characteristic: ENA-LAST-UPDATE

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: A

text: ArrayExpress

text: thale cress

text: Proliferative tissue

text: Mild drought

text: Arabidopsis thaliana

text: Arabidopsis thaliana

text: rosette leaf

text: Arabidopsis thaliana


status: PUBLIC

tag: attribute

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: External Id

characteristic: INSDC center name

text: public

tag: Namespace:Department of Plant Biotechnology and Bioinformatics, Ghent University, Gent, Belgium Department of Plant Systems Biology,VIB, Gent, Belgium

characteristic: Submitter Id

text: B

characteristic: batch

text: ArrayExpress

characteristic: broker name

text: thale cress

characteristic: common name

text: Protocols: Seeds of Blh-1 were provided by Olivier Loudet (INRA, Versailles). Other accessions were obtained from NASC (N22660). Plants were flash-frozen in liquid nitrogen immediately upon harvest. RNAlater-ICE (Ambion), which prevents RNA from degrading, was cooled at -70 degree centigrade, added to the samples and was allowed to penetrate the tissue at -20 degree centigrade for 5 days. The third leaf was collected by microdissection under a microscope. Samples were microdissected in a Petri dish on dry ice to keep the samples below room temperature. Six Arabidopsis thaliana (L.) Heynh accessions (An-1, Blh-1, Col-0, Cvi-0, Oy-0 and Sha) were grown in a growth chamber under controlled environmental conditions (21 degree centigrade, 55% relative humidity, 16 h day/ 8 h night, 110-120 micromol m-2 s-1 light intensity). Plants were germinated in soil-filled 96-well plates after four days of stratification at 4 degreee centigrade in the dark. Seedlings were transferred to pots at four days after stratification (DAS). The 54 average-sized seedlings were selected (Fig. 1A) using an in-house developed image algorithm in order to reduce seedling size effects at the beginning of the experiment. Before transfer, the relative water content of the pots was set at 1.2 g H2O/g dry soil for the mild drought treatment, the control condition was set at 2.2 g H2O/g dry soil (Fig. 1D). Once the seedlings were transferred to pots (Fig. 1B), they were placed on the automated phenotyping platform WIWAM (Skirycz et al., 2011b). The water content of the soil was kept constant until 10 DAS, after which it was lowered daily to target 0.7 g H2O/g dry soil for the mild drought treated plants (Fig. 1D). Pictures of the rosette of each plant were taken daily until 21 DAS and analyzed for the projected rosette area (PRA) (Skirycz et al., 2011b). Dissected leaves were ground with a Retsch machine (Retsch) and 3-mm metal balls. Samples were obtained from 3 independent biological repeats. RNA was extracted with TriZol (Invitrogen) according to the manufacturers instructions. RNA samples were subjected to DNA digestion with RNase-free DNase I kit (Qiagen), and subsequently, impurities were removed with the RNeasy mini kit (Qiagen). Library preparation was done using the TruSeq RNA Sample Preparation Kit v2 (Illumina). In brief, polyA containing mRNA molecules are reverse transcribed, double-stranded cDNA is generated and adapters are ligated. After quality control using 2100 Bioanalyzer (Agilent), clusters are generated through amplification using the TruSeq PE Cluster Kit v3-cBot-HS kit (Illumina) followed by sequencing on a Illumina HiSeq2000 with the TruSeq SBS Kit v3-HS (Illumina).

characteristic: description

text: Proliferative tissue

characteristic: developmental stage

text: Sha

characteristic: ecotype

text: Mild drought

characteristic: growth condition

text: Arabidopsis thaliana

characteristic: organism

text: Arabidopsis thaliana

text: rosette leaf

characteristic: organism part

text: Arabidopsis thaliana

characteristic: title

type: has member


characteristic: ENA-LAST-UPDATE

text: Department of Plant Biotechnology and Bioinformatics, Ghent University, Gent, Belgium Department of Plant Systems Biology,VIB, Gent, Belgium

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: B

text: ArrayExpress

text: thale cress

text: Proliferative tissue

text: Mild drought

text: Arabidopsis thaliana

text: Arabidopsis thaliana

text: rosette leaf

text: Arabidopsis thaliana


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: External Id

text: public

characteristic: SRA accession

text: E

text: ArrayExpress

text: thale cress

text: Protocols: Seeds of Blh-1 were provided by Olivier Loudet (INRA, Versailles). Other accessions were obtained from NASC (N22660). Plants were flash-frozen in liquid nitrogen immediately upon harvest. RNAlater-ICE (Ambion), which prevents RNA from degrading, was cooled at -70 degree centigrade, added to the samples and was allowed to penetrate the tissue at -20 degree centigrade for 5 days. The third leaf was collected by microdissection under a microscope. Samples were microdissected in a Petri dish on dry ice to keep the samples below room temperature. Six Arabidopsis thaliana (L.) Heynh accessions (An-1, Blh-1, Col-0, Cvi-0, Oy-0 and Sha) were grown in a growth chamber under controlled environmental conditions (21 degree centigrade, 55% relative humidity, 16 h day/ 8 h night, 110-120 micromol m-2 s-1 light intensity). Plants were germinated in soil-filled 96-well plates after four days of stratification at 4 degree centigrade in the dark. Seedlings were transferred to pots at four days after stratification (DAS). The 54 average-sized seedlings were selected (Fig. 1A) using an in-house developed image algorithm in order to reduce seedling size effects at the beginning of the experiment. Before transfer, the relative water content of the pots was set at 1.2 g H2O/g dry soil for the mild drought treatment, the control condition was set at 2.2 g H2O/g dry soil (Fig. 1D). Once the seedlings were transferred to pots (Fig. 1B), they were placed on the automated phenotyping platform WIWAM (Skirycz et al., 2011b). The water content of the soil was kept constant until 10 DAS, after which it was lowered daily to target 0.7 g H2O/g dry soil for the mild drought treated plants (Fig. 1D). Pictures of the rosette of each plant were taken daily until 21 DAS and analyzed for the projected rosette area (PRA) (Skirycz et al., 2011b). Dissected leaves were ground with a Retsch machine (Retsch) and 3-mm metal balls. Samples were obtained from 3 independent biological repeats. RNA was extracted with TriZol (Invitrogen) according to the manufacturers instructions. RNA samples were subjected to DNA digestion with RNase-free DNase I kit (Qiagen), and subsequently, impurities were removed with the RNeasy mini kit (Qiagen). Library preparation was done using the TruSeq RNA Sample Preparation Kit v2 (Illumina). In brief, polyA containing mRNA molecules are reverse transcribed, double-stranded cDNA is generated and adapters are ligated. After quality control using 2100 Bioanalyzer (Agilent), clusters are generated through amplification using the TruSeq PE Cluster Kit v3-cBot-HS kit (Illumina) followed by sequencing on a Illumina HiSeq2000 with the TruSeq SBS Kit v3-HS (Illumina).

text: Proliferative tissue

text: Control

text: Arabidopsis thaliana

text: Arabidopsis thaliana

text: rosette leaf

text: Arabidopsis thaliana


characteristic: INSDC center name

text: public

characteristic: Submitter Id

text: A

characteristic: batch

text: ArrayExpress

characteristic: broker name

text: thale cress

text: Proliferative tissue

text: Sha

text: Control

text: Arabidopsis thaliana

text: Arabidopsis thaliana

text: rosette leaf

text: Arabidopsis thaliana


text: public

text: D

text: ArrayExpress

text: thale cress

characteristic: common name

characteristic: description

text: Proliferative tissue

characteristic: developmental stage

characteristic: ecotype

text: Mild drought

text: Arabidopsis thaliana

text: Arabidopsis thaliana

text: rosette leaf

text: Arabidopsis thaliana


text: public

text: D

text: ArrayExpress

text: thale cress

text: Proliferative tissue

text: Control

characteristic: growth condition

text: Arabidopsis thaliana

characteristic: organism

text: Arabidopsis thaliana

text: rosette leaf

characteristic: organism part

text: Arabidopsis thaliana

characteristic: title


characteristic: ENA-LAST-UPDATE

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: A

text: ArrayExpress

text: thale cress

text: Proliferative tissue

text: Control

text: Arabidopsis thaliana

text: Arabidopsis thaliana

text: rosette leaf

text: Arabidopsis thaliana


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: External Id

text: public

characteristic: SRA accession

text: C

text: ArrayExpress

text: thale cress

text: Proliferative tissue

text: Control

text: Arabidopsis thaliana

text: Arabidopsis thaliana

text: rosette leaf

text: Arabidopsis thaliana


characteristic: INSDC center name

text: public

characteristic: Submitter Id

text: B

characteristic: batch

text: ArrayExpress

characteristic: broker name

text: thale cress

text: Proliferative tissue

text: Control

text: Arabidopsis thaliana

text: Arabidopsis thaliana

text: rosette leaf

text: Arabidopsis thaliana


text: public

text: C

text: ArrayExpress

text: thale cress

characteristic: common name

characteristic: description

text: Proliferative tissue

characteristic: developmental stage

text: Sha

characteristic: ecotype

text: Control

text: Arabidopsis thaliana

text: Arabidopsis thaliana

text: rosette leaf

text: Arabidopsis thaliana


text: public

text: C

text: ArrayExpress

text: thale cress

text: Proliferative tissue

text: Mild drought

characteristic: growth condition

text: Arabidopsis thaliana

characteristic: organism

text: Arabidopsis thaliana

text: rosette leaf

characteristic: organism part

text: Arabidopsis thaliana

characteristic: title


characteristic: ENA-LAST-UPDATE

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: C

text: ArrayExpress

text: thale cress

text: Proliferative tissue

text: Sha

text: Mild drought

text: Arabidopsis thaliana

text: Arabidopsis thaliana

text: rosette leaf

text: Arabidopsis thaliana


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: External Id

text: public

characteristic: SRA accession

text: B

text: ArrayExpress

text: thale cress

text: Proliferative tissue

text: Sha

text: Control

text: Arabidopsis thaliana

text: Arabidopsis thaliana

text: rosette leaf

text: Arabidopsis thaliana


characteristic: INSDC center name

text: public

characteristic: Submitter Id

text: A

characteristic: batch

text: ArrayExpress

characteristic: broker name

text: thale cress

text: Proliferative tissue

text: Sha

text: Mild drought

text: Arabidopsis thaliana

text: Arabidopsis thaliana

text: rosette leaf

text: Arabidopsis thaliana


text: mus musculus

characteristic: ArrayExpress-Species

text: SC

text: public

text: house mouse

characteristic: common name

text: Mus musculus

text: Screen 8 Wild Type Knock-out Embryonic Stem Cell Derived Macrophages stimulated with Poly I:C (Toll-like receptor agonist)

