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characteristic: project name

text: gut metagenome

text: Illumina

characteristic: sequencing method


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: DUKE UNIV

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

characteristic: amount or size of sample collected

characteristic: collection date

text: control protein mouse 9 day 14

characteristic: description

text: fecal environment

text: feces

text: feces

text: USA

text: gut

text: feces

text: host-associated

text: metagenome

text: control protein day 14

text: gut metagenome

characteristic: organism count

text: gut metagenome

text: Illumina

characteristic: title


text: DUKE UNIV

text: public

text: control protein mouse 10 day 0

text: fecal environment

characteristic: environment (biome)

text: feces

characteristic: environment (feature)

text: feces

characteristic: environment (material)

text: USA

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: gut

characteristic: host body habitat

text: feces

characteristic: host body product

characteristic: host subject id

text: host-associated

characteristic: host-associated environmental package

text: metagenome

characteristic: investigation type

text: control protein day 0

characteristic: miscellaneous parameter

text: gut metagenome

characteristic: organism

characteristic: project name

characteristic: sample storage temperature

text: gut metagenome

text: Illumina


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: DUKE UNIV

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

characteristic: amount or size of sample collected

characteristic: collection date

text: control protein mouse 10 day 1

characteristic: description

text: fecal environment

text: feces

text: feces

text: USA

text: gut

text: feces

text: host-associated

text: metagenome

text: control protein day 1

text: gut metagenome

characteristic: organism count

text: gut metagenome

text: Illumina

characteristic: sequencing method


text: DUKE UNIV

text: public

text: control protein mouse 10 day 2

text: fecal environment

characteristic: environment (biome)

text: feces

characteristic: environment (feature)

text: feces

characteristic: environment (material)

text: USA

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: gut

characteristic: host body habitat

text: feces

characteristic: host body product

characteristic: host subject id

text: host-associated

characteristic: host-associated environmental package

text: metagenome

characteristic: investigation type

text: control protein day 2

characteristic: miscellaneous parameter

text: gut metagenome

characteristic: organism

characteristic: project name

text: gut metagenome

text: Illumina

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: DUKE UNIV

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

characteristic: amount or size of sample collected

characteristic: collection date

text: control protein mouse 10 day 7

characteristic: description

text: fecal environment

text: feces

text: feces

text: USA

text: gut

text: feces

text: host-associated

text: metagenome

text: control protein day 7

text: gut metagenome

characteristic: organism count

characteristic: sample storage temperature

text: gut metagenome

text: Illumina


text: DUKE UNIV

text: public

text: control protein mouse 10 day 14

text: fecal environment

characteristic: environment (biome)

text: feces

characteristic: environment (feature)

text: feces

characteristic: environment (material)

text: USA

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: gut

characteristic: host body habitat

text: feces

characteristic: host body product

characteristic: host subject id

text: host-associated

characteristic: host-associated environmental package

text: metagenome

characteristic: investigation type

text: control protein day 14

characteristic: miscellaneous parameter

text: gut metagenome

characteristic: organism

characteristic: project name

text: gut metagenome

text: Illumina

characteristic: sequencing method


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: DUKE UNIV

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

characteristic: amount or size of sample collected

characteristic: collection date

text: control protein mouse 9 day 2

characteristic: description

text: fecal environment

text: feces

text: feces

text: USA

text: gut

text: feces

text: host-associated

text: metagenome

text: control protein day 2

text: gut metagenome

characteristic: organism count

text: gut metagenome

text: Illumina

characteristic: title


text: DUKE UNIV

text: public

text: control protein mouse 9 day 7

text: fecal environment

characteristic: environment (biome)

text: feces

characteristic: environment (feature)

text: feces

characteristic: environment (material)

text: USA

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: gut

characteristic: host body habitat

text: feces

characteristic: host body product

characteristic: host subject id

text: host-associated

characteristic: host-associated environmental package

text: metagenome

characteristic: investigation type

text: control protein day 7

characteristic: miscellaneous parameter

text: gut metagenome

characteristic: organism

characteristic: project name

characteristic: sample storage temperature

text: gut metagenome

text: Illumina


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Wellcome Trust Sanger Institute

