695

text: house mouse

text: Mus musculus

text: Mus musculus


characteristic: ENA-CHECKLIST

text: SRA-Webin

characteristic: ENA-SUBMISSION-TOOL

text: ISB-USA

text: public

text: baker's yeast

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

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


text: Homo Sapien

text: SC

text: public

text: ILBHuGRC5514810-sc-2013-04-09T14:46:14Z-1609540

text: human

text: Homo sapiens

text: Homo sapiens


text: Mus musculus

text: SC

text: public

text: SC_MHT5376385-sc-2012-08-02T07:41:16Z-1458364

text: house mouse

text: Mus musculus

text: Mus musculus


text: Aarhus University, Department of Molecular Biology and Genetics

text: public

text: ArrayExpress

characteristic: broker name

text: pig

text: Protocols: At an average weight of approximately 30 kg the offspring was transferred to the finishing unit. Slaughtering was done when the largest pig in the pen reached 110 kg. Blood samples were collected from the sows and muscle, lung and liver tissue from the boar and offspring were sampled at slaughter. The RNA fragments were then copied into first strand cDNA using reverse transcriptase and random hexamer primers followed by second strand cDNA synthesis using DNA Polymerase I and RNaseH. The short cDNA fragments were finally prepared for sequencing on the Illumina Genome Analyzer using reagents provided in the Illumina Genomic DNA Sequencing Sample Prep Kit. The cDNA fragments were end-repaired using T4 DNA polymerase and Klenow DNA polymerase and a single adenine nucleotide base was added to the cDNA fragments by using 3prime to 5prime exonuclease. This was followed by ligation of Illumina adaptors, gel purification of fragments of approximately 200 bases in size and finally PCR enrichment for 15 cycles. The concentrations of the libraries were measured using Invitrogen Qubit fluorometer and the size and purity were determined using the Agilent DNA 1000 Kit on Agilent 2100 Bioanalyzer. The 89 libraries were diluted in buffer EB from QIAGEN to 10 nM, denaturated with 2 N NaOH to a final DNA concentration of 1.0 nM, diluted to 4 pM with pre-chilled hybridization buffer from Illumina and loaded in individual lanes into a 1.0 mm flowcell together with a single lane of a 2 pM PhiX control library from Illumina.

characteristic: description

text: Single boar founder family

characteristic: family history

characteristic: individual

text: Sus scrofa

text: Sus scrofa

text: longissimus dorsi

characteristic: organism part

text: Sus scrofa


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: SRA-Webin

text: IPK-Gatersleben

text: public

text: domesticated barley

text: Exome capture of Barley cv. Bonus

text: Hordeum vulgare subsp. vulgare

text: Hordeum vulgare subsp. vulgare

text: Bonus

characteristic: title


characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

tag: Namespace:Centre for Organismal Studies (COS) - University of Heidelberg

text: ArrayExpress

characteristic: cell line

text: house mouse

text: Protocols: Neural stem cells cultured in either proliferation-promoting medium (proNSC) or quiescence-promoting medium (quiNSC) Chromatin Immunoprecipitation with antibodies to H3K27ac (Abcam, ab4729), p300 (Santa Cruz, sc-585) and NFI transcription factors (Santa Cruz, sc-30918).

text: wild type

characteristic: genotype

text: proliferation-promoting medium

characteristic: growth condition

text: Mus musculus

text: Mus musculus

text: Mus musculus


text: Streptococcus pneumoniae

characteristic: ArrayExpress-Species

characteristic: ArrayExpress-StrainOrLine

characteristic: External Id

text: SC

characteristic: INSDC center name

text: public

characteristic: SRA accession

characteristic: Submitter Id

text: Streptococcus pneumoniae

characteristic: organism

text: Streptococcus pneumoniae

characteristic: strain


text: female

characteristic: ArrayExpress-Sex

text: Homo Sapien

characteristic: ENA-FIRST-PUBLIC

text: SC

text: public

text: 2042STDY5251931-sc-2012-03-08T09:50:54Z-1309262

text: human

characteristic: common name

text: Homo sapiens

text: Homo sapiens


text: Streptococcus pneumoniae

characteristic: ENA-LAST-UPDATE

text: SC

characteristic: INSDC first public

text: public

text: Sample60-sc-2012-01-06T08:06:32Z-1330253

text: Streptococcus pneumoniae

text: Streptococcus pneumoniae


text: Mus Musculus

text: SC

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: 2042STDY5305526-sc-2012-03-05T08:24:04Z-1370526