characteristic: sample description

text: Mus musculus


text: mus musculus

text: SC

text: public

text: house mouse

text: Mus musculus

characteristic: organism

text: Screen 8 Wild Type 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 8 Wild Type 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 8 Wild Type 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 8 Wild Type 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 8 Wild Type 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 8 Wild Type 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 8 Unstimulated Wild Type Knock-out Embryonic Stem Cell Derived Macrophages 24hr

text: Mus musculus


text: mus musculus

text: SC

text: public

text: house mouse

text: Mus musculus

text: Screen 8 Unstimulated Stat5b 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 8 Stat5b 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 8 Stat5b 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 8 Stat5b 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 8 Stat5b 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 8 Stat5b 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 8 Stat5b 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 8 Stat5b 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 8 Unstimulated Stat5b Knock-out Embryonic Stem Cell Derived Macrophages 24hr

text: Mus musculus


text: mus musculus

text: SC

text: public

text: house mouse

text: Mus musculus

text: Screen 8 Unstimulated tmem165 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 8 tmem165 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 8 tmem165 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 8 tmem165 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 8 tmem165 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 8 tmem165 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 8 tmem165 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 8 tmem165 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 8 Unstimulated tmem165 Knock-out Embryonic Stem Cell Derived Macrophages 24hr

text: Mus musculus


text: mus musculus

text: SC

text: public

text: house mouse

text: Mus musculus

text: Screen 8 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 8 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 8 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 8 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 8 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 8 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 8 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 8 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 8 Unstimulated mapk1 Knock-out Embryonic Stem Cell Derived Macrophages 24hr

text: Mus musculus


text: mus musculus

text: SC

text: public

text: house mouse

text: Mus musculus

text: Screen 8 Unstimulated Plekhm2 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 8 Plekhm2 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 8 Plekhm2 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 8 Plekhm2 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 8 Plekhm2 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 8 Plekhm2 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 8 Plekhm2 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 8 Plekhm2 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 8 Unstimulated Plekhm2 Knock-out Embryonic Stem Cell Derived Macrophages 24hr

text: Mus musculus


text: mus musculus

text: SC

text: public

text: house mouse

text: Mus musculus

text: Screen 8 Unstimulated Atp2b4 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 8 Atp2b4 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 8 Atp2b4 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 8 Atp2b4 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 8 Atp2b4 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 8 Atp2b4 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 8 Atp2b4 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 8 Atp2b4 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 8 Unstimulated Atp2b4 Knock-out Embryonic Stem Cell Derived Macrophages 24hr

text: Mus musculus


text: mus musculus

text: SC

text: public

text: house mouse

text: Mus musculus

text: Screen 8 Unstimulated Lmnb2 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 8 Lmnb2 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 8 Lmnb2 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 8 Lmnb2 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 8 Lmnb2 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 8 Lmnb2 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 8 Lmnb2 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 8 Lmnb2 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 8 Unstimulated Lmnb2 Knock-out Embryonic Stem Cell Derived Macrophages 24hr

text: Mus musculus


text: mus musculus

text: SC

text: public

text: house mouse

text: Mus musculus

text: Screen 8 Unstimulated Wild Type Knock-out Embryonic Stem Cell Derived Macrophages 4hr

text: Mus musculus


text: public

text: E-MTAB-3301:Mueller_Lab_Feb2015_MDCK_biorep2_techrep4

tag: Namespace:Institute of Animal Breeding & Genetics, University of Veterinary Medicine Vienna

text: ArrayExpress

text: MDCK

characteristic: cell line

text: dog

text: Protocols: MDCK and MDCK-Ras cells were cultivated in DMEM/F12 +10%FCS. Confluent cultures were used for the experiment. Starting with an amount of 15 µg total RNA poly(A)+ selected cDNA samples were generated following a protocol preserving the strand information based on the dUTP method [Mortazavi et al., Nature Methods 2008]. Total RNA was isolated from 4 biological replicates from each cell type (MDCK and MDCK-Ras) using peqGOLD TriFast (Peqlab) according to the manufacturer’s instructions. Quality and quantity of total RNA was checked on Agilent Bioanalyzer according to manufacturer’s instructions. Strand specific and indexed cDNA libraries with 200 - 700 bp insert size were generated for sequencing using the NEBNext® Ultra™ DNA Library Prep Kit for Illumina® (New England BioLabs).

characteristic: description

text: Canis lupus familiaris

text: Canis lupus familiaris

text: epithelial

characteristic: phenotype

text: Canis lupus familiaris

characteristic: title


characteristic: ENA-LAST-UPDATE

text: Institute of Animal Breeding & Genetics, University of Veterinary Medicine Vienna

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: E-MTAB-3301:Mueller_Lab_Feb2015_MDCK-Ras_biorep3_techrep4

text: ArrayExpress

text: MDCK-Ras

text: dog

text: Canis lupus familiaris

text: Canis lupus familiaris

text: mesenchymal

text: Canis lupus familiaris


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: External Id

text: public

characteristic: SRA accession

text: E-MTAB-3301:Mueller_Lab_Feb2015_MDCK_biorep1_techrep1

text: ArrayExpress

text: MDCK

text: dog

text: Canis lupus familiaris

text: Canis lupus familiaris

text: epithelial

text: Canis lupus familiaris


characteristic: INSDC center name

text: public

text: E-MTAB-3301:Mueller_Lab_Feb2015_MDCK-Ras_biorep1_techrep4

characteristic: Submitter Id

text: ArrayExpress

characteristic: broker name

text: MDCK-Ras

text: dog

text: Canis lupus familiaris

text: Canis lupus familiaris

text: mesenchymal

text: Canis lupus familiaris


text: public

text: E-MTAB-3301:Mueller_Lab_Feb2015_MDCK_biorep3_techrep2

text: ArrayExpress

text: MDCK

text: dog

characteristic: common name

text: Canis lupus familiaris

text: Canis lupus familiaris

text: epithelial

text: Canis lupus familiaris


text: public

text: E-MTAB-3301:Mueller_Lab_Feb2015_MDCK_biorep3_techrep1

text: ArrayExpress

text: MDCK

text: dog

text: Canis lupus familiaris

characteristic: organism

text: Canis lupus familiaris

text: epithelial

text: Canis lupus familiaris


text: public

text: E-MTAB-3301:Mueller_Lab_Feb2015_MDCK-Ras_biorep4_techrep3

text: ArrayExpress

text: MDCK-Ras

characteristic: cell line

text: dog

text: Canis lupus familiaris

text: Canis lupus familiaris

text: mesenchymal

text: Canis lupus familiaris


text: public

text: E-MTAB-3301:Mueller_Lab_Feb2015_MDCK-Ras_biorep4_techrep2

text: ArrayExpress

text: MDCK-Ras

text: dog

characteristic: description

text: Canis lupus familiaris

text: Canis lupus familiaris

text: mesenchymal

text: Canis lupus familiaris


text: public

text: E-MTAB-3301:Mueller_Lab_Feb2015_MDCK_biorep1_techrep3

text: ArrayExpress

text: MDCK

text: dog

text: Canis lupus familiaris

text: Canis lupus familiaris

text: epithelial

characteristic: phenotype

text: Canis lupus familiaris


text: public

text: E-MTAB-3301:Mueller_Lab_Feb2015_MDCK-Ras_biorep1_techrep2

text: ArrayExpress

text: MDCK-Ras

text: dog

text: Canis lupus familiaris

text: Canis lupus familiaris

text: mesenchymal

text: Canis lupus familiaris

characteristic: title


characteristic: ENA-LAST-UPDATE

text: public

text: E-MTAB-3301:Mueller_Lab_Feb2015_MDCK_biorep3_techrep4

text: ArrayExpress

text: MDCK

text: dog

text: Canis lupus familiaris

text: Canis lupus familiaris

text: epithelial

text: Canis lupus familiaris


characteristic: INSDC first public

text: public

text: E-MTAB-3301:Mueller_Lab_Feb2015_MDCK_biorep1_techrep4

text: ArrayExpress

text: MDCK

text: dog

text: Canis lupus familiaris

text: Canis lupus familiaris

text: epithelial

text: Canis lupus familiaris


characteristic: INSDC last update

text: public

text: E-MTAB-3301:Mueller_Lab_Feb2015_MDCK-Ras_biorep1_techrep1

text: ArrayExpress

text: MDCK-Ras

text: dog

text: Canis lupus familiaris

text: Canis lupus familiaris

text: mesenchymal

text: Canis lupus familiaris


text: public

characteristic: INSDC status

text: E-MTAB-3301:Mueller_Lab_Feb2015_MDCK-Ras_biorep4_techrep4

text: ArrayExpress

text: MDCK-Ras

text: dog

text: Canis lupus familiaris

text: Canis lupus familiaris

text: mesenchymal

text: Canis lupus familiaris


characteristic: ENA-CHECKLIST

text: public

text: E-MTAB-3301:Mueller_Lab_Feb2015_MDCK_biorep4_techrep2

text: ArrayExpress

text: MDCK

text: dog

text: Canis lupus familiaris

text: Canis lupus familiaris

text: epithelial

text: Canis lupus familiaris


characteristic: ENA-FIRST-PUBLIC

text: public

text: E-MTAB-3301:Mueller_Lab_Feb2015_MDCK_biorep2_techrep3

text: ArrayExpress

text: MDCK

text: dog

text: Canis lupus familiaris

text: Canis lupus familiaris

text: epithelial

text: Canis lupus familiaris


characteristic: External Id

text: public

text: E-MTAB-3301:Mueller_Lab_Feb2015_MDCK_biorep4_techrep3

text: ArrayExpress

text: MDCK

text: dog

text: Protocols: MDCK and MDCK-Ras cells were cultivated in DMEM/F12 +10%FCS. Confluent cultures were used for the experiment. Starting with an amount of 15 µg total RNA poly(A)+ selected cDNA samples were generated following a protocol preserving the strand information based on the dUTP method [Mortazavi et al., Nature Methods 2008]. Total RNA was isolated from 4 biological replicates from each cell type (MDCK and MDCK-Ras) using peqGOLD TriFast (Peqlab) according to the manufacturer’s instructions. Quality and quantity of total RNA was checked on Agilent Bioanalyzer according to manufacturer’s instructions. Strand specific and indexed cDNA libraries with 200 - 700 bp insert size were generated for sequencing using the NEBNext® Ultra™ DNA Library Prep Kit for Illumina® (New England BioLabs).

