E-MTAB-3823:Sample 49

text: public

characteristic: INSDC status

text: E-MTAB-3823:Sample 49

text: ArrayExpress

text: human

text: normal

text: Homo sapiens

text: Homo sapiens

text: blood

text: Homo sapiens

text: Sample 49


E-MTAB-3823:Sample 50

status: PUBLIC

tag: attribute

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: SRA accession

text: E-MTAB-3823:Sample 50

tag: Namespace:Goethe University of Frankfurt am Main, Institute of Molecular BioSciences

characteristic: Submitter Id

text: ArrayExpress

characteristic: broker name

text: human

characteristic: common name

text: Protocols: Sample collection was approved by the Ethics Committee of the Technical University of Munich and written informed consent was obtained from all patients. All following methods/experimental protocols were carried out in accordance with the approved guidelines of the Ethics committee of the Technische Universitaet Muenchen, Munich, Germany. Whole blood (5 ml) from each participant was drawn into two PAXgene tubes (PreAnalyticX) and incubated at room temperature for 3 h before being frozen at -80°C. Initial marker candidate selection was carried out by MACE of blood samples from 25 CTR and 47 PDAC patients. Validation was performed on whole blood from a cohort of 222 CTR, 75 PDAC, 13 CP, and seven IPMN patients. Total RNA (including small RNA) was extracted from both PAXgene blood tubes using the PAXgene blood miRNA extraction kit (Qiagen) according to the manufacturer’s protocol. The RNA concentration and quality in each sample was evaluated by the RNA HS Assay Kit using the Qubit Fluorometer (Life Technologies) and the RNA Nano Chip using the 2100 Bioanalyser (Agilent), respectively. Total RNA preparations with an RNA integrity number (RIN) number >7.5 and sufficient quantity were used for the mRNA expression analysis. Globin depletion was performed using the GLOBINclear kit (Ambion). MACE libraries were prepared as previously describe using the MACE kit by GenXPro GmbH (Germany). Briefly, polyadenylated RNA was extracted from 2 μg Globin-depleted total RNA and reverse-transcribed with biotinylated poly(dT) primers. The resulting cDNA was fragmented and biotinylated ends were captured by streptavidin beads. TrueQuant DNA adapters (GenXPro) were ligated. to the enriched ends, and subsequent to PCR amplification the libraries were sequenced on the HiSeq2000 platform (Illumina).

characteristic: description

text: normal

characteristic: disease

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: blood

characteristic: organism part

text: Homo sapiens

text: Sample 50

characteristic: title

type: has member


E-MTAB-3823:Sample 51

text: Goethe University of Frankfurt am Main, Institute of Molecular BioSciences

text: public

characteristic: INSDC status

text: E-MTAB-3823:Sample 51

text: ArrayExpress

text: human

text: normal

text: Homo sapiens

text: Homo sapiens

text: blood

text: Homo sapiens

text: Sample 51


E-MTAB-3823:Sample 52

characteristic: ENA-CHECKLIST

text: public

text: E-MTAB-3823:Sample 52

text: ArrayExpress

text: human

text: normal

text: Homo sapiens

text: Homo sapiens

text: blood

text: Homo sapiens

text: Sample 52


E-MTAB-3823:Sample 53

characteristic: ENA-FIRST-PUBLIC

text: public

text: E-MTAB-3823:Sample 53

text: ArrayExpress

text: human

text: normal

text: Homo sapiens

text: Homo sapiens

text: blood

text: Homo sapiens

text: Sample 53


E-MTAB-3823:Sample 54

characteristic: ENA-LAST-UPDATE

text: public

text: E-MTAB-3823:Sample 54

text: ArrayExpress

text: human

text: normal

text: Homo sapiens

text: Homo sapiens

text: blood

text: Homo sapiens

text: Sample 54


E-MTAB-3823:Sample 55

characteristic: External Id

text: public

text: E-MTAB-3823:Sample 55

text: ArrayExpress

text: human

text: normal

text: Homo sapiens

text: Homo sapiens

text: blood

text: Homo sapiens

text: Sample 55


E-MTAB-3823:Sample 56

characteristic: INSDC center name

text: public

text: E-MTAB-3823:Sample 56

text: ArrayExpress

text: human

text: normal

text: Homo sapiens

text: Homo sapiens

text: blood

text: Homo sapiens

text: Sample 56


E-MTAB-3823:Sample 57

characteristic: INSDC first public

text: public

text: E-MTAB-3823:Sample 57

text: ArrayExpress

text: human

text: normal

text: Homo sapiens

text: Homo sapiens

text: blood

text: Homo sapiens

text: Sample 57


E-MTAB-3823:Sample 58

characteristic: INSDC last update

text: public

text: E-MTAB-3823:Sample 58

text: ArrayExpress

text: human

text: normal

text: Homo sapiens

text: Homo sapiens

text: blood

text: Homo sapiens

text: Sample 58


E-MTAB-3823:Sample 59

text: public

characteristic: SRA accession

text: E-MTAB-3823:Sample 59

text: ArrayExpress

text: human

text: normal

text: Homo sapiens

text: Homo sapiens

text: blood

text: Homo sapiens

text: Sample 59


E-MTAB-3823:Sample 60

text: public

text: E-MTAB-3823:Sample 60

characteristic: Submitter Id

text: ArrayExpress

text: human

text: normal

text: Homo sapiens

text: Homo sapiens

text: blood

text: Homo sapiens

text: Sample 60


E-MTAB-3823:Sample 61

text: public

text: E-MTAB-3823:Sample 61

text: ArrayExpress

characteristic: broker name

text: human

text: normal

text: Homo sapiens

text: Homo sapiens

text: blood

text: Homo sapiens

text: Sample 61


E-MTAB-3823:Sample 62

text: public

text: E-MTAB-3823:Sample 62

text: ArrayExpress

text: human

characteristic: common name

text: normal

text: Homo sapiens

text: Homo sapiens

text: blood

text: Homo sapiens

text: Sample 62


E-MTAB-3823:Sample 63

text: public

text: E-MTAB-3823:Sample 63

text: ArrayExpress

text: human

characteristic: description

text: normal

text: Homo sapiens

text: Homo sapiens

text: blood

text: Homo sapiens

text: Sample 63


E-MTAB-3823:Sample 64

text: public

text: E-MTAB-3823:Sample 64

text: ArrayExpress

text: human

text: normal

characteristic: disease

text: Homo sapiens

text: Homo sapiens

text: blood

text: Homo sapiens

text: Sample 64


E-MTAB-3823:Sample 65

text: public

text: E-MTAB-3823:Sample 65

text: ArrayExpress

text: human

text: normal

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: blood

text: Homo sapiens

text: Sample 65


E-MTAB-3823:Sample 66

text: public

text: E-MTAB-3823:Sample 66

text: ArrayExpress

text: human

text: normal

text: Homo sapiens

text: Homo sapiens

text: blood

characteristic: organism part

text: Homo sapiens

text: Sample 66


E-MTAB-3823:Sample 67

text: public

text: E-MTAB-3823:Sample 67

text: ArrayExpress

text: human

text: normal

text: Homo sapiens

text: Homo sapiens

text: blood

text: Homo sapiens

text: Sample 67

characteristic: title


E-MTAB-3823:Sample 68

text: public

characteristic: INSDC status

text: E-MTAB-3823:Sample 68

text: ArrayExpress

text: human

text: normal

text: Homo sapiens

text: Homo sapiens

text: blood

text: Homo sapiens

text: Sample 68


E-MTAB-3823:Sample 69

characteristic: ENA-CHECKLIST

text: public

text: E-MTAB-3823:Sample 69

text: ArrayExpress

text: human

text: normal

text: Homo sapiens

text: Homo sapiens

text: blood

text: Homo sapiens

text: Sample 69


E-MTAB-3823:Sample 70

characteristic: ENA-FIRST-PUBLIC

text: public

text: E-MTAB-3823:Sample 70

text: ArrayExpress

text: human

text: normal

text: Homo sapiens

text: Homo sapiens

text: blood

text: Homo sapiens

text: Sample 70


E-MTAB-3823:Sample 71

characteristic: ENA-LAST-UPDATE

text: public

text: E-MTAB-3823:Sample 71

text: ArrayExpress

text: human

text: normal

text: Homo sapiens

text: Homo sapiens

text: blood

text: Homo sapiens

text: Sample 71


E-MTAB-3823:Sample 72

characteristic: External Id

text: public

text: E-MTAB-3823:Sample 72

text: ArrayExpress

text: human

text: normal

text: Homo sapiens

text: Homo sapiens

text: blood

text: Homo sapiens

text: Sample 72


status: KILLED

text: EBI

characteristic: INSDC center name

text: killed

text: fruit fly

text: Drosophila melanogaster

text: Drosophila melanogaster

text: Test Sample


text: EBI

characteristic: INSDC first public

text: killed

text: fruit fly

text: Drosophila melanogaster

text: Drosophila melanogaster

text: Test Sample


text: Bone marrow

characteristic: ArrayExpress-CellType

text: Bone marrow

characteristic: ArrayExpress-OrganismPart

text: female

characteristic: ArrayExpress-Sex

text: Mus musculus

characteristic: ArrayExpress-Species

text: SC

characteristic: INSDC last update

text: public

text: house mouse

text: Mus musculus

text: Total RNA extracted from Lin_neg_bone marrow

characteristic: sample description

text: Mus musculus


text: Bone marrow

text: Bone marrow

text: male

text: Mus musculus

text: SC

text: public

characteristic: SRA accession

characteristic: Submitter Id

text: house mouse

characteristic: common name

text: Mus musculus

text: Mus musculus


text: Leibniz Institute on Aging - Fritz Lipmann Institute (FLI)

text: public

tag: Namespace:Leibniz Institute on Aging – Fritz Lipmann Institute (FLI)

text: turquoise killifish

characteristic: individual name

text: Nothobranchius furzeri

characteristic: organism

text: Nothobranchius furzeri

text: male

characteristic: sex

text: GRZ

characteristic: strain

text: Nothobranchius furzeri GRZ GRZ_M004 (male)

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: public

characteristic: INSDC status

text: turquoise killifish

text: Nothobranchius furzeri

text: Nothobranchius furzeri

text: male

text: GRZ

text: Nothobranchius furzeri GRZ GRZ_M005 (male)


text: Mus musculus

text: SC

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: house mouse

text: Mus musculus

text: DNA library

text: Mus musculus


text: Larval:Day 5 - ZFS:0000037

characteristic: ArrayExpress-DevelopmentalStage

text: Whole embryo

characteristic: ArrayExpress-OrganismPart

text: Danio rerio

characteristic: ArrayExpress-Species

text: mixed

characteristic: ArrayExpress-StrainOrLine

text: SC

characteristic: INSDC last update

text: public

text: zebrafish

text: Danio rerio

text: Total RNA from a single zebrafish embryo from the SAT Sanger AB T?bingen) strain collected at 5dpf.