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

tag: Namespace:Wellcome Trust Sanger Institute

characteristic: Submitter Id

text: ArrayExpress

characteristic: broker name

characteristic: cell line

text: mouse embryonic stem cell

characteristic: cell type

text: house mouse

characteristic: common name

text: Protocols: Cells were grown to a final concentration of 5x107 cells for each ChIP-seq experiment. To stabilize Dpf2 on chromatin, cells were treated with 2 mM disuccinimidyl glutarate (DSG) for 10 minutes prior to formaldehyde crosslinking. For all other targets, cells were chemically cross-linked at room temperature by the addition of formaldehyde to 1% final concentration for 10 minutes and quenched with 0.125 M final concentration of glycine. Cross-linked cells were re-suspended in sonication buffer (50mM HEPES-KOH pH 7.5, 140mM NaCl, 1mM EDTA, 1% TritonX-100, 0.1% Na-deoxycholate, 0.1% SDS) and sonicated using a Diagenode Bioruptor for three 10-minute rounds using pulsing settings (30 sec ON; 1 min OFF). 10 µg of sonicated chromatin was then incubated overnight at 4ºC with 5 µg of Flag antibody conjugated to magnetic beads. Following the IP, beads were washed twice with RIPA buffer (50mM Tris-HCl pH8, 150 mM NaCl, 2mM EDTA, 1% NP-40, 0.1% Na-deocycholate, 0.1% SDS), low salt buffer (20mM Tris pH 8.1, 150mM NaCl, 2mM EDTA, 1% Triton X-100, 0.1% SDS), high salt buffer (20mM Tris pH 8.1, 500mM NaCl, 2mM EDTA, 1% Triton X-100, 0.1% SDS), LiCl buffer (10mM Tris pH 8.1, 250mM LiCl, 1mM EDTA, 1% Na-deoxycholate, 1% NP-40), and 1X TE. Finally, DNA was extracted by reverse crosslinking at 65ºC overnight with proteinase K (20ug/µL) and 1% SDS followed by phenol:chloroform:isoamyl alcohol purification and ethanol precipitation. Libraries were constructed as indicated above and sequenced using Illumina HiSeq 2500. ChIPed DNA was purified using Qiagen MinElute PCR Purification Kit. Library DNA was purified using AmpureXP beads using 1:1 ratio. Libraries were constructed using Diagenode MicroPlex ChIP kit.

characteristic: description

text: normal

characteristic: disease

text: Dpf2 flox/flox

characteristic: genotype

text: Mus musculus

text: Mus musculus

text: inner cell mass

characteristic: organism part

text: Mus musculus


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: Wellcome Trust Sanger Institute

text: public

text: ArrayExpress

text: mouse embryonic stem cell

text: house mouse

text: normal

text: wild type genotype

text: Mus musculus

characteristic: organism

text: Mus musculus

text: inner cell mass

text: Mus musculus

characteristic: title


E-MTAB-6737:Sample 11

characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: E-MTAB-6737:Sample 11

tag: Namespace:Institut de Biologie de l'Ecole Normale Superieure

text: ArrayExpress

text: human

text: Protocols: RNA was extracted from treated cells using the RNeasy midi kit from Qiagen. GR18 cells were grown to approximately 90% confluence according to standard protocols in DMEM medium with 5% FBS 5 million U2OS-GR cells were transfected with 5 μg library-DNA by nucleofection using kit V (Lonza). The next day, cells were treated for 4 h with 1 µM dexamethasone or with 0.1% ethanol as vehicle control. The poly(A) fraction was isolated from total RNA using oligo d(T) beads. RNA was treated with turboDNase (Ambion) for 30 minutes at 37°C and cleaned up using the RNeasy MinElute kit (Qiagen). Reverse transcription and amplification of cDNA for subsequence Illumina sequencing were done as described (PMID 23328393).

