text: Queen's University Belfast

text: public

text: 14 day

characteristic: block

text: ArrayExpress

characteristic: broker name

text: velvet grass

text: Hogland solution phosphatelus phosphate

characteristic: growth condition

characteristic: individual

text: Holcus lanatus

text: Holcus lanatus L

text: Arsenic-non-tolerant

text: Holcus lanatus

text: fresh specimen


status: PUBLIC

tag: attribute

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Queen's University Belfast

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

tag: Namespace:Queen's University Belfast

characteristic: Submitter Id

text: 14 day

characteristic: age

text: ArrayExpress

text: velvet grass

characteristic: common name

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

characteristic: description

text: Hogland solution minus phosphate

text: Holcus lanatus

characteristic: organism

text: Holcus lanatus L

text: Arsenic-non-tolerant

characteristic: phenotype

text: Holcus lanatus

text: fresh specimen

characteristic: specimen with known storage state

characteristic: title

type: has member


text: Queen's University Belfast

text: public

text: 14 day

characteristic: block

text: ArrayExpress

characteristic: broker name

text: velvet grass

text: Hogland solution minus phosphate

characteristic: growth condition

characteristic: individual

text: Holcus lanatus

text: Holcus lanatus L

text: Arsenic-tolerant

text: Holcus lanatus

text: fresh specimen


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Queen's University Belfast

characteristic: INSDC center name

text: public

text: 14 day

text: ArrayExpress

text: velvet grass

text: Protocols: Arsenate tolerant and non-tolerant Holcus lanatus L. Genovars were selected randomly from a screened population, the arsenic uncontaminated Cruickshank Botanic Garden (CBG) and tillers of the plants were grown hydroponically for 2 weeks in 50ml individual centrifuge tubes with base of the tubes covered in tin-foil to block out light, in heated glasshouse at around 18C under supplemental sodium lamps. Plant tillers from arsenic tolerant (T) and non-tolerant (N) plants were grown hydroponically for 2 weeks in 50ml complete Hogland solution (plusP treatment) or 50ml Hogland solution minus Phosphate (minusP treatment). The experiment therefore investigated 4 treatments (TplusP, TminusP, NplusP, NminusP) and was repeated 2 time. Experiment1 was conducted on 4 plants (n=1), Experiment2 was conducted on 16 plants (n=4). dry roots and shoots for each replicate were ground under liquid nitrogen and total RNA was extrected using the Plant Rneasy kit (Qiagen), with additional on-column Dnase treatment. Extracted RNA of each sample was stored at -80C until shipping on dry ice for sequencing 454-TITANIUM, normalised total RNA