text: Danio rerio

text: mixed


text: olfactory mucosa

text: male

characteristic: ArrayExpress-Sex

text: Canis familiaris

text: Mixed breed

text: SC

text: public

characteristic: SRA accession

characteristic: Submitter Id

text: dog

characteristic: common name

text: Canis lupus familiaris

text: olfactory mucosa 1

characteristic: sample description

text: Canis lupus familiaris

text: Mixed breed


text: 7 years

text: olfactory mucosa

text: male

text: Canis familiaris

text: Mixed breed

characteristic: ENA-CHECKLIST

text: SC

text: public

text: dog

text: Canis lupus familiaris

characteristic: organism

text: olfactory mucosa 2

text: Canis lupus familiaris

text: Mixed breed

characteristic: strain


text: 7 years

text: olfactory mucosa

text: male

text: Canis familiaris

text: Mixed breed

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: SC

text: public

text: dog

text: Canis lupus familiaris

text: olfactory mucosa 3

text: Canis lupus familiaris

text: Mixed breed


E-MTAB-3830:Sample 13

characteristic: INSDC center name

characteristic: INSDC first public

text: public

characteristic: INSDC status

text: E-MTAB-3830:Sample 13

tag: Namespace:Institute of Molecular BioSciences, University of Frankfurt am Main

text: ArrayExpress

characteristic: broker name

text: tomato

text: Protocols: The short-term heat stress treatment and collection of pollen samples were performed according to the protocol developed by the SPOT-ITN consortium. For heat treatment plants were transferred in a preheated growth chamber and exposed to 38oC for 1 h (Figure S 1) under artificial light (Photosynthetically active radiation (PAR) = 85,927±4,7 μmol photons m−2s−1). The temperature was then gradually decreased to 25oC within 30 minutes and plants were allowed to recover for an additional hour at 25oC. Untreated plants were kept in the growth chamber for the same time period at control temperature of 25oC. In a preliminary experiment (data not shown) the tomato flower bud size has been correlated with three stages of pollen development, using DAPI (4, 6-diamidino-2-phenylindole) staining as shown by Chaturvedi et al. (38). Flower material was harvested 1.5 h after HS and immediately collected in the containers kept on ice. Control samples were harvested from a parallel set of non‐stressed plants while performing the HS treatments. Flower buds were sorted according to the corresponding stages as follow: flower buds of 4‐6 mm in length for tetrad (T) (meiotic stage/microspore mother cell), 6‐8 mm in length for post-meiotic (PM) stage (microspores), and =/> 10 mm in length for mature (M) (bicellular pollen) pollen grains (Figure S 1). Sepals from the flower buds of tetrad stage and sepals and petals from the flower buds of post‐meiotic and mature stages were gently removed using forceps. Additionally stigma and the style from the flower buds of post‐meiotic and mature stages were excised in order to avoid the contamination by parts of the gynoecium during pollen preparation. Immediately after removing aforementioned parts of the flower buds, released anthers were immersed in germination solution [KNO3 (1 mM); Ca(NO3)2 (3 mM); MgSO4 (0,8 mM), H3BO3 (1,6 mM)] kept on ice prior pollen isolation and purification. Pollen was isolated from anthers by squeezing the stamens with a pipette tip 200 μl in the germination solution, followed by vortexing for 15 seconds. To ensure that the material was free of contaminants from other anther tissues, isolated pollen was passed through gauze cloth, washed twice with germination solution, and centrifuged at 4°C for 2 min at 100g. The supernatant was discarded, while pollen cell pellet re‐suspended in 200 μl of germination solution, followed by centrifugation at 100 g for 2 minutes at 4°C. The supernatant was discarded and pollen samples were stored in the liquid nitrogen. Prior to first centrifugation the pollen stage and purity were confirmed by staining with 1 μg mL-1 DAPI and visualized under a fluorescent microscope [38] (Figure S 1). Control and heat-stressed pollen samples were collected from three independent experiments performed during three consecutive days. Samples derived from one day were treated as biological replica. Growth conditions included a 12 hour light-dark cycle with a day temperature of 24-26°C and night temperature of 18-20°C, and relative humidity at 65-70%. The daily solar radiation in the greenhouse was supplemented to at least 190 μmol photons m-2 s-1 from a series of high-pressure sodium lamps 400 W SON-T (Philips Electronics N.V. Amsterdam, Netherlands) after the appearance of the first inflorescence. During the first 6 weeks of development, plants were watered every two days and subsequently every day. RNA was isolated using the Macherey-Nagel NucleoSpin miRNA isolation kit according to manufacturer’s protocol. sncRNA libraries were prepared using the proprietary TrueQuant method for elimination of PCR bias [39]. Briefly, adapters were ligated to the 3’- and 5’-ends to total RNA by T4 RNA ligase, reverse transcribed and PCR amplified. The final PCR product was size-selected on a PAA-gel .

characteristic: description

text: mature

characteristic: developmental stage

text: Solanum lycopersicum

text: Solanum lycopersicum

text: pollen

characteristic: organism part

text: Solanum lycopersicum

text: Sample 13

characteristic: title


E-MTAB-3830:Sample 14

text: Institute of Molecular BioSciences, University of Frankfurt am Main

characteristic: INSDC last update

text: public

characteristic: SRA accession

text: E-MTAB-3830:Sample 14

characteristic: Submitter Id

text: ArrayExpress

text: tomato

text: mature

text: Solanum lycopersicum

text: Solanum lycopersicum

text: pollen

text: Solanum lycopersicum

text: Sample 14


E-MTAB-3830:Sample 15

characteristic: ENA-CHECKLIST

text: public

text: E-MTAB-3830:Sample 15

text: ArrayExpress

text: tomato

characteristic: common name

text: mature

text: Solanum lycopersicum

text: Solanum lycopersicum

text: pollen

text: Solanum lycopersicum

text: Sample 15


E-MTAB-3830:Sample 7

text: public

text: E-MTAB-3830:Sample 7

text: ArrayExpress

text: tomato

text: post-meiotic

text: Solanum lycopersicum

characteristic: organism

text: Solanum lycopersicum

text: pollen

text: Solanum lycopersicum

text: Sample 7


E-MTAB-3830:Sample 8

characteristic: ENA-FIRST-PUBLIC

text: public

text: E-MTAB-3830:Sample 8

text: ArrayExpress

text: tomato

text: post-meiotic

text: Solanum lycopersicum

text: Solanum lycopersicum

text: pollen

text: Solanum lycopersicum

text: Sample 8


E-MTAB-3830:Sample 9

characteristic: ENA-LAST-UPDATE

text: public

text: E-MTAB-3830:Sample 9

text: ArrayExpress

text: tomato

text: post-meiotic

text: Solanum lycopersicum

text: Solanum lycopersicum

text: pollen

text: Solanum lycopersicum

text: Sample 9


E-MTAB-3830:Sample 1

characteristic: External Id

text: public

text: E-MTAB-3830:Sample 1

text: ArrayExpress

text: tomato

text: tetrad

text: Solanum lycopersicum

text: Solanum lycopersicum

text: pollen

text: Solanum lycopersicum

text: Sample 1


E-MTAB-3830:Sample 2

characteristic: INSDC center name

text: public

text: E-MTAB-3830:Sample 2

text: ArrayExpress

text: tomato

text: tetrad

text: Solanum lycopersicum

text: Solanum lycopersicum

text: pollen

text: Solanum lycopersicum

text: Sample 2


E-MTAB-3830:Sample 3

characteristic: INSDC first public

text: public

text: E-MTAB-3830:Sample 3

text: ArrayExpress

text: tomato

text: tetrad

text: Solanum lycopersicum

text: Solanum lycopersicum

text: pollen

text: Solanum lycopersicum

text: Sample 3


E-MTAB-3830:Sample 16

text: public

characteristic: INSDC status

text: E-MTAB-3830:Sample 16

text: ArrayExpress

text: tomato

text: mature

text: Solanum lycopersicum

text: Solanum lycopersicum

text: pollen

text: Solanum lycopersicum

text: heat stress

characteristic: stimulus

text: Sample 16


E-MTAB-3830:Sample 17

text: public

text: E-MTAB-3830:Sample 17

text: ArrayExpress

characteristic: broker name

text: tomato

characteristic: description

text: mature

text: Solanum lycopersicum

text: Solanum lycopersicum

text: pollen

text: Solanum lycopersicum

text: heat stress

text: Sample 17


E-MTAB-3830:Sample 18

text: public

text: E-MTAB-3830:Sample 18

text: ArrayExpress

text: tomato

text: mature

characteristic: developmental stage

text: Solanum lycopersicum

text: Solanum lycopersicum

text: pollen

characteristic: organism part

text: Solanum lycopersicum

text: heat stress

text: Sample 18


E-MTAB-3830:Sample 10

characteristic: INSDC last update

text: public

text: E-MTAB-3830:Sample 10

text: ArrayExpress

text: tomato

text: post-meiotic

text: Solanum lycopersicum

text: Solanum lycopersicum

text: pollen

text: Solanum lycopersicum

text: heat stress

text: Sample 10

characteristic: title


E-MTAB-3830:Sample 11

text: public

characteristic: SRA accession

text: E-MTAB-3830:Sample 11

characteristic: Submitter Id

text: ArrayExpress

text: tomato

text: post-meiotic

text: Solanum lycopersicum

text: Solanum lycopersicum

text: pollen

text: Solanum lycopersicum

text: heat stress

text: Sample 11


E-MTAB-3830:Sample 12

characteristic: ENA-CHECKLIST

text: public

text: E-MTAB-3830:Sample 12

text: ArrayExpress

text: tomato

characteristic: common name

text: post-meiotic

text: Solanum lycopersicum

text: Solanum lycopersicum

text: pollen

text: Solanum lycopersicum

text: heat stress

text: Sample 12


E-MTAB-3830:Sample 4

characteristic: ENA-FIRST-PUBLIC

text: public

text: E-MTAB-3830:Sample 4

text: ArrayExpress

text: tomato

text: tetrad

text: Solanum lycopersicum

characteristic: organism

text: Solanum lycopersicum

text: pollen

text: Solanum lycopersicum

text: heat stress

text: Sample 4


E-MTAB-3830:Sample 5

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: public

text: E-MTAB-3830:Sample 5

text: ArrayExpress

text: tomato

text: tetrad

text: Solanum lycopersicum

text: Solanum lycopersicum

text: pollen

text: Solanum lycopersicum

text: heat stress

text: Sample 5


E-MTAB-3830:Sample 6

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: E-MTAB-3830:Sample 6

text: ArrayExpress

text: tomato

text: tetrad

text: Solanum lycopersicum

text: Solanum lycopersicum

text: pollen

text: Solanum lycopersicum

text: heat stress

text: Sample 6


text: EBI

text: killed

characteristic: INSDC status

text: fruit fly

text: Drosophila melanogaster

text: Drosophila melanogaster

text: Test Sample


text: EBI

text: killed

text: fruit fly

text: Drosophila melanogaster

text: Drosophila melanogaster

text: Test Sample


text: Homo Sapiens

characteristic: ArrayExpress-Species

text: SC

text: public

text: human

text: Homo sapiens

text: Amplicon library

characteristic: sample description

text: Homo sapiens


text: Mus musculus

text: SC

text: public

text: house mouse

text: Mus musculus

text: 3' end enriched mRNA from single cells. An 11 base indexing sequence ( CCCTATGGCCC ) is bases 11 to 21 of read 1 followed by CG and polyT.

text: Mus musculus


text: Mus musculus

text: SC

text: public

text: house mouse

text: Mus musculus

text: 3' end enriched mRNA from single cells. An 11 base indexing sequence ( GACAAAGAGAA ) is bases 11 to 21 of read 1 followed by CG and polyT.

text: Mus musculus


text: Mus musculus

text: SC

text: public

text: house mouse

text: Mus musculus

text: 3' end enriched mRNA from single cells. An 11 base indexing sequence ( AACCACAGCAC ) is bases 11 to 21 of read 1 followed by CG and polyT.

text: Mus musculus


text: Mus musculus

text: SC

text: public

text: house mouse

text: Mus musculus

text: 3' end enriched mRNA from single cells. An 11 base indexing sequence ( CAGGTGACGGC ) is bases 11 to 21 of read 1 followed by CG and polyT.

text: Mus musculus


text: Mus musculus

text: SC

text: public

text: house mouse

text: Mus musculus

text: 3' end enriched mRNA from single cells. An 11 base indexing sequence ( GAGTCGCGACG ) is bases 11 to 21 of read 1 followed by CG and polyT.

text: Mus musculus


text: Mus musculus

text: SC

text: public

text: house mouse

text: Mus musculus

text: 3' end enriched mRNA from single cells. An 11 base indexing sequence ( AGGAACTACAC ) is bases 11 to 21 of read 1 followed by CG and polyT.

text: Mus musculus


text: Mus musculus

text: SC

text: public

text: house mouse

text: Mus musculus

text: 3' end enriched mRNA from single cells. An 11 base indexing sequence ( GGGCTCCGACA ) is bases 11 to 21 of read 1 followed by CG and polyT.

text: Mus musculus


text: Mus musculus

text: SC

text: public

text: house mouse

text: Mus musculus

text: 3' end enriched mRNA from single cells. An 11 base indexing sequence ( CAACGCCAAAA ) is bases 11 to 21 of read 1 followed by CG and polyT.

text: Mus musculus


text: Mus musculus

text: SC

text: public

text: house mouse

text: Mus musculus

text: 3' end enriched mRNA from single cells. An 11 base indexing sequence ( TACCTAACGCA ) is bases 11 to 21 of read 1 followed by CG and polyT.

text: Mus musculus


text: Mus musculus

text: SC

text: public

text: house mouse

text: Mus musculus

text: 3' end enriched mRNA from single cells. An 11 base indexing sequence ( CATAATGGCGA ) is bases 11 to 21 of read 1 followed by CG and polyT.

text: Mus musculus


text: Mus musculus

text: SC

text: public

text: house mouse

text: Mus musculus

text: 3' end enriched mRNA from single cells. An 11 base indexing sequence ( ACGAGACACCC ) is bases 11 to 21 of read 1 followed by CG and polyT.

text: Mus musculus


text: Mus musculus

text: SC

text: public

text: house mouse

text: Mus musculus

text: 3' end enriched mRNA from single cells. An 11 base indexing sequence ( AGTACTACGCG ) is bases 11 to 21 of read 1 followed by CG and polyT.