text: Canis lupus familiaris

text: Canis lupus familiaris

text: epithelial

text: Canis lupus familiaris


text: Institute of Animal Breeding & Genetics, University of Veterinary Medicine Vienna

text: public

characteristic: SRA accession

text: E-MTAB-3301:Mueller_Lab_Feb2015_MDCK-Ras_biorep1_techrep3

text: ArrayExpress

text: MDCK-Ras

text: dog

text: Canis lupus familiaris

text: Canis lupus familiaris

text: mesenchymal

text: Canis lupus familiaris


characteristic: INSDC center name

text: public

text: E-MTAB-3301:Mueller_Lab_Feb2015_MDCK-Ras_biorep2_techrep2

text: ArrayExpress

text: MDCK-Ras

text: dog

text: Canis lupus familiaris

text: Canis lupus familiaris

text: mesenchymal

text: Canis lupus familiaris


text: public

text: E-MTAB-3301:Mueller_Lab_Feb2015_MDCK-Ras_biorep3_techrep3

characteristic: Submitter Id

text: ArrayExpress

text: MDCK-Ras

text: dog

text: Canis lupus familiaris

text: Canis lupus familiaris

text: mesenchymal

text: Canis lupus familiaris


text: public

text: E-MTAB-3301:Mueller_Lab_Feb2015_MDCK-Ras_biorep2_techrep3

text: ArrayExpress

characteristic: broker name

text: MDCK-Ras

text: dog

text: Canis lupus familiaris

text: Canis lupus familiaris

text: mesenchymal

text: Canis lupus familiaris


text: public

text: E-MTAB-3301:Mueller_Lab_Feb2015_MDCK_biorep2_techrep1

text: ArrayExpress

text: MDCK

text: dog

characteristic: common name

text: Canis lupus familiaris

text: Canis lupus familiaris

text: epithelial

text: Canis lupus familiaris


text: public

text: E-MTAB-3301:Mueller_Lab_Feb2015_MDCK_biorep4_techrep4

text: ArrayExpress

text: MDCK

text: dog

text: Canis lupus familiaris

characteristic: organism

text: Canis lupus familiaris

text: epithelial

text: Canis lupus familiaris


text: public

text: E-MTAB-3301:Mueller_Lab_Feb2015_MDCK_biorep3_techrep3

text: ArrayExpress

text: MDCK

characteristic: cell line

text: dog

text: Canis lupus familiaris

text: Canis lupus familiaris

text: epithelial

text: Canis lupus familiaris


text: public

text: E-MTAB-3301:Mueller_Lab_Feb2015_MDCK_biorep2_techrep2

text: ArrayExpress

text: MDCK

text: dog

characteristic: description

text: Canis lupus familiaris

text: Canis lupus familiaris

text: epithelial

text: Canis lupus familiaris


text: public

text: E-MTAB-3301:Mueller_Lab_Feb2015_MDCK-Ras_biorep4_techrep1

text: ArrayExpress

text: MDCK-Ras

text: dog

text: Canis lupus familiaris

text: Canis lupus familiaris

text: mesenchymal

characteristic: phenotype

text: Canis lupus familiaris


text: public

text: E-MTAB-3301:Mueller_Lab_Feb2015_MDCK_biorep4_techrep1

text: ArrayExpress

text: MDCK

text: dog

text: Canis lupus familiaris

text: Canis lupus familiaris

text: epithelial

text: Canis lupus familiaris

characteristic: title


characteristic: ENA-LAST-UPDATE

text: public

text: E-MTAB-3301:Mueller_Lab_Feb2015_MDCK-Ras_biorep3_techrep1

text: ArrayExpress

text: MDCK-Ras

text: dog

text: Canis lupus familiaris

text: Canis lupus familiaris

text: mesenchymal

text: Canis lupus familiaris


characteristic: INSDC first public

text: public

text: E-MTAB-3301:Mueller_Lab_Feb2015_MDCK-Ras_biorep2_techrep4

text: ArrayExpress

text: MDCK-Ras

text: dog

text: Canis lupus familiaris

text: Canis lupus familiaris

text: mesenchymal

text: Canis lupus familiaris


characteristic: INSDC last update

text: public

text: E-MTAB-3301:Mueller_Lab_Feb2015_MDCK_biorep1_techrep2

text: ArrayExpress

text: MDCK

text: dog

text: Canis lupus familiaris

text: Canis lupus familiaris

text: epithelial

text: Canis lupus familiaris


text: public

characteristic: INSDC status

text: E-MTAB-3301:Mueller_Lab_Feb2015_MDCK-Ras_biorep3_techrep2

text: ArrayExpress

text: MDCK-Ras

text: dog

text: Canis lupus familiaris

text: Canis lupus familiaris

text: mesenchymal

text: Canis lupus familiaris


characteristic: ENA-CHECKLIST

text: public

text: E-MTAB-3301:Mueller_Lab_Feb2015_MDCK-Ras_biorep2_techrep1

text: ArrayExpress

text: MDCK-Ras

text: dog

text: Canis lupus familiaris

text: Canis lupus familiaris

text: mesenchymal

text: Canis lupus familiaris


characteristic: ENA-FIRST-PUBLIC

text: public

tag: Namespace:Translational Bioinformatics Group NIHR GSTFT/KCL Comprehensive Biomedical Research Centre

text: ArrayExpress

text: western European house mouse

text: Protocols: Mice were sacrificed at the age of 11 to 13 weeks. All dissections were done by the same person following personal instructions and standardized protocols designed by Valery Grinevich (MPI for Medical Research Heidelberg for HYP). Brains were removed and further dissection was performed on wet ice using gross anatomical borders (i.e., optic chiasm arms, optic tracts, and mammillary body) as markers. Prepared tissues were immediately frozen on dry ice and kept at -70 degree centigrade until RNA preparation. Using TRIzol Reagent with the PureLink RNA Mini Kit, invitrogen/ambion With On-Column PureLink DNase Treatment during Purification Illumina TruSeq RNA Sample Preparation Kit v2

characteristic: individual

text: Mus musculus domesticus

text: Mus musculus domesticus

text: hypothalamus

characteristic: organism part

text: Mus musculus domesticus

text: Male

characteristic: sex

text: Massif Central

characteristic: strain


characteristic: External Id

text: Translational Bioinformatics Group NIHR GSTFT/KCL Comprehensive Biomedical Research Centre

characteristic: INSDC center name

text: public

characteristic: SRA accession

characteristic: Submitter Id

text: ArrayExpress

characteristic: broker name

text: western European house mouse

text: Mus musculus domesticus

text: Mus musculus domesticus

text: hypothalamus

text: Mus musculus domesticus

text: Male

text: Koeln


text: public

text: ArrayExpress

text: western European house mouse

characteristic: common name

characteristic: description

text: Mus musculus domesticus

characteristic: organism

text: Mus musculus domesticus

text: hypothalamus

text: Mus musculus domesticus

text: Female

text: Massif Central


characteristic: ENA-LAST-UPDATE

characteristic: INSDC first public

text: public

text: ArrayExpress

text: western European house mouse

text: Mus musculus domesticus

text: Mus musculus domesticus

text: hypothalamus

text: Mus musculus domesticus

text: Male

text: Massif Central

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: ArrayExpress

text: western European house mouse

text: Mus musculus domesticus

text: Mus musculus domesticus

text: hypothalamus

text: Mus musculus domesticus

text: Female

text: Koeln


characteristic: ENA-FIRST-PUBLIC

text: Institute of Animal Breeding & Genetics, University of Veterinary Medicine Vienna

text: public

text: E-MTAB-3302:Mueller_Lab_Feb2015_MDCK_miRNA_biorep3

text: ArrayExpress

text: MDCK

characteristic: cell line

text: dog

text: Protocols: MDCK and MDCK-Ras cells were cultivated in DMEM/F12 +10%FCS. Confluent cultures were used for the experiment. Total RNA was isolated from 4 biological replicates from each cell type (MDCK and MDCK-Ras) using peqGOLD TriFast (Peqlab) according to the manufacturer’s instructions. Quality and quantity of total RNA was checked on Agilent Bioanalyzer according to manufacturer’s instructions. Libraries for sequencing were prepared using Illumina Small RNA Sample Prep kit v1.5 (Illumina, San Diago, CA USA) as described in the corresponding protocol. Amplified libraries were size fractionated on a 2 % low-melt agarose gel and fragments with a length between 90 to 110 nucleotides were excised. Eluated template libraries were quantified and quality checked using Qubit dsDNA HS Assay Kit (Invitrogen) and on an Agilent Bioanalyzer (Agilent).

text: Canis lupus familiaris

text: Canis lupus familiaris

text: epithelial

characteristic: phenotype

text: Canis lupus familiaris


characteristic: External Id

text: public

text: E-MTAB-3302:Mueller_Lab_Feb2015_MDCK-Ras_miRNA_biorep3

text: ArrayExpress

text: MDCK-Ras

text: dog

text: Canis lupus familiaris

text: Canis lupus familiaris

text: mesenchymal

text: Canis lupus familiaris


characteristic: INSDC center name

text: public

text: E-MTAB-3302:Mueller_Lab_Feb2015_MDCK-Ras_miRNA_biorep2

text: ArrayExpress

text: MDCK-Ras

text: dog

text: Canis lupus familiaris

text: Canis lupus familiaris

text: mesenchymal

text: Canis lupus familiaris


text: public

characteristic: SRA accession

text: E-MTAB-3302:Mueller_Lab_Feb2015_MDCK_miRNA_biorep4

text: ArrayExpress

text: MDCK

text: dog

text: Canis lupus familiaris

text: Canis lupus familiaris

text: epithelial

text: Canis lupus familiaris


text: public

text: E-MTAB-3302:Mueller_Lab_Feb2015_MDCK-Ras_miRNA_biorep1

characteristic: Submitter Id

text: ArrayExpress

text: MDCK-Ras

text: dog

text: Canis lupus familiaris

text: Canis lupus familiaris

text: mesenchymal

text: Canis lupus familiaris


text: public

text: E-MTAB-3302:Mueller_Lab_Feb2015_MDCK_miRNA_biorep1

text: ArrayExpress

characteristic: broker name

text: MDCK

text: dog

text: Canis lupus familiaris

text: Canis lupus familiaris

text: epithelial

text: Canis lupus familiaris


text: public

text: E-MTAB-3302:Mueller_Lab_Feb2015_MDCK-Ras_miRNA_biorep4

text: ArrayExpress

text: MDCK-Ras

text: dog

characteristic: common name

text: Canis lupus familiaris

text: Canis lupus familiaris

text: mesenchymal

text: Canis lupus familiaris


text: public

text: E-MTAB-3302:Mueller_Lab_Feb2015_MDCK_miRNA_biorep2

text: ArrayExpress

text: MDCK

text: dog

characteristic: description

text: Canis lupus familiaris

text: Canis lupus familiaris

text: epithelial

text: Canis lupus familiaris


text: Maastricht University

text: public

tag: Namespace:Maastricht University

text: ArrayExpress

text: hepatocyte

characteristic: cell type

text: human

text: Protocols: Human hepatocellular carcinoma HepG2 cells obtained from ATCC (HB-6065) were used as a cell model. HepG2 cells were cultured as a monolayer in 95% humidity, with 5% CO2 atmosphere at 37 ˚C. The cells were cultured in a Minimal Essential Medium (MEM) with 10% of Fetal Bovine Serum (FBS), 1% penicillin/streptomycin, 1% sodium-pyruvate and 1% non-essential amino acids. All reagents were obtained from Gibco BRL (Breda, the Netherlands). Passages were done at pre-confluent densities by standard trypsin-EDTA solution. Three hundred thousand cells were used in each well of a 6-wells microtiter plate. At 80% confluence, the medium was replaced with fresh medium containing either 3 mM of BaP or by the control vehicule (0.5 % DMSO) during six different exposure time (6h, 12h, 18h, 24h, 36h and 48h) in two independent experiments (biological replicates). First, Total RNA was treated with the Epicentre Ribo-Zero kit (cat.#MRZH11124) to remove the all the rRNAs. The remaining RNAs were processed using the TruSeq RNA Sample PrepKit according to the Illumina protocol. After cDNA synthesis, 6.5 pmol of DNA from each sample were clustered and sequenced on the Illumina HiSeq 2000 (Illumina) in 100 bp paired-end reads.