text: house mouse

text: Mus musculus

text: Mus musculus


E-MTAB-1628:MPP dH19/dIgf1r

text: Stowers Institute for Medical Research

text: public

text: E-MTAB-1628:MPP dH19/dIgf1r

text: 6 week

characteristic: age

text: ArrayExpress

characteristic: broker name

text: MPP (Lin- Sca1+ cKit+ CD34+ Flk2+)

characteristic: cell type

text: house mouse

text: Protocols: All mice used in this study were housed in the animal facility at the Stowers Institute for Medical Research (SIMR) and handled according to SIMR and National Institutes of Health (NIH) guidelines. All procedures were approved by the Institutional Animal Care and Use Committee (IACUC) of SIMR. H19-DMR flDMR/flDMR mice on B6 background were kindly provided by Dr. Marisa S. Bartolomei (University of Pennsylvania Perelman School of Medicine). Conditional mutant Igf1rfl/+ was kindly provided by Thomas L Clemens (Center for Musculoskeletal Research, Johns Hopkins Medicine, 601 North Caroline Street, Baltimore, MD 21287). Interferon inducible Mx1-Cre or tamoxifen inducible Scl-Cre mouse strains were used to delete the floxed H19-DMR and Igf1r. For Mx1-Cre activation, 250ug of pIpC was injected intraperitoneal every other day for 14 days at 5 weeks of age. For Scl-CreER activation, 2mg tamoxifen dissolved in 0.1 ml of corn oil was injected intraperitoneal every day for 5 days. Illumina TruSeq RNA Sample Prep Kit (Catalog #: FC-122-1001) The RNA-sequencing library was prepared from approximately 200 ng of total RNA (mH19dDMR/+ Igf1r-/- , mH19dDMR/+Igf1rf-/- and mH19flDMR/+) for each sample. The fragment size in the generated library ranged from 220 to 500 bps with a peak at 280 bps.