text: Mus musculus


text: Mus musculus

text: SC

text: public

text: house mouse

text: Mus musculus

text: 3' end enriched mRNA from single cells. An 11 base indexing sequence ( CGGCGAGCCAG ) is bases 11 to 21 of read 1 followed by CG and polyT.

text: Mus musculus


text: Mus musculus

text: SC

text: public

text: house mouse

text: Mus musculus

text: 3' end enriched mRNA from single cells. An 11 base indexing sequence ( TAGGTGAGAAA ) is bases 11 to 21 of read 1 followed by CG and polyT.

text: Mus musculus


text: Mus musculus

text: SC

text: public

text: house mouse

text: Mus musculus

text: 3' end enriched mRNA from single cells. An 11 base indexing sequence ( GCTTGAGGACC ) is bases 11 to 21 of read 1 followed by CG and polyT.

text: Mus musculus


text: Mus musculus

text: SC

text: public

text: house mouse

text: Mus musculus

text: 3' end enriched mRNA from single cells. An 11 base indexing sequence ( AATGAGCAGAG ) is bases 11 to 21 of read 1 followed by CG and polyT.

text: Mus musculus


text: Mus musculus

text: SC

text: public

text: house mouse

text: Mus musculus

text: 3' end enriched mRNA from single cells. An 11 base indexing sequence ( ACGCAGAGAGA ) is bases 11 to 21 of read 1 followed by CG and polyT.

text: Mus musculus


text: Mus musculus

text: SC

text: public

text: house mouse

text: Mus musculus

text: 3' end enriched mRNA from single cells. An 11 base indexing sequence ( GCAATTAGGAG ) is bases 11 to 21 of read 1 followed by CG and polyT.

text: Mus musculus


text: Mus musculus

text: SC

text: public

text: house mouse

text: Mus musculus

text: 3' end enriched mRNA from single cells. An 11 base indexing sequence ( TGAGTGGGCCA ) is bases 11 to 21 of read 1 followed by CG and polyT.

text: Mus musculus


text: Mus musculus

text: SC

text: public

text: house mouse

text: Mus musculus

text: 3' end enriched mRNA from single cells. An 11 base indexing sequence ( CCAAGCAGGCC ) is bases 11 to 21 of read 1 followed by CG and polyT.

text: Mus musculus


text: Mus musculus

text: SC

text: public

text: house mouse

text: Mus musculus

text: 3' end enriched mRNA from single cells. An 11 base indexing sequence ( AAAGAATCGCC ) is bases 11 to 21 of read 1 followed by CG and polyT.

text: Mus musculus


text: Mus musculus

text: SC

text: public

text: house mouse

text: Mus musculus

text: 3' end enriched mRNA from single cells. An 11 base indexing sequence ( GGCTTAAGAGA ) is bases 11 to 21 of read 1 followed by CG and polyT.

text: Mus musculus


text: Mus musculus

text: SC

text: public

text: house mouse

text: Mus musculus

text: 3' end enriched mRNA from single cells. An 11 base indexing sequence ( CTCCACGCAAG ) is bases 11 to 21 of read 1 followed by CG and polyT.

text: Mus musculus


text: Mus musculus

text: SC

text: public

text: house mouse

text: Mus musculus

text: 3' end enriched mRNA from single cells. An 11 base indexing sequence ( TAGGATGGACC ) is bases 11 to 21 of read 1 followed by CG and polyT.

text: Mus musculus


text: Mus musculus

text: SC

text: public

text: house mouse

text: Mus musculus

text: 3' end enriched mRNA from single cells. An 11 base indexing sequence ( GTTACGGGCCG ) is bases 11 to 21 of read 1 followed by CG and polyT.

text: Mus musculus


text: Mus musculus

text: SC

text: public

text: house mouse

text: Mus musculus

text: 3' end enriched mRNA from single cells. An 11 base indexing sequence ( TCCCGGAGCCA ) is bases 11 to 21 of read 1 followed by CG and polyT.

text: Mus musculus


text: Mus musculus

text: SC

text: public

text: house mouse

text: Mus musculus

text: 3' end enriched mRNA from single cells. An 11 base indexing sequence ( GCCAAGGCGCC ) is bases 11 to 21 of read 1 followed by CG and polyT.

text: Mus musculus


text: Mus musculus

text: SC

text: public

text: house mouse

text: Mus musculus

text: 3' end enriched mRNA from single cells. An 11 base indexing sequence ( GGATCGCACAG ) is bases 11 to 21 of read 1 followed by CG and polyT.

text: Mus musculus


text: Mus musculus

text: SC

text: public

text: house mouse

text: Mus musculus

text: 3' end enriched mRNA from single cells. An 11 base indexing sequence ( CATCAGCGAAC ) is bases 11 to 21 of read 1 followed by CG and polyT.

text: Mus musculus


text: Mus musculus

text: SC

text: public

text: house mouse

text: Mus musculus

text: 3' end enriched mRNA from single cells. An 11 base indexing sequence ( AACATTCACCA ) is bases 11 to 21 of read 1 followed by CG and polyT.

text: Mus musculus


text: Mus musculus

text: SC

text: public

text: house mouse

text: Mus musculus

text: 3' end enriched mRNA from single cells. An 11 base indexing sequence ( AGGGACCCACC ) is bases 11 to 21 of read 1 followed by CG and polyT.

text: Mus musculus


text: Mus musculus

text: SC

text: public

text: house mouse

text: Mus musculus

text: 3' end enriched mRNA from single cells. An 11 base indexing sequence ( GCGGGAAAGGC ) is bases 11 to 21 of read 1 followed by CG and polyT.

text: Mus musculus


text: Mus musculus

text: SC

text: public

text: house mouse

text: Mus musculus

text: 3' end enriched mRNA from single cells. An 11 base indexing sequence ( GATACACCGGC ) is bases 11 to 21 of read 1 followed by CG and polyT.

text: Mus musculus


text: Mus musculus

text: SC

text: public

text: house mouse

text: Mus musculus

text: 3' end enriched mRNA from single cells. An 11 base indexing sequence ( TCGAAACGAGG ) is bases 11 to 21 of read 1 followed by CG and polyT.

text: Mus musculus


text: Mus musculus

text: SC

text: public

text: house mouse

text: Mus musculus

text: 3' end enriched mRNA from single cells. An 11 base indexing sequence ( ATTCAAGGAAA ) is bases 11 to 21 of read 1 followed by CG and polyT.

text: Mus musculus


text: Mus musculus

text: SC

text: public

text: house mouse

text: Mus musculus

text: 3' end enriched mRNA from single cells. An 11 base indexing sequence ( AGGGGGAAGCG ) is bases 11 to 21 of read 1 followed by CG and polyT.

text: Mus musculus


text: Mus musculus

text: SC

text: public

text: house mouse

text: Mus musculus

text: 3' end enriched mRNA from single cells. An 11 base indexing sequence ( ACCGATCCAGA ) is bases 11 to 21 of read 1 followed by CG and polyT.

text: Mus musculus


text: Mus musculus

text: SC

text: public

text: house mouse

text: Mus musculus

text: 3' end enriched mRNA from single cells. An 11 base indexing sequence ( GACGGCGCACA ) is bases 11 to 21 of read 1 followed by CG and polyT.

text: Mus musculus


text: Mus musculus

text: SC

text: public

text: house mouse

text: Mus musculus

text: 3' end enriched mRNA from single cells. An 11 base indexing sequence ( GGGACAGAAGG ) is bases 11 to 21 of read 1 followed by CG and polyT.

text: Mus musculus


text: Mus musculus

text: SC

text: public

text: house mouse

text: Mus musculus

text: 3' end enriched mRNA from single cells. An 11 base indexing sequence ( CCTTGCGACAG ) is bases 11 to 21 of read 1 followed by CG and polyT.

text: Mus musculus


text: Mus musculus

text: SC

text: public

text: house mouse

text: Mus musculus

text: 3' end enriched mRNA from single cells. An 11 base indexing sequence ( GCACTGGGCGC ) is bases 11 to 21 of read 1 followed by CG and polyT.

text: Mus musculus


text: Mus musculus

text: SC

text: public

text: house mouse

text: Mus musculus

text: 3' end enriched mRNA from single cells. An 11 base indexing sequence ( GTGAAGTGGAC ) is bases 11 to 21 of read 1 followed by CG and polyT.

text: Mus musculus


text: Mus musculus

text: SC

text: public

text: house mouse

text: Mus musculus

text: 3' end enriched mRNA from single cells. An 11 base indexing sequence ( TTCGCACCCGA ) is bases 11 to 21 of read 1 followed by CG and polyT.

text: Mus musculus


text: Mus musculus

text: SC

text: public

text: house mouse

text: Mus musculus

text: 3' end enriched mRNA from single cells. An 11 base indexing sequence ( TGACTGCAGCG ) is bases 11 to 21 of read 1 followed by CG and polyT.

text: Mus musculus


text: Mus musculus

text: SC

text: public

text: house mouse

text: Mus musculus

text: 3' end enriched mRNA from single cells. An 11 base indexing sequence ( TTGGACAGGGC ) is bases 11 to 21 of read 1 followed by CG and polyT.

text: Mus musculus


text: Mus musculus

text: SC

text: public

text: house mouse

text: Mus musculus

text: 3' end enriched mRNA from single cells. An 11 base indexing sequence ( GGTATAAAACC ) is bases 11 to 21 of read 1 followed by CG and polyT.

text: Mus musculus


text: Mus musculus

text: SC

text: public

text: house mouse

text: Mus musculus

text: 3' end enriched mRNA from single cells. An 11 base indexing sequence ( GATTGACCAAA ) is bases 11 to 21 of read 1 followed by CG and polyT.

text: Mus musculus


text: Mus musculus

text: SC

text: public

text: house mouse

text: Mus musculus

text: 3' end enriched mRNA from single cells. An 11 base indexing sequence ( CAAGACTGCCA ) is bases 11 to 21 of read 1 followed by CG and polyT.

text: Mus musculus


text: public

tag: Namespace:Duke Molecular Physiology Institute, Duke University

text: ArrayExpress

characteristic: broker name

text: QNR/D

characteristic: cell line

text: neuroretina cell

characteristic: cell type

text: Japanese quail

text: Protocols: 'QNR/D cell lines were purchased from ATCC and cultured by following the instruction. The base medium for this cell line is ATCC-formulated Dulbecco''s Modified Eagle''s Medium, Catalog No. 30-2002. To make the complete growth medium, add the following components to the base medium: fetal bovine serum to a final concentration of 10%. Protocol: Remove and discard culture medium. Briefly rinse the cell layer with 0.25% (w/v) Trypsin- 0.53 mM EDTA solution to remove all traces of serum which contains trypsin inhibitor. Add 2.0 to 3.0 ml of Trypsin-EDTA solution to flask and observe cells under an inverted microscope until cell layer is dispersed (usually within 5 to 15 minutes). Note: To avoid clumping do not agitate the cells by hitting or shaking the flask while waiting for the cells to detach. Cells that are difficult to detach may be placed at 37°C to facilitate dispersal. Add 6.0 to 8.0 ml of complete growth medium and aspirate cells by gently pipetting. Add appropriate aliquots of the cell suspension to new culture vessels. Incubate cultures at 38.5°C.to 39°C Subcultivation Ratio: A subcultivation ratio of 1:3 to 1:5 is recommended Medium Renewal: Every 2 to 3 days.' Illumina TruSeq Stranded RNA-Seq kit. Poly-A enriched mRNA. default insert size is around 200bp.