text: Hogland solution phosphatelus phosphate

text: Holcus lanatus

text: Holcus lanatus L

text: Arsenic-non-tolerant

text: Holcus lanatus

text: fresh specimen


text: Queen's University Belfast

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: 14 day

text: ArrayExpress

text: velvet grass

text: Hogland solution phosphatelus phosphate

text: Holcus lanatus

text: Holcus lanatus L

text: Arsenic-tolerant

text: Holcus lanatus

text: fresh specimen


text: Mus Musculus

characteristic: ArrayExpress-Species

text: SC

text: public

text: mES_i2m_s1_cell88-sc-2013-06-06T21:59:37Z-1643402

characteristic: Submitter Id

text: house mouse

characteristic: common name

text: Mus musculus

text: mRNA-seq Nextera library

characteristic: sample description

text: Mus musculus


text: Mus Musculus

text: SC

text: public

text: mES_i2m_s1_cell91-sc-2013-06-06T21:59:42Z-1643405

text: house mouse

text: Mus musculus

characteristic: organism

text: mRNA-seq Nextera library

text: Mus musculus


text: Mus Musculus

text: SC

text: public

text: mES_i2m_s1_cell94-sc-2013-06-06T21:59:45Z-1643408

text: house mouse

text: Mus musculus

text: mRNA-seq Nextera library

text: Mus musculus


text: Mus Musculus

text: SC

text: public

text: mES_i2m_s1_cell23-sc-2013-06-06T21:57:38Z-1643337

text: house mouse

text: Mus musculus

text: mRNA-seq Nextera library

text: Mus musculus


text: Mus Musculus

text: SC

text: public

text: mES_i2m_s1_cell26-sc-2013-06-06T21:57:44Z-1643340

text: house mouse

text: Mus musculus

text: mRNA-seq Nextera library

text: Mus musculus


text: Mus Musculus

text: SC

text: public

text: mES_i2m_s1_cell29-sc-2013-06-06T21:57:50Z-1643343

text: house mouse

text: Mus musculus

text: mRNA-seq Nextera library

text: Mus musculus


text: Mus Musculus

text: SC

text: public

text: mES_i2m_s1_cell32-sc-2013-06-06T21:57:55Z-1643346

text: house mouse

text: Mus musculus

text: mRNA-seq Nextera library

text: Mus musculus


text: Mus Musculus

text: SC

text: public

text: mES_i2m_s1_cell35-sc-2013-06-06T21:57:59Z-1643349

text: house mouse

text: Mus musculus

text: mRNA-seq Nextera library

text: Mus musculus


text: Mus Musculus

text: SC

text: public

text: mES_i2m_s1_cell38-sc-2013-06-06T21:58:05Z-1643352

text: house mouse

text: Mus musculus

text: mRNA-seq Nextera library

text: Mus musculus


text: Mus Musculus

text: SC

text: public

text: mES_i2m_s1_cell41-sc-2013-06-06T21:58:10Z-1643355

text: house mouse

text: Mus musculus

text: mRNA-seq Nextera library

text: Mus musculus


text: Mus Musculus

text: SC

text: public

text: mES_i2m_s1_cell44-sc-2013-06-06T21:58:15Z-1643358

text: house mouse

text: Mus musculus

text: mRNA-seq Nextera library

text: Mus musculus


text: Mus Musculus

text: SC

text: public

text: mES_i2m_s1_cell47-sc-2013-06-06T21:58:21Z-1643361

text: house mouse

text: Mus musculus

text: mRNA-seq Nextera library

text: Mus musculus


text: Mus Musculus

text: SC

text: public

text: mES_i2m_s1_cell50-sc-2013-06-06T21:58:26Z-1643364

text: house mouse

text: Mus musculus

text: mRNA-seq Nextera library

text: Mus musculus


text: Mus Musculus

text: SC

text: public

text: mES_i2m_s1_cell53-sc-2013-06-06T21:58:32Z-1643367

text: house mouse

text: Mus musculus

text: mRNA-seq Nextera library

text: Mus musculus


text: Mus Musculus

text: SC

text: public

text: mES_i2m_s1_cell56-sc-2013-06-06T21:58:40Z-1643370

text: house mouse

text: Mus musculus

text: mRNA-seq Nextera library

text: Mus musculus


text: Mus Musculus

text: SC

text: public

text: mES_i2m_s1_cell59-sc-2013-06-06T21:58:45Z-1643373

text: house mouse

text: Mus musculus

text: mRNA-seq Nextera library

text: Mus musculus


text: Mus Musculus

text: SC

text: public

text: mES_i2m_s1_cell62-sc-2013-06-06T21:58:49Z-1643376

text: house mouse

text: Mus musculus

text: mRNA-seq Nextera library

text: Mus musculus


text: Mus Musculus

text: SC

text: public

text: mES_i2m_s1_cell68-sc-2013-06-06T21:58:58Z-1643382

text: house mouse

text: Mus musculus

text: mRNA-seq Nextera library

text: Mus musculus


text: Mus Musculus

text: SC

text: public

text: mES_i2m_s1_cell71-sc-2013-06-06T21:59:03Z-1643385

text: house mouse

text: Mus musculus

text: mRNA-seq Nextera library

text: Mus musculus


text: Mus Musculus

text: SC

text: public

text: mES_i2m_s1_cell74-sc-2013-06-06T21:59:08Z-1643388

text: house mouse

text: Mus musculus

text: mRNA-seq Nextera library

text: Mus musculus


text: Mus Musculus

text: SC

text: public

text: mES_i2m_s1_cell77-sc-2013-06-06T21:59:16Z-1643391

text: house mouse

text: Mus musculus

text: mRNA-seq Nextera library

text: Mus musculus


text: Mus Musculus

text: SC

text: public

text: mES_i2m_s1_cell80-sc-2013-06-06T21:59:20Z-1643394

text: house mouse

text: Mus musculus

text: mRNA-seq Nextera library

text: Mus musculus


text: Mus Musculus

text: SC

text: public

text: mES_i2m_s1_cell83-sc-2013-06-06T21:59:30Z-1643397

text: house mouse

text: Mus musculus

text: mRNA-seq Nextera library

text: Mus musculus


text: Mus Musculus

text: SC

text: public

text: mES_i2m_s1_cell86-sc-2013-06-06T21:59:34Z-1643400

text: house mouse

text: Mus musculus

text: mRNA-seq Nextera library

text: Mus musculus


text: Mus Musculus

text: SC

text: public

text: mES_i2m_s1_cell89-sc-2013-06-06T21:59:39Z-1643403

text: house mouse

text: Mus musculus

text: mRNA-seq Nextera library

text: Mus musculus


text: Mus Musculus

text: SC

text: public

text: mES_i2m_s1_cell92-sc-2013-06-06T21:59:43Z-1643406

text: house mouse

text: Mus musculus

text: mRNA-seq Nextera library

text: Mus musculus


text: Mus Musculus

text: SC

text: public

text: mES_i2m_s1_cell95-sc-2013-06-06T21:59:47Z-1643409

text: house mouse

text: Mus musculus

text: mRNA-seq Nextera library

text: Mus musculus


text: male

characteristic: ArrayExpress-Sex

text: Mus musculus

text: SC

text: public

text: JM8_5_control-sc-2013-06-10T14:50:48Z-1645591

text: house mouse

text: Mus musculus

text: PCR products

text: Mus musculus


text: Anopheles gambiae

text: SC

text: public

text: African malaria mosquito

text: Anopheles gambiae

text: Anopheles gambiae


text: spleen

characteristic: ArrayExpress-OrganismPart

text: Mus Musculus

text: SC

text: public

text: Foxp3Mut1_K44_deltaE1_3-sc-2013-06-07T19:01:52Z-1643508

text: house mouse

text: Mus musculus

text: RNA extracted from cells

text: Mus musculus


text: spleen

text: Mus Musculus

text: SC

text: public

text: Foxp3Mut2_K44_deltaE1_3-sc-2013-06-07T19:01:56Z-1643511

text: house mouse

text: Mus musculus

text: RNA extracted from cells

text: Mus musculus


E-MTAB-1683:CKI alpha KO

text: public

text: E-MTAB-1683:CKI alpha KO

tag: Namespace:Institute for Molecular Biology and Tumor Research

text: ArrayExpress

characteristic: broker name

text: epithelial cell

characteristic: cell type

text: house mouse