characteristic: description

text: mH19 dDMR/+ Igf1r -/-

characteristic: genotype

text: Mus musculus

text: Mus musculus

text: FACS-sorted bone marrow

characteristic: organism part

text: Mus musculus

text: fresh specimen

characteristic: specimen with known storage state

text: MPP dH19/dIgf1r

characteristic: title


text: Danio rerio

characteristic: ArrayExpress-Species

text: TL/AB

characteristic: ArrayExpress-StrainOrLine

characteristic: External Id

text: SC

characteristic: INSDC center name

text: public

characteristic: SRA accession

text: SL6_08_F9-sc-2013-02-21T15:14:40Z-1513763

characteristic: Submitter Id

text: zebrafish

text: Danio rerio

characteristic: organism

text: Exome

characteristic: sample description

text: Danio rerio

text: TL/AB


text: Mus musculus

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

text: house mouse

characteristic: common name

text: Mus musculus

text: Mus musculus


text: Homo sapiens

text: SC

text: public

text: human

text: Homo sapiens

text: Homo sapiens


text: Mus Musculus

text: SC

text: public

text: 2042STDY5252509-sc-2012-02-22T11:50:57Z-1309826

text: house mouse

text: Mus musculus

text: Mus musculus


text: Mus musculus

text: SC

text: public

text: akap9_5_rnaseq-sc-2012-02-06T13:06:48Z-1001701

text: house mouse

text: Mus musculus

text: Mus musculus


text: Pancreas

characteristic: ArrayExpress-CellType

characteristic: ArrayExpress-Immunoprecipitate

text: Pancreas

characteristic: ArrayExpress-OrganismPart

text: Cancer

characteristic: ArrayExpress-Phenotype

text: Mus Musculus

text: SC

text: public

text: house mouse

text: Mus musculus

text: Chromatin IP

text: Mus musculus


text: Danio rerio

characteristic: ArrayExpress-Species

text: TL

characteristic: ArrayExpress-StrainOrLine

characteristic: External Id

text: SC

text: public

text: SL3_08_B7b-sc-2011-10-31T09:33:47Z-1281831

text: zebrafish

text: Danio rerio

text: Exome

text: Danio rerio

text: TL

characteristic: strain


text: E9.5 (18-25 somites)

characteristic: ArrayExpress-DevelopmentalStage

text: Whole Embryo

text: Mus musculus

text: SC

characteristic: INSDC center name

text: public

characteristic: SRA accession

text: Mouse_Tbx1_WT1-sc-2012-04-30T14:46:20Z-1407956

characteristic: Submitter Id

text: house mouse

text: Mus musculus

characteristic: organism

text: wild type mouse embryo of allele Tbx1tm1Bld (MGI: 2179136) reference PMID: 11242049

text: Mus musculus


text: Danio rerio

text: TL/AB

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: SC

characteristic: INSDC first public

text: public

text: SL6_09_A3-sc-2013-02-21T15:15:20Z-1513806

text: zebrafish

text: Danio rerio

text: Exome

characteristic: sample description

text: Danio rerio

text: TL/AB


text: Danio rerio

text: TL/AB

text: SC

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: SL6_09_B1-sc-2013-02-21T15:15:06Z-1513791