text: osteosarcoma

text: expression of rat glucocorticoid receptor alpha

text: Homo sapiens

text: Homo sapiens

text: bone tissue

text: Homo sapiens

text: Sgk and Cgt GBS

characteristic: synthetic library

text: Sample 11


E-MTAB-6737:Sample 12

text: Institut de Biologie de l'Ecole Normale Superieure

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-6737:Sample 12

characteristic: Submitter Id

text: ArrayExpress

characteristic: broker name

text: human

text: osteosarcoma

text: Homo sapiens

text: Homo sapiens

text: bone tissue

text: Homo sapiens

text: Sgk and Cgt GBS

text: Sample 12


E-MTAB-6737:Sample 4

text: public

text: E-MTAB-6737:Sample 4

text: ArrayExpress

characteristic: cell line

text: human

characteristic: common name

characteristic: description

text: osteosarcoma

characteristic: disease

text: Homo sapiens

text: Homo sapiens

text: bone tissue

text: Homo sapiens

text: Half-site GBS

text: Sample 4


E-MTAB-6737:Sample 5

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: public

text: E-MTAB-6737:Sample 5

text: ArrayExpress

text: human

text: osteosarcoma

characteristic: genotype

text: Homo sapiens

text: Homo sapiens

text: bone tissue

characteristic: organism part

text: Homo sapiens

text: Half-site GBS

text: Sample 5


E-MTAB-6737:Sample 6

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: public

text: E-MTAB-6737:Sample 6

text: ArrayExpress

text: human

text: osteosarcoma

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: bone tissue

text: Homo sapiens

text: Half-site GBS

text: Sample 6

characteristic: title


E-MTAB-6737:Sample 8

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: E-MTAB-6737:Sample 8

text: ArrayExpress

text: human

text: osteosarcoma

text: Homo sapiens

text: Homo sapiens

text: bone tissue

text: Homo sapiens

text: Sgk and Cgt GBS

characteristic: synthetic library

text: Sample 8


E-MTAB-6737:Sample 1

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-6737:Sample 1

characteristic: Submitter Id

text: ArrayExpress

characteristic: broker name

text: human

text: osteosarcoma

text: Homo sapiens

text: Homo sapiens

text: bone tissue

text: Homo sapiens

text: Half-site GBS

text: Sample 1


E-MTAB-6737:Sample 10

text: public

text: E-MTAB-6737:Sample 10

text: ArrayExpress

characteristic: cell line

text: human

characteristic: common name

characteristic: description

text: osteosarcoma

characteristic: disease

text: Homo sapiens

text: Homo sapiens

text: bone tissue

text: Homo sapiens

text: Sgk and Cgt GBS

text: Sample 10


E-MTAB-6737:Sample 2

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: public

text: E-MTAB-6737:Sample 2

text: ArrayExpress

text: human

text: osteosarcoma

characteristic: genotype

text: Homo sapiens

text: Homo sapiens

text: bone tissue

characteristic: organism part

text: Homo sapiens

text: Half-site GBS

text: Sample 2


E-MTAB-6737:Sample 3

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: public

text: E-MTAB-6737:Sample 3

text: ArrayExpress

text: human

text: osteosarcoma

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: bone tissue

text: Homo sapiens

text: Half-site GBS

text: Sample 3

characteristic: title


E-MTAB-6737:Sample 7

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: E-MTAB-6737:Sample 7

text: ArrayExpress

text: human

text: osteosarcoma

text: Homo sapiens

text: Homo sapiens

text: bone tissue

text: Homo sapiens

text: Sgk and Cgt GBS

characteristic: synthetic library

text: Sample 7


E-MTAB-6737:Sample 9

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-6737:Sample 9

characteristic: Submitter Id

text: ArrayExpress

characteristic: broker name

text: human

text: osteosarcoma

text: Homo sapiens

text: Homo sapiens

text: bone tissue

text: Homo sapiens

text: Sgk and Cgt GBS

text: Sample 9


text: public

text: ArrayExpress

characteristic: cell line

text: human

characteristic: common name

text: Protocols: RNA was isolated from 1-2 million cells using an RNeasy kit from Qiagen. GR18 cells where grown to approximately 90% confluence according to standard protocols in DMEM medium with 5% FBS. Cells were treated for 4 hours with 1uM Dexamethasone or 0.1% ethanol as vehicle control Prior to reverse transcription, poly adenylated RNA was isolated using oligo d(T) beads. Sequencing libraries were prepared using the TruSeq RNA library Prep Kit (Illumina)

characteristic: description

text: osteosarcoma

characteristic: disease

text: Homo sapiens

text: Homo sapiens

text: bone tissue

text: Homo sapiens


E-MTAB-6740:Sample 10

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: public

text: E-MTAB-6740:Sample 10

tag: Namespace:Research Centre for Genomics and Bioinformatics, Consiglio per la Ricerca in Agricoltura e l’Analisi dell’Economia Agraria, Fiorenzuola d’Arda, Italy