text: Protocols: For generation of conditional CKI knockout mice, Cre was transiently expressed in ES cells to produce specific deletion of the neomycin cassette and an intact floxed CKI alpha allele. A second aggregation was done, and Vilin-Cre-ERT2 transgenic mice were used as a gut-specific deleter to generate a conditional CKI floxed/floxed Villin-Cre-ERT2 knockout mouse (CKI alpha KO). Inducible double-knockout mice (p53 and CKI alpha) were generated by crossing mice in which CKI alpha was floxed with mice in which p53 was floxed (CKI alpha/p53 DKO). Mice were kept under specific pathogen-free conditions at the Hadassah Medical School of the Hebrew University. Mice were injected with 150 milligram/kilogram Tamoxifen (Sigma) subcutaneously, at a regimen of 6 injections every other day. Sulindac (Sigma) was administered in the drinking water at 0.6 gram/liter, one week before the first Tamoxifen injection, and throughout the 2 weeks of knockout induction, for a total period of 3 weeks. BV6 (Genentech) was injected intraperitoneally at 10 milligram/kilogram, every other day, from day 2 of knockout induction. BOT64 (Santa Cruz) was injected intraperitoneally at 30 milligram/kilogram, every day, from day 2 of knockout induction. 1-2 days after the last Tamoxifen injection, mice were injected intraperitoneally with 10 microliter/gram of 5-bromo-2-deoxyuridine (BrdU; GE Healthcare) and sacrificed 2 hours later, on day 10-12 of knockout induction. Jejunum, ileum and the entire large intestine were flushed with ice-cold PBS, cut open longitudinally, and subjected to fixation in 4% formaldehyde and paraffin embedding(FFPE). Intestinal epithelial cells (IECs) were isolated from the middle part of the small intestine and separated into single cells in HBSS containing 10 millimolar HEPES, 5 millimolar EDTA and 0.5 mM DTT, at 37C for 30 minutes. Total RNA was extracted from IECs using TRI-reagent (Sigma) and phenol/chloroform methods. Total RNA from IECs of three mice per genotype was pooled, processed with the mRNA Sequencing Kit (Illumina). Library construction was done with the Illumina TRUSeq kit according maufacturers instructions.

characteristic: description

text: flox sites around both CKI alpha alleles

characteristic: genomic modification

text: CKI alpha -/-

characteristic: genotype

text: Mus musculus

text: Mus musculus

text: intestine

characteristic: organism part

text: Mus musculus

text: CKI alpha KO

characteristic: title


E-MTAB-1683:CKI alpha and p53 DKO

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Institute for Molecular Biology and Tumor Research

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: E-MTAB-1683:CKI alpha and p53 DKO

text: ArrayExpress

text: epithelial cell

text: house mouse

text: flox sites around CKI alpha and p53

text: CKI alpha -/- p53 -/-

text: Mus musculus

text: Mus musculus

text: intestine

text: Mus musculus

text: CKI alpha and p53 DKO


text: spleen

text: Mus Musculus

characteristic: ArrayExpress-Species

text: SC

text: public

characteristic: INSDC status

characteristic: SRA accession

text: Foxp3Mut1_J100_M5-sc-2013-06-07T19:01:53Z-1643509

characteristic: Submitter Id

text: house mouse

characteristic: common name

text: Mus musculus

text: RNA extracted from cells

characteristic: sample description

text: Mus musculus


text: spleen

characteristic: ArrayExpress-OrganismPart

text: Mus Musculus

text: SC

text: public

text: Foxp3Mut2_J100_M5-sc-2013-06-07T19:01:57Z-1643512

text: house mouse

text: Mus musculus

characteristic: organism

text: RNA extracted from cells

text: Mus musculus


E-MTAB-1683:CKI alpha Het

text: public

text: E-MTAB-1683:CKI alpha Het

text: ArrayExpress

characteristic: broker name

text: epithelial cell

characteristic: cell type

text: house mouse

characteristic: description

text: flox sites around one CKI alpha allele

characteristic: genomic modification

text: cki alpha -/+

characteristic: genotype

text: Mus musculus

text: Mus musculus

text: intestine

text: Mus musculus

text: CKI alpha Het


E-MTAB-1628:ST-HSC WT

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Stowers Institute for Medical Research

text: public

text: E-MTAB-1628:ST-HSC WT

tag: Namespace:Stowers Institute for Medical Research

text: 6 week

characteristic: age

text: ArrayExpress

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

text: house mouse

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

text: WT

text: Mus musculus

text: Mus musculus

text: FACS-sorted bone marrow

characteristic: organism part

text: Mus musculus

text: fresh specimen

characteristic: specimen with known storage state

characteristic: strain

text: ST-HSC WT

characteristic: title


E-MTAB-1628:LT-HSC dH19

text: Stowers Institute for Medical Research

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-1628:LT-HSC dH19

characteristic: Submitter Id

text: 6 week

text: ArrayExpress

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

text: house mouse

characteristic: common name

text: mH19 flDMR/+

text: Mus musculus

text: Mus musculus

text: FACS-sorted bone marrow

text: Mus musculus

text: fresh specimen

text: LT-HSC dH19


text: Mus musculus

characteristic: ArrayExpress-Species

text: SC

text: public

text: MD4953d3-sc-2013-06-11T11:10:08Z-1471175

text: house mouse

text: Mus musculus

characteristic: organism

text: Mus musculus


text: Mus musculus

characteristic: ENA-FIRST-PUBLIC

text: SC

text: public

text: house mouse

text: Mus musculus

text: Mus musculus


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

characteristic: ENA-LAST-UPDATE

text: Stowers Institute for Medical Research

text: public

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

text: 6 week

text: ArrayExpress

characteristic: broker name

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

characteristic: cell type

text: house mouse

characteristic: description

text: mH19 dDMR/+ Igf1r -/-

characteristic: genotype

text: Mus musculus

text: Mus musculus

text: FACS-sorted bone marrow

text: Mus musculus

text: fresh specimen

text: LT-HSC dH19/dIgf1r


E-MTAB-1628:LT-HSC WT

characteristic: External Id

text: Stowers Institute for Medical Research

text: public

text: E-MTAB-1628:LT-HSC WT

text: 6 week

characteristic: age

text: ArrayExpress

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

text: house mouse

text: WT

text: Mus musculus

text: Mus musculus

text: FACS-sorted bone marrow

characteristic: organism part

text: Mus musculus

text: fresh specimen

characteristic: specimen with known storage state

characteristic: strain

text: LT-HSC WT


E-MTAB-1628:MPP dH19

text: Stowers Institute for Medical Research

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: E-MTAB-1628:MPP dH19

text: 6 week

text: ArrayExpress

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

text: house mouse

text: mH19 flDMR/+

text: Mus musculus

text: Mus musculus

text: FACS-sorted bone marrow

text: Mus musculus

text: fresh specimen

text: MPP dH19

characteristic: title


E-MTAB-1628:MPP WT

text: Stowers Institute for Medical Research

text: public

characteristic: SRA accession

text: E-MTAB-1628:MPP WT

characteristic: Submitter Id

text: 6 week

text: ArrayExpress

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

text: house mouse

characteristic: common name

text: WT

text: Mus musculus

characteristic: organism

text: Mus musculus

text: FACS-sorted bone marrow

text: Mus musculus

text: fresh specimen

text: MPP WT


E-MTAB-1628:MPP dIgf1r

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: Stowers Institute for Medical Research