text: zebrafish

characteristic: common name

text: Danio rerio

text: Exome

text: Danio rerio

text: TL/AB


text: male

characteristic: ArrayExpress-Sex

text: Homo Sapien

text: SC

text: public

text: SC_GMFUL5306373-sc-2012-05-09T14:46:01Z-1371757

text: human

text: Homo sapiens

text: Homo sapiens


text: male

text: Mus Musculus

characteristic: ArrayExpress-Species

text: SC

text: public

text: 2042STDY5252236-sc-2011-11-30T14:51:14Z-1309501

text: house mouse

text: Mus musculus

text: Mus musculus


text: Saccharomyces cerevisiae

text: SC

text: public

text: SC_MFY5515330-sc-2013-04-16T12:02:02Z-1610060

text: baker's yeast

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae


text: female

text: Mus Musculus

text: SC

text: public

text: 2042STDY5252362-sc-2011-11-30T14:55:06Z-1309731

text: house mouse

text: Mus musculus

text: Mus musculus


text: Haemonchus contortus

characteristic: ArrayExpress-StrainOrLine

text: SC

text: public

text: Haemonchus_contortus-sc-2011-10-14T15:56:11Z-1289491

text: barber pole worm

text: Haemonchus contortus

text: Haemonchus contortus


text: Mus Musculus

characteristic: External Id

text: SC

text: public

text: 2042STDY5252827-sc-2012-02-22T11:53:40Z-1310124

text: house mouse

text: Mus musculus

text: Mus musculus


text: Mus Musculus

text: SC

text: public

text: 2042STDY5252837-sc-2012-02-22T11:53:56Z-1310145

text: house mouse

text: Mus musculus

text: Mus musculus


text: Mus musculus

text: SC

text: public

text: psd93_c_rnaseq-sc-2012-02-06T13:07:38Z-1001745

text: house mouse

text: Mus musculus

text: Mus musculus


characteristic: ArrayExpress-CellType

characteristic: ArrayExpress-Compound

characteristic: ArrayExpress-DiseaseState

characteristic: ArrayExpress-Dose

characteristic: ArrayExpress-Genotype

characteristic: ArrayExpress-GrowthCondition

characteristic: ArrayExpress-Immunoprecipitate

characteristic: ArrayExpress-OrganismPart

characteristic: ArrayExpress-Phenotype

text: not applicable

text: Homo sapiens

characteristic: ArrayExpress-TimePoint

characteristic: EGA-Disease

characteristic: EGA-Treatment

text: SC

text: killed

text: Nugen Liver

characteristic: Sample Description

characteristic: Strain

text: THKPSC385-sc-2012-02-06T13:18:31Z-1305580

text: human

text: Homo sapiens

text: Homo sapiens


text: Mus Musculus

characteristic: ArrayExpress-Species

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: SC

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: 2042STDY5305528-sc-2012-03-05T08:24:06Z-1370530

characteristic: Submitter Id

text: house mouse

characteristic: common name

text: Mus musculus

characteristic: organism

text: Mus musculus


text: Anopheles gambiae

characteristic: External Id

text: SC

text: public

text: African malaria mosquito

text: Anopheles gambiae

text: Anopheles gambiae


text: Homo Sapien

text: SC

text: public

text: 2019STDY5279473-sc-2012-01-27T12:25:38Z-1340743

text: human

text: Homo sapiens

text: Homo sapiens


text: Plasmodium falciparum

characteristic: ENA-CHECKLIST

text: SC

text: public

text: malaria parasite P. falciparum

text: Plasmodium falciparum

text: Plasmodium falciparum


text: male

characteristic: ArrayExpress-Sex

text: Homo Sapien

text: SC

text: public

text: SC_GMJOL5309942-sc-2012-07-20T11:56:26Z-1376508

text: human

text: Homo sapiens

text: Homo sapiens


text: Plasmodium falciparum

text: IT

characteristic: ArrayExpress-StrainOrLine

text: SC

text: public

text: A4posMboHiC-sc-2012-02-06T13:14:27Z-1243353

text: malaria parasite P. falciparum

text: Plasmodium falciparum

text: Plasmodium falciparum

text: IT

characteristic: strain


text: male

text: Homo Sapien

text: SC

text: public

text: 2042STDY5251926-sc-2012-03-08T09:10:50Z-1309252

text: human

text: Homo sapiens

text: Homo sapiens


text: female

text: Homo Sapien

text: SC

text: public

text: 2042STDY5251916-sc-2011-11-29T10:16:30Z-1309233

text: human

text: Homo sapiens

text: Homo sapiens


text: Mus musculus

text: SC

text: public

text: camk2a_d_rnaseq-sc-2012-02-06T13:06:59Z-1001711

text: house mouse

text: Mus musculus

text: Mus musculus


text: Mus musculus

text: SC

text: public

text: tnik_9_rnaseq-sc-2012-02-06T13:09:01Z-1001816

text: house mouse

text: Mus musculus

text: Mus musculus


text: TGAC

text: public

text: bread wheat

text: Wheat CS42 CSS 6AL flow-sorted DNA

characteristic: description

text: Triticum aestivum

text: Triticum aestivum

text: Wheat CS42 CSS 6AL flow-sorted DNA

characteristic: title


characteristic: ENA-FIRST-PUBLIC

text: Science for Life Laboratory, Stockholm, Sweden

text: public

text: ArrayExpress

characteristic: broker name

text: human

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

text: adult

characteristic: developmental stage

characteristic: individual

text: Homo sapiens

text: Homo sapiens

text: endometrium

characteristic: organism part

text: Homo sapiens

text: frozen specimen

characteristic: specimen with known storage state


text: Danio rerio

characteristic: ArrayExpress-Species

text: TL/AB

characteristic: ENA-LAST-UPDATE

text: SC

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: SL6_07_A11-sc-2013-02-21T15:13:13Z-1513678