characteristic: description

text: gene knock in

characteristic: genetic modification

text: AES overexpression

characteristic: genotype

text: Coturnix japonica

text: Coturnix japonica

text: Coturnix japonica


characteristic: ENA-CHECKLIST

text: Duke Molecular Physiology Institute, Duke University

characteristic: INSDC last update

text: public

characteristic: SRA accession

characteristic: Submitter Id

text: ArrayExpress

text: QNR/D

text: neuroretina cell

text: Japanese quail

text: gene knock in

text: AES overexpression

text: Coturnix japonica

text: Coturnix japonica

text: Coturnix japonica

characteristic: title


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: public

text: ArrayExpress

text: QNR/D

text: neuroretina cell

text: Japanese quail

characteristic: common name

text: wild type genotype

text: Coturnix japonica

characteristic: organism

text: Coturnix japonica

text: Coturnix japonica


characteristic: INSDC center name

characteristic: INSDC first public

text: public

characteristic: INSDC status

text: ArrayExpress

text: QNR/D

text: neuroretina cell

text: Japanese quail

text: gene knock in

text: SIX6 overexpression

text: Coturnix japonica

text: Coturnix japonica

text: Coturnix japonica


text: public

text: ArrayExpress

characteristic: broker name

text: QNR/D

characteristic: cell line

text: neuroretina cell

characteristic: cell type

text: Japanese quail

text: gene knock in

text: SIX6 and AES overexpression

text: Coturnix japonica

text: Coturnix japonica

text: Coturnix japonica


text: public

text: ArrayExpress

text: QNR/D

text: neuroretina cell

text: Japanese quail

characteristic: description

text: gene knock in

characteristic: genetic modification

text: SIX6 and TLE1 overexpression

characteristic: genotype

text: Coturnix japonica

text: Coturnix japonica

text: Coturnix japonica


characteristic: ENA-CHECKLIST

characteristic: INSDC last update

text: public

characteristic: SRA accession

text: ArrayExpress

text: QNR/D

text: neuroretina cell

text: Japanese quail

text: gene knock in

text: TLE1 overexpression

text: Coturnix japonica

text: Coturnix japonica

text: Coturnix japonica


E-MTAB-3834:Sample 1

characteristic: ENA-FIRST-PUBLIC

text: public

text: E-MTAB-3834:Sample 1

tag: Namespace:Department of Agronomy, National Taiwan University

characteristic: Submitter Id

text: ArrayExpress

text: rice

text: Protocols: Sterilized seeds were germinated on moist kimwipe tissues in capped glass tubes in a growth chamber with a photoperiod 16hr-light (150 μmole m-2 s-1) 8hr-dark cycle at 25°C for 7 days as control condition For submergence treatment, the seeds were germinated in 5 cm water-filled glass tube for 7 days. Total RNA from shoot tissue of 7-day-old seedlings was extracted using TRI Reagent® (Ambion) and Direct-zolTM RNA MiniPrep Kit (ZymoResearch). Poly-A RNA containing mRNA was purified using poly-T oligo-attached magnetic beads and fragmented. Complementary DNA (cDNA) was synthesized using random hexamer priming, followed by purification, end repair, poly-A tailing and adaptor ligation.

text: 0 seed germination stage

characteristic: developmental stage

text: normal air

characteristic: growth condition

text: Oryza sativa

text: Oryza sativa

text: Oryza sativa

text: Sample 1

characteristic: title


E-MTAB-3834:Sample 10

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Department of Agronomy, National Taiwan University

characteristic: INSDC center name

text: public

text: E-MTAB-3834:Sample 10

text: ArrayExpress

text: rice

characteristic: common name

text: 0 seed germination stage

text: submergence low oxygen

text: Oryza sativa

characteristic: organism

text: Oryza sativa

text: Oryza sativa

text: Sample 10


E-MTAB-3834:Sample 11

characteristic: INSDC first public

text: public

characteristic: INSDC status

text: E-MTAB-3834:Sample 11

text: ArrayExpress

characteristic: broker name

text: rice

text: 0 seed germination stage

text: normal air

text: Oryza sativa

text: Oryza sativa

text: Oryza sativa

text: Sample 11


E-MTAB-3834:Sample 12

text: public

text: E-MTAB-3834:Sample 12

text: ArrayExpress

text: rice

characteristic: description

text: 0 seed germination stage

text: submergence low oxygen

text: Oryza sativa

text: Oryza sativa

text: Oryza sativa

text: Sample 12


E-MTAB-3834:Sample 2

characteristic: ENA-CHECKLIST

text: public

text: E-MTAB-3834:Sample 2

text: ArrayExpress

text: rice

text: 0 seed germination stage

text: submergence low oxygen

text: Oryza sativa

text: Oryza sativa

text: Oryza sativa

text: Sample 2


E-MTAB-3834:Sample 3

characteristic: INSDC last update

text: public

text: E-MTAB-3834:Sample 3

text: ArrayExpress

text: rice

text: 0 seed germination stage

text: normal air

text: Oryza sativa

text: Oryza sativa

text: Oryza sativa

text: Sample 3


E-MTAB-3834:Sample 4

text: public

characteristic: SRA accession

text: E-MTAB-3834:Sample 4

text: ArrayExpress

text: rice

text: 0 seed germination stage

text: submergence low oxygen

text: Oryza sativa

text: Oryza sativa

text: Oryza sativa

text: Sample 4


E-MTAB-3834:Sample 5

characteristic: ENA-FIRST-PUBLIC

text: public

text: E-MTAB-3834:Sample 5

text: ArrayExpress

text: rice

text: 0 seed germination stage

text: normal air

text: Oryza sativa

text: Oryza sativa

text: Oryza sativa

text: Sample 5


E-MTAB-3834:Sample 6

text: public

text: E-MTAB-3834:Sample 6

characteristic: Submitter Id

text: ArrayExpress

text: rice

text: 0 seed germination stage

text: submergence low oxygen

text: Oryza sativa

text: Oryza sativa

text: Oryza sativa

text: Sample 6


E-MTAB-3834:Sample 7

text: public

text: E-MTAB-3834:Sample 7

text: ArrayExpress

text: rice

text: 0 seed germination stage

characteristic: developmental stage

text: normal air

text: Oryza sativa

text: Oryza sativa

text: Oryza sativa

text: Sample 7


E-MTAB-3834:Sample 8

text: public

text: E-MTAB-3834:Sample 8

text: ArrayExpress

text: rice

text: 0 seed germination stage

text: submergence low oxygen

characteristic: growth condition

text: Oryza sativa

text: Oryza sativa

text: Oryza sativa

text: Sample 8


E-MTAB-3834:Sample 9

text: public

text: E-MTAB-3834:Sample 9

text: ArrayExpress

text: rice

text: 0 seed germination stage

text: normal air

text: Oryza sativa

text: Oryza sativa

text: Oryza sativa

text: Sample 9

characteristic: title


characteristic: ENA-LAST-UPDATE

text: EBI

text: killed

text: fruit fly

text: Drosophila melanogaster

text: Drosophila melanogaster

text: Test Sample


characteristic: External Id

text: EBI

text: killed

text: fruit fly

text: Drosophila melanogaster

text: Drosophila melanogaster

text: Test Sample


text: Danio rerio

characteristic: ArrayExpress-Species

text: SC

characteristic: INSDC center name

text: public

text: zebrafish

text: Danio rerio

text: DNA libraries made by the addition of tailed oligos in a second round of PCR.

characteristic: sample description

text: Danio rerio


text: Danio rerio

text: SC

characteristic: INSDC first public

text: public

text: zebrafish

characteristic: common name

text: Danio rerio

characteristic: organism

text: Danio rerio


text: ESC

characteristic: ArrayExpress-CellType

text: male

characteristic: ArrayExpress-Sex

text: Mus musculus

characteristic: ArrayExpress-StrainOrLine

text: SC

text: public

characteristic: INSDC status

text: house mouse

text: Mus musculus

text: Mus musculus

characteristic: strain


text: DIFF

text: male

text: Mus musculus

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: SC

characteristic: INSDC last update

text: public

characteristic: SRA accession

characteristic: Submitter Id

text: house mouse

text: Mus musculus

text: Mus musculus


text: Homo Sapien

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: SC

text: killed

characteristic: Sample Description

characteristic: Strain

text: human

text: Homo sapiens

text: Homo sapiens


text: Liver

text: female

text: Mus spretus

characteristic: ArrayExpress-Species

text: SPRET/Ei

text: SC

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: western wild mouse

text: Mus spretus

text: RNA

characteristic: sample description

text: Mus spretus

text: SPRET/Ei


text: Liver

characteristic: ArrayExpress-CellType

text: female

characteristic: ArrayExpress-Sex

text: Mus musculus

text: PWK/PhJ

text: SC

text: public

text: eastern European house mouse

characteristic: common name

text: Mus musculus musculus

characteristic: organism

text: RNA

text: Mus musculus musculus

text: PWK/PhJ


text: Liver

text: female

text: Mus musculus

text: CAST/EiJ

characteristic: ArrayExpress-StrainOrLine

characteristic: ENA-CHECKLIST

text: SC

text: public

characteristic: INSDC status

text: southeastern Asian house mouse

text: Mus musculus castaneus

text: RNA

text: Mus musculus castaneus

text: CAST/EiJ

characteristic: strain


text: Liver

text: female

text: Mus musculus

characteristic: ENA-FIRST-PUBLIC

text: SC

characteristic: INSDC last update

text: public

characteristic: SRA accession

characteristic: Submitter Id

text: house mouse

text: Mus musculus

text: RNA

text: Mus musculus


text: Spleen

text: female

text: Mus musculus

text: PWK/PhJ

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: SC

text: public

text: eastern European house mouse

text: Mus musculus musculus

text: RNA

text: Mus musculus musculus

text: PWK/PhJ


text: Spleen

text: female

text: Mus musculus

characteristic: ArrayExpress-Species

text: CAST/EiJ

text: SC

characteristic: INSDC center name

text: public

text: southeastern Asian house mouse

text: Mus musculus castaneus

text: RNA

text: Mus musculus castaneus

text: CAST/EiJ


text: Spleen

text: female

text: Mus musculus

text: SC

characteristic: INSDC first public

text: public

text: house mouse

text: Mus musculus

text: RNA

characteristic: sample description

text: Mus musculus


text: Brain

characteristic: ArrayExpress-CellType

text: female

characteristic: ArrayExpress-Sex

text: Mus musculus

text: FVB/NJ

text: SC

text: public

text: house mouse

text: Mus musculus

text: RNA

text: Mus musculus

text: FVB/NJ


text: male

text: Homo Sapien

text: SC

text: killed

characteristic: Sample Description

characteristic: Strain

text: human

characteristic: common name

text: Homo sapiens

characteristic: organism

text: Homo sapiens


text: Homo Sapien

characteristic: ArrayExpress-StrainOrLine

characteristic: ENA-CHECKLIST

text: SC

text: public

characteristic: INSDC status

text: human

text: Homo sapiens

text: Homo sapiens

characteristic: strain


text: Mus musculus

characteristic: ENA-FIRST-PUBLIC

text: SC

characteristic: INSDC last update

text: public

characteristic: SRA accession

characteristic: Submitter Id

text: house mouse

text: Mus musculus

text: Mus musculus


text: female

text: Mus musculus

characteristic: ArrayExpress-Species

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: SC

characteristic: INSDC center name

text: public

text: house mouse

text: Mus musculus

text: Mus musculus


text: Bone Marrow

characteristic: ArrayExpress-CellType

text: Bone Marrow

characteristic: ArrayExpress-OrganismPart

text: Mus musculus

text: SC

characteristic: INSDC first public

text: public

text: house mouse

text: Mus musculus

text: mRNAseq Nextera library made from RNA extracted from mutant Ba/F3 cells

characteristic: sample description

text: Mus musculus


text: Clintec, Karolinska Institutet

text: public

text: ArrayExpress

characteristic: broker name

characteristic: cell line

text: Human embryonic stem cell

characteristic: cell type

text: human

characteristic: common name

text: Protocols: The hESC line HS401 (46,XY) was cultured on hESC-qualified Matrigel (Corning) -coated plates using mTeSR1 medium (StemCell Technologies) in 5% CO2 and atmospheric oxygen at 37°C. The cells were passaged using Accutase (Life Technologies), followed by an over night incubation with 5 μM Y-27632 (Millipore). hESCs were co-transfected with 2.5 μg piggyBac transposon (IFP2) and 2.5 μg transposase vector (MOCK, NANOS3, or DAZL) in a 6-well format using 5 μl PLUS reagent and 10 μl Lipofectamine LTX (Life Technologies) according to the manufacturer’s instructions. Two days after the transfection, cells were selected with 1 μg/ml puromycin (Life Technologies) for 6 days. Transfection was repeted three times for each transposase vector and cells were collected for RNA isolation at passage 1 after transfection. RNA libraries for sequencing were prepared using TruSeq Stranded mRNA Sample prep kit with 96 dual indexes (Illumina, CA, USA) according to the manufacturers instructions with the following changes. The protocols were automated using an Agilent NGS workstation (Agilent, CA, USA) using purification steps as described in: S. Lundin/ H. Stranneheim PLoS ONE 2010) and (E. Borgstrom/ S.Lundin et al. 2011 PLoS ONE).

characteristic: description

text: piggyBac over expression construct

characteristic: genetic modification

text: construct without open reading frame

characteristic: genotype

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: Homo sapiens

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: Clintec, Karolinska Institutet

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: ArrayExpress

text: Human embryonic stem cell

text: human

text: piggyBac over expression construct

text: over expression NANOS3

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Clintec, Karolinska Institutet