text: public

text: E-MTAB-1628:MPP dIgf1r

text: 6 week

text: ArrayExpress

characteristic: broker name

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

characteristic: cell type

text: house mouse

text: mH19 dDMR/+ Igf1r f-/-

text: Mus musculus

text: Mus musculus

text: FACS-sorted bone marrow

text: Mus musculus

text: fresh specimen

text: MPP dIgf1r


text: Pancreas

characteristic: ArrayExpress-CellType

characteristic: ArrayExpress-Immunoprecipitate

text: Pancreas

characteristic: ArrayExpress-OrganismPart

text: Cancer

characteristic: ArrayExpress-Phenotype

text: Mus Musculus

characteristic: ArrayExpress-Species

characteristic: External Id

text: SC

text: public

text: house mouse

text: Mus musculus

text: Chromatin IP

characteristic: sample description

text: Mus musculus


text: Liver

text: Liver

text: Cancer

text: Mus Musculus

text: SC

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: Foxp2_4_9i-sc-2013-06-10T13:41:50Z-1645595

text: house mouse

text: Mus musculus

text: Chromatin IP

text: Mus musculus


text: GIS

text: public

characteristic: SRA accession

characteristic: Submitter Id

text: ArrayExpress

characteristic: cell line

text: embryonic stem cell

text: human

characteristic: common name

text: Protocols: The hESC line H1 (WA-01, passage 30) was cultured feeder-free in conditioned medium on Matrigel (BD). Conditioned medium contains 20% Knock-out serum replacement (Gibco), 1 mM L-glutamine (Gibco), 1% non-essential amino acids (Gibco) and 0.1 mM 2-mercaptoethanol (Gibco), 4 ng/ml human basic fibroblast growth factor (bFGF) (Invitrogen), and medium was supplemented with additional bFGF (8ng/ml) before use. The hESCs were passaged for expansion with 1 mg/ml collagenase IV (Gibco) every 5-7 days. For transfection, the hESCs were passaged with 0.25% trypsin (Invitrogen) for dissociation and transfected with 1.5 ug shRNA and 4.5 ulMirus LT1 transfection reagents the following day. Cells were harvested for mRNA 3 days after transfection of SON shRNA1. Trizol (Invitrogen) was used for extraction of total RNA from hESCs treated with control shRNA or SON shRNA for 3 days. 4 ug RNA extracted from biological duplicate samples was poly (A) enriched by incubating with oligo(dT) coated sepherose beads for two rounds (Ambion). The resultant enriched mRNA was fragmented, size selected and reverse transcribed according to the IlluminaTruSeq RNA Sample Preparation Guide.

characteristic: description

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens

text: male

characteristic: sex

text: hESCs

characteristic: title


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: European Bioinformatics Institute (EBI)

text: public

tag: Namespace:European Bioinformatics Institute (EBI)

text: ArrayExpress

characteristic: broker name

text: embryonic cell

characteristic: cell type

text: fruit fly

text: Protocols: S2 cells were grown in Schneiders Media (Invitrogen) supplemented with 10% of heat-inactivated bovine fetal serum to a density of 1 million cells per ml. 30ml cell suspension were spun down and the cell pellet was resuspended in 1 ml of cross-linking solution (50 mM HEPES, 100 mM NaCl, 1 mM EDTA, 0.5 mM EGTA). 37% formaldehyde was added to a final concentration of 1.8%. The tube was rotated at room temperature for 15 minutes and the reaction was quenched with 2.5 M glycine at a final concentration of 125 mM for 5 minutes. The fixed cells were washed 3 times for 5 minutes each with rinse buffer 1 (10 mM HEPES pH 7.5, 10 mM EDTA, 0.5 mM EGTA, 0.25% Triton X-100) and 5 times for 5 minutes each with rinse buffer 2 (10 mM HEPES pH 7.6, 1 mM EDTA, 0.5 mM EGTA, 200 mM NaCl). Finally, the cells were washed 3 times in RIPA buffer (25 mM HEPES pH 7.5, 140 mM NaCl, 1 mM EDTA, 1% Triton-X 100, 0.1% SDS, 0.1% DOC). The cells were sonicated 30 x 20 seconds using a Branson 250 sonicator at pulse 40, intensity 3%. The chromatin should be sheared into fragments with average length of 200 bp. Samples were centrifuged at maximum speed and the supernatant was used for the subsequent steps. To reverse cross-linking, samples were incubated at 65C overnight in TE buffer, followed by a treatment with RNaseA (0.2 mg/ml) for 30 min at 37C, and with Proteinase K (0.05 mg/ml) for 2 hours at 50C. Finally, DNA was purified using Minelute columns (Qiagen). The libraries were prepared following Illumina's TruSeq ChIP sample prep kit (http://www.illumina.com/products/truseq_chip_sample_prep_kit.ilmn)

text: wild type

characteristic: genotype

text: Drosophila melanogaster

characteristic: organism

text: Drosophila melanogaster

text: Drosophila melanogaster

text: male


characteristic: External Id

text: UCSF

characteristic: INSDC center name

text: public

text: 0 day

characteristic: age

text: ArrayExpress

text: house mouse

text: Protocols: Embryonic BAT (Brown Adipose Tissue) from mice at postnatal stage P0 or Interscapular BAT from 12-weeks old. RiboZol reagent (AMRESCO) following the manufacturer's protocol Ultralow DR library kit (NuGEN): www.nugeninc.com/nugen/index.cfm/products/cs/ngs/rna-seq-v2

text: postnatal

characteristic: developmental stage

text: wild type

text: Mus musculus

text: Mus musculus

text: embryonic brown fat

characteristic: organism part

text: normal

characteristic: phenotype

text: Mus musculus

text: frozen specimen

characteristic: specimen with known storage state

characteristic: strain


text: UCSF

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: 12 week

text: ArrayExpress

text: house mouse

characteristic: common name

characteristic: description

text: adult

text: Ehmt1adipo KO

text: Mus musculus

text: Mus musculus

text: interscapular brown fat

text: brown adipose tissue dysfunction

text: Mus musculus

text: frozen specimen

text: Adipo-Cre+/-; Ehmt1flox/flox

text: AdipKO


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: UCSF

text: public

text: 12 week

text: ArrayExpress

characteristic: broker name

text: house mouse

text: adult

text: wild type

characteristic: genotype

text: Mus musculus

text: Mus musculus

text: interscapular brown fat

text: normal

text: Mus musculus

text: frozen specimen

characteristic: title


characteristic: External Id

text: UCSF

characteristic: INSDC center name

text: public

text: 0 day

characteristic: age

text: ArrayExpress

text: house mouse

text: postnatal

characteristic: developmental stage

text: Ehmt1Myf5 KO

text: Mus musculus

characteristic: organism

text: Mus musculus

text: embryonic brown fat

text: brown adipose tissue developmental defect

text: Mus musculus

text: frozen specimen

text: Myf5-Cre+/-; Ehmt1flox/flox


text: OMP-GFP +/-

characteristic: ArrayExpress-Genotype

text: MOE

characteristic: ArrayExpress-OrganismPart

text: Wildtype

characteristic: ArrayExpress-Phenotype

text: male

characteristic: ArrayExpress-Sex

text: Mouse

characteristic: ArrayExpress-Species

text: 129 x C57BL/6

characteristic: ArrayExpress-StrainOrLine

text: SC

characteristic: INSDC first public

text: public

text: OMP_GFP_MOE-sc-2013-06-05T09:01:53Z-1640345

text: house mouse

text: Mus musculus

text: RNA from MOE

characteristic: sample description

text: Mus musculus

text: 129 x C57BL/6

characteristic: strain


text: OMP-GFP +/-

text: MOE

text: Wildtype

text: mixed

text: Mouse

text: 129 x C57BL/6

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: SC

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: OMP_GFP_OSN-sc-2013-06-05T09:01:59Z-1640348