text: ArrayExpress

text: rice

text: weedy

characteristic: cultivar

text: Protocols: Dormant red rice spikelets (<1% germination) were stored at -15 °C till use. Fully germinating (nondormant, > 99% germination) seeds were obtained by dry-after ripening dormant spikelets at 30 °C for 16 weeks. Naked (dehulled) caryopses were prepared by manually dehulling the spikelets prior to the start of the experiment. For each treatment, three replicated dishes were each prepared by placing 15 caryopses on two filter paper discs with 5 mL of water. At every sampling time, for each replicate, all 15 imbibed seeds (approximately 450 mg) were transferred into 1.5 mL Eppendorf tubes and immediately frozen in liquid nitrogen and stored at -80°C. Samples were subsequently ground in liquid nitrogen and further stored at -80°C. Additional germination tests were performed as above but with 20 caryopses per dish to assay germinative capability. Dehulled red rice caryopses were incubated in water in Petri dishes enclosed in a humidity box. Dormant caryopses were incubated either at 30 °C or 10 °C for either 8 hours or 8 days. For comparison, fully afterripened (non dormant) caryopses were incubated for either 8 hours at 30 °C or 8 days at 10 °C. Total RNA was extracted by a protocol modified after López-Gómez and Gómez-Lim (1992). Briefly, 15 mL Falcon tubes with samples were kept in liquid nitrogen and singularly transferred to ice; then, 1.4 mL of cold ethanol containing 6.8% -mercaptoethanol was added to the tube, which was then closed, turned upside down and hit against the counter a few times, to suspend the frozen powdered pellet. Thereafter, the tube was vortexed till the sample was fully suspended in the ethanol/-mercaptoethanol mixture. One mL of TE-saturated phenol (pH 8) was then added to the single tube, and after quick vortexing, one mL of 24:1 chloroform/isopropanol was added, and the tube was shortly vortexed once more. Thereafter, 5 mL of extraction buffer (150 mM Tris/borate pH 8 containing 50 mM EDTA and 2% SDS) was added, the tube was vortexed 1’, and left on ice while processing the other samples. Once all samples had been extracted, 0.6 mL of 5M potassium acetate was added to each one, and they were then turned upside down ten times and left on ice for one hour. Tubes were centrifuged 5’ at 15000g and 5 mL of the upper phase of each sample was transferred to a new 15 mL Falcon tube. Five mL of 6M LiCl was added and the tubes were gently turned upside down several times and left 30’ on ice. They were centrifuged 10’ at 20000g and the upper phase was then poured away; open tubes were left to drain upside down for >1’. Pellets were washed with 2 mL 80% ethanol, and tubes were centrifuged 5’ at 15000g. The liquid was carefully removed and the tubes left 10’ upside down. Pellets were re-suspended in 700 µL DEPC-treated water, tubes were warmed 1’ at 65 °C and each sample was transferred to a 2 mL Eppendorf tube. Thirty-three microliters of 5M NaCl and 1.3 mL cold ethanol were added; tubes were turned upside down a few times and left 30’ on ice. They were centrifuged 12’ at 20000g and the liquid was carefully removed. Pellets were washed with 0.2 mL 80% ethanol, and tubes were centrifuged 5’ at 20000g. Any liquid was carefully removed and open tubes were left (upside down) to dry 5’ at 37 °C. Pellets were dissolved in 100 µL DEPC-treated water by warming up 1’ at 65 °C. DNA was removed by treating 20’ with RNase-free DNAse (0.2 enzyme unit per every µg of RNA) at 37°C. The enzyme was inactivated at 75 °C for 5’. Samples were stored at -80°C. For every sample, the RNA integrity number (RIN) was determined with a 2100 Bioanalyzer (Agilent) using the Agilent RNA 6000 Nano Kit and following provided instructions. RNA-Seq libraries were prepared with the TruSeq RNA sample preparation kit (Illumina), according to manufacturers’ instructions, starting from 1 µg of total RNA for each sample. This protocol involves removal of rRNA. The quality of libraries was checked with a 2100 Bioanalyzer (Agilent) using the Agilent DNA 1000 Kit and following provided instructions. Libraries were quantified through qRT-PCR, as recommended by the manufacturers’ instructions, and single-end sequenced for 70 bases on an Illumina Genome Analyzer (GAIIx).

text: seed dormant stage

characteristic: developmental stage

text: wild type genotype

characteristic: genotype

text: Oryza sativa

text: Oryza sativa

text: caryopsis fruit

characteristic: organism part

text: Oryza sativa

text: Sample 10


E-MTAB-6740:Sample 11

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Research Centre for Genomics and Bioinformatics, Consiglio per la Ricerca in Agricoltura e l’Analisi dell’Economia Agraria, Fiorenzuola d’Arda, Italy