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: ArrayExpress

text: Human embryonic stem cell

text: human

text: piggyBac over expression construct

text: over expression DAZL

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens


text: H. sapiens

characteristic: ArrayExpress-Species

text: Hapmap

characteristic: ArrayExpress-StrainOrLine

text: SC

text: public

text: human

text: Homo sapiens

text: Hapmap

characteristic: sample description

text: Homo sapiens

text: Hapmap

characteristic: strain


text: embryonic stem cell

characteristic: ArrayExpress-CellType

text: male

characteristic: ArrayExpress-Sex

text: Mus musculus

text: mus musculus

text: SC

text: public

text: house mouse

characteristic: common name

text: Mus musculus

text: ATAC-seq library, has nucleosomal distribution

text: Mus musculus

text: mus musculus


text: Mus musculus

characteristic: ENA-CHECKLIST

text: SC

text: public

text: house mouse

text: Mus musculus

characteristic: organism

text: Bisulphite library

text: Mus musculus


text: Mouse

characteristic: ENA-FIRST-PUBLIC

text: SC

characteristic: INSDC last update

text: public

text: house mouse

text: Mus musculus

text: Amplicon

text: Mus musculus


text: EBI

text: killed

characteristic: INSDC status

characteristic: SRA accession

text: fruit fly

text: Drosophila melanogaster

text: Drosophila melanogaster

text: Test Sample

characteristic: title


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: EBI

text: killed

characteristic: Submitter Id

text: fruit fly

text: Drosophila melanogaster

text: Drosophila melanogaster

text: Test Sample


text: Plasmodium Falciparum

characteristic: ArrayExpress-Species

text: SC

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: malaria parasite P. falciparum

text: Plasmodium falciparum

text: Plasmodium falciparum


text: Mus musculus

characteristic: ArrayExpress-StrainOrLine

text: SC

text: public

text: house mouse

text: Mus musculus

text: DNA from earclip

characteristic: sample description

text: Mus musculus

characteristic: strain


text: Mus musculus

text: SC

text: public

text: house mouse

characteristic: common name

text: Mus musculus

text: DNA from blastocyst

text: Mus musculus


text: Mus musculus

characteristic: ENA-CHECKLIST

text: SC

text: public

text: house mouse

text: Mus musculus

text: Amplicon library

text: Mus musculus


E-MTAB-3858:F1.II-10 (08S381)

text: public

text: E-MTAB-3858:F1.II-10 (08S381)

tag: Namespace:Centro Nacional de Investigaciones Oncológicas: CNIO

characteristic: age

text: ArrayExpress

characteristic: broker name

text: lymphocyte

characteristic: cell type

text: Li-Fraumeni-like family

characteristic: clinical history

text: human

text: Protocols: Blood samples were taken directly from patients. DNA was extracted from lympohcytes from using standard methods DNA was captured and enriched using the SureSelect Human All Exon Kit (78 Mb)

characteristic: description

text: angiosarcoma

characteristic: disease

characteristic: genotype

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: whole organism

characteristic: organism part

text: Homo sapiens

text: female

characteristic: sex

text: F1.II-10 (08S381)


E-MTAB-3858:F1.III-13 (10S763)

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Centro Nacional de Investigaciones Oncológicas: CNIO

characteristic: INSDC center name

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-3858:F1.III-13 (10S763)

characteristic: Submitter Id

text: ArrayExpress

text: lymphocyte

text: Li-Fraumeni-like family

text: human

text: angiosarcoma

text: Homo sapiens

text: Homo sapiens

text: whole organism

text: Homo sapiens

text: female

text: F1.III-13 (10S763)

characteristic: title


characteristic: ENA-CHECKLIST

text: University of Manchester

characteristic: INSDC first public

text: public

tag: Namespace:University of Manchester

text: ArrayExpress

characteristic: broker name

text: house mouse

characteristic: common name

text: Protocols: Palatal shelves from 5 embryos were dissected from E10.5 mouse embryos and pooled for RNA extraction. The same was done for E11.5, E12.5, E13.5 and E14.5 mouse embryos. All mice were housed with free access to food and water under specific pathogen free conditions at the University of Manchester. Temperature 20-22 Â°C, Humidity 40-60%, Specified mouse pathogen free conditions, 12 hours light/dark cycle. Nutrients Rat and Mouse Standard Diet no.1 expanded (Ban Kingman). All experiments were performed under regulations of The UK Home Office Scientific Procedures Act (1986). BALB/c mouse strain (Charles River Ltd, UK) were used for the experiment. Embryos were obtained after matings, the morning of the vaginal plug being considered embryonic day (E) 0.5. RNA was isolated mouse palatal shelves using the Qiagen RNeasy kit. SOLiDTM Total RNA-Seq Kit (PN 4445374)

text: embryonic day 10.5

characteristic: developmental stage

text: Mus musculus

text: Mus musculus

text: palate

text: Mus musculus


text: University of Manchester

text: public

text: ArrayExpress

text: house mouse

characteristic: description

text: embryonic day 11.5

text: Mus musculus

characteristic: organism

text: Mus musculus

text: palate

text: Mus musculus


text: University of Manchester

text: public

text: ArrayExpress

text: house mouse

text: embryonic day 12.5

text: Mus musculus

text: Mus musculus

text: palate

characteristic: organism part

text: Mus musculus


characteristic: ENA-FIRST-PUBLIC

text: public

tag: Namespace:Telethon Institute of Genetics and Medicine (Tigem)

text: ArrayExpress

text: embryonic cell line

characteristic: cell line

text: epiblast cell

characteristic: cell type

text: house mouse

text: Protocols: ChIP-assay were performed from 10e7 cells per experiment. Cells were crosslinked with 1% formaldehyde for 10 min at room temperature. Glycine at a final concentration of 0.125 M was added to quench the reaction. Cells were collected and lysed in SDS buffer and chromatin was then sonicated to an average size of 0,2-0,3 kb. After a 30 minute step of chromatin preclearing with the Protein A Agarose/Salmon Sperm DNA 50% gel slurry (Millipore), rabbit polyclonal antibody against Otx2 was added to the chromatin and incubated overnight at 4°C. The immunoprecipitated complex was subsequently incubated with the Protein A Agarose for 2-4 hours at 4°C. Agarose beads were then washed, chromatin was eluted and reverse-crosslinked overnight at 65°C. EpiSCs were induced from ESCs on serum-coated dishes in N2B27 medium supplemented with activin A and Fgf2. Proteinase K treatment and phenol/chloroform purification. Libraries were prepared according to Illumina standard protocols with internal barcodes.

text: Otx2 knockout

characteristic: genotype

text: Mus musculus

text: Mus musculus

text: Mus musculus


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Telethon Institute of Genetics and Medicine (Tigem)

characteristic: INSDC center name

characteristic: INSDC last update

text: public

text: ArrayExpress

text: embryonic cell line

text: epiblast cell

text: house mouse

text: Otx2 knockout

text: Mus musculus

text: Mus musculus

text: Mus musculus


text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: ArrayExpress

text: embryonic cell line

text: epiblast cell

text: house mouse

text: wild type genotype

text: Mus musculus

text: Mus musculus

text: Mus musculus

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: INSDC first public

text: public

text: ArrayExpress

characteristic: broker name

text: embryonic cell line

text: embryonic stem cell

text: house mouse

characteristic: common name

text: Protocols: ChIP-assay were performed from 10e7 cells per experiment. Cells were crosslinked with 1% formaldehyde for 10 min at room temperature. Glycine at a final concentration of 0.125 M was added to quench the reaction. Cells were collected and lysed in SDS buffer and chromatin was then sonicated to an average size of 0,2-0,3 kb. After a 30 minute step of chromatin preclearing with the Protein A Agarose/Salmon Sperm DNA 50% gel slurry (Millipore), rabbit polyclonal antibody against Otx2 was added to the chromatin and incubated overnight at 4°C. The immunoprecipitated complex was subsequently incubated with the Protein A Agarose for 2-4 hours at 4°C. Agarose beads were then washed, chromatin was eluted and reverse-crosslinked overnight at 65°C. E14Tg2a wt and Obs3 mutant ESCs were routinely grown in GMEM medium plus 12% FBS (Hyclone) and LIF (Millipore). Proteinase K treatment and phenol/chloroform purification. Libraries were prepared according to Illumina standard protocols with internal barcodes.

text: Otx2 knockout

text: Mus musculus

text: Mus musculus

text: Mus musculus


text: public

text: ArrayExpress

text: embryonic cell line

text: embryonic stem cell

text: house mouse

characteristic: description

text: wild type genotype

text: Mus musculus

characteristic: organism

text: Mus musculus

text: Mus musculus


E-MTAB-3856:NanogObs3/Obs3 ESC1

characteristic: ENA-FIRST-PUBLIC

text: public

text: E-MTAB-3856:NanogObs3/Obs3 ESC1

text: ArrayExpress

text: embryonic cell line

characteristic: cell line

text: embryonic stem cell

text: house mouse

text: Protocols: E14Tg2a wt and Obs3 mutant ESCs were routinely grown in GMEM medium plus 12% FBS (Hyclone) and LIF (Millipore). RNA was extracted with Trizol (Invitrogen) Indexed sequencing libraries were generated from 1ug RNA, using the TruSeq Stranded Total RNA Sample Prep Kit with Ribo-Zero ribosomal RNA reduction chemistry (Illumina, San Diego, CA), according to the manufacturer’s instructions.

text: Mus musculus

text: Mus musculus

text: Mus musculus

text: NanogObs3/Obs3 ESC1


E-MTAB-3856:NanogObs3/Obs3 ESC2

text: public

text: E-MTAB-3856:NanogObs3/Obs3 ESC2

text: ArrayExpress

text: embryonic cell line

text: embryonic stem cell

characteristic: cell type

text: house mouse

characteristic: genotype

text: Mus musculus

text: Mus musculus

text: Mus musculus

text: NanogObs3/Obs3 ESC2


E-MTAB-3856:wt EpiSC1

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: public

text: E-MTAB-3856:wt EpiSC1

text: ArrayExpress

text: embryonic cell line

text: epiblast cell

text: house mouse

text: Protocols: EpiSCs were induced from ESCs on serum-coated dishes in N2B27 medium supplemented with activin A and Fgf2. RNA was extracted with Trizol (Invitrogen) Indexed sequencing libraries were generated from 1ug RNA, using the TruSeq Stranded Total RNA Sample Prep Kit with Ribo-Zero ribosomal RNA reduction chemistry (Illumina, San Diego, CA), according to the manufacturer’s instructions.

text: wild type genotype

text: Mus musculus

text: Mus musculus

text: Mus musculus

text: wt EpiSC1


E-MTAB-3856:wt EpiSC2

characteristic: INSDC center name

characteristic: INSDC last update

text: public

text: E-MTAB-3856:wt EpiSC2

text: ArrayExpress

text: embryonic cell line

text: epiblast cell

text: house mouse

text: wild type genotype

text: Mus musculus

text: Mus musculus

text: Mus musculus

text: wt EpiSC2


E-MTAB-3856:wt ESC1

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-3856:wt ESC1

text: ArrayExpress

text: embryonic cell line

text: embryonic stem cell

text: house mouse

text: wild type genotype

text: Mus musculus

text: Mus musculus

text: Mus musculus

text: wt ESC1


E-MTAB-3856:wt ESC2

text: public

text: E-MTAB-3856:wt ESC2

characteristic: Submitter Id

text: ArrayExpress

text: embryonic cell line

text: embryonic stem cell

text: house mouse

text: wild type genotype

text: Mus musculus

text: Mus musculus

text: Mus musculus

text: wt ESC2

characteristic: title


text: Mus Musculus

characteristic: ArrayExpress-Species

characteristic: ENA-CHECKLIST

text: SC

characteristic: INSDC first public

text: public

text: house mouse

text: Mus musculus

text: Mus musculus


text: ESC-Like

characteristic: ArrayExpress-CellType

text: female

characteristic: ArrayExpress-Sex

text: Mus musculus

text: SC

text: public

text: house mouse

characteristic: common name

text: Mus musculus

text: Mus musculus


text: MEF

text: female

text: Mus musculus

characteristic: ENA-FIRST-PUBLIC

text: SC

text: public

text: house mouse

text: Mus musculus

characteristic: organism

text: Mus musculus


text: Xenopus tropicalis

text: SC

text: public

text: western clawed frog

text: Xenopus (Silurana) tropicalis

text: Xenopus (Silurana) tropicalis


text: Yeast

characteristic: ArrayExpress-Phenotype

text: Saccharomyces cerevisiae

text: SC

text: public

text: baker's yeast

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae


characteristic: ENA-LAST-UPDATE

text: public

tag: Namespace:European Molecular Biology Laboratory EMBL-EBI

text: ArrayExpress

characteristic: broker name

characteristic: cell line

text: Neural stem cell

characteristic: cell type

text: human

text: Protocols: GNS and NS cells were cultured using serum-free basal media supplemented with B27 and N2 culture supplements (Life Technologies). Growth factors EGF and FGF-2 (20 ng/ml) were added. Culture vessels were coated with Laminin (Sigma) for 3 hr at 10 ug/ml prior to use. Alternatively media was directly supplemented with 1 ug/ml Laminin. GNS cells were routinely grown to confluence, dissociated using Accutase (Sigma), and then split 1:3 to 1:7. Medium was replaced every 3-7 days. GNS and NS cells were split as appropriate to maintain a plating density of ~10 cells/mm2; differentiating cells were maintained in media supplemented with bone morphogenic protein (BMP) without EGF and FGF-2. After 8 daysâ treatment cells were harvested, counted and pelleted in aliquots of 50,000 cells. Cells were lysed and the nuclei were pelleted then suspended in buffer and treated with Tn5 transposase for 30 min. ATAC library preparation was undertaken according to published protocols (Buenrostro et al. 2013, Nat Methods 10:1213-8). DNA was purified using Qiagen MinElute columns, followed by 12 cycles of PCR amplification using NEBNext High Fidelity Master Mix and custom primers, with adapter sequences previously specified for ATAC-seq (Buenrostro et al., 2013), followed by further purification on MinElute columns.