text: zebrafish

text: Danio rerio

text: Exome

characteristic: sample description

text: Danio rerio

text: TL/AB


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

characteristic: ENA-CHECKLIST

characteristic: External Id

text: SC

text: public

text: m_Input_Control_Liver-sc-2013-07-18T13:26:47Z-1669279

characteristic: Submitter Id

text: house mouse

characteristic: common name

text: Mus musculus

characteristic: organism

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

text: Mus musculus

text: Bl6 MeCP2 GFP

characteristic: strain


text: Danio rerio

characteristic: ArrayExpress-Species

text: TL

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: SC

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: SL3_08_C9b-sc-2011-10-31T09:34:41Z-1281911

text: zebrafish

text: Danio rerio

text: Exome

text: Danio rerio

text: TL


text: Mus Musculus

text: SC

text: public

characteristic: SRA accession

text: 2042STDY5252925-sc-2012-02-22T11:55:05Z-1310233

text: house mouse

text: Mus musculus

text: Mus musculus


text: Danio rerio

text: TL/AB

text: SC

text: public

text: SL6_10_D3-sc-2013-02-21T15:16:56Z-1513905

text: zebrafish

text: Danio rerio

text: Exome

characteristic: sample description

text: Danio rerio

text: TL/AB


text: Aarhus University, Department of Molecular Biology and Genetics

text: public

text: ArrayExpress

characteristic: broker name

text: pig

text: Protocols: At an average weight of approximately 30 kg the offspring was transferred to the finishing unit. Slaughtering was done when the largest pig in the pen reached 110 kg. Blood samples were collected from the sows and muscle, lung and liver tissue from the boar and offspring were sampled at slaughter. The RNA fragments were then copied into first strand cDNA using reverse transcriptase and random hexamer primers followed by second strand cDNA synthesis using DNA Polymerase I and RNaseH. The short cDNA fragments were finally prepared for sequencing on the Illumina Genome Analyzer using reagents provided in the Illumina Genomic DNA Sequencing Sample Prep Kit. The cDNA fragments were end-repaired using T4 DNA polymerase and Klenow DNA polymerase and a single adenine nucleotide base was added to the cDNA fragments by using 3prime to 5prime exonuclease. This was followed by ligation of Illumina adaptors, gel purification of fragments of approximately 200 bases in size and finally PCR enrichment for 15 cycles. The concentrations of the libraries were measured using Invitrogen Qubit fluorometer and the size and purity were determined using the Agilent DNA 1000 Kit on Agilent 2100 Bioanalyzer. The 89 libraries were diluted in buffer EB from QIAGEN to 10 nM, denaturated with 2 N NaOH to a final DNA concentration of 1.0 nM, diluted to 4 pM with pre-chilled hybridization buffer from Illumina and loaded in individual lanes into a 1.0 mm flowcell together with a single lane of a 2 pM PhiX control library from Illumina.

characteristic: description

text: Single boar founder family

characteristic: family history

characteristic: individual

text: Sus scrofa

text: Sus scrofa

text: longissimus dorsi

characteristic: organism part

text: Sus scrofa

characteristic: title


text: Mus musculus

text: WSB/EiJ

characteristic: ArrayExpress-StrainOrLine

characteristic: External Id

text: SC

text: public

characteristic: Submitter Id

text: house mouse

characteristic: common name

text: Mus musculus

characteristic: organism

text: Mus musculus

text: WSB/EiJ


text: male

characteristic: ArrayExpress-Sex

text: Homo Sapien

characteristic: ArrayExpress-Species

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: SC

characteristic: INSDC center name

text: public

text: SC_GMJOL5309941-sc-2012-07-20T11:56:25Z-1376506

text: human

text: Homo sapiens

text: Homo sapiens


text: Danio rerio

text: SC

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: CH73_116F2-sc-2013-05-28T14:22:35Z-1633972

text: zebrafish

text: Danio rerio

text: Danio rerio


text: male

text: Homo Sapien

text: SC

text: public

text: SC_GMJOL5309926-sc-2012-08-22T15:41:51Z-1376478

text: human

text: Homo sapiens

text: Homo sapiens


text: Dendritic cells (Cd11c+ sorted)