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: E-MTAB-6740:Sample 11

text: ArrayExpress

text: rice

text: weedy

text: seed dormant stage

text: wild type genotype

text: Oryza sativa

characteristic: organism

text: Oryza sativa

text: caryopsis fruit

text: Oryza sativa

text: Sample 11

characteristic: title


E-MTAB-6740:Sample 12

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-6740:Sample 12

characteristic: Submitter Id

text: ArrayExpress

characteristic: broker name

text: rice

text: weedy

text: seed dormant stage

text: wild type genotype

text: Oryza sativa

text: Oryza sativa

text: caryopsis fruit

text: Oryza sativa

text: Sample 12


E-MTAB-6740:Sample 4

characteristic: ENA-CHECKLIST

text: public

text: E-MTAB-6740:Sample 4

text: ArrayExpress

text: rice

characteristic: common name

text: weedy

characteristic: description

text: seed dormant stage

text: wild type genotype

text: Oryza sativa

text: Oryza sativa

text: caryopsis fruit

text: Oryza sativa

text: Sample 4


E-MTAB-6740:Sample 5

characteristic: ENA-FIRST-PUBLIC

text: public

text: E-MTAB-6740:Sample 5

text: ArrayExpress

text: rice

text: weedy

characteristic: cultivar

text: seed dormant stage

characteristic: developmental stage

text: wild type genotype

text: Oryza sativa

text: Oryza sativa

text: caryopsis fruit

text: Oryza sativa

text: Sample 5


E-MTAB-6740:Sample 6

characteristic: ENA-LAST-UPDATE

text: public

text: E-MTAB-6740:Sample 6

text: ArrayExpress

text: rice

text: weedy

text: seed dormant stage

text: wild type genotype

characteristic: genotype

text: Oryza sativa

text: Oryza sativa

text: caryopsis fruit

characteristic: organism part

text: Oryza sativa

text: Sample 6


E-MTAB-6740:Sample 1

characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: E-MTAB-6740:Sample 1