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: Homo sapiens

text: 6 hour

characteristic: time


characteristic: ENA-LAST-UPDATE

text: Maastricht University

characteristic: INSDC first public

text: public

text: ArrayExpress

text: hepatocyte

text: human

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens

text: 36 hour

characteristic: title


characteristic: ENA-CHECKLIST

text: Maastricht University

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: ArrayExpress

text: hepatocyte

text: human

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens

text: 18 hour


characteristic: ENA-FIRST-PUBLIC

text: Maastricht University

text: public

text: ArrayExpress

characteristic: cell line

text: hepatocyte

text: human

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens

text: 24 hour


characteristic: External Id

text: Maastricht University

characteristic: INSDC center name

text: public

text: ArrayExpress

text: hepatocyte

text: human

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens

text: 12 hour


text: Maastricht University

text: public

characteristic: SRA accession

characteristic: Submitter Id

text: ArrayExpress

text: hepatocyte

text: human

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens

text: 48 hour


text: Plasmodium falciparum

characteristic: ArrayExpress-Species

text: SC

text: public

text: malaria parasite P. falciparum

characteristic: common name

text: Plasmodium falciparum

text: Plasmodium falciparum


text: The Roslin Institute

text: public

text: E-MTAB-3311:Smith_Roslin_quail_con_lung_1_rep2.fastq.gz

tag: Namespace:The Roslin Institute

text: ArrayExpress

characteristic: broker name

text: Japanese quail

text: Protocols: Virus Strains: A/Mallard/British Columbia/500/2005 (H5N2) was used for LPAI challenge. A/Vietnam/1203/2004 (H5N1) was used for HPAI challenge. The viruses were grown in the allantoic cavities of 10-day-old embryonated chicken eggs for 48 hours at 35 degree centigrade. Allantoic fluid containing virus was harvested and stored at minus 80 degree centigrade until use. Virus yield was determined as 50% egg infectious dose (EID50) per millilitre of virus stock by the method of Reed and Muench. All experiments involving animals were approved by the Animal Care and Use Committee of St. Jude Childrens Research Hospital and performed in compliance with relevant policies of the National Institutes of Health and the Animal Welfare Act. All animal challenge experiments were performed in an animal biosafety level 2 containment facilities for the LPAI challenges and in biosafety level 3 enhanced containment laboratories for the HPAI challenges. Viral Challenge: Quail, except the mock infection control group, were challenged with 106 EID50 intranasally, intratracheally, and intraocularly of LPAI A/Mallard/British Columbia/500/2005 (H5N2) in phosphate buffered saline (PBS). Quail, except the mock infection control group, were challenged with 101.5 EID50 intranasally, intratracheally, and intraocularly of HPAI A/Vietnam/1203/2004 (H5N1) in PBS. During LPAI and HPAI infections, mock infection control groups were also inoculated. Mock infection control birds received an equivalent volume and route of administration with PBS. Animals were monitored daily for clinical signs. Tissue Sampling: Lung and ileum samples were collected from all birds on days 1 and 3 dpi. Tissue homogenates were inoculated into 10-day-old embryonated chicken eggs in triplicate to screen for positive samples. Positive samples were then titrated in eggs and expressed as log10EID50/mL. The lower limit of detection was 0.75 log10EID50/mL. For each ileum and lung tissue, the tissue sample was homogenized in Trizol (Invitrogen Life Technologies), 0.1g tissue/1.0ml Trizol with handheld homogenizer Power Gen125 (Thermo Fisher Scientific). After homogenates were prepared, the samples were centrifuged to separate the liquid phases of Trizol homogenates. 0.5ml of the aqueous phase was passed through a QIagen RNeasy (Qiagen, Valencia, CA) spin column according to manufacturers instructions for RNA extraction. Samples were frozen and stored at -80 degree centigrade until all samples were collected for analysis. Samples were prepared for mRNA sequencing using 5ug of total RNA starting material following the Illumina mRNA sequencing 8 sample preparation kit protocol. Resulting libraries were quality checked on an Agilent DNA 1000 bioanalyzer (Agilent Technologies, South Queensferry, UK) and then clustered onto a Single Read flowcell using the Illumina v2 cluster generation kit at a 4.75pM concentration. Thirty-six cycle single-ended sequencing was carried out on the Genome Analyser IIx using Illumina v3 Sequencing by Synthesis kits (Illumina, Little Chesterford, UK).

characteristic: description

text: control

characteristic: disease

text: Coturnix japonica

text: Coturnix japonica

text: lung

characteristic: organism part

text: Coturnix japonica

text: 1 day


characteristic: ENA-LAST-UPDATE

text: The Roslin Institute

characteristic: INSDC first public

text: public

text: E-MTAB-3311:Smith_Roslin_quail_con_ileum_1_rep2.fastq.gz

text: ArrayExpress

text: Japanese quail

text: control

text: Coturnix japonica

characteristic: organism

text: Coturnix japonica

text: ileum

text: Coturnix japonica

text: 1 day

characteristic: time


characteristic: ENA-CHECKLIST

text: The Roslin Institute

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: E-MTAB-3311:Smith_Roslin_quail_LP_lung_3_rep1.fastq.gz

text: ArrayExpress

text: Japanese quail

text: Coturnix japonica

text: Coturnix japonica

text: lung

text: Coturnix japonica

text: 3 day

characteristic: title


characteristic: ENA-FIRST-PUBLIC

characteristic: External Id

text: The Roslin Institute

characteristic: INSDC center name

text: public

text: E-MTAB-3311:Smith_Roslin_quail_LP_lung_3_rep3.fastq.gz

text: ArrayExpress

text: Japanese quail

text: Coturnix japonica

text: Coturnix japonica

text: lung

text: Coturnix japonica

text: 3 day


text: The Roslin Institute

text: public

characteristic: SRA accession

text: E-MTAB-3311:Smith_Roslin_quail_con_lung_1_rep3.fastq.gz

characteristic: Submitter Id

text: ArrayExpress

text: Japanese quail

text: control

text: Coturnix japonica

text: Coturnix japonica

text: lung

text: Coturnix japonica

text: 1 day


text: The Roslin Institute

text: public

text: E-MTAB-3311:Smith_Roslin_quail_con_lung_3_rep2.fastq.gz

text: ArrayExpress

characteristic: broker name

text: Japanese quail

characteristic: common name

text: control

text: Coturnix japonica

text: Coturnix japonica

text: lung

text: Coturnix japonica

text: 3 day


text: The Roslin Institute

text: public

text: E-MTAB-3311:Smith_Roslin_quail_con_ileum_3_rep1.fastq.gz

text: ArrayExpress

text: Japanese quail

characteristic: description

text: control

characteristic: disease

text: Coturnix japonica

text: Coturnix japonica

text: ileum

text: Coturnix japonica

text: 3 day


characteristic: ENA-LAST-UPDATE

text: The Roslin Institute

text: public

text: E-MTAB-3311:Smith_Roslin_quail_LP_ileum_1_rep3.fastq.gz

text: ArrayExpress

text: Japanese quail

text: Coturnix japonica

text: Coturnix japonica

text: ileum

characteristic: organism part

text: Coturnix japonica

text: 1 day


text: The Roslin Institute

characteristic: INSDC first public

text: public

text: E-MTAB-3311:Smith_Roslin_quail_HP_lung_3_rep3.fastq.gz

text: ArrayExpress

text: Japanese quail

text: Coturnix japonica

characteristic: organism

text: Coturnix japonica

text: lung

text: Coturnix japonica

text: 3 day


characteristic: ENA-CHECKLIST

text: The Roslin Institute

text: public

text: E-MTAB-3311:Smith_Roslin_quail_con_ileum_3_rep3.fastq.gz

text: ArrayExpress

text: Japanese quail

text: control

text: Coturnix japonica

text: Coturnix japonica

text: ileum

text: Coturnix japonica

text: 3 day

characteristic: time


text: The Roslin Institute

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: E-MTAB-3311:Smith_Roslin_quail_HP_ileum_1_rep1.fastq.gz