characteristic: ArrayExpress-CellType

text: Anti H3K4me3 Millipore 07-473

characteristic: ArrayExpress-Immunoprecipitate

text: Mus musculus

text: SC

text: public

text: m_DC_H3K4me3_P-sc-2011-11-09T13:40:41Z-43056

text: house mouse

text: Mus musculus

text: DNA isolated from ChIP

characteristic: sample description

text: Mus musculus


characteristic: ENA-CHECKLIST

text: public

text: ArrayExpress

characteristic: broker name

text: human

characteristic: description

text: adult

characteristic: developmental stage

characteristic: individual

text: Homo sapiens

text: Homo sapiens

text: colon

characteristic: organism part

text: Homo sapiens

text: frozen specimen

characteristic: specimen with known storage state

characteristic: title


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: public

characteristic: Submitter Id

text: ArrayExpress

text: pig

characteristic: common name

text: Protocols: Ten different tissues from two unrelated one year old Landrace boars were included in the study. Hence, total RNA was extracted from heart, spleen, liver, kidney, lung, musculus longissimus dorsi, occipital cortex, hypothalamus, frontal cortex, and cerebellum employing the mirVanaTM RNA extraction kit (Ambion) according to manufacturers protocol, yielding a total of 20 samples. RNA integrity was assessed by manual inspection of the individual RNA samples on a 2% agarose gel. The RNA fragments were then copied into first strand cDNA using reverse transcriptase and random hexamer primers followed by second strand cDNA synthesis using DNA Polymerase I and RNaseH. The short cDNA fragments were finally prepared for sequencing on the Illumina Genome Analyzer using reagents provided in the Illumina Genomic DNA Sequencing Sample Prep Kit. The cDNA fragments were end-repaired using T4 DNA polymerase and Klenow DNA polymerase and a single adenine nucleotide base was added to the cDNA fragments by using 3 prime to 5 prime exonuclease. This was followed by ligation of Illumina adaptors, gel purification of fragments of approximately 200 bases in size and finally PCR enrichment for 15 cycles. The concentrations of the libraries were measured using Invitrogen Qubit fluorometer and the size and purity were determined using the Agilent DNA 1000 Kit on Agilent 2100 Bioanalyzer. The 89 libraries were diluted in buffer EB from QIAGEN to 10 nM, denaturated with 2 N NaOH to a final DNA concentration of 1.0 nM, diluted to 4 pM with pre-chilled hybridization buffer from Illumina and loaded in individual lanes into a 1.0 mm flowcell together with a single lane of a 2 pM PhiX control library from Illumina.

text: Sus scrofa

characteristic: organism

text: Sus scrofa

text: cerebellum

text: Sus scrofa

text: male

characteristic: sex


text: diseased

characteristic: ArrayExpress-DiseaseState

text: cancer

characteristic: ArrayExpress-Phenotype

text: Mus Musculus

characteristic: ArrayExpress-Species

text: cancer

characteristic: EGA-Disease

text: SC

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: 5__SB_induced_tumour_18-sc-2011-11-07T15:36:24Z-1297003

text: house mouse

text: Mus musculus

text: transposon-induced tumour

text: Mus musculus


text: Danio rerio

text: TL

characteristic: ArrayExpress-StrainOrLine

text: SC

text: public

text: SL3_07_G10b-sc-2011-10-31T09:32:33Z-1281716

text: zebrafish

text: Danio rerio

text: Exome

characteristic: sample description

text: Danio rerio

text: TL

characteristic: strain


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: SRA-Webin

characteristic: ENA-SUBMISSION-TOOL

characteristic: External Id

text: ISB-USA

text: public

text: baker's yeast

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

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

characteristic: title


text: EMBL-EBI

text: public

characteristic: Submitter Id

text: ArrayExpress

characteristic: broker name

text: human

characteristic: common name

text: Protocols: to be confirmed to be confirmed For each sample, one paired-end mRNA library with approximately 150bp insert size was prepared using the TruSeq RNA Sample Preparation Kit v2 (Illumina).