text: ArrayExpress

text: rice

text: weedy

text: seed dormant stage

text: wild type genotype

text: Oryza sativa

text: Oryza sativa

text: caryopsis fruit

text: Oryza sativa

text: Sample 1


E-MTAB-6740:Sample 2

characteristic: INSDC last update

text: public

text: E-MTAB-6740:Sample 2

text: ArrayExpress

text: rice

text: weedy

text: seed dormant stage

text: wild type genotype

text: Oryza sativa

characteristic: organism

text: Oryza sativa

text: caryopsis fruit

text: Oryza sativa

text: Sample 2

characteristic: title


E-MTAB-6740:Sample 3

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-6740:Sample 3

characteristic: Submitter Id

text: ArrayExpress

text: rice

text: weedy

text: seed dormant stage

text: wild type genotype

text: Oryza sativa

text: Oryza sativa

text: caryopsis fruit

text: Oryza sativa

text: Sample 3


E-MTAB-6740:Sample 7

characteristic: ENA-CHECKLIST

text: public

text: E-MTAB-6740:Sample 7

text: ArrayExpress

characteristic: broker name

text: rice

characteristic: common name

text: weedy

text: seed dormant stage

text: wild type genotype

text: Oryza sativa

text: Oryza sativa

text: caryopsis fruit

text: Oryza sativa

text: Sample 7


E-MTAB-6740:Sample 8

characteristic: ENA-FIRST-PUBLIC

text: public

text: E-MTAB-6740:Sample 8

text: ArrayExpress

text: rice

text: weedy

characteristic: cultivar

characteristic: description

text: seed dormant stage

text: wild type genotype

text: Oryza sativa

text: Oryza sativa

text: caryopsis fruit

text: Oryza sativa

text: Sample 8


E-MTAB-6740:Sample 9

characteristic: ENA-LAST-UPDATE

text: public

text: E-MTAB-6740:Sample 9

text: ArrayExpress

text: rice

text: weedy

text: seed dormant stage

characteristic: developmental stage

text: wild type genotype

characteristic: genotype

text: Oryza sativa

text: Oryza sativa

text: caryopsis fruit

text: Oryza sativa

text: Sample 9


E-MTAB-6740:Sample 16

characteristic: External Id

characteristic: INSDC center name

text: public

text: E-MTAB-6740:Sample 16

text: ArrayExpress

text: rice

text: weedy

text: seed germination stage

text: wild type genotype

text: Oryza sativa

text: Oryza sativa

text: caryopsis fruit

characteristic: organism part

text: Oryza sativa

text: Sample 16


E-MTAB-6740:Sample 17

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: E-MTAB-6740:Sample 17

text: ArrayExpress

text: rice

text: weedy

text: seed germination stage

text: wild type genotype

text: Oryza sativa

characteristic: organism

text: Oryza sativa

text: caryopsis fruit

text: Oryza sativa

text: Sample 17


E-MTAB-6740:Sample 18

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-6740:Sample 18

text: ArrayExpress

text: rice

text: weedy

text: seed germination stage

text: wild type genotype

text: Oryza sativa

text: Oryza sativa

text: caryopsis fruit

text: Oryza sativa

text: Sample 18

characteristic: title


E-MTAB-6740:Sample 13

characteristic: ENA-CHECKLIST

text: public

text: E-MTAB-6740:Sample 13

characteristic: Submitter Id

text: ArrayExpress

characteristic: broker name

text: rice

text: weedy

text: seed germination stage

text: wild type genotype

text: Oryza sativa

text: Oryza sativa

text: caryopsis fruit

text: Oryza sativa

text: Sample 13


E-MTAB-6740:Sample 14

characteristic: ENA-FIRST-PUBLIC

text: public

text: E-MTAB-6740:Sample 14

text: ArrayExpress

text: rice

characteristic: common name

text: weedy

characteristic: cultivar

text: seed germination stage

text: wild type genotype

text: Oryza sativa

text: Oryza sativa

text: caryopsis fruit

text: Oryza sativa

text: Sample 14


E-MTAB-6740:Sample 15

characteristic: ENA-LAST-UPDATE

text: public

text: E-MTAB-6740:Sample 15

text: ArrayExpress

text: rice

text: weedy

characteristic: description

text: seed germination stage

characteristic: developmental stage

text: wild type genotype

text: Oryza sativa

text: Oryza sativa

text: caryopsis fruit

text: Oryza sativa

text: Sample 15


characteristic: External Id

characteristic: INSDC center name

text: public

tag: Namespace:European Bioinformatics Institute (EMBL-EBI)

text: Texas laboratory of the U.S. department of agriculture

characteristic: collected by

text: The use of the new genomic technologies has led to major advances in control of several arboviruses of medical importance. However, the development of tools and resources available for vectors of non-zoonotic arboviruses remains neglected. Biting midges of the genus Culicoides transmit some of the most important arboviruses of wildlife and livestock worldwide, with a global impact on economic productivity, health and welfare. The absence of a suitable reference genome has hindered genomic analyses to date in this important group of vectors. In the present study, the genome of Culicoides sonorensis, a vector of bluetongue virus (BTV) in the USA, has been sequenced to be used as reference genome for transcriptomic analyses of vector competence for BTV. Results: The genome has a size of 197.4 Mb and has been assembled in 7,974 scaffolds. Its annotation using the transcriptomic data has identified 15,629 genes. Gene expression analyses of C. sonorensis females infected with BTV have identified 165 genes that were differentially expressed between vector competent and refractory females. Two candidate genes, glutathione S-transferase (gst) and the antiviral helicase ski2, were previously recognized as involved in vector competence for BTV in C. sonorensis (gst) and repressing dsRNA virus propagation (ski2). Conclusions: The genome of C. sonorensis has enabled preliminary analyses of the genetic profiles of vector competent and refractory individuals. The C. sonorensis genome and transcriptomes generated in this study provide suitable platforms for future research on arbovirus transmission. They will be a valuable source of comparative data for other important Dipteran vector families including mosquitoes (Culicidae) and sandflies (Psychodidae).

text: Adult

characteristic: dev stage

text: USA

characteristic: geographic location (country and/or sea)

text: Culicoides sonorensis

text: Culicoides sonorensis

text: Male/Female

characteristic: sex

text: Whole organism

characteristic: tissue type

text: The genome of the biting midge Culicoides sonorensis comprised in 197.4Mb and assembled in 7,974 scaffolds.