characteristic: Submitter Id

text: house mouse

characteristic: common name

text: Mus musculus

text: RNA from MOE OSNs

text: Mus musculus

text: 129 x C57BL/6


E-MTAB-1628:LT-HSC dIgf1r

characteristic: External Id

text: Stowers Institute for Medical Research

characteristic: INSDC center name

text: public

text: E-MTAB-1628:LT-HSC dIgf1r

text: 6 week

characteristic: age

text: ArrayExpress

characteristic: broker name

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

characteristic: cell type

text: house mouse

characteristic: description

text: mH19 dDMR/+ Igf1r f-/-

characteristic: genotype

text: Mus musculus

characteristic: organism

text: Mus musculus

text: FACS-sorted bone marrow

characteristic: organism part

text: Mus musculus

text: fresh specimen

characteristic: specimen with known storage state

text: LT-HSC dIgf1r

characteristic: title


E-MTAB-1628:ST-HSC dIgf1r

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: Stowers Institute for Medical Research

characteristic: INSDC first public

text: public

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

text: 6 week

text: ArrayExpress

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

text: house mouse

text: mH19 dDMR/+ Igf1r f-/-

text: Mus musculus

text: Mus musculus

text: FACS-sorted bone marrow

text: Mus musculus

text: fresh specimen

characteristic: strain

text: ST-HSC dIgf1r


E-MTAB-1628:ST-HSC dH19

text: Stowers Institute for Medical Research

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

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

characteristic: Submitter Id

text: 6 week

text: ArrayExpress

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

text: house mouse

text: mH19 flDMR/+

text: Mus musculus

text: Mus musculus

text: FACS-sorted bone marrow

text: Mus musculus

text: fresh specimen

text: ST-HSC dH19


text: OMP-GFP +/-

characteristic: ArrayExpress-Genotype

text: MOE

characteristic: ArrayExpress-OrganismPart

text: Wildtype

characteristic: ArrayExpress-Phenotype

text: male

characteristic: ArrayExpress-Sex

text: Mouse

characteristic: ArrayExpress-Species

text: 129 x C57BL/6

characteristic: ArrayExpress-StrainOrLine

characteristic: External Id

text: SC

characteristic: INSDC center name

text: public

text: OMP_GFP_MOE-sc-2013-06-05T09:01:56Z-1640346

text: house mouse

characteristic: common name

text: Mus musculus

text: RNA from MOE

characteristic: sample description

text: Mus musculus

text: 129 x C57BL/6


text: OMP-GFP +/-

text: MOE

text: Wildtype

text: mixed

text: Mouse

text: 129 x C57BL/6

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: SC

text: public

text: OMP_GFP_OSN-sc-2013-06-05T09:02:00Z-1640349

text: house mouse

text: Mus musculus

characteristic: organism

text: RNA from MOE OSNs

text: Mus musculus

text: 129 x C57BL/6


text: Mus musculus

text: SC

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: house mouse

text: Mus musculus

text: Mus musculus


text: Plasmodium falciparum

text: SC

text: public

characteristic: INSDC status

characteristic: SRA accession

text: malaria parasite P. falciparum

text: Plasmodium falciparum

text: Plasmodium falciparum


text: male

text: Mus musculus

text: SC

text: public

text: JM8_5_clone2-sc-2013-06-06T20:56:12Z-1643296

characteristic: Submitter Id

text: house mouse

text: Mus musculus

text: PCR products

text: Mus musculus


text: male

text: Mus musculus

text: SC

text: public

text: Control_set_2-sc-2013-06-06T20:57:32Z-1643294

text: house mouse

text: Mus musculus

text: PCR products

text: Mus musculus


text: male

text: Mus musculus

text: SC

text: public

text: JM8_5_clone9-sc-2013-06-06T20:58:52Z-1643303

text: house mouse

text: Mus musculus

text: PCR products

text: Mus musculus


text: male

text: Mus musculus

text: SC

text: public

text: JM8_5_clone6-sc-2013-06-06T21:02:06Z-1643300

text: house mouse

text: Mus musculus

text: PCR products

text: Mus musculus


text: male

text: Mus musculus

text: SC

text: public

text: JM8_5_clone10-sc-2013-06-06T21:03:49Z-1643304

text: house mouse

text: Mus musculus

text: PCR products

text: Mus musculus


text: male

text: Mus musculus

text: SC

text: public

text: JM8_8_clone3-sc-2013-06-06T21:05:22Z-1643307

text: house mouse

text: Mus musculus

text: PCR products

text: Mus musculus


text: male

text: Mus musculus

text: SC

text: public

text: JM8_8_clone8-sc-2013-06-06T21:08:53Z-1643312

text: house mouse

text: Mus musculus

text: PCR products

text: Mus musculus


text: male

text: Mus musculus

text: SC

text: public

text: JM8_8_clone5-sc-2013-06-06T21:11:58Z-1643309

text: house mouse

text: Mus musculus

text: PCR products

text: Mus musculus


text: Mus Musculus

text: SC

text: public

text: mES_i2m_s1_cell1-sc-2013-06-06T21:56:59Z-1643315

text: house mouse

text: Mus musculus

text: mRNA-seq Nextera library

text: Mus musculus


text: Mus Musculus

text: SC

text: public

text: mES_i2m_s1_cell4-sc-2013-06-06T21:57:07Z-1643318

text: house mouse

text: Mus musculus

text: mRNA-seq Nextera library

text: Mus musculus


text: male

text: Mus musculus

text: SC

text: public

text: GPI_geneset_2-sc-2013-06-06T20:56:35Z-1643292

text: house mouse

text: Mus musculus

text: PCR products

text: Mus musculus


text: male

text: Mus musculus

text: SC

text: public

text: JM8_5_clone3-sc-2013-06-06T20:58:06Z-1643297

text: house mouse

text: Mus musculus

text: PCR products

text: Mus musculus


text: male

text: Mus musculus

text: SC

text: public

text: JM8_5_clone5-sc-2013-06-06T20:59:17Z-1643299

text: house mouse

text: Mus musculus

text: PCR products

text: Mus musculus


text: male

text: Mus musculus

text: SC

text: public

text: JM8_5_clone7-sc-2013-06-06T21:02:38Z-1643301

text: house mouse

text: Mus musculus

text: PCR products

text: Mus musculus


text: male

text: Mus musculus

text: SC

text: public

text: JM8_8_clone1-sc-2013-06-06T21:04:10Z-1643305

text: house mouse

text: Mus musculus

text: PCR products

text: Mus musculus


text: male

text: Mus musculus

text: SC

text: public

text: JM8_8_clone4-sc-2013-06-06T21:06:15Z-1643308

text: house mouse

text: Mus musculus

text: PCR products

text: Mus musculus


text: male

text: Mus musculus

text: SC

text: public

text: JM8_8_clone9-sc-2013-06-06T21:09:56Z-1643313

text: house mouse

text: Mus musculus

text: PCR products

text: Mus musculus


text: male

text: Mus musculus

text: SC

text: public

text: JM8_8_clone6-sc-2013-06-06T21:14:19Z-1643310

text: house mouse

text: Mus musculus

text: PCR products

text: Mus musculus


text: Mus Musculus

text: SC

text: public

text: mES_i2m_s1_cell2-sc-2013-06-06T21:57:04Z-1643316

text: house mouse

text: Mus musculus

text: mRNA-seq Nextera library

text: Mus musculus


text: Mus Musculus

text: SC

text: public

text: mES_i2m_s1_cell5-sc-2013-06-06T21:57:09Z-1643319

text: house mouse

text: Mus musculus

text: mRNA-seq Nextera library

text: Mus musculus


text: Mus Musculus

text: SC

text: public

text: mES_i2m_s1_cell11-sc-2013-06-06T21:57:19Z-1643325

text: house mouse

text: Mus musculus

text: mRNA-seq Nextera library

text: Mus musculus


text: Mus Musculus

text: SC

text: public

text: mES_i2m_s1_cell14-sc-2013-06-06T21:57:25Z-1643328

text: house mouse

text: Mus musculus

text: mRNA-seq Nextera library

text: Mus musculus


text: Mus Musculus

text: SC

text: public

text: mES_i2m_s1_cell17-sc-2013-06-06T21:57:30Z-1643331

text: house mouse

text: Mus musculus

text: mRNA-seq Nextera library

text: Mus musculus


text: Mus Musculus

text: SC

text: public

text: mES_i2m_s1_cell20-sc-2013-06-06T21:57:34Z-1643334

text: house mouse

text: Mus musculus

text: mRNA-seq Nextera library

text: Mus musculus


text: Mus Musculus

text: SC

text: public

text: mES_i2m_s1_cell10-sc-2013-06-06T21:57:18Z-1643324

text: house mouse

text: Mus musculus

text: mRNA-seq Nextera library

text: Mus musculus


text: Mus Musculus

text: SC

text: public

text: mES_i2m_s1_cell13-sc-2013-06-06T21:57:22Z-1643327

text: house mouse

text: Mus musculus

text: mRNA-seq Nextera library

text: Mus musculus


text: Mus Musculus

text: SC

text: public

text: mES_i2m_s1_cell16-sc-2013-06-06T21:57:29Z-1643330

text: house mouse

text: Mus musculus

text: mRNA-seq Nextera library

text: Mus musculus


text: Mus Musculus

text: SC

text: public

text: mES_i2m_s1_cell19-sc-2013-06-06T21:57:33Z-1643333

text: house mouse

text: Mus musculus

text: mRNA-seq Nextera library

text: Mus musculus


text: Mus Musculus

text: SC

text: public

text: mES_i2m_s1_cell22-sc-2013-06-06T21:57:37Z-1643336

text: house mouse

text: Mus musculus

text: mRNA-seq Nextera library

text: Mus musculus


text: Mus Musculus

text: SC

text: public

text: mES_i2m_s1_cell25-sc-2013-06-06T21:57:42Z-1643339

text: house mouse

text: Mus musculus

text: mRNA-seq Nextera library

text: Mus musculus


text: Mus Musculus

text: SC

text: public

text: mES_i2m_s1_cell28-sc-2013-06-06T21:57:48Z-1643342

text: house mouse

text: Mus musculus

text: mRNA-seq Nextera library

text: Mus musculus


text: Mus Musculus

text: SC

text: public

text: mES_i2m_s1_cell31-sc-2013-06-06T21:57:53Z-1643345

text: house mouse

text: Mus musculus

text: mRNA-seq Nextera library

text: Mus musculus


text: Mus Musculus

text: SC

text: public

text: mES_i2m_s1_cell34-sc-2013-06-06T21:57:58Z-1643348

text: house mouse

text: Mus musculus

text: mRNA-seq Nextera library

text: Mus musculus


text: Mus Musculus

text: SC

text: public

text: mES_i2m_s1_cell37-sc-2013-06-06T21:58:03Z-1643351

text: house mouse

text: Mus musculus

text: mRNA-seq Nextera library

text: Mus musculus


text: Mus Musculus

text: SC

text: public

text: mES_i2m_s1_cell40-sc-2013-06-06T21:58:08Z-1643354

text: house mouse

text: Mus musculus

text: mRNA-seq Nextera library

text: Mus musculus


text: Mus Musculus

text: SC

text: public

text: mES_i2m_s1_cell43-sc-2013-06-06T21:58:13Z-1643357

text: house mouse

text: Mus musculus

text: mRNA-seq Nextera library

text: Mus musculus


text: Mus Musculus

text: SC

text: public

text: mES_i2m_s1_cell46-sc-2013-06-06T21:58:19Z-1643360

text: house mouse

text: Mus musculus

text: mRNA-seq Nextera library

text: Mus musculus


text: Mus Musculus

text: SC

text: public

text: mES_i2m_s1_cell49-sc-2013-06-06T21:58:24Z-1643363

text: house mouse

text: Mus musculus

text: mRNA-seq Nextera library

text: Mus musculus


text: Mus Musculus

text: SC

text: public

text: mES_i2m_s1_cell52-sc-2013-06-06T21:58:30Z-1643366

text: house mouse

text: Mus musculus

text: mRNA-seq Nextera library

text: Mus musculus


text: Mus Musculus