text: ArrayExpress

text: Japanese quail

text: Coturnix japonica

text: Coturnix japonica

text: ileum

text: Coturnix japonica

text: 1 day


characteristic: ENA-FIRST-PUBLIC

text: The Roslin Institute

text: public

text: E-MTAB-3311:Smith_Roslin_quail_HP_ileum_1_rep2.fastq.gz

text: ArrayExpress

text: Japanese quail

text: Coturnix japonica

text: Coturnix japonica

text: ileum

text: Coturnix japonica

text: 1 day

characteristic: title


characteristic: External Id

text: The Roslin Institute

characteristic: INSDC center name

text: public

text: E-MTAB-3311:Smith_Roslin_quail_LP_ileum_1_rep2.fastq.gz

text: ArrayExpress

text: Japanese quail

text: Coturnix japonica

text: Coturnix japonica

text: ileum

text: Coturnix japonica

text: 1 day


text: The Roslin Institute

text: public

characteristic: SRA accession

text: E-MTAB-3311:Smith_Roslin_quail_con_ileum_3_rep2.fastq.gz

characteristic: Submitter Id

text: ArrayExpress

text: Japanese quail

text: control

text: Coturnix japonica

text: Coturnix japonica

text: ileum

text: Coturnix japonica

text: 3 day


text: The Roslin Institute

text: public

text: E-MTAB-3311:Smith_Roslin_quail_LP_lung_1_rep2.fastq.gz

text: ArrayExpress

characteristic: broker name

text: Japanese quail

characteristic: common name

text: Coturnix japonica

text: Coturnix japonica

text: lung

text: Coturnix japonica

text: 1 day


text: The Roslin Institute

text: public

text: E-MTAB-3311:Smith_Roslin_quail_HP_lung_3_rep1.fastq.gz

text: ArrayExpress

text: Japanese quail

characteristic: description

characteristic: disease

text: Coturnix japonica

text: Coturnix japonica

text: lung

text: Coturnix japonica

text: 3 day


characteristic: ENA-LAST-UPDATE

text: The Roslin Institute

text: public

text: E-MTAB-3311:Smith_Roslin_quail_HP_lung_1_rep2.fastq.gz

text: ArrayExpress

text: Japanese quail

text: Coturnix japonica

text: Coturnix japonica

text: lung

characteristic: organism part

text: Coturnix japonica

text: 1 day


text: The Roslin Institute

characteristic: INSDC first public

text: public

text: E-MTAB-3311:Smith_Roslin_quail_LP_ileum_3_rep1b.fastq.gz

text: ArrayExpress

text: Japanese quail

text: Protocols: Virus Strains: A/Mallard/British Columbia/500/2005 (H5N2) was used for LPAI challenge. A/Vietnam/1203/2004 (H5N1) was used for HPAI challenge. The viruses were grown in the allantoic cavities of 10-day-old embryonated chicken eggs for 48 hours at 35 degree centigrade. Allantoic fluid containing virus was harvested and stored at minus 80 degree centigrade until use. Virus yield was determined as 50% egg infectious dose (EID50) per millilitre of virus stock by the method of Reed and Muench. All experiments involving animals were approved by the Animal Care and Use Committee of St. Jude Childrens Research Hospital and performed in compliance with relevant policies of the National Institutes of Health and the Animal Welfare Act. All animal challenge experiments were performed in an animal biosafety level 2 containment facilities for the LPAI challenges and in biosafety level 3 enhanced containment laboratories for the HPAI challenges. Viral Challenge: Quail, except the mock infection control group, were challenged with 106 EID50 intranasally, intratracheally, and intraocularly of LPAI A/Mallard/British Columbia/500/2005 (H5N2) in phosphate buffered saline (PBS). Quail, except the mock infection control group, were challenged with 101.5 EID50 intranasally, intratracheally, and intraocularly of HPAI A/Vietnam/1203/2004 (H5N1) in PBS. During LPAI and HPAI infections, mock infection control groups were also inoculated. Mock infection control birds received an equivalent volume and route of administration with PBS. Animals were monitored daily for clinical signs. Tissue Sampling: Lung and ileum samples were collected from all birds on days 1 and 3 dpi. Tissue homogenates were inoculated into 10-day-old embryonated chicken eggs in triplicate to screen for positive samples. Positive samples were then titrated in eggs and expressed as log10EID50/mL. The lower limit of detection was 0.75 log10EID50/mL. For each ileum and lung tissue, the tissue sample was homogenized in Trizol (Invitrogen Life Technologies), 0.1g tissue/1.0ml Trizol with handheld homogenizer Power Gen125 (Thermo Fisher Scientific). After homogenates were prepared, the samples were centrifuged to separate the liquid phases of Trizol homogenates. 0.5ml of the aqueous phase was passed through a QIagen RNeasy (Qiagen, Valencia, CA) spin column according to manufacturers instructions for RNA extraction. Samples were frozen and stored at -80 degree centigrade until all samples were collected for analysis. Samples were prepared for mRNA sequencing using 5ug of total RNA starting material following the Illumina mRNA sequencing 8 sample preparation kit protocol. Resulting libraries were quality checked on an Agilent DNA 1000 bioanalyzer (Agilent Technologies, South Queensferry, UK) and then clustered onto a Single Read flowcell using the Illumina v2 cluster generation kit at a 4.75pM concentration. Thirty-six cycle single-ended sequencing was carried out on the Genome Analyser IIx using Illumina v3 Sequencing by Synthesis kits (Illumina, Little Chesterford, UK).

text: Coturnix japonica

characteristic: organism

text: Coturnix japonica

text: ileum

text: Coturnix japonica

text: 3 day


characteristic: ENA-CHECKLIST

text: The Roslin Institute

text: public

text: E-MTAB-3311:Smith_Roslin_quail_con_lung_3_rep3.fastq.gz

text: ArrayExpress

text: Japanese quail

text: control

text: Coturnix japonica

text: Coturnix japonica

text: lung

text: Coturnix japonica

text: 3 day

characteristic: time


text: The Roslin Institute

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: E-MTAB-3311:Smith_Roslin_quail_HP_ileum_3_rep3.fastq.gz

text: ArrayExpress

text: Japanese quail

text: Coturnix japonica

text: Coturnix japonica

text: ileum

text: Coturnix japonica

text: 3 day


characteristic: ENA-FIRST-PUBLIC

text: The Roslin Institute

text: public

text: E-MTAB-3311:Smith_Roslin_quail_HP_lung_1_rep3.fastq.gz

text: ArrayExpress

text: Japanese quail

text: Coturnix japonica

text: Coturnix japonica

text: lung

text: Coturnix japonica

text: 1 day

characteristic: title


characteristic: External Id

text: The Roslin Institute

characteristic: INSDC center name

text: public

text: E-MTAB-3311:Smith_Roslin_quail_con_ileum_1_rep1.fastq.gz

text: ArrayExpress

text: Japanese quail

text: control

text: Coturnix japonica

text: Coturnix japonica

text: ileum

text: Coturnix japonica

text: 1 day


text: The Roslin Institute

text: public

characteristic: SRA accession

text: E-MTAB-3311:Smith_Roslin_quail_LP_ileum_3_rep1a.fastq.gz

characteristic: Submitter Id

text: ArrayExpress

text: Japanese quail

text: Coturnix japonica

text: Coturnix japonica

text: ileum

text: Coturnix japonica

text: 3 day


text: The Roslin Institute

text: public

text: E-MTAB-3311:Smith_Roslin_quail_con_lung_3_rep1.fastq.gz

text: ArrayExpress

characteristic: broker name

text: Japanese quail

characteristic: common name

text: control

text: Coturnix japonica

text: Coturnix japonica

text: lung

text: Coturnix japonica

text: 3 day


text: The Roslin Institute

text: public

text: E-MTAB-3311:Smith_Roslin_quail_LP_lung_1_rep3.fastq.gz

text: ArrayExpress

text: Japanese quail

characteristic: description

characteristic: disease

text: Coturnix japonica

text: Coturnix japonica

text: lung

text: Coturnix japonica

text: 1 day


characteristic: ENA-LAST-UPDATE

text: The Roslin Institute

text: public

text: E-MTAB-3311:Smith_Roslin_quail_con_lung_1_rep1b.fastq.gz

text: ArrayExpress

text: Japanese quail

text: control

text: Coturnix japonica

text: Coturnix japonica

text: lung

characteristic: organism part

text: Coturnix japonica

text: 1 day


text: The Roslin Institute

characteristic: INSDC first public

text: public

text: E-MTAB-3311:Smith_Roslin_quail_LP_ileum_3_rep2.fastq.gz

text: ArrayExpress

text: Japanese quail

text: Coturnix japonica

characteristic: organism

text: Coturnix japonica

text: ileum

text: Coturnix japonica

text: 3 day


characteristic: ENA-CHECKLIST

text: The Roslin Institute

text: public

text: E-MTAB-3311:Smith_Roslin_quail_con_ileum_1_rep3.fastq.gz

text: ArrayExpress

text: Japanese quail

text: control

text: Coturnix japonica

text: Coturnix japonica

text: ileum

text: Coturnix japonica

text: 1 day

characteristic: time


text: The Roslin Institute

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: E-MTAB-3311:Smith_Roslin_quail_HP_lung_1_rep1a.fastq.gz

text: ArrayExpress

text: Japanese quail

text: Coturnix japonica

text: Coturnix japonica

text: lung

text: Coturnix japonica

text: 1 day


characteristic: ENA-FIRST-PUBLIC

text: The Roslin Institute

text: public

text: E-MTAB-3311:Smith_Roslin_quail_HP_lung_3_rep2.fastq.gz

text: ArrayExpress

text: Japanese quail

text: Coturnix japonica

text: Coturnix japonica

text: lung

text: Coturnix japonica

text: 3 day

characteristic: title


characteristic: External Id

text: The Roslin Institute

characteristic: INSDC center name

text: public

text: E-MTAB-3311:Smith_Roslin_quail_HP_ileum_3_rep2.fastq.gz

text: ArrayExpress

text: Japanese quail

text: Coturnix japonica

text: Coturnix japonica

text: ileum

text: Coturnix japonica

text: 3 day


text: The Roslin Institute

text: public

characteristic: SRA accession

text: E-MTAB-3311:Smith_Roslin_quail_LP_ileum_1_rep1.fastq.gz

characteristic: Submitter Id

text: ArrayExpress

text: Japanese quail

text: Coturnix japonica

text: Coturnix japonica

text: ileum

text: Coturnix japonica

text: 1 day


text: The Roslin Institute

text: public

text: E-MTAB-3311:Smith_Roslin_quail_HP_ileum_3_rep1.fastq.gz

text: ArrayExpress

characteristic: broker name

text: Japanese quail

characteristic: common name

text: Coturnix japonica

text: Coturnix japonica

text: ileum

text: Coturnix japonica

text: 3 day


text: The Roslin Institute

text: public

text: E-MTAB-3311:Smith_Roslin_quail_con_lung_1_rep1a.fastq.gz

text: ArrayExpress

text: Japanese quail

characteristic: description

text: control

characteristic: disease

text: Coturnix japonica

text: Coturnix japonica

text: lung

text: Coturnix japonica

text: 1 day


characteristic: ENA-LAST-UPDATE

text: The Roslin Institute

text: public

text: E-MTAB-3311:Smith_Roslin_quail_LP_lung_3_rep2.fastq.gz

text: ArrayExpress

text: Japanese quail

text: Protocols: Virus Strains: A/Mallard/British Columbia/500/2005 (H5N2) was used for LPAI challenge. A/Vietnam/1203/2004 (H5N1) was used for HPAI challenge. The viruses were grown in the allantoic cavities of 10-day-old embryonated chicken eggs for 48 hours at 35 degree centigrade. Allantoic fluid containing virus was harvested and stored at minus 80 degree centigrade until use. Virus yield was determined as 50% egg infectious dose (EID50) per millilitre of virus stock by the method of Reed and Muench. All experiments involving animals were approved by the Animal Care and Use Committee of St. Jude Childrens Research Hospital and performed in compliance with relevant policies of the National Institutes of Health and the Animal Welfare Act. All animal challenge experiments were performed in an animal biosafety level 2 containment facilities for the LPAI challenges and in biosafety level 3 enhanced containment laboratories for the HPAI challenges. Viral Challenge: Quail, except the mock infection control group, were challenged with 106 EID50 intranasally, intratracheally, and intraocularly of LPAI A/Mallard/British Columbia/500/2005 (H5N2) in phosphate buffered saline (PBS). Quail, except the mock infection control group, were challenged with 101.5 EID50 intranasally, intratracheally, and intraocularly of HPAI A/Vietnam/1203/2004 (H5N1) in PBS. During LPAI and HPAI infections, mock infection control groups were also inoculated. Mock infection control birds received an equivalent volume and route of administration with PBS. Animals were monitored daily for clinical signs. Tissue Sampling: Lung and ileum samples were collected from all birds on days 1 and 3 dpi. Tissue homogenates were inoculated into 10-day-old embryonated chicken eggs in triplicate to screen for positive samples. Positive samples were then titrated in eggs and expressed as log10EID50/mL. The lower limit of detection was 0.75 log10EID50/mL. For each ileum and lung tissue, the tissue sample was homogenized in Trizol (Invitrogen Life Technologies), 0.1g tissue/1.0ml Trizol with handheld homogenizer Power Gen125 (Thermo Fisher Scientific). After homogenates were prepared, the samples were centrifuged to separate the liquid phases of Trizol homogenates. 0.5ml of the aqueous phase was passed through a QIagen RNeasy (Qiagen, Valencia, CA) spin column according to manufacturers instructions for RNA extraction. Samples were frozen and stored at -80 degree centigrade until all samples were collected for analysis. Samples were prepared for mRNA sequencing using 5ug of total RNA starting material following the Illumina mRNA sequencing 8 sample preparation kit protocol. Resulting libraries were quality checked on an Agilent DNA 1000 bioanalyzer (Agilent Technologies, South Queensferry, UK) and then clustered onto a Single Read flowcell using the Illumina v2 cluster generation kit at a 4.75pM concentration. Thirty-six cycle single-ended sequencing was carried out on the Genome Analyser IIx using Illumina v3 Sequencing by Synthesis kits (Illumina, Little Chesterford, UK).