text: female

characteristic: ArrayExpress-SEX

text: Tasmanian devil

characteristic: ArrayExpress-SPECIES

text: SC

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: Tasmanian devil

text: Female

characteristic: gender

text: Sarcophilus harrisii

characteristic: organism

text: Sarcophilus harrisii

characteristic: subject id

characteristic: title


text: male

text: Tasmanian devil

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: SC

text: public

characteristic: Submitter Id

text: Tasmanian devil

characteristic: common name

text: Male

text: Sarcophilus harrisii

text: Sarcophilus harrisii


text: Tasmanian devil

text: SC

characteristic: INSDC center name

text: public

text: Tasmanian devil

text: Sarcophilus harrisii

text: Sarcophilus harrisii


text: University of Bath

text: public

tag: Namespace:University of Bath

characteristic: collection date

text: Chile

characteristic: geographic location (country and/or sea)

text: diseased

characteristic: host health state

text: Salmo salar

characteristic: host scientific name

characteristic: isolate

text: host

characteristic: isolation source

text: Renibacterium salmoninarum

text: Renibacterium salmoninarum


text: University of Bath

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: Chile

text: diseased

text: Oncorhynchus mykiss

text: host

text: Renibacterium salmoninarum

text: Renibacterium salmoninarum


characteristic: ENA-CHECKLIST

text: University of Bath

text: public

text: Chile

text: diseased

text: Oncorhynchus kisutch

text: host

text: Renibacterium salmoninarum

characteristic: organism

text: Renibacterium salmoninarum

characteristic: title


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: JIC

text: public

text: thale cress

text: Arabidopsis thaliana

text: Arabidopsis thaliana

text: White Rust Resistance gene cloning using RenSeq


E-MTAB-6729:Sample 1

text: high

characteristic: HER3-EGFR status

characteristic: INSDC center name

text: public

text: E-MTAB-6729:Sample 1

tag: Namespace:Georgia State University, Department of Biology

characteristic: Submitter Id

unit: year

characteristic: age

text: ArrayExpress

characteristic: broker name

text: human

characteristic: common name

text: Protocols: Pre-marked tumor areas in n=60 formalin-fixed paraffin-embedded (FFPE) primary breast tumor resection samples obtained prior to treatment from unique triple-negative breast cancer patients were obtained from the Nottingham Primary Breast Carcinoma series, selected based on the presence of sufficient tissue quantity for the analysis. The FFPE samples were deparaffinized with xylene, after which RNA was extracted using the Omega Mag-Bind XP FFPE RNA isolation kit (Omega, M2595-01) and the KingFisher Flex magnetic particle separator (ThermoFisher). Integrity was evaluated using the Agilent 2200 TapeStation instrument (Agilent Technologies, Santa Clara, CA). First-strand cDNA synthesis using random hexamers and reverse transcriptase was performed on ~100 ng RNA (25°C for 10 min, 42°C for 15 min, and 70°C for 15 min). Second-strand synthesis and RNA sequencing libraries were prepared per the manufacturer’s instructions using the TruSeq RNA Access library kit (Illumina, Inc., San Diego, CA, USA). RNA templates were removed and a second replacement strand was created by incorporating dUTP to generate double-stranded cDNA. Clean up was performed using Mag-Bind RxnPure Plus magnetic beads (Omega Bio-tek, Norcross, GA). cDNA 3’ ends were adenylated, and indexing adaptors were ligated. DNA fragments with adapter molecules on both ends were enriched using PCR (15 cycles of 98°C for 10 sec, 60°C for 30 sec, and 72°C for 30 sec). The Agilent 2200 TapeStation and QuantiFluor dsDNA System (Promega, Madiosn, WI) were used for library qualification and quantitation, respectively. 200 ng of each DNA library was combined to create a 4-plex pool of libraries, which were then mixed with capture probes specific to regions of interest, followed by hybridization (18 cycles of 1 min incubation, starting at 94°C, and then lowering by 2°C/cycle). Probes hybridized to the target regions were captured using streptavidin-coated magnetic beads. Enriched libraries were eluted and subjected to a second hybridization, then they were amplified by 10 cycles of PCR (98°C for 10 sec, 60°C for 30 sec, and 72°C for 30 sec). RxnPure magnetic beads were then used for clean-up. Final libraries were validated with the Agilent High Sensitivity D1000 ScreenTape on an Agilent 2200 Tapestation instrument.