text: SC

text: public

text: mES_i2m_s1_cell55-sc-2013-06-06T21:58:38Z-1643369

text: house mouse

text: Mus musculus

text: mRNA-seq Nextera library

text: Mus musculus


text: Mus Musculus

text: SC

text: public

text: mES_i2m_s1_cell58-sc-2013-06-06T21:58:43Z-1643372

text: house mouse

text: Mus musculus

text: mRNA-seq Nextera library

text: Mus musculus


text: Mus Musculus

text: SC

text: public

text: mES_i2m_s1_cell61-sc-2013-06-06T21:58:48Z-1643375

text: house mouse

text: Mus musculus

text: mRNA-seq Nextera library

text: Mus musculus


text: Mus Musculus

text: SC

text: public

text: mES_i2m_s1_cell64-sc-2013-06-06T21:58:52Z-1643378

text: house mouse

text: Mus musculus

text: mRNA-seq Nextera library

text: Mus musculus


text: Mus Musculus

text: SC

text: public

text: mES_i2m_s1_cell67-sc-2013-06-06T21:58:57Z-1643381

text: house mouse

text: Mus musculus

text: mRNA-seq Nextera library

text: Mus musculus


text: Mus Musculus

text: SC

text: public

text: mES_i2m_s1_cell70-sc-2013-06-06T21:59:02Z-1643384

text: house mouse

text: Mus musculus

text: mRNA-seq Nextera library

text: Mus musculus


text: Mus Musculus

text: SC

text: public

text: mES_i2m_s1_cell73-sc-2013-06-06T21:59:07Z-1643387

text: house mouse

text: Mus musculus

text: mRNA-seq Nextera library

text: Mus musculus


text: Mus Musculus

text: SC

text: public

text: mES_i2m_s1_cell76-sc-2013-06-06T21:59:14Z-1643390

text: house mouse

text: Mus musculus

text: mRNA-seq Nextera library

text: Mus musculus


text: Mus Musculus

text: SC

text: public

text: mES_i2m_s1_cell82-sc-2013-06-06T21:59:26Z-1643396

text: house mouse

text: Mus musculus

text: mRNA-seq Nextera library

text: Mus musculus


text: Mus Musculus

text: SC

text: public

text: mES_i2m_s1_cell39-sc-2013-06-06T21:58:07Z-1643353

text: house mouse

text: Mus musculus

text: mRNA-seq Nextera library

text: Mus musculus


text: Mus Musculus

text: SC

text: public

text: mES_i2m_s1_cell42-sc-2013-06-06T21:58:11Z-1643356

text: house mouse

text: Mus musculus

text: mRNA-seq Nextera library

text: Mus musculus


text: Mus Musculus

text: SC

text: public

text: mES_i2m_s1_cell45-sc-2013-06-06T21:58:17Z-1643359

text: house mouse

text: Mus musculus

text: mRNA-seq Nextera library

text: Mus musculus


text: Mus Musculus

text: SC

text: public

text: mES_i2m_s1_cell48-sc-2013-06-06T21:58:22Z-1643362

text: house mouse

text: Mus musculus

text: mRNA-seq Nextera library

text: Mus musculus


text: Mus Musculus

text: SC

text: public

text: mES_i2m_s1_cell51-sc-2013-06-06T21:58:28Z-1643365

text: house mouse

text: Mus musculus

text: mRNA-seq Nextera library

text: Mus musculus


text: Mus Musculus

text: SC

text: public

text: mES_i2m_s1_cell54-sc-2013-06-06T21:58:36Z-1643368

text: house mouse

text: Mus musculus

text: mRNA-seq Nextera library

text: Mus musculus


text: Mus Musculus

text: SC

text: public

text: mES_i2m_s1_cell57-sc-2013-06-06T21:58:42Z-1643371

text: house mouse

text: Mus musculus

text: mRNA-seq Nextera library

text: Mus musculus


text: Mus Musculus

text: SC

text: public

text: mES_i2m_s1_cell60-sc-2013-06-06T21:58:47Z-1643374

text: house mouse

text: Mus musculus

text: mRNA-seq Nextera library

text: Mus musculus


text: Mus Musculus

text: SC

text: public

text: mES_i2m_s1_cell63-sc-2013-06-06T21:58:51Z-1643377

text: house mouse

text: Mus musculus

text: mRNA-seq Nextera library

text: Mus musculus


text: Mus Musculus

text: SC

text: public

text: mES_i2m_s1_cell66-sc-2013-06-06T21:58:55Z-1643380

text: house mouse

text: Mus musculus

text: mRNA-seq Nextera library

text: Mus musculus


text: Mus Musculus

text: SC

text: public

text: mES_i2m_s1_cell69-sc-2013-06-06T21:59:00Z-1643383

text: house mouse

text: Mus musculus

text: mRNA-seq Nextera library

text: Mus musculus


text: Mus Musculus

text: SC

text: public

text: mES_i2m_s1_cell72-sc-2013-06-06T21:59:05Z-1643386

text: house mouse

text: Mus musculus

text: mRNA-seq Nextera library

text: Mus musculus


text: Mus Musculus

text: SC

text: public

text: mES_i2m_s1_cell75-sc-2013-06-06T21:59:10Z-1643389

text: house mouse

text: Mus musculus

text: mRNA-seq Nextera library

text: Mus musculus


text: Mus Musculus

text: SC

text: public

text: mES_i2m_s1_cell78-sc-2013-06-06T21:59:17Z-1643392

text: house mouse

text: Mus musculus

text: mRNA-seq Nextera library

text: Mus musculus


text: Mus Musculus

text: SC

text: public

text: mES_i2m_s1_cell81-sc-2013-06-06T21:59:22Z-1643395

text: house mouse

text: Mus musculus

text: mRNA-seq Nextera library

text: Mus musculus


text: Mus Musculus

text: SC

text: public

text: mES_i2m_s1_cell87-sc-2013-06-06T21:59:36Z-1643401

text: house mouse

text: Mus musculus

text: mRNA-seq Nextera library

text: Mus musculus


text: Mus Musculus

text: SC

text: public

text: mES_i2m_s1_cell90-sc-2013-06-06T21:59:40Z-1643404

text: house mouse

text: Mus musculus

text: mRNA-seq Nextera library

text: Mus musculus


text: Mus Musculus

text: SC

text: public

text: mES_i2m_s1_cell93-sc-2013-06-06T21:59:44Z-1643407

text: house mouse

text: Mus musculus

text: mRNA-seq Nextera library

text: Mus musculus


text: Mus Musculus

text: SC

text: public

text: mES_i2m_s1_cell96-sc-2013-06-06T21:59:48Z-1643410

text: house mouse

text: Mus musculus

text: mRNA-seq Nextera library

text: Mus musculus


text: Anopheles gambiae

text: SC

text: public

text: African malaria mosquito

text: Anopheles gambiae

text: Anopheles gambiae


text: CR-UK Cambridge Institute

text: public

tag: Namespace:CR-UK Cambridge Institute

text: ArrayExpress

characteristic: broker name

characteristic: cell line

text: epithelial

characteristic: cell type

text: human

text: Protocols: The ER-AR+ molecular apocrine breast cancer cell line, MDA-MB-453, was obtained from American Type Culture Collection (ATCC). Cells were grown in DMEM media supplemented with 10% Fetal Bovine Serum, 2 mM L-glutamine, 50U/ml penicillin and 50ug/ml streptomycin in 37oC incubator with 5% CO2. Cells were transfected with 50nM Allstars Negative Control siRNA (Qiagen) using Lipofectamine2000 (Invitrogen). Cells were harvested 48hours after treatment. For all experiments, 1x10^8 cells were cross-linked with 1% formaldehyde as previously described (Schmidt et al, Methods 48(3) July 2009 doi:10.1016/j.ymeth.2009.03.001). ChIP-seq assays were performed as previously described (Schmidt 2009). Protein-bound DNA was immunoprecipitated with antibodies against AR (Santa Cruz, sc-816), AP2alpha (Santa Cruz, sc-12726) or the histone modifications H3K27Ac (Abcam, ab4729) and H3K4me1 (Abcam, 8895). Immunoprecipitated DNA was end-repaired, A-tailed and single-end Illumina sequencing adapters ligated before 18 cycles of PCR amplification. A 2% agarose gel was used to select 200-300 bp DNA fragments.

characteristic: description

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens

text: female

characteristic: sex

text: fresh specimen

characteristic: specimen with known storage state

characteristic: title


text: spleen

characteristic: ArrayExpress-OrganismPart

text: Mus Musculus

characteristic: ArrayExpress-Species

characteristic: External Id

text: SC

characteristic: INSDC center name

text: public

text: Foxp3Mut1_J26_Ctrl-sc-2013-06-07T19:01:50Z-1643507

text: house mouse

characteristic: common name

text: Mus musculus

text: RNA extracted from cells

text: Mus musculus


text: spleen

text: Mus Musculus

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: SC

characteristic: INSDC first public

text: public

text: Foxp3Mut2_J26_Ctrl-sc-2013-06-07T19:01:55Z-1643510

text: house mouse

text: Mus musculus

characteristic: organism

text: RNA extracted from cells

characteristic: sample description

text: Mus musculus


text: Mus musculus

text: SC

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: MD4954f4-sc-2013-06-19T14:26:22Z-1471177

characteristic: Submitter Id

text: house mouse

text: Mus musculus

text: Mus musculus


text: Pancreas

characteristic: ArrayExpress-CellType

characteristic: ArrayExpress-Immunoprecipitate

text: Pancreas

text: Cancer

characteristic: ArrayExpress-Phenotype

text: Mus Musculus

text: SC

text: public

text: Bcl6_C19-sc-2013-06-10T13:41:47Z-1645593

text: house mouse

text: Mus musculus

text: Chromatin IP

text: Mus musculus


text: Pancreas

text: Pancreas

characteristic: ArrayExpress-OrganismPart

text: Cancer

text: Mus Musculus

text: SC

text: public

text: Foxp2_12_2g-sc-2013-06-10T13:41:51Z-1645596

text: house mouse

text: Mus musculus

text: Chromatin IP

text: Mus musculus


text: European Bioinformatics Institute (EBI)

text: public

text: ArrayExpress

characteristic: broker name

characteristic: cell line

text: fruit fly

text: Protocols: S2 cells were grown in Schneiders Media (Invitrogen) supplemented with 10% of heat-inactivated bovine fetal serum to a density of 1 million cells per ml. HITS-CLIP was performed as described in (Chi et al., 2009) with the following modifications: Nuclear extracts prepared from Drosophila S2 cells were used for immunoprecipitations. After high-salt washes, the 3'-ends of bound RNAs were de-phosphorylated first with PNK in MES-PNK buffer (25mM MES at pH 6.0, 50mM NaCl, 10mM MgCl2, 0.1% Tween20, 5mM DTT, NO ATP, 1U/uL PNK [NEB]) by incubating the beads at 37 degrees C for 10 minutes and then with CIP (NEB) before ligation of the 3'-RNA tag. The libraries were prepared following Illumina's TruSeq ChIP sample prep kit (http://www.illumina.com/products/truseq_chip_sample_prep_kit.ilmn)

characteristic: description

text: wild type

characteristic: genotype

text: Drosophila melanogaster

text: Drosophila melanogaster

text: Drosophila melanogaster

text: male

characteristic: sex

text: embryonic cell

characteristic: strain

characteristic: title


text: OMP-GFP +/-

characteristic: ArrayExpress-Genotype

text: MOE

text: Wildtype

text: female

characteristic: ArrayExpress-Sex

text: Mouse

characteristic: ArrayExpress-Species

text: 129 x C57BL/6

characteristic: ArrayExpress-StrainOrLine

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: SC

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: OMP_GFP_MOE-sc-2013-06-05T09:01:57Z-1640347

text: house mouse

characteristic: common name

text: Mus musculus

characteristic: organism

text: RNA from MOE

text: Mus musculus

text: 129 x C57BL/6


text: OMP-GFP +/-

text: MOE

characteristic: ArrayExpress-OrganismPart

text: Wildtype

characteristic: ArrayExpress-Phenotype

text: mixed

text: Mouse

text: 129 x C57BL/6

text: SC

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: OMP_GFP_OSN-sc-2013-06-05T09:02:01Z-1640350