text: Coturnix japonica

text: Coturnix japonica

text: lung

characteristic: organism part

text: Coturnix japonica

text: 3 day


text: The Roslin Institute

characteristic: INSDC first public

text: public

text: E-MTAB-3311:Smith_Roslin_quail_LP_ileum_3_rep3.fastq.gz

text: ArrayExpress

text: Japanese quail

text: Coturnix japonica

characteristic: organism

text: Coturnix japonica

text: ileum

text: Coturnix japonica

text: 3 day


characteristic: ENA-CHECKLIST

text: The Roslin Institute

text: public

text: E-MTAB-3311:Smith_Roslin_quail_LP_lung_1_rep1.fastq.gz

text: ArrayExpress

text: Japanese quail

text: Coturnix japonica

text: Coturnix japonica

text: lung

text: Coturnix japonica

text: 1 day

characteristic: time


text: The Roslin Institute

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: E-MTAB-3311:Smith_Roslin_quail_HP_lung_1_rep1b.fastq.gz

text: ArrayExpress

text: Japanese quail

text: Coturnix japonica

text: Coturnix japonica

text: lung

text: Coturnix japonica

text: 1 day


text: 2.5 months

characteristic: ArrayExpress-Age

text: 1 mM

characteristic: ArrayExpress-Dose

text: WT

characteristic: ArrayExpress-Genotype

text: MOE

characteristic: ArrayExpress-OrganismPart

text: male

characteristic: ArrayExpress-Sex

text: Mus musculus

characteristic: ArrayExpress-Species

characteristic: ArrayExpress-StrainOrLine

characteristic: ArrayExpress-TimePoint

text: control

characteristic: ArrayExpress-Treatment

characteristic: ENA-FIRST-PUBLIC

text: SC

text: public

text: house mouse

text: Mus musculus

text: control

characteristic: sample description

text: Mus musculus

characteristic: strain


text: 2.5 months

text: 1 mM

text: WT

text: MOE

text: female

text: Mus musculus

text: control

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: SC

characteristic: INSDC center name

characteristic: INSDC first public

text: public

characteristic: SRA accession

characteristic: Submitter Id

text: house mouse

characteristic: common name

text: Mus musculus

characteristic: organism

text: control

text: Mus musculus


text: 2.5 months

characteristic: ArrayExpress-Age

text: carvone

characteristic: ArrayExpress-Compound

text: 1 mM

characteristic: ArrayExpress-Dose

text: WT

characteristic: ArrayExpress-Genotype

text: MOE

characteristic: ArrayExpress-OrganismPart

text: male

text: Mus musculus

text: exposed

characteristic: ENA-CHECKLIST

text: SC

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: house mouse

text: Mus musculus

text: exposed to carvone

text: Mus musculus


text: 2.5 months

text: carvone

text: 1 mM

text: WT

text: MOE

text: female

characteristic: ArrayExpress-Sex

text: Mus musculus

characteristic: ArrayExpress-Species

characteristic: ArrayExpress-StrainOrLine

characteristic: ArrayExpress-TimePoint

text: exposed

characteristic: ArrayExpress-Treatment

characteristic: ENA-FIRST-PUBLIC

text: SC

text: public

text: house mouse

text: Mus musculus

text: exposed to carvone

characteristic: sample description

text: Mus musculus

characteristic: strain


text: 2.5 months

text: heptanal

text: 1 mM

text: WT

text: MOE

text: male

text: Mus musculus

text: exposed

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: SC

characteristic: INSDC center name

characteristic: INSDC first public

text: public

characteristic: SRA accession

characteristic: Submitter Id

text: house mouse

characteristic: common name

text: Mus musculus

characteristic: organism

text: exposed to heptanal

text: Mus musculus


text: 2.5 months

characteristic: ArrayExpress-Age

text: heptanal

characteristic: ArrayExpress-Compound

text: 1 mM

characteristic: ArrayExpress-Dose

text: WT

characteristic: ArrayExpress-Genotype

text: MOE

characteristic: ArrayExpress-OrganismPart

text: female

text: Mus musculus

text: exposed

characteristic: ENA-CHECKLIST

text: SC

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: house mouse

text: Mus musculus

text: exposed to heptanal

text: Mus musculus


text: 2.5 months

text: carvone and heptanal

text: 1 mM

text: WT

text: MOE

text: male

characteristic: ArrayExpress-Sex

text: Mus musculus

characteristic: ArrayExpress-Species

characteristic: ArrayExpress-StrainOrLine

characteristic: ArrayExpress-TimePoint

text: exposed

characteristic: ArrayExpress-Treatment

characteristic: ENA-FIRST-PUBLIC

text: SC

text: public

text: house mouse

text: Mus musculus

text: exposed to a mix of carvone and heptanal

characteristic: sample description

text: Mus musculus

characteristic: strain


text: 2.5 months

text: carvone and heptanal

text: 1 mM

text: WT

text: MOE

text: female

text: Mus musculus

text: exposed

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: SC

characteristic: INSDC center name

characteristic: INSDC first public

text: public

characteristic: SRA accession

characteristic: Submitter Id

text: house mouse

characteristic: common name

text: Mus musculus

characteristic: organism

text: Mus musculus


characteristic: ENA-CHECKLIST

characteristic: INSDC last update

text: public

characteristic: INSDC status

tag: Namespace:Max Plank Institute for Molecular Biomedicine

text: ArrayExpress

characteristic: broker name

characteristic: cell line

text: embryonic stem cell

characteristic: cell type

text: house mouse

text: Protocols: ES cells were cultured in DMEM with GlutaMax (Life technologies) containing 15% FCS and LIF Lipofectamine RNAi MAX (Life technologies) were used to transfect siRNA. Total RNA was extracted with GenElute total RNA miniprep kit, treated with turbo DNase and purified with RNeasy MinElute Cleanup kit. The quality was assessed on a bioanalyzer. Libraries were prepared with Truseq Stranded Total RNA with Ribo-Zero Gold Prep kit (Illumina).

characteristic: description

text: MERVL-LTR::EGFP reporter construct

characteristic: genotype

text: Mus musculus

text: Mus musculus

text: FACS-sorted EGFP positive

characteristic: phenotype

text: Mus musculus

characteristic: title


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Max Plank Institute for Molecular Biomedicine

text: public

text: ArrayExpress

text: embryonic stem cell

text: house mouse

text: MERVL-LTR::EGFP reporter construct

text: Mus musculus

text: Mus musculus

text: FACS-sorted EGFP negative

text: Mus musculus

characteristic: strain


characteristic: INSDC center name

characteristic: INSDC first public

text: public

characteristic: SRA accession

characteristic: Submitter Id

text: ArrayExpress

text: embryonic stem cell

text: house mouse

text: MERVL-LTR::EGFP reporter construct

text: Mus musculus

text: Mus musculus

text: FACS-sorted EGFP positive

text: Mus musculus


characteristic: ENA-CHECKLIST

text: Translational Bioinformatics Group NIHR GSTFT/KCL Comprehensive Biomedical Research Centre

characteristic: INSDC last update

text: public

text: ArrayExpress

text: house mouse

characteristic: common name

text: Protocols: female offspring (3 to 6 individuals per genotype and cross direction were sacrificed at the age of 11 to 13 weeks to prepare the HYP, the VNO, and the LIV from the same individuals. All dissections were done by the same person following personal instructions and standardized protocols designed by Valery Grinevich (MPI for Medical Research Heidelberg for HYP) and Masayo Omura (MPI for Biophysics, Frankfurt for VNO). For the HYP, brains were removed and further dissection was performed on wet ice using gross anatomical borders (i.e., optic chiasm arms, optic tracts, and mammillary body) as markers to remove the HYP. For the VNO, we followed the first steps of the procedure described in Meeks and Holy (2009). Prepared tissues were immediately frozen on dry ice and kept at minus 70 degree centigrade until RNA preparation Using TRIzol Reagent with the PureLink RNA Mini Kit, invitrogen/ambion With On-Column PureLink DNase Treatment during Purification Illumina TruSeq RNA Sample Preparation Kit v2

text: WSB/EiJ mother, PWD/PhJ father

characteristic: individual

text: Mus musculus

characteristic: organism

text: Mus musculus

text: vomeronasal organ

characteristic: organism part

text: Mus musculus

text: cross M.m musulus (PWD/PhJ) and M. m. domesticus (WSB/EiJ)


text: public

characteristic: INSDC status

tag: Namespace:University of Massachusetts Medical School,

text: ArrayExpress

characteristic: broker name

text: splenocyte

characteristic: cell type

text: western European house mouse

text: Protocols: C57BL/6 mice (Jackson Laboratory, Bar Harbor, ME) were maintained in specific pathogen-free conditions and used in accordance with the Institutional Animal Care and Use Committee. PBS was used as a control for infections as described in PMID 24477914 Single cell suspensions from spleens were used to make total RNA. 4 μg of total RNA was used to generate libraries for RNA-sequencing (Illumina unstranded mRNA kits). Samples were sized, quantified and validated on a Bioanalyzer.