characteristic: description

text: allergic bronchopulmonary aspergillosis

characteristic: disease state

characteristic: individual

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: Homo sapiens


text: Danio rerio

characteristic: ArrayExpress-Species

text: TL/AB

text: SC

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: SL6_06_B11-sc-2013-02-21T15:11:36Z-1513583

text: zebrafish

text: Danio rerio

text: Exome

text: Danio rerio

text: TL/AB


text: Streptococcus pneumoniae

characteristic: ArrayExpress-StrainOrLine

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: SC

text: public

text: Streptococcus pneumoniae

text: Streptococcus pneumoniae

characteristic: strain


text: Eidolon helvum

characteristic: External Id

text: SC

text: public

characteristic: Submitter Id

text: straw-colored fruit bat

text: Eidolon helvum

text: Bat urine for virus discovery

characteristic: sample description

text: Eidolon helvum


characteristic: ENA-CHECKLIST

text: Science for Life Laboratory, Stockholm, Sweden

text: public

text: ArrayExpress

characteristic: broker name

text: human

characteristic: common name

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

characteristic: description

text: adult

characteristic: developmental stage

text: Homo sapiens

text: Homo sapiens

text: salivary gland

characteristic: organism part

text: Homo sapiens

text: frozen specimen

characteristic: specimen with known storage state

characteristic: title


text: Homo Sapien

characteristic: ArrayExpress-Species

text: SC

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: SC_GCIGC5375908-sc-2012-08-02T07:46:05Z-1457593

text: human

text: Homo sapiens

characteristic: organism

text: Homo sapiens


text: Danio rerio

text: TL/AB

characteristic: ArrayExpress-StrainOrLine

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: SC

text: public

characteristic: SRA accession

text: SL6_08_B9-sc-2013-02-21T15:14:36Z-1513759

text: zebrafish

text: Danio rerio

text: Exome

text: Danio rerio

text: TL/AB

characteristic: strain


text: Mus musculus

text: SC

text: public

text: Mouse_MK_megakaryocyte__TPO-sc-2011-04-05T13:26:04Z-1093867

characteristic: Submitter Id

text: house mouse

characteristic: common name

text: Mus musculus

text: Mus musculus


text: female

characteristic: ArrayExpress-Sex

text: Mus Musculus

text: SC

text: public

text: SC_DSCC15506262-sc-2013-03-21T10:41:19Z-1600184

text: house mouse

text: Mus musculus

text: Tumour

characteristic: sample description

text: Mus musculus


characteristic: ENA-CHECKLIST

text: public

text: ArrayExpress

characteristic: broker name

text: human

characteristic: description

text: adult

characteristic: developmental stage

characteristic: individual

text: Homo sapiens

text: Homo sapiens

text: testis

characteristic: organism part

text: Homo sapiens

text: frozen specimen

characteristic: specimen with known storage state

characteristic: title


text: diseased

characteristic: ArrayExpress-DiseaseState

text: cancer

characteristic: ArrayExpress-Phenotype

text: Mus Musculus

characteristic: ArrayExpress-Species

text: cancer

characteristic: EGA-Disease

characteristic: ENA-FIRST-PUBLIC

text: SC

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: 5__SB_induced_tumour_38-sc-2011-11-07T15:36:38Z-1297023