characteristic: description

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens


characteristic: External Id

text: European Molecular Biology Laboratory EMBL-EBI

characteristic: INSDC center name

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: ArrayExpress

text: Neural stem cell

text: human

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens


characteristic: ENA-CHECKLIST

characteristic: INSDC first public

text: public

characteristic: Submitter Id

text: ArrayExpress

text: Neural stem cell

text: human

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens

text: bone morphogenic protein

characteristic: stimulus

unit: day

characteristic: time

characteristic: title


characteristic: ENA-FIRST-PUBLIC

text: public

text: ArrayExpress

text: Neural stem cell

text: human

characteristic: common name

text: glioblastoma multiforme

characteristic: disease

text: Grade IV

characteristic: disease staging

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: Homo sapiens


characteristic: ENA-LAST-UPDATE

text: public

text: ArrayExpress

characteristic: broker name

characteristic: cell line

text: Neural stem cell

characteristic: cell type

text: human

characteristic: description

text: glioblastoma multiforme

text: Grade IV

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens

text: bone morphogenic protein


text: Pluripotent cell line

characteristic: ArrayExpress-CellType

text: EPSCM

characteristic: ArrayExpress-GrowthCondition

characteristic: ArrayExpress-Immunoprecipitate

text: Normal

characteristic: ArrayExpress-Phenotype

text: male

characteristic: ArrayExpress-Sex

text: Mus musculus

characteristic: ArrayExpress-Species

text: EPSCM

characteristic: ArrayExpress-Treatment

characteristic: External Id

text: SC

characteristic: INSDC center name

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: house mouse

text: Mus musculus

text: Pluripotent cell line

characteristic: sample description

text: Mus musculus


text: Pluripotent cell line

text: EPSCM

text: INPUT

text: Normal

text: male

text: Mus musculus

text: EPSCM

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: SC

characteristic: INSDC first public

text: public

characteristic: Submitter Id

text: house mouse

characteristic: common name

text: Mus musculus

characteristic: organism

text: Pluripotent cell line

text: Mus musculus


text: public

tag: Namespace:Copenhagen Center for Glycomics, University of Copenhagen

text: ArrayExpress

characteristic: broker name

characteristic: cell line

text: human

text: Protocols: The analysis was performed on total RNA from two clones each of HepG2WTΔT1, ΔT2, +T3, and two pools of HepG2WT cells, Total RNA was extracted from exponentially growing cells using RNeasy®kit (Qiagen) Library was constructed using Illumina Truseq RNA Sample Preparation Kit. High quality total RNA was DNase I treated, mRNA isolated by magnetic bead Oligo (dT) enrichment, followed by mRNA fragmentation, cDNA synthesis, single nucleotide A (adenine) addition, and adapter ligation.

characteristic: description

text: gene knock out

characteristic: genetic modification

text: GALNT1 knockout

characteristic: genotype

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens

characteristic: title


characteristic: External Id

text: Copenhagen Center for Glycomics, University of Copenhagen

characteristic: INSDC center name

characteristic: INSDC last update

text: public

text: ArrayExpress

text: human

text: gene knock out

text: GALNT1 knockout

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens


text: public

characteristic: INSDC status

characteristic: SRA accession

text: ArrayExpress

text: human

text: gene knock out

text: GALNT2 knockout

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: public

text: ArrayExpress

text: human

text: gene knock in

text: GALNT3 knock-in

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens


characteristic: ENA-LAST-UPDATE

characteristic: INSDC first public

text: public

text: ArrayExpress

text: human

text: wild type genotype

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens


characteristic: ArrayExpress-DevelopmentalStage

text: whole embryo

characteristic: ArrayExpress-OrganismPart

text: Mus musculus

characteristic: ArrayExpress-Species

characteristic: ArrayExpress-StrainOrLine

text: SC

text: public

characteristic: Submitter Id

text: house mouse

characteristic: common name

text: Mus musculus

text: Total RNA from a single second generation genotypically wildtype C57BL/6N mouse embryo with 5 somites, collected at E8.5. The embryo comes from a mixed G0 lineage of heterozygous Setd5 animals. This study forms part of the Deciphering the Mechanisms of Developmental Disorders (DMDD) project.

characteristic: sample description

text: Mus musculus

characteristic: strain


text: whole embryo

text: Mus musculus

characteristic: External Id

text: SC

text: public

text: house mouse

text: Mus musculus

characteristic: organism

text: Total RNA from a single second generation genotypically wildtype C57BL/6N mouse embryo with 5 somites, collected at E8.5. The embryo comes from a mixed G0 lineage of heterozygous Pold3(b) animals. This study forms part of the Deciphering the Mechanisms of Developmental Disorders (DMDD) project.

text: Mus musculus


text: whole embryo

text: Mus musculus

text: SC

characteristic: INSDC center name

characteristic: INSDC last update

text: public

text: house mouse

text: Mus musculus

text: Total RNA from a single second generation genotypically wildtype C57BL/6N mouse embryo with 12 somites, collected at E8.5. The embryo comes from a mixed G0 lineage of heterozygous Pold3(b) animals. This study forms part of the Deciphering the Mechanisms of Developmental Disorders (DMDD) project.

text: Mus musculus


text: whole embryo

text: Mus musculus

text: SC

text: public

characteristic: INSDC status

characteristic: SRA accession

text: house mouse

text: Mus musculus

text: Total RNA from a single second generation genotypically wildtype C57BL/6N mouse embryo with 27 somites, collected at E9.5. The embryo comes from a mixed G0 lineage of heterozygous Pold3(b) animals. This study forms part of the Deciphering the Mechanisms of Developmental Disorders (DMDD) project.

text: Mus musculus


text: whole embryo

text: Mus musculus

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: SC

text: public

text: house mouse

text: Mus musculus

text: Total RNA from a single second generation genotypically wildtype C57BL/6N mouse embryo with 34 somites, collected at E10.5. The embryo comes from a mixed G0 lineage of heterozygous Setd5 animals. This study forms part of the Deciphering the Mechanisms of Developmental Disorders (DMDD) project.

text: Mus musculus


text: male

characteristic: ArrayExpress-Sex

text: Homo Sapien

characteristic: ENA-LAST-UPDATE

text: SC

characteristic: INSDC first public

text: public

text: human

text: Homo sapiens

text: Homo sapiens


text: Tumour

characteristic: ArrayExpress-Phenotype

text: Homo Sapien

characteristic: ArrayExpress-Species

text: SC

text: public

text: human

text: Homo sapiens

text: Homo sapiens


text: Mus musculus

text: SC

text: public

characteristic: Submitter Id

text: house mouse

text: Mus musculus

text: Screen 16 Unstimulated Wild Type Knock-out Embryonic Stem Cell Derived Macrophages 4hr p7

text: Mus musculus


text: Mus musculus

text: SC

text: public

text: house mouse

characteristic: common name

text: Mus musculus

text: Screen 16 Wild Type Knock-out Embryonic Stem Cell Derived Macrophages stimulated with Poly I:C (Toll-like receptor agonist) p7

text: Mus musculus


text: Mus musculus

text: SC

text: public

text: house mouse

text: Mus musculus

text: Screen 16 Wild Type Knock-out Embryonic Stem Cell Derived Macrophages stimulated with ODN 1826 (CpG) p7

characteristic: sample description

text: Mus musculus


text: Mus musculus

text: SC

text: public

text: house mouse

text: Mus musculus

text: Screen 16 Wild Type Knock-out Embryonic Stem Cell Derived Macrophages stimulated with M TRI-dap (NOD agonist) p7

text: Mus musculus


text: Mus musculus

text: SC

text: public

text: house mouse

text: Mus musculus

text: Screen 16 Wild Type Knock-out Embryonic Stem Cell Derived Macrophages stimulated with LPS (Toll-like receptor agonist) p7

text: Mus musculus


text: Mus musculus

text: SC

text: public

text: house mouse

text: Mus musculus

text: Screen 16 Wild Type Knock-out Embryonic Stem Cell Derived Macrophages stimulated with Salmonella p7

text: Mus musculus


text: Mus musculus

text: SC

text: public

text: house mouse

text: Mus musculus

text: Screen 16 Wild Type Knock-out Embryonic Stem Cell Derived Macrophages stimulated with Influenza 6 hr p7

text: Mus musculus


text: Mus musculus

text: SC

text: public

text: house mouse

text: Mus musculus

text: Screen 16 Wild Type Knock-out Embryonic Stem Cell Derived Macrophages stimulated with Influenza 24 hr p7

text: Mus musculus


text: Mus musculus

text: SC

text: public

text: house mouse

text: Mus musculus

text: Screen 16 Unstimulated Wild Type Knock-out Embryonic Stem Cell Derived Macrophages 24hr p7

text: Mus musculus


text: Mus musculus

text: SC

text: public

text: house mouse

text: Mus musculus

text: Screen 16 Unstimulated Wild Type Knock-out Embryonic Stem Cell Derived Macrophages 4hr p10 1:4

text: Mus musculus


text: Mus musculus

text: SC

text: public

text: house mouse

text: Mus musculus

text: Screen 16 Wild Type Knock-out Embryonic Stem Cell Derived Macrophages stimulated with Poly I:C (Toll-like receptor agonist) p10 1:4

text: Mus musculus


text: Mus musculus

text: SC

text: public

text: house mouse

text: Mus musculus

text: Screen 16 Wild Type Knock-out Embryonic Stem Cell Derived Macrophages stimulated with ODN 1826 (CpG) p10 1:4

text: Mus musculus


text: Mus musculus

text: SC

text: public

text: house mouse

text: Mus musculus

text: Screen 16 Wild Type Knock-out Embryonic Stem Cell Derived Macrophages stimulated with M TRI-dap (NOD agonist) p10 1:4

text: Mus musculus


text: Mus musculus

text: SC

text: public

text: house mouse

text: Mus musculus

text: Screen 16 Wild Type Knock-out Embryonic Stem Cell Derived Macrophages stimulated with LPS (Toll-like receptor agonist) p10 1:4

text: Mus musculus


text: Mus musculus

text: SC

text: public

text: house mouse

text: Mus musculus

text: Screen 16 Wild Type Knock-out Embryonic Stem Cell Derived Macrophages stimulated with Salmonella p10 1:4

text: Mus musculus


text: Mus musculus

text: SC

text: public

text: house mouse

text: Mus musculus

text: Screen 16 Wild Type Knock-out Embryonic Stem Cell Derived Macrophages stimulated with Influenza 6 hr p10 1:4

text: Mus musculus


text: Mus musculus

text: SC

text: public

text: house mouse

text: Mus musculus

text: Screen 16 Wild Type Knock-out Embryonic Stem Cell Derived Macrophages stimulated with Influenza 24 hr p10 1:4

text: Mus musculus


text: Mus musculus

text: SC

text: public

text: house mouse

text: Mus musculus

text: Screen 16 Unstimulated Wild Type Knock-out Embryonic Stem Cell Derived Macrophages 24hr p10 1:4

text: Mus musculus


text: Mus musculus

text: SC

text: public

text: house mouse

text: Mus musculus

text: Screen 16 Unstimulated Wild Type Knock-out Embryonic Stem Cell Derived Macrophages 4hr p10 1:2