characteristic: description

text: none (PBS control)

characteristic: infect

text: Mus musculus domesticus

text: Mus musculus domesticus

text: Mus musculus domesticus

text: SamplePBS


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: University of Massachusetts Medical School,

text: public

text: ArrayExpress

text: splenocyte

text: western European house mouse

text: Protocols: C57BL/6 mice (Jackson Laboratory, Bar Harbor, ME) were maintained in specific pathogen-free conditions and used in accordance with the Institutional Animal Care and Use Committee. Listeria monocytogenes (clinical isolate 10403s) was from V. Boyartchuk (NTNU, Trondheim, Norway) and infected as described in PMID 24477914 for 24 hours before harvesting the spleen. Single cell suspensions from spleens were used to make total RNA. 4 μg of total RNA was used to generate libraries for RNA-sequencing (Illumina unstranded mRNA kits). Samples were sized, quantified and validated on a Bioanalyzer.

text: Mus musculus domesticus

text: Mus musculus domesticus

text: Mus musculus domesticus

characteristic: title


text: mus musculus

characteristic: ArrayExpress-Species

text: SC

characteristic: INSDC center name

characteristic: INSDC first public

text: public

characteristic: SRA accession

text: house mouse

text: Mus musculus

text: Screen 9 Unstimulated Wild Type Knock-out Embryonic Stem Cell Derived Macrophages 4hr

characteristic: sample description

text: Mus musculus


text: mus musculus

characteristic: ENA-CHECKLIST

text: SC

characteristic: INSDC last update

text: public

characteristic: Submitter Id

text: house mouse

characteristic: common name

text: Mus musculus

text: Screen 9 Wild Type 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

characteristic: INSDC status

text: house mouse

text: Mus musculus

characteristic: organism

text: Screen 9 Wild Type 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 9 Wild Type 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 9 Wild Type 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 9 Wild Type 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 9 Unstimulated Atp2b4 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 9 Atp2b4 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 9 Atp2b4 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 9 Atp2b4 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 9 Atp2b4 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 9 Atp2b4 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 9 Unstimulated Stat5b 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 9 Stat5b 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 9 Stat5b 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 9 Stat5b 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 9 Stat5b 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 9 Stat5b 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 9 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 9 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 9 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 9 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 9 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 9 Mapk1 Knock-out Embryonic Stem Cell Derived Macrophages stimulated with Salmonella

text: Mus musculus


status: KILLED

text: Homo sapiens

text: SC

text: killed

characteristic: Sample Description

characteristic: Strain

text: human

text: Homo sapiens

text: Homo sapiens


E-MTAB-3322:Sample 15

characteristic: ENA-FIRST-PUBLIC

text: King's College London

text: public

text: E-MTAB-3322:Sample 15

tag: Namespace:King's College London

text: ArrayExpress

characteristic: broker name

text: bone marrow haematopoietic stem and progenitor cells

characteristic: cell type

text: non mixed-lineage leukemia

characteristic: clinical history

text: house mouse

text: Protocols: Haematopoietic progenitors and stem cells harvested from 4-10 week old C57BL/6 mice were transduced with named fusion, immortalised, and subsequently prmt1 or kdm4c expression was inhibited mirVana miRNA extraction kit (Ambion) or Nucleopsin RNA extraction kit (Macherey-Nagel) Truseq Stranded RNA LT kit (Illumina)

characteristic: description

text: leukemia

characteristic: disease

text: wild type genotype

characteristic: genotype

text: Mus musculus

text: Mus musculus

text: haemopoietic system

characteristic: organism part

text: Mus musculus

text: Sample 15


E-MTAB-3322:Sample 4

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: King's College London

characteristic: INSDC center name

characteristic: INSDC first public

text: public

characteristic: SRA accession

text: E-MTAB-3322:Sample 4

text: ArrayExpress

text: mixed-lineage leukemia

text: house mouse

text: leukemia

text: KDM4C knock-down

text: Mus musculus

text: Mus musculus

text: haemopoietic system

text: Mus musculus

text: Sample 4

characteristic: title


E-MTAB-3322:Sample 13

characteristic: ENA-CHECKLIST

text: King's College London

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: E-MTAB-3322:Sample 13

characteristic: Submitter Id

text: ArrayExpress

text: non mixed-lineage leukemia

text: house mouse

characteristic: common name

text: leukemia

text: PRMT1 gene knock out

text: Mus musculus

characteristic: organism

text: Mus musculus

text: haemopoietic system

text: Mus musculus

text: Sample 13


E-MTAB-3322:Sample 5

characteristic: ENA-FIRST-PUBLIC

text: King's College London

text: public

text: E-MTAB-3322:Sample 5

text: ArrayExpress

characteristic: broker name

characteristic: cell type

text: mixed-lineage leukemia

characteristic: clinical history

text: house mouse

text: leukemia

text: KDM4C knock-down

text: Mus musculus

text: Mus musculus

text: haemopoietic system

text: Mus musculus

text: Sample 5


E-MTAB-3322:Sample 12

text: King's College London

text: public

text: E-MTAB-3322:Sample 12

text: ArrayExpress

text: non mixed-lineage leukemia

text: house mouse

characteristic: description

text: leukemia

characteristic: disease

text: PRMT1 gene knock out

characteristic: genotype

text: Mus musculus

text: Mus musculus

text: haemopoietic system

characteristic: organism part

text: Mus musculus

text: Sample 12


E-MTAB-3322:Sample 16

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: King's College London

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: E-MTAB-3322:Sample 16

text: ArrayExpress

text: non mixed-lineage leukemia

text: house mouse

text: leukemia

text: wild type genotype

text: Mus musculus

text: Mus musculus

text: haemopoietic system

text: Mus musculus

text: Sample 16


E-MTAB-3322:Sample 6

characteristic: ENA-CHECKLIST

text: King's College London

characteristic: INSDC last update

text: public

characteristic: SRA accession

text: E-MTAB-3322:Sample 6

text: ArrayExpress

text: mixed-lineage leukemia

text: house mouse

text: leukemia

text: PRMT1 gene knock out

text: Mus musculus

text: Mus musculus

text: haemopoietic system

text: Mus musculus

text: Sample 6

characteristic: title


E-MTAB-3322:Sample 3

text: King's College London

text: public

characteristic: INSDC status

text: E-MTAB-3322:Sample 3

characteristic: Submitter Id

text: ArrayExpress

text: mixed-lineage leukemia

text: house mouse

characteristic: common name

text: leukemia

text: wild type genotype

text: Mus musculus

characteristic: organism

text: Mus musculus

text: haemopoietic system

text: Mus musculus

text: Sample 3


E-MTAB-3322:Sample 2

characteristic: ENA-FIRST-PUBLIC

text: King's College London

text: public

text: E-MTAB-3322:Sample 2

text: ArrayExpress

characteristic: broker name

characteristic: cell type

text: mixed-lineage leukemia

characteristic: clinical history

text: house mouse

text: leukemia

text: KDM4C knock-down

text: Mus musculus

text: Mus musculus

text: haemopoietic system

text: Mus musculus

text: Sample 2


E-MTAB-3322:Sample 7

text: King's College London

text: public

text: E-MTAB-3322:Sample 7

text: ArrayExpress

text: mixed-lineage leukemia

text: house mouse

characteristic: description

text: leukemia

characteristic: disease

text: PRMT1 gene knock out

characteristic: genotype

text: Mus musculus

text: Mus musculus

text: haemopoietic system

characteristic: organism part

text: Mus musculus

text: Sample 7


E-MTAB-3322:Sample 8

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: King's College London

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: E-MTAB-3322:Sample 8

text: ArrayExpress

text: mixed-lineage leukemia

text: house mouse

text: leukemia

text: wild type genotype

text: Mus musculus

text: Mus musculus

text: haemopoietic system

text: Mus musculus

text: Sample 8


E-MTAB-3322:Sample 11

characteristic: ENA-CHECKLIST

text: King's College London

characteristic: INSDC last update

text: public

characteristic: SRA accession

text: E-MTAB-3322:Sample 11

text: ArrayExpress

text: non mixed-lineage leukemia

text: house mouse

text: leukemia

text: KDM4C knock-down

text: Mus musculus

text: Mus musculus

text: haemopoietic system

text: Mus musculus

text: Sample 11

characteristic: title


E-MTAB-3322:Sample 9

text: King's College London

text: public

characteristic: INSDC status

text: E-MTAB-3322:Sample 9

characteristic: Submitter Id

text: ArrayExpress

text: mixed-lineage leukemia

text: house mouse

characteristic: common name

text: leukemia

text: wild type genotype

text: Mus musculus

characteristic: organism

text: Mus musculus

text: haemopoietic system

text: Mus musculus

text: Sample 9


E-MTAB-3322:Sample 1

characteristic: ENA-FIRST-PUBLIC

text: King's College London

text: public

text: E-MTAB-3322:Sample 1

text: ArrayExpress

characteristic: broker name

characteristic: cell type

text: non mixed-lineage leukemia

characteristic: clinical history

text: house mouse

text: leukemia

text: wild type genotype

text: Mus musculus

text: Mus musculus

text: haemopoietic system

text: Mus musculus

text: Sample 1


E-MTAB-3322:Sample 14

text: King's College London

text: public

text: E-MTAB-3322:Sample 14

text: ArrayExpress

text: non mixed-lineage leukemia

text: house mouse

characteristic: description

text: leukemia

characteristic: disease

text: wild type genotype

characteristic: genotype

text: Mus musculus

text: Mus musculus

text: haemopoietic system

characteristic: organism part

text: Mus musculus

text: Sample 14


E-MTAB-3322:Sample 10

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: King's College London

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: E-MTAB-3322:Sample 10

text: ArrayExpress

text: non mixed-lineage leukemia

text: house mouse

text: leukemia

text: KDM4C knock-down

text: Mus musculus

text: Mus musculus

text: haemopoietic system

text: Mus musculus

text: Sample 10


text: Dracunculus medinensis

characteristic: ArrayExpress-Species

characteristic: ENA-CHECKLIST

text: SC

characteristic: INSDC last update

text: public

characteristic: SRA accession

text: Guinea worm

text: Dracunculus medinensis

text: Dracunculus medinensis


text: Cell line DNA

characteristic: ArrayExpress-Phenotype

text: male

characteristic: ArrayExpress-Sex

text: Homo Sapien

text: SC

text: public

characteristic: INSDC status

characteristic: Submitter Id

text: human

characteristic: common name

text: Homo sapiens

characteristic: organism

text: Homo sapiens


characteristic: ENA-FIRST-PUBLIC

text: public

tag: Namespace:Institute of Biochemistry and Molecular Biology, National Yang-Ming University, Taipei, Taiwan