characteristic: description

text: triple-negative breast cancer

characteristic: disease

characteristic: disease staging

text: yes

characteristic: distant metastasis status

unit: month

characteristic: distant metastasis time

text: Homo sapiens

text: Homo sapiens

text: mammary gland

characteristic: organism part

text: died from breast cancer

characteristic: organism status

text: primary neoplasm

characteristic: sampling site

text: Homo sapiens

text: female

characteristic: sex

characteristic: survival time

text: Sample 1


E-MTAB-6729:Sample 10

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: high

text: Georgia State University, Department of Biology

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-6729:Sample 10

text: ArrayExpress

text: human

text: triple-negative breast cancer

text: yes

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: mammary gland

text: died from breast cancer

text: primary neoplasm

text: Homo sapiens

text: female

text: Sample 10

characteristic: title


E-MTAB-6729:Sample 11

text: high

characteristic: HER3-EGFR status

characteristic: INSDC center name

text: public

text: E-MTAB-6729:Sample 11

characteristic: Submitter Id

characteristic: age

text: ArrayExpress

characteristic: broker name

text: human

characteristic: common name

characteristic: description

text: triple-negative breast cancer

characteristic: disease

characteristic: disease staging

text: no

characteristic: distant metastasis status

text: Homo sapiens

text: Homo sapiens

text: mammary gland

text: alive

text: primary neoplasm

text: Homo sapiens

text: female

text: Sample 11


E-MTAB-6729:Sample 12

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: high

text: public

text: E-MTAB-6729:Sample 12

text: ArrayExpress

text: human

text: triple-negative breast cancer

text: no

characteristic: distant metastasis time

text: Homo sapiens

text: Homo sapiens

text: mammary gland

characteristic: organism part

text: alive

characteristic: organism status

text: primary neoplasm

characteristic: sampling site

text: Homo sapiens

text: female

characteristic: sex

characteristic: survival time

text: Sample 12


E-MTAB-6729:Sample 13

text: high

characteristic: HER3-EGFR status

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-6729:Sample 13

characteristic: Submitter Id

characteristic: age

text: ArrayExpress

text: human

text: triple-negative breast cancer

text: no

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: mammary gland

text: alive

text: primary neoplasm

text: Homo sapiens

text: female

text: Sample 13

characteristic: title


E-MTAB-6729:Sample 14

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: high

text: public

text: E-MTAB-6729:Sample 14

text: ArrayExpress

characteristic: broker name

text: human

characteristic: common name

characteristic: description

text: triple-negative breast cancer

characteristic: disease

characteristic: disease staging

text: yes

characteristic: distant metastasis status

text: Homo sapiens

text: Homo sapiens

text: mammary gland

text: died from breast cancer

text: primary neoplasm

text: Homo sapiens

text: female

text: Sample 14


E-MTAB-6729:Sample 15

text: high

characteristic: HER3-EGFR status

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: E-MTAB-6729:Sample 15

text: ArrayExpress

text: human

text: triple-negative breast cancer

text: yes

characteristic: distant metastasis time

text: Homo sapiens

text: Homo sapiens

text: mammary gland

characteristic: organism part

text: died from breast cancer

characteristic: organism status

text: primary neoplasm

characteristic: sampling site

text: Homo sapiens

text: female

characteristic: sex

characteristic: survival time

text: Sample 15


E-MTAB-6729:Sample 16

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: high

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-6729:Sample 16

characteristic: Submitter Id

characteristic: age

text: ArrayExpress

text: human

text: triple-negative breast cancer

text: yes

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: mammary gland

text: died from breast cancer

text: primary neoplasm

text: Homo sapiens

text: female

text: Sample 16

characteristic: title


E-MTAB-6729:Sample 17

text: high

characteristic: HER3-EGFR status

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: E-MTAB-6729:Sample 17

text: ArrayExpress

characteristic: broker name

text: human

characteristic: common name

characteristic: description

text: triple-negative breast cancer

characteristic: disease

characteristic: disease staging

text: no

characteristic: distant metastasis status

text: Homo sapiens

text: Homo sapiens

text: mammary gland

text: alive

text: primary neoplasm

text: Homo sapiens

text: female

text: Sample 17


E-MTAB-6729:Sample 18

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: high

text: public

text: E-MTAB-6729:Sample 18

text: ArrayExpress

text: human

text: triple-negative breast cancer

text: no

characteristic: distant metastasis time

text: Homo sapiens

text: Homo sapiens

text: mammary gland

characteristic: organism part

text: alive

characteristic: organism status

text: primary neoplasm

characteristic: sampling site

text: Homo sapiens

text: female

characteristic: sex

characteristic: survival time

text: Sample 18