text: Mus musculus


text: Mus musculus

text: SC

text: public

text: house mouse

text: Mus musculus

text: Screen 16 Wild Type Knock-out Embryonic Stem Cell Derived Macrophages stimulated with Poly I:C (Toll-like receptor agonist) p10 1:2

text: Mus musculus


text: Mus musculus

text: SC

text: public

text: house mouse

text: Mus musculus

text: Screen 16 Wild Type Knock-out Embryonic Stem Cell Derived Macrophages stimulated with ODN 1826 (CpG) p10 1:2

text: Mus musculus


text: Mus musculus

text: SC

text: public

text: house mouse

text: Mus musculus

text: Screen 16 Wild Type Knock-out Embryonic Stem Cell Derived Macrophages stimulated with M TRI-dap (NOD agonist) p10 1:2

text: Mus musculus


text: Mus musculus

text: SC

text: public

text: house mouse

text: Mus musculus

text: Screen 16 Wild Type Knock-out Embryonic Stem Cell Derived Macrophages stimulated with LPS (Toll-like receptor agonist) p10 1:2

text: Mus musculus


text: Mus musculus

text: SC

text: public

text: house mouse

text: Mus musculus

text: Screen 16 Wild Type Knock-out Embryonic Stem Cell Derived Macrophages stimulated with Salmonella p10 1:2

text: Mus musculus


text: Mus musculus

text: SC

text: public

text: house mouse

text: Mus musculus

text: Screen 16 Wild Type Knock-out Embryonic Stem Cell Derived Macrophages stimulated with Influenza 6 hr p10 1:2

text: Mus musculus


text: Mus musculus

text: SC

text: public

text: house mouse

text: Mus musculus

text: Screen 16 Wild Type Knock-out Embryonic Stem Cell Derived Macrophages stimulated with Influenza 24 hr p10 1:2

text: Mus musculus


text: Mus musculus

text: SC

text: public

text: house mouse

text: Mus musculus

text: Screen 16 Unstimulated Wild Type Knock-out Embryonic Stem Cell Derived Macrophages 24hr p10 1:2

text: Mus musculus


text: Mus musculus

text: SC

text: public

text: house mouse

text: Mus musculus

text: Screen 16 Unstimulated mapk1 Knock-out Embryonic Stem Cell Derived Macrophages 4hr

text: Mus musculus


text: Mus musculus

text: SC

text: public

text: house mouse

text: Mus musculus

text: Screen 16 mapk1 Knock-out Embryonic Stem Cell Derived Macrophages stimulated with Poly I:C (Toll-like receptor agonist)

text: Mus musculus


text: Mus musculus

text: SC

text: public

text: house mouse

text: Mus musculus

text: Screen 16 mapk1 Knock-out Embryonic Stem Cell Derived Macrophages stimulated with ODN 1826 (CpG)

text: Mus musculus


text: Mus musculus

text: SC

text: public

text: house mouse

text: Mus musculus

text: Screen 16 mapk1 Knock-out Embryonic Stem Cell Derived Macrophages stimulated with M TRI-dap (NOD agonist)

text: Mus musculus


text: Mus musculus

text: SC

text: public

text: house mouse

text: Mus musculus

text: Screen 16 mapk1 Knock-out Embryonic Stem Cell Derived Macrophages stimulated with LPS (Toll-like receptor agonist)

text: Mus musculus


text: Mus musculus

text: SC

text: public

text: house mouse

text: Mus musculus

text: Screen 16 mapk1 Knock-out Embryonic Stem Cell Derived Macrophages stimulated with Salmonella

text: Mus musculus


text: Mus musculus

text: SC

text: public

text: house mouse

text: Mus musculus

text: Screen 16 mapk1 Knock-out Embryonic Stem Cell Derived Macrophages stimulated with Influenza 6 hr

text: Mus musculus


text: Mus musculus

text: SC

text: public

text: house mouse

text: Mus musculus

text: Screen 16 mapk1 Knock-out Embryonic Stem Cell Derived Macrophages stimulated with Influenza 24 hr

text: Mus musculus


text: Mus musculus

text: SC

text: public

text: house mouse

text: Mus musculus

text: Screen 16 Unstimulated mapk1 Knock-out Embryonic Stem Cell Derived Macrophages 24hr

text: Mus musculus


text: EBI

text: killed

text: fruit fly

text: Drosophila melanogaster

text: Drosophila melanogaster

text: Test Sample

characteristic: title


characteristic: External Id

text: EBI

text: killed

text: fruit fly

text: Drosophila melanogaster

text: Drosophila melanogaster

text: Test Sample


E-MTAB-3884:Heterozygote rep1

text: University of Dundee

text: public

text: E-MTAB-3884:Heterozygote rep1

tag: Namespace:University of Dundee

text: ArrayExpress

characteristic: broker name

text: house mouse

text: Protocols: Mice were sacrificed by CO2 asphyxiation Full thickness corneas were dissected, snap frozen and stored at -80Â°C RNA from frozen corneas was extracted after douncing and lysis using the RNeasy Plus Minikit (Qiagen) Illumina TruSeqRNA v2 with polyA capture

characteristic: description

text: 7-9 weeks

characteristic: development stage

text: humanised KRT12 heterozygote

characteristic: genotype

text: Mus musculus

characteristic: organism

text: Mus musculus

text: cornea

characteristic: organism part

text: Mus musculus

characteristic: strain

text: Heterozygote rep1


E-MTAB-3884:Heterozygote rep2

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: University of Dundee

characteristic: INSDC center name

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-3884:Heterozygote rep2

text: ArrayExpress

text: house mouse

text: 7-9 weeks

text: humanised KRT12 heterozygote

text: Mus musculus

text: Mus musculus

text: cornea

text: Mus musculus

text: Heterozygote rep2


E-MTAB-3884:Heterozygote rep3

characteristic: ENA-LAST-UPDATE

text: University of Dundee

characteristic: INSDC first public

text: public

text: E-MTAB-3884:Heterozygote rep3

characteristic: Submitter Id

text: ArrayExpress

text: house mouse

characteristic: common name

text: 7-9 weeks

text: humanised KRT12 heterozygote

text: Mus musculus

text: Mus musculus

text: cornea

text: Mus musculus

text: Heterozygote rep3


E-MTAB-3884:Heterozygote rep4

characteristic: External Id

text: University of Dundee

text: public

text: E-MTAB-3884:Heterozygote rep4

text: ArrayExpress

characteristic: broker name

text: house mouse

text: 7-9 weeks

text: humanised KRT12 heterozygote

text: Mus musculus

text: Mus musculus

text: cornea

text: Mus musculus

text: Heterozygote rep4

characteristic: title


E-MTAB-3884:Heterozygote rep5

text: University of Dundee

text: public

text: E-MTAB-3884:Heterozygote rep5

text: ArrayExpress

text: house mouse

characteristic: description

text: 7-9 weeks

characteristic: development stage

text: humanised KRT12 heterozygote

characteristic: genotype

text: Mus musculus

text: Mus musculus

text: cornea

text: Mus musculus

text: Heterozygote rep5


E-MTAB-3884:Heterozygote rep6

text: University of Dundee

text: public

text: E-MTAB-3884:Heterozygote rep6

text: ArrayExpress

text: house mouse

text: 7-9 weeks

text: humanised KRT12 heterozygote

text: Mus musculus

characteristic: organism

text: Mus musculus

text: cornea

characteristic: organism part

text: Mus musculus

characteristic: strain

text: Heterozygote rep6


E-MTAB-3884:Homozygote rep1

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: University of Dundee

characteristic: INSDC center name

text: public

text: E-MTAB-3884:Homozygote rep1

text: ArrayExpress

text: house mouse

text: 7-9 weeks

text: humanised KRT12 homozygote

text: Mus musculus

text: Mus musculus

text: cornea

text: Mus musculus

text: Homozygote rep1


E-MTAB-3884:Homozygote rep2

text: University of Dundee

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-3884:Homozygote rep2

text: ArrayExpress

text: house mouse

text: 7-9 weeks

text: humanised KRT12 homozygote

text: Mus musculus

text: Mus musculus

text: cornea

text: Mus musculus

text: Homozygote rep2


E-MTAB-3884:Homozygote rep3

characteristic: ENA-LAST-UPDATE

text: University of Dundee

characteristic: INSDC first public

text: public

text: E-MTAB-3884:Homozygote rep3

characteristic: Submitter Id

text: ArrayExpress

text: house mouse

text: 7-9 weeks

text: humanised KRT12 homozygote

text: Mus musculus

text: Mus musculus

text: cornea

text: Mus musculus

text: Homozygote rep3


E-MTAB-3884:Homozygote rep4

characteristic: External Id

text: University of Dundee

text: public

text: E-MTAB-3884:Homozygote rep4

text: ArrayExpress

characteristic: broker name

text: house mouse

characteristic: common name

text: 7-9 weeks

text: humanised KRT12 homozygote

text: Mus musculus

text: Mus musculus

text: cornea

text: Mus musculus

text: Homozygote rep4


E-MTAB-3884:Homozygote rep5

text: University of Dundee

text: public

text: E-MTAB-3884:Homozygote rep5

text: ArrayExpress

text: house mouse

characteristic: description

text: 7-9 weeks

characteristic: development stage

text: humanised KRT12 homozygote

text: Mus musculus

text: Mus musculus

text: cornea

text: Mus musculus

text: Homozygote rep5

characteristic: title


E-MTAB-3884:Homozygote rep6

text: University of Dundee

text: public

text: E-MTAB-3884:Homozygote rep6

text: ArrayExpress

text: house mouse

text: 7-9 weeks

text: humanised KRT12 homozygote

characteristic: genotype

text: Mus musculus

characteristic: organism

text: Mus musculus

text: cornea

characteristic: organism part

text: Mus musculus

text: Homozygote rep6


E-MTAB-3884:Wild type rep1

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: University of Dundee

text: public

text: E-MTAB-3884:Wild type rep1

text: ArrayExpress

text: house mouse

text: 7-9 weeks

text: wild type genotype

text: Mus musculus

text: Mus musculus

text: cornea

text: Mus musculus

characteristic: strain

text: Wild type rep1


E-MTAB-3884:Wild type rep2

text: University of Dundee

characteristic: INSDC center name

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: E-MTAB-3884:Wild type rep2

text: ArrayExpress

text: house mouse

text: 7-9 weeks

text: wild type genotype

text: Mus musculus

text: Mus musculus

text: cornea

text: Mus musculus

text: Wild type rep2


E-MTAB-3884:Wild type rep3

characteristic: ENA-LAST-UPDATE

text: University of Dundee

characteristic: INSDC first public

text: public

characteristic: SRA accession

text: E-MTAB-3884:Wild type rep3

text: ArrayExpress

text: house mouse

text: 7-9 weeks

text: wild type genotype

text: Mus musculus

text: Mus musculus

text: cornea

text: Mus musculus

text: Wild type rep3


E-MTAB-3884:Wild type rep4

characteristic: External Id

text: University of Dundee

text: public

text: E-MTAB-3884:Wild type rep4

characteristic: Submitter Id

text: ArrayExpress

characteristic: broker name

text: house mouse

text: 7-9 weeks

text: wild type genotype

text: Mus musculus

text: Mus musculus

text: cornea

text: Mus musculus

text: Wild type rep4


E-MTAB-3884:Wild type rep5

text: University of Dundee

text: public

text: E-MTAB-3884:Wild type rep5

text: ArrayExpress

text: house mouse

characteristic: common name

characteristic: description

text: 7-9 weeks

characteristic: development stage

text: wild type genotype

text: Mus musculus

text: Mus musculus

text: cornea

text: Mus musculus

text: Wild type rep5


E-MTAB-3884:Wild type rep6

text: University of Dundee

text: public

text: E-MTAB-3884:Wild type rep6

text: ArrayExpress

text: house mouse

text: 7-9 weeks

text: wild type genotype

characteristic: genotype

text: Mus musculus

characteristic: organism

text: Mus musculus

text: cornea

text: Mus musculus

text: Wild type rep6

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: Sallk Institute for Biological Studies

text: public

tag: Namespace:Sallk Institute for Biological Studies

text: ArrayExpress

text: human

text: Protocols: post-mortem tissue collection Capture of L1-containing fragments followed by Illumina library prep