text: ArrayExpress

characteristic: broker name

characteristic: cell line

text: human

text: Protocols: MCF-7 cells were cultured in RPMI1640 medium (GIBCO/BRL) supplemented with 10% (v/v) fetal bovine serum (GIBCO/BRL), 2.0 g/L sodium bicarbonate, and were incubated in a humidified 37 degrees C incubator with 5% CO2. MCF-7 cells were transfected with H2ac siRNA duplex (a mixture of equimolar concentrations of 5'-CUGCUAGGCCGGGUGACCA-3' and 5'-UGGUCACCCGGCCUAGCAG-3'). Cells transfected with siRNAs were harvested 48 hours post transfection. MCF-7 cells were washed with 1X PBS and resuspended with cell lysis buffer. Cells were treated with 0.1 mg/mL of RNaseA for an hour at 37 degrees C and 0.3 mg/mL proteinase K for 12-16 hr at 55 degrees C. DNA was extracted with an equal volume of phenol/chloroform/isoamyl alcohol mixture (24:25:1). The extraction procedure was repeated until the interface is clean. An equal volume of chloroform was then added and the mixture centrifuged for 10 minutes at 13000x g. Finally, the aqueous phase was removed and precipitated with ethanol. After removal of the supernatant, the DNA pellet was washed with 70% ethanol, air-dried, and dissolved in triple distilled H2O. The integrity of the DNA extracted was checked by 1.2 % (w/v) agarose gel electrophoresis. The concentration of DNA was estimated by ultraviolet spectrophotometry. Bisulfite-seq library was prepared using a method based on Lister et al. Briefly, 3-5 ug of DNA was fragmented by sonication with a Bioruptor (Diagenode, Sparta, NJ) following by adapter ligation using the Pair End DNA Sample Prep kit (Illumina Inc., USA) with the use of methylated adapter (Illumina Inc., USA) according to manufacturer's instruction. For each sample, four adapter-ligated DNA fragments of 200-250 bp, 250-300 bp, 300-350 bp and 350-400 bp were isolated by gel electrophoresis and subjected to bisulfite conversion and PCR enrichment independently to generate 4 separate libraries for each sample. Bisulfite treatment was performed using an EZ DNA Methylation-Gold Kit (Zymo Research) that converts unmethylated cytosines to uracils and leaves methylated cytosines unchanged. Four separate PCR were performed for each library using PfuTurbo(r) Cx Hotstart DNA polymerase (Stratagene) and then pooling the enrichment products following by gel purification. PCR-amplified library was quantified by quantitative PCR and the library size was determined on an Agilent 2100 Bioanalyzer with High Sensitivity DNA chip.

characteristic: description

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens

characteristic: title


text: Mus musculus

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: SC

characteristic: INSDC center name

text: public

text: __Spreadsheet__Formula_0x6dd1674a_-sc-2231315

text: house mouse

text: Mus musculus

characteristic: sample description

text: Mus musculus


text: Mus musculus

characteristic: ArrayExpress-Species

characteristic: ENA-CHECKLIST

text: SC

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: __Spreadsheet__Formula_0x3996082_-sc-2231316

text: house mouse

text: Mus musculus

text: Mus musculus


text: Mus musculus

text: SC

text: public

characteristic: INSDC status

characteristic: SRA accession

text: __Spreadsheet__Formula_0x477f1cf3_-sc-2231317

text: house mouse

text: Mus musculus

text: Mus musculus


text: Mus musculus

text: SC

text: public

text: __Spreadsheet__Formula_0x48b1afd8_-sc-2231318

characteristic: Submitter Id

text: house mouse

characteristic: common name

text: Mus musculus

text: Mus musculus


text: Mus musculus

characteristic: ENA-FIRST-PUBLIC

text: SC

text: public

text: __Spreadsheet__Formula_0x4bf836c7_-sc-2231319

text: house mouse

text: Mus musculus

characteristic: organism

text: Mus musculus


text: Mus musculus

text: SC

text: public

text: __Spreadsheet__Formula_0x4a2b2d_-sc-2231320

text: house mouse

text: Mus musculus

text: Mus musculus


text: Mus musculus

text: SC

text: public

text: __Spreadsheet__Formula_0x74713188_-sc-2231321

text: house mouse

text: Mus musculus

text: Mus musculus


text: Mus musculus

text: SC

text: public

text: __Spreadsheet__Formula_0xa7047ba_-sc-2231322

text: house mouse

text: Mus musculus

text: Mus musculus


text: Mus musculus

text: SC

text: public

text: __Spreadsheet__Formula_0x350e5ae8_-sc-2231323

text: house mouse

text: Mus musculus

text: Mus musculus


text: Mus musculus

text: SC

text: public

text: __Spreadsheet__Formula_0x3f493201_-sc-2231324

text: house mouse

text: Mus musculus

text: Mus musculus


text: Mus musculus

text: SC

text: public

text: __Spreadsheet__Formula_0x2b8aae78_-sc-2231325

text: house mouse

text: Mus musculus

text: Mus musculus


text: Mus musculus

text: SC

text: public

text: __Spreadsheet__Formula_0x5fdb9827_-sc-2231326

text: house mouse

text: Mus musculus

text: Mus musculus


text: Mus musculus

text: SC

text: public

text: __Spreadsheet__Formula_0x15045733_-sc-2231327

text: house mouse

text: Mus musculus

text: Mus musculus


text: Mus musculus

text: SC

text: public

text: __Spreadsheet__Formula_0x6e20224c_-sc-2231328

text: house mouse

text: Mus musculus

text: Mus musculus


text: Mus musculus

text: SC

text: public

text: __Spreadsheet__Formula_0x6ab03d75_-sc-2231329

text: house mouse

text: Mus musculus

text: Mus musculus


text: Mus musculus

text: SC

text: public

text: __Spreadsheet__Formula_0x39d54a2d_-sc-2231330

text: house mouse

text: Mus musculus

text: Mus musculus


text: Mus musculus

text: SC

text: public

text: __Spreadsheet__Formula_0x75b0473a_-sc-2231331

text: house mouse

text: Mus musculus

text: Mus musculus


text: Mus musculus

text: SC

text: public

text: __Spreadsheet__Formula_0x2a101417_-sc-2231332

text: house mouse

text: Mus musculus

text: Mus musculus


text: Mus musculus

text: SC

text: public

text: __Spreadsheet__Formula_0x3e35db43_-sc-2231333

text: house mouse

text: Mus musculus

text: Mus musculus


text: National Institute for Medical Research

text: public

tag: Namespace:National Institute for Medical Research

text: ArrayExpress

characteristic: broker name

text: house mouse

text: Protocols: E12.5 mouse embryos ventral midbrain has been dissected using zeiss laser capture microdissection Picopure RNA Isolation Kit Ovation RNA-Seq system (Nugen)

text: embryonic day 12.5

characteristic: developmental stage

text: Foxa1/2 Flox/ Flox

characteristic: genotype

text: Mus musculus

text: Mus musculus

text: 10um thick cryostat coronal sections of the midbrain

characteristic: organism part

text: Mus musculus


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: National Institute for Medical Research

text: public

text: ArrayExpress

text: house mouse

characteristic: description

text: embryonic day 12.5

text: wild type genotype

text: Mus musculus

text: Mus musculus

text: Mus musculus

characteristic: title


text: Kidney

characteristic: ArrayExpress-Phenotype

text: male

characteristic: ArrayExpress-Sex

text: Mus musculus

characteristic: ArrayExpress-Species

characteristic: ENA-CHECKLIST

text: SC

characteristic: INSDC center name

text: public

text: house mouse

text: Mus musculus

text: Mus musculus


text: Normal

text: Mus musculus

text: SC

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: house mouse

text: Mus musculus

text: Mus musculus


characteristic: ENA-FIRST-PUBLIC

text: public

tag: Namespace:Department of Internal Medicine Division of Gastroenterology

text: 110 day

characteristic: age

text: A+

characteristic: blood type

text: ArrayExpress

characteristic: broker name

text: embryonic stem cell line WA09 (H9) NIH registry #0062.

characteristic: cell line

text: human

characteristic: common name

text: Protocols: 4-day Activin A (R&D systems) differentiation protocol was used to derive definitive endoderm from human pluripotent stem cells (hPSCs). Cells were treated with Activin A (100 ng ml−1) for three consecutive days in RPMI 1640 media (Life Technologies) with increasing concentrations of 0%, 0.2% and 2% HyClone defined fetal bovine serum (dFBS, Thermo Scientific). The fourth day was a repeat of day 3 media (2% HyClone FBS). After differentiation into definitive endoderm, cells were incubated in foregut media (advanced DMEM/F12 plus N-2 and B27 supplement, 10mM Hepes, 1x L-Glutamine (200mM), 1x Penicillin-streptomycin (5,000 U/mL, all from Life Technologies)) with 200ng/mL Noggin (NOG, R&D Systems) and 10µM SB431542 (SB, Stemgent) for 4 days, SB, 500ng/mL FGF4 (R&D Systems), and 2 µM CHIR99021 (Chiron, Stemgent), and 1µM SAG (Enzo Life Sciences) for 4-6 days. After 4 days with treatment of growth factors, three-dimensional floating spheroids were present in the culture. Three-dimensional spheroids were transferred into Matrigel to support 3D growth. Spheroids were embedded in a droplet of Matrigel (BD Bioscience #356237) in one well of a 24 well plate, and incubated at room temperature for 10 minutes. After the Matrigel solidified, foregut media with 1% Fetal bovine serum (FBS, CAT#: 16000-044, Life Technologies) and 500ng/mL FGF10 (R&D Systems) were overlaid and replaced every 4 days. Organoids were transferred into new Matrigel droplets every 10 to 15 days. Illumina TrueSeq RNA sample prep

text: Organoid culture

characteristic: growth condition

text: 46, XX

characteristic: karyotype

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: Homo sapiens

text: female

characteristic: sex


characteristic: ENA-CHECKLIST

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Department of Internal Medicine Division of Gastroenterology

text: public

text: 110 day

text: A+

text: ArrayExpress

text: human

characteristic: description

text: Organoid culture

text: 46, XX

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens

text: female

characteristic: title


characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: 65 day

text: A+

text: ArrayExpress

text: human

text: Organoid culture

text: 46, XX

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens

text: female


text: Saccharomyces cerevisiae

characteristic: ArrayExpress-Species

characteristic: ENA-FIRST-PUBLIC

text: SC

text: public

characteristic: Submitter Id

text: baker's yeast

text: Saccharomyces cerevisiae

text: Lane 1

characteristic: sample description

text: Saccharomyces cerevisiae


text: Saccharomyces cerevisiae

text: SC

text: public

text: baker's yeast

characteristic: common name

text: Saccharomyces cerevisiae

text: Lane 4

text: Saccharomyces cerevisiae


text: Saccharomyces cerevisiae

text: SC

text: public

text: baker's yeast

text: Saccharomyces cerevisiae

characteristic: organism

text: Lane 2

text: Saccharomyces cerevisiae


text: Saccharomyces cerevisiae

text: SC

text: public

text: baker's yeast

text: Saccharomyces cerevisiae

text: Lane 3

text: Saccharomyces cerevisiae


text: Homo sapiens

text: SC

text: public

text: human

text: Homo sapiens

text: Homo sapiens