characteristic: Submitter Id

text: house mouse

text: Mus musculus

text: RNA from MOE OSNs

characteristic: sample description

text: Mus musculus

text: 129 x C57BL/6


text: male

characteristic: ArrayExpress-Sex

text: Mus musculus

text: SC

text: public

text: Control_set_1-sc-2013-06-06T20:57:08Z-1643293

text: house mouse

text: Mus musculus

text: PCR products

text: Mus musculus


text: male

text: Mus musculus

characteristic: ArrayExpress-Species

text: SC

text: public

text: JM8_5_clone4-sc-2013-06-06T20:58:28Z-1643298

text: house mouse

text: Mus musculus

text: PCR products

text: Mus musculus


text: male

text: Mus musculus

text: SC

text: public

text: JM8_5_clone8-sc-2013-06-06T21:03:02Z-1643302

text: house mouse

text: Mus musculus

text: PCR products

text: Mus musculus


text: male

text: Mus musculus

text: SC

text: public

text: JM8_8_clone2-sc-2013-06-06T21:04:41Z-1643306

text: house mouse

text: Mus musculus

text: PCR products

text: Mus musculus


text: male

text: Mus musculus

text: SC

text: public

text: JM8_8_clone7-sc-2013-06-06T21:07:51Z-1643311

text: house mouse

text: Mus musculus

text: PCR products

text: Mus musculus


text: male

text: Mus musculus

text: SC

text: public

text: JM8_8_clone10-sc-2013-06-06T21:11:20Z-1643314

text: house mouse

text: Mus musculus

text: PCR products

text: Mus musculus


text: Mus Musculus

text: SC

text: public

text: mES_i2m_s1_cell3-sc-2013-06-06T21:57:06Z-1643317

text: house mouse

text: Mus musculus

text: mRNA-seq Nextera library

text: Mus musculus


text: Mus Musculus

text: SC

text: public

text: mES_i2m_s1_cell6-sc-2013-06-06T21:57:11Z-1643320

text: house mouse

text: Mus musculus

text: mRNA-seq Nextera library

text: Mus musculus


text: Mus Musculus

text: SC

text: public

text: mES_i2m_s1_cell9-sc-2013-06-06T21:57:16Z-1643323

text: house mouse

text: Mus musculus

text: mRNA-seq Nextera library

text: Mus musculus


text: Mus Musculus

text: SC

text: public

text: mES_i2m_s1_cell12-sc-2013-06-06T21:57:21Z-1643326

text: house mouse

text: Mus musculus

text: mRNA-seq Nextera library

text: Mus musculus


text: Mus Musculus

text: SC

text: public

text: mES_i2m_s1_cell15-sc-2013-06-06T21:57:27Z-1643329

text: house mouse

text: Mus musculus

text: mRNA-seq Nextera library

text: Mus musculus


text: Mus Musculus

text: SC

text: public

text: mES_i2m_s1_cell18-sc-2013-06-06T21:57:31Z-1643332

text: house mouse

text: Mus musculus

text: mRNA-seq Nextera library

text: Mus musculus


text: Mus Musculus

text: SC

text: public

text: mES_i2m_s1_cell21-sc-2013-06-06T21:57:36Z-1643335

text: house mouse

text: Mus musculus

text: mRNA-seq Nextera library

text: Mus musculus


text: Mus Musculus

text: SC

text: public

text: mES_i2m_s1_cell24-sc-2013-06-06T21:57:40Z-1643338

text: house mouse

text: Mus musculus

text: mRNA-seq Nextera library

text: Mus musculus


text: Mus Musculus

text: SC

text: public

text: mES_i2m_s1_cell27-sc-2013-06-06T21:57:46Z-1643341

text: house mouse

text: Mus musculus

text: mRNA-seq Nextera library

text: Mus musculus


text: Mus Musculus

text: SC

text: public

text: mES_i2m_s1_cell30-sc-2013-06-06T21:57:51Z-1643344

text: house mouse

text: Mus musculus

text: mRNA-seq Nextera library

text: Mus musculus


text: Mus Musculus

text: SC

text: public

text: mES_i2m_s1_cell33-sc-2013-06-06T21:57:56Z-1643347

text: house mouse

text: Mus musculus

text: mRNA-seq Nextera library

text: Mus musculus


text: Mus Musculus

text: SC

text: public

text: mES_i2m_s1_cell36-sc-2013-06-06T21:58:01Z-1643350

text: house mouse

text: Mus musculus

text: mRNA-seq Nextera library

text: Mus musculus


text: public

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

text: ArrayExpress

characteristic: broker name

text: bread wheat

characteristic: cultivar

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

characteristic: description

text: anthesis

characteristic: developmental stage

text: mock inoculation

characteristic: infect

text: Triticum aestivum

text: Triticum aestivum

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

characteristic: organism part

text: Triticum aestivum

text: frozen specimen

characteristic: specimen with known storage state

characteristic: title


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

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

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: ArrayExpress

text: bread wheat

characteristic: common name

text: anthesis

text: Fusarium graminearum inoculation

text: Triticum aestivum

characteristic: organism

text: Triticum aestivum

text: Triticum aestivum

text: frozen specimen


text: Plasmodium falciparum

characteristic: ENA-CHECKLIST

text: SC

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: malaria parasite P. falciparum

text: Plasmodium falciparum

text: Plasmodium falciparum


text: University College London

text: public

tag: Namespace:University College London

text: ArrayExpress

characteristic: broker name

text: HEKn

characteristic: cell line

text: keratinocyte

characteristic: cell type

text: human

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

characteristic: description

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens

text: fresh specimen


text: SRA-Webin

characteristic: ENA-SUBMISSION-TOOL

text: ISB-USA

text: public

text: baker's yeast

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

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

characteristic: title


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: public

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

text: ArrayExpress

text: human

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

text: adult

characteristic: developmental stage

characteristic: individual

text: Homo sapiens

text: Homo sapiens

text: colon

characteristic: organism part

text: Homo sapiens

text: frozen specimen

characteristic: specimen with known storage state


characteristic: ENA-CHECKLIST

characteristic: External Id

text: Science for Life Laboratory, Stockholm, Sweden

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: ArrayExpress

text: human

characteristic: common name

text: adult

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: lung

text: Homo sapiens

text: frozen specimen


text: Mouse

characteristic: ArrayExpress-Species

text: SC

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: SC_HUWE5569741-sc-2013-07-16T08:26:38Z-1667119

characteristic: Submitter Id

text: house mouse

text: Mus musculus

text: Mus musculus


characteristic: ENA-FIRST-PUBLIC

text: public

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

text: ArrayExpress

characteristic: broker name

text: apple

text: Protocols: Plant material comprised young Malus x domestica (Borkh.) cv. Golden Delicious saplings grafted on M9T337 rootstock. Plants were kept in active growth with a 16h/8h (day/night) photoperiod and a minimum of 65.5 umol m-2 s-1 light intensity provided with white fluorescent lamps (Philips Master TL-D 36W/830) and fertilized once with Obstdunger 12:8:16:2:0.2 (N:P:K:Mg:B; OBA-Lanze, Hauert AG, Switzerland) one week prior the start of the experiment. Plants were grown under greenhouse condition at 20 +/- degrees C and 70% RH until 10 to 15 leaves stadium. Rape-seed oil (Maag AG, Switzerland) mixed with Alaxon 50 (Maag AG, Switzerland) and two weeks later Vertimec (Maag AG, Switzerland) have been used as chemical treatment before starting the experiment to keep plants free of pest-insects. For inoculation, conidia of Venturia inaequalis (Cooke) single spore isolate no. 1639 were used.Inoculation, with a spore suspension of 5 x 105 spores ml-1, was performed at 17 +/- 2 degrees C and >98% RH. . Half of the plants were challenged with the apple scab pathogen and half were mock inoculated. After the treatment (scab or mock inoculation), plants were grown at 17 +/- 2 degrees C and 70% RH until sampling. The first sets of samples have been collected 72 hours post inoculation (hpi). The second sets of samples have been collected at 96 hpi. Samples have been collected from leaf 1 (L1) and leaf 7 (L7) by removing the leaf tip (< 100 mg) of each leaf in three biological replicates for inoculated and not inoculated shoots, 12 samples for each time points (72 and 96 hpi), 24 in total. Total RNA was extracted using SV Total RNA Isolation System (Promega Corporation, USA) with column purification Complementary DNA (cDNA) libraries were constructed, starting from 1 ug of total RNA, at the Functional Genomic Center Zurich (FGCZ) following the TruSeq RNA Sample preparation protocol v. 2 instructions (Low Throughput protocol, Illumina, Inc.).

characteristic: description

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

text: inoculated with Venturia inaequalis

characteristic: infect

text: Malus domestica

text: Malus domestica

text: leaf

text: Malus domestica

text: fresh specimen

text: 17 +/- 2 degree celsius

characteristic: temperature

text: 72 hour

characteristic: time post inoculation

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-LAST-UPDATE

characteristic: External Id

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

text: public

text: ArrayExpress

text: apple

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

characteristic: developmental stage

text: inoculated with Venturia inaequalis

text: Malus domestica

text: Malus domestica

text: leaf

characteristic: organism part

text: Malus domestica

text: fresh specimen

characteristic: specimen with known storage state

text: 17 +/- 2 degree celsius

text: 96 hour


text: male

characteristic: ArrayExpress-Sex

text: Mus musculus

characteristic: ArrayExpress-Species

text: SC

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: 6TGR_3_2-sc-2013-06-26T16:19:50Z-1654037

text: house mouse

characteristic: common name

text: Mus musculus

characteristic: organism

text: PCR products

characteristic: sample description

text: Mus musculus


text: Danio rerio

characteristic: ENA-FIRST-PUBLIC

text: SC

text: public

characteristic: INSDC status

characteristic: SRA accession

text: CH73_346J6-sc-2013-07-05T13:38:43Z-1660473

characteristic: Submitter Id

text: zebrafish

text: Danio rerio

text: Danio rerio


characteristic: ENA-CHECKLIST

characteristic: ENA-LAST-UPDATE

text: public

text: ArrayExpress

characteristic: broker name

text: apple

characteristic: description

text: mock inoculation

characteristic: infect

text: Malus domestica

text: Malus domestica

text: leaf

text: Malus domestica

text: fresh specimen

text: 17 +/- 2 degree celsius

characteristic: temperature

text: 72 hour

characteristic: time post inoculation

characteristic: title


text: Mus Musculus

characteristic: ArrayExpress-Species

characteristic: External Id

text: SC

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: mES_lif_s1_cell10-sc-2013-07-11T08:56:30Z-1661107