text: Homo sapiens

text: Homo sapiens

text: cerebellum

characteristic: organism part

text: Homo sapiens


text: Sallk Institute for Biological Studies

characteristic: INSDC center name

characteristic: INSDC last update

text: public

text: ArrayExpress

text: human

text: Homo sapiens

text: Homo sapiens

text: hippocampus

text: Homo sapiens


characteristic: ENA-LAST-UPDATE

text: Sallk Institute for Biological Studies

text: public

characteristic: INSDC status

text: ArrayExpress

text: human

text: Homo sapiens

text: Homo sapiens

text: hippocampus

text: NeuN+ staining

characteristic: phenotype

text: Homo sapiens


characteristic: External Id

text: Sallk Institute for Biological Studies

characteristic: INSDC first public

text: public

characteristic: SRA accession

text: ArrayExpress

text: human

text: Homo sapiens

text: Homo sapiens

text: hippocampus

text: NeuN- staining

text: Homo sapiens


text: Sallk Institute for Biological Studies

text: public

characteristic: Submitter Id

text: ArrayExpress

characteristic: broker name

text: human

characteristic: common name

text: Homo sapiens

text: Homo sapiens

text: cortex

text: Homo sapiens


text: Sallk Institute for Biological Studies

text: public

text: ArrayExpress

text: human

characteristic: description

text: Homo sapiens

text: Homo sapiens

text: cortex

text: NeuN+ staining

text: Homo sapiens


text: Sallk Institute for Biological Studies

text: public

text: ArrayExpress

text: human

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: cortex

text: NeuN- staining

text: Homo sapiens


text: Sallk Institute for Biological Studies

text: public

text: ArrayExpress

text: human

text: Homo sapiens

text: Homo sapiens

text: heart

text: Homo sapiens

characteristic: title


characteristic: ENA-CHECKLIST

text: Sallk Institute for Biological Studies

text: public

text: ArrayExpress

text: human

text: Homo sapiens

text: Homo sapiens

text: liver

text: Homo sapiens


characteristic: ENA-FIRST-PUBLIC

text: The Francis Crick Institute

text: public

tag: Namespace:The Francis Crick Institute

text: ArrayExpress

text: fetal liver cell

characteristic: cell type

text: house mouse

text: Protocols: Fetal livers were dissected from C57BL/6 mouse embryos at day 14.5 (E14.5) of development. Fetal liver cells were filtered through a cell strainer (70 μm) and directly fixed in formaldehyde. Hi-C was performed essentially as described in Lieberman-Aiden et al. (2009.), with some modifications. Thirty to 50 million cells were fixed in 2 % formaldehyde for 10 min, quenched with 0.125 M glycine, spun down (400 x g, 5 min) and washed once with PBS. The cells were incubated in 50 ml permeabilisation buffer (10 mM Tris-HCl pH 8, 10 mM NaCl, 0.2 % Igepal CA- 630, Complete EDTA-free protease inhibitor cocktail [Roche]) for 30 min on ice with occasional agitation, spun down (650 x g, 5 min, 4 °C), and the cell pellets were resuspended in 358 μl of 1.25 x NEBuffer2 (NEB) per 5 million cell aliquot. Eleven μl of 10 % SDS was added to each aliquot, followed by an incubation at 37 °C for 60 min with continuous agitation (950 rpm). To quench the SDS, 75 μl of 10 % Triton X-100 was then added per aliquot, followed by an incubation at 37 °C for 60 min with continuous agitation (950 rpm). To digest chromatin, 1500 U of Hind III (NEB) was added per aliquot and incubated at 37 °C overnight with continuous agitation (950 rpm). After digestion, restriction sites were filled in with Klenow (NEB) in the presence of biotin-14-dATP (Life Technologies), dCTP, dGTP and dTTP (all 30 μM) for 60 min at 37 °C. For in-solution ligation, 86 μl of 10 % SDS was added per aliquot and incubated at 65 °C for 30 min with continuous agitation (950 rpm), followed by addition of 7.61 ml of ligation mix (745 μl of 10 % Triton X-100, 820 μl of 10 x T4 DNA ligase reaction buffer [NEB], 82 μl of 10 mg/ml BSA [NEB] and 5.965 ml water) per aliquot and incubation at 37 °C for 60 min with occasional agitation. For in-nucleus ligation, 7.61 ml of ligation mix (820 μl of 10 x T4 DNA ligase reaction buffer [NEB], 82 μl of 10 mg/ml BSA [NEB] and 6.71 ml water) was added per aliquot (compared to the in-solution ligation, SDS addition and incubation at 65 °C were omitted). For the ligation reaction (both in-solution and in-nucleus variants), 50 μl of 1 U/μl T4 DNA ligase (Life Technologies) was added per aliquot, followed by incubation at 16 °C for 4 h. The cross-links were reversed by adding 60 μl of 10 mg/ml proteinase K (Roche) per aliquot and incubating at 65 °C overnight. After overnight incubation, another 60 μl of proteinase K per aliquot was added, followed by incubation at 65 °C for an additional two hours. RNA was removed by adding 12.5 μl of 10 mg/ml RNase A (Roche) per aliquot and incubating at 37 °C for 60 min. DNA was isolated by a phenol (Sigma) extraction, followed by a phenol/chloroform/isoamylalcohol (Sigma) extraction and standard ethanol precipitation. The precipitated DNA was washed three times with 70 % ethanol, and dissolved in 25 μl TE per aliquot. Subsequently all aliquots were pooled and the Hi-C DNA was quantified (Quant-iT Pico Green, Life Technologies). Biotin was removed from non-ligated restriction fragment ends by incubating 30 to 40 μg of Hi-C library DNA with T4 DNA polymerase (NEB) for 4 h at 20 °C in the presence of dATP. After DNA purification (QIAquick PCR purification kit [Qiagen]) and sonication (Covaris E220), the sonicated DNA was end-repaired with T4 DNA polymerase, T4 DNA polynucleotide kinase, Klenow (all NEB) and dNTPs in 1 x T4 DNA ligase reaction buffer (NEB). Double size selection of DNA was performed using AMPure XP beads (Beckman Coulter), before dATP-addition with Klenow exo- (NEB). Biotin- marked ligation products were isolated with MyOne Streptavidin C1 Dynabeads (Life Technologies) in binding buffer (5 mM Tris pH8, 0.5 mM EDTA, 1 M NaCl) for 30 min at room temperature, followed by two washes in binding buffer, and one wash in 1 x T4 DNA ligase reaction buffer (NEB). PE adapters (Illumina) were ligated onto Hi-C ligation products bound to streptavidin beads for 2 h at room temperature (T4 DNA ligase in 1 x T4 DNA ligase reaction buffer [NEB], slowly rotating). After washes in wash buffer (5 mM Tris, 0.5 mM EDTA, 1 M NaCl, 0.05 % Tween-20) and binding buffer, the DNA-bound beads were resuspended in NEBuffer 2. Bead-bound Hi-C DNA was amplified with 12 PCR amplification cycles using PE PCR 1.0 and PE PCR 2.0 primers (Illumina). The concentration and size distribution of Hi-C library DNA after PCR amplification was determined by Bioanalyzer profiles (Agilent Technologies) and quantitative PCR.

text: Mus musculus

text: Mus musculus

text: Mus musculus


text: male

characteristic: ArrayExpress-Sex

text: Mus musculus

characteristic: ArrayExpress-Species

text: SC

characteristic: INSDC center name

text: public

text: house mouse

text: Mus musculus

text: Mus musculus


text: Mus musculus

characteristic: ENA-LAST-UPDATE

text: SC

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: house mouse

text: Mus musculus

text: Mus musculus


text: Larval:Day 5 - ZFS:0000037

characteristic: ArrayExpress-DevelopmentalStage

text: Whole embryo

characteristic: ArrayExpress-OrganismPart

text: Danio rerio

text: Mixed

characteristic: ArrayExpress-StrainOrLine

characteristic: External Id

text: SC

characteristic: INSDC first public

text: public

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from a single genotyped zebrafish embryo homozygous for dicer, allele sa9205 from ZMP phenotype 183 clutch 1 plus ERCC spike mix 2 (Ambion). A 8 base indexing sequence (GCAACATT) is bases 13 to 20 of read 1 followed by CG and polyT. More information describing the mutant phenotype can be found at the Wellcome Trust Sanger Institute Zebrafish Mutation Project website http://www.sanger.ac.uk/sanger/Zebrafish_Zmpsearch/zmp_ph183

characteristic: sample description

text: Danio rerio

text: Mixed

characteristic: strain


text: Larval:Day 5 - ZFS:0000037

text: Whole embryo

text: Danio rerio

text: Mixed

text: SC

text: public

characteristic: SRA accession

characteristic: Submitter Id

text: zebrafish

characteristic: common name

text: Danio rerio

characteristic: organism

text: 3' end enriched mRNA from a single genotyped zebrafish embryo homozygous for dicer, allele sa9205 from ZMP phenotype 183 clutch 1 plus ERCC spike mix 2 (Ambion). A 8 base indexing sequence (GGTCGTGT) is bases 13 to 20 of read 1 followed by CG and polyT. More information describing the mutant phenotype can be found at the Wellcome Trust Sanger Institute Zebrafish Mutation Project website http://www.sanger.ac.uk/sanger/Zebrafish_Zmpsearch/zmp_ph183

text: Danio rerio

text: Mixed


text: Larval:Day 5 - ZFS:0000037

text: Whole embryo

text: Danio rerio

text: Mixed

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: SC

text: public

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from a single genotyped zebrafish embryo homozygous for dicer, allele sa9205 from ZMP phenotype 183 clutch 1 plus ERCC spike mix 2 (Ambion). A 8 base indexing sequence (GAATCTGT) is bases 13 to 20 of read 1 followed by CG and polyT. More information describing the mutant phenotype can be found at the Wellcome Trust Sanger Institute Zebrafish Mutation Project website http://www.sanger.ac.uk/sanger/Zebrafish_Zmpsearch/zmp_ph183

text: Danio rerio

text: Mixed


text: Larval:Day 5 - ZFS:0000037

text: Whole embryo

text: Danio rerio

characteristic: ArrayExpress-Species

text: Mixed

text: SC

characteristic: INSDC center name

text: public

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from a single genotyped zebrafish embryo homozygous for dicer, allele sa9205 from ZMP phenotype 183 clutch 1 plus ERCC spike mix 2 (Ambion). A 8 base indexing sequence (GTACATCT) is bases 13 to 20 of read 1 followed by CG and polyT. More information describing the mutant phenotype can be found at the Wellcome Trust Sanger Institute Zebrafish Mutation Project website http://www.sanger.ac.uk/sanger/Zebrafish_Zmpsearch/zmp_ph183

text: Danio rerio

text: Mixed


text: Larval:Day 5 - ZFS:0000037

text: Whole embryo

text: Danio rerio

text: Mixed

characteristic: ENA-LAST-UPDATE

text: SC

characteristic: INSDC last update

text: public

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from a single genotyped zebrafish embryo homozygous for dicer, allele sa9205 from ZMP phenotype 183 clutch 1 plus ERCC spike mix 2 (Ambion). A 8 base indexing sequence (GAGGTGCT) is bases 13 to 20 of read 1 followed by CG and polyT. More information describing the mutant phenotype can be found at the Wellcome Trust Sanger Institute Zebrafish Mutation Project website http://www.sanger.ac.uk/sanger/Zebrafish_Zmpsearch/zmp_ph183

text: Danio rerio

text: Mixed


text: Larval:Day 5 - ZFS:0000037

characteristic: ArrayExpress-DevelopmentalStage

text: Whole embryo

text: Danio rerio

text: Mixed

text: SC

text: public

characteristic: INSDC status

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from a single genotyped zebrafish embryo homozygous for dicer, allele sa9205 from ZMP phenotype 183 clutch 1 plus ERCC spike mix 2 (Ambion). A 8 base indexing sequence (GCATGGCT) is bases 13 to 20 of read 1 followed by CG and polyT. More information describing the mutant phenotype can be found at the Wellcome Trust Sanger Institute Zebrafish Mutation Project website http://www.sanger.ac.uk/sanger/Zebrafish_Zmpsearch/zmp_ph183

text: Danio rerio

text: Mixed


text: Larval:Day 5 - ZFS:0000037

text: Whole embryo

characteristic: ArrayExpress-OrganismPart

text: Danio rerio

text: Mixed

characteristic: ArrayExpress-StrainOrLine

text: SC

text: public

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from a single genotyped zebrafish embryo homozygous for dicer, allele sa9205 from ZMP phenotype 183 clutch 1 plus ERCC spike mix 2 (Ambion). A 8 base indexing sequence (GTTAGCCT) is bases 13 to 20 of read 1 followed by CG and polyT. More information describing the mutant phenotype can be found at the Wellcome Trust Sanger Institute Zebrafish Mutation Project website http://www.sanger.ac.uk/sanger/Zebrafish_Zmpsearch/zmp_ph183

text: Danio rerio

text: Mixed