text: house mouse

text: Mus musculus

characteristic: organism

text: transposon-induced tumour

text: Mus musculus


text: Plasmodium falciparum

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: SC

text: public

characteristic: SRA accession

text: Expt1IC_Pf_RNA-sc-2012-02-06T12:58:31Z-30383

characteristic: Submitter Id

text: malaria parasite P. falciparum

characteristic: common name

text: Plasmodium falciparum

text: Plasmodium falciparum


text: Mus Musculus

text: SC

text: public

text: SC_GCIGC5375913-sc-2012-08-02T09:00:54Z-1457598

text: house mouse

text: Mus musculus

text: Mus musculus


text: Mus musculus

text: SC

text: public

text: sscam_b_rnaseq-sc-2012-02-06T13:07:27Z-1001735

text: house mouse

text: Mus musculus

text: Mus musculus


text: female

characteristic: ArrayExpress-Sex

text: Mus Musculus

text: SC

text: public

text: 2042STDY5252055-sc-2011-11-30T14:48:21Z-1309325

text: house mouse

text: Mus musculus

text: Mus musculus


text: Danio rerio

text: TL/AB

characteristic: ArrayExpress-StrainOrLine

text: SC

text: public

text: SL4_10_H12-sc-2012-04-25T15:12:05Z-1404506

text: zebrafish

text: Danio rerio

text: Exome

characteristic: sample description

text: Danio rerio

text: TL/AB

characteristic: strain


text: EMBL-EBI

text: public

text: ArrayExpress

characteristic: broker name

text: baker's yeast

text: Protocols: Human feces were plated on YPD (yeast extract 1%, peptone 2%, D-Glucose 2%) agar plates added with antibiotics to prevent bacterial growth. Yeast colonies were then collected and species was assessed by ITS1-4 sequencing. Cells were grown in YPD liquid medium for genomic DNA extraction DNA was extracted from 10^9 pelleted cells with the Qiagen Genomic DNA Isolation Kit following the manufacturer's instructions.

characteristic: description

text: clinical strain

characteristic: environmental history

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

text: frozen sample

characteristic: specimen with known storage state

characteristic: title


text: Mus musculus

characteristic: ArrayExpress-Species

characteristic: ENA-FIRST-PUBLIC

text: SC

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: 2042STDY5261072-sc-2011-12-15T14:33:03Z-1319371

text: house mouse

text: Mus musculus

text: Mus musculus


text: Human

text: Promega

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: SC

text: public

characteristic: INSDC status

characteristic: SRA accession

text: Homo_sapiens-sc-2013-04-03T15:18:48Z-1607046

text: human

text: Homo sapiens

characteristic: organism

text: genomic DNA

text: Homo sapiens

text: Promega


text: Mus musculus

text: SC

text: public

text: WI1_2651L20_-sc-2011-10-17T17:51:40Z-1289913

characteristic: Submitter Id

text: house mouse

characteristic: common name

text: Mus musculus

text: Mus musculus


text: Streptococcus pneumoniae

characteristic: ArrayExpress-StrainOrLine

text: SC

text: public

text: Streptococcus pneumoniae

text: Streptococcus pneumoniae

characteristic: strain


text: Mus musculus

text: SC

text: public

text: RP23_196E17_-sc-2011-10-17T17:51:12Z-1289875

text: house mouse

text: Mus musculus

text: Mus musculus


text: Anopheles gambiae

text: SC

text: public

text: African malaria mosquito

text: Anopheles gambiae

text: Anopheles gambiae


text: University College London

text: public

tag: Namespace:University College London

text: ArrayExpress

characteristic: broker name

text: HEKn

characteristic: cell line

text: keratinocyte

characteristic: cell type

text: human

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

characteristic: description

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens

text: fresh specimen


text: Danio rerio

characteristic: ArrayExpress-Species

text: TL/AB

characteristic: ENA-FIRST-PUBLIC

text: SC

text: public

text: SL6_09_H2-sc-2013-02-21T15:15:19Z-1513805

text: zebrafish

text: Danio rerio

text: Exome

characteristic: sample description

text: Danio rerio

text: TL/AB


text: male

characteristic: ArrayExpress-Sex

text: Mus Musculus

text: SC

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: 2042STDY5252429-sc-2011-11-30T14:54:18Z-1309693

text: house mouse

text: Mus musculus

text: Mus musculus