text: house mouse

text: Mus musculus

text: mRNA-seq Nextera library

text: Mus musculus


characteristic: INSDC last update

text: public

text: ArrayExpress

text: human

characteristic: common name

text: adult

characteristic: developmental stage

characteristic: individual

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: stomach

characteristic: organism part

text: Homo sapiens

text: frozen specimen

characteristic: specimen with known storage state


text: Danio rerio

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: SC

text: public

characteristic: INSDC status

characteristic: SRA accession

text: CH73_66I11-sc-2013-07-05T13:37:51Z-1660412

characteristic: Submitter Id

text: zebrafish

text: Danio rerio

text: Danio rerio


characteristic: ENA-CHECKLIST

text: public

text: ArrayExpress

characteristic: broker name

text: human

characteristic: description

text: adult

text: Homo sapiens

text: Homo sapiens

text: appendix

text: Homo sapiens

text: frozen specimen

characteristic: title


text: Danio rerio

characteristic: ArrayExpress-Species

characteristic: External Id

text: SC

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: CH1073_472N9-sc-2013-07-05T13:36:50Z-1660346

text: zebrafish

text: Danio rerio

text: Danio rerio


characteristic: INSDC last update

text: public

text: ArrayExpress

text: human

characteristic: common name

text: adult

characteristic: developmental stage

characteristic: individual

text: Homo sapiens

text: Homo sapiens

text: adipose tissue

text: Homo sapiens

text: frozen specimen


characteristic: ENA-FIRST-PUBLIC

text: public

tag: Namespace:Max Planck Institute, Department of Genetics

text: ArrayExpress

text: house mouse

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

text: adult

text: domestic animal house

characteristic: environmental history

text: Mus musculus

characteristic: organism

text: Mus musculus

text: liver

characteristic: organism part

text: Mus musculus

text: fresh specimen

characteristic: specimen with known storage state

characteristic: strain


text: Danio rerio

characteristic: ENA-LAST-UPDATE

text: SC

text: public

characteristic: INSDC status

characteristic: SRA accession

text: CH1073_573O10-sc-2013-07-05T13:37:13Z-1660370

characteristic: Submitter Id

text: zebrafish

text: Danio rerio

text: Danio rerio


text: Danio rerio

characteristic: ArrayExpress-Species

characteristic: External Id

text: SC

text: public

text: CH73_358G1-sc-2013-07-05T13:37:56Z-1660418

text: zebrafish

text: Danio rerio

text: Danio rerio


text: Plasmodium falciparum

characteristic: ENA-CHECKLIST

text: SC

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: malaria parasite P. falciparum

text: Plasmodium falciparum

text: Plasmodium falciparum


text: SRA-Webin

characteristic: ENA-SUBMISSION-TOOL

text: ISB-USA

characteristic: INSDC last update

text: public

text: baker's yeast

characteristic: common name

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

characteristic: title


text: Mus Musculus

characteristic: ENA-FIRST-PUBLIC

text: SC

text: public

text: mES_lif_s1_cell31-sc-2013-07-11T08:56:51Z-1661128

text: house mouse

text: Mus musculus

characteristic: organism

text: mRNA-seq Nextera library

characteristic: sample description

text: Mus musculus


E-MTAB-1746:Mutant 2

text: University of Dublin, Trinity College

text: public

text: E-MTAB-1746:Mutant 2

tag: Namespace:University of Dublin, Trinity College

text: ArrayExpress

characteristic: broker name

text: house mouse

text: Protocols: Heterozygous matings of Splotch-delayed mice were harvested at E14.5 (TS23) Splotch-delayed homozogous mutant and control (homozygous wild-type and heterozygote) embryos were dissected and Humerus forelimb tissue was dissected at embronic day 14.5 (Theiler Stage 23) RNA was extracted following manufacturers guidlines ( SV. Total RNA Isolation system, Promega, UK) The DNase-treated RNA (3ug) was used to prepare RNA-Seq libraries with the TruSeq RNA Sample Prep kit. A total of six cDNA libraries were constructed, representing triplicate biological replicates for each group.

characteristic: description

text: Theiler stage 23

characteristic: developmental stage

text: Splotch-delayed (Pax3Spd/Spd)

characteristic: genotype

text: Mus musculus

text: Mus musculus

text: humerus

characteristic: organism part

text: Mus musculus

text: Mutant 2


text: Danio rerio

characteristic: ArrayExpress-Species

characteristic: ENA-LAST-UPDATE

text: SC

text: public

characteristic: INSDC status

characteristic: SRA accession

text: CH73_305K11-sc-2013-07-05T13:39:04Z-1660495

characteristic: Submitter Id

text: zebrafish

text: Danio rerio

text: Danio rerio


text: Danio rerio

characteristic: External Id

text: SC

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: zFOS_827H5-sc-2013-07-05T13:36:46Z-1660342

text: zebrafish

text: Danio rerio

text: Danio rerio


text: Mus Musculus

characteristic: ENA-CHECKLIST

text: SC

characteristic: INSDC last update

text: public

text: mES_lif_s1_cell54-sc-2013-07-11T08:57:14Z-1661151

text: house mouse

characteristic: common name

text: Mus musculus

text: mRNA-seq Nextera library

text: Mus musculus


characteristic: ENA-FIRST-PUBLIC

text: Science for Life Laboratory, Stockholm, Sweden

text: public

text: ArrayExpress

text: human

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

text: adult

characteristic: individual

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: placenta

text: Homo sapiens

text: frozen specimen

characteristic: specimen with known storage state

characteristic: title


E-MTAB-1746:Mutant 3

text: University of Dublin, Trinity College

text: public

text: E-MTAB-1746:Mutant 3

text: ArrayExpress

characteristic: broker name

text: house mouse

characteristic: description

text: Theiler stage 23

characteristic: developmental stage

text: Splotch-delayed (Pax3Spd/Spd)

characteristic: genotype

text: Mus musculus

text: Mus musculus

text: humerus

characteristic: organism part

text: Mus musculus

text: Mutant 3


text: Danio rerio

characteristic: ArrayExpress-Species

characteristic: ENA-LAST-UPDATE

text: SC

text: public

characteristic: INSDC status

characteristic: SRA accession

text: CH1073_392E1-sc-2013-07-05T13:37:12Z-1660369

characteristic: Submitter Id

text: zebrafish

text: Danio rerio

text: Danio rerio


text: Mus Musculus

characteristic: ENA-CHECKLIST

characteristic: External Id

text: SC

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: mES_lif_s1_cell38-sc-2013-07-11T08:56:57Z-1661135

text: house mouse

text: Mus musculus

text: mRNA-seq Nextera library

characteristic: sample description

text: Mus musculus


characteristic: ENA-FIRST-PUBLIC

text: University College London

text: public

text: ArrayExpress

text: HEKn

characteristic: cell line

text: keratinocyte

characteristic: cell type

text: human

characteristic: common name

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

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: Homo sapiens

text: fresh specimen

characteristic: specimen with known storage state

characteristic: title


E-MTAB-1754:EpiSC (XY)

characteristic: ENA-LAST-UPDATE

text: The Babraham Institute

text: public

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

tag: Namespace:The Babraham Institute

text: ArrayExpress

characteristic: broker name

text: epiblast stem cell

text: house mouse

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

characteristic: description

text: XY

characteristic: karyotype

text: Mus musculus

text: Mus musculus

text: Mus musculus

text: fresh specimen

text: EpiSC (XY)


characteristic: ENA-CHECKLIST

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

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: ArrayExpress

text: apple

text: Protocols: Plant material comprised young Malus x domestica (Borkh.) cv. Golden Delicious saplings grafted on M9T337 rootstock. Plants were kept in active growth with a 16h/8h (day/night) photoperiod and a minimum of 65.5 umol m-2 s-1 light intensity provided with white fluorescent lamps (Philips Master TL-D 36W/830) and fertilized once with Obstdunger 12:8:16:2:0.2 (N:P:K:Mg:B; OBA-Lanze, Hauert AG, Switzerland) one week prior the start of the experiment. Plants were grown under greenhouse condition at 20 +/- degrees C and 70% RH until 10 to 15 leaves stadium. Rape-seed oil (Maag AG, Switzerland) mixed with Alaxon 50 (Maag AG, Switzerland) and two weeks later Vertimec (Maag AG, Switzerland) have been used as chemical treatment before starting the experiment to keep plants free of pest-insects. For inoculation, conidia of Venturia inaequalis (Cooke) single spore isolate no. 1639 were used.Inoculation, with a spore suspension of 5 x 105 spores ml-1, was performed at 17 +/- 2 degrees C and >98% RH. . Half of the plants were challenged with the apple scab pathogen and half were mock inoculated. After the treatment (scab or mock inoculation), plants were grown at 17 +/- 2 degrees C and 70% RH until sampling. The first sets of samples have been collected 72 hours post inoculation (hpi). The second sets of samples have been collected at 96 hpi. Samples have been collected from leaf 1 (L1) and leaf 7 (L7) by removing the leaf tip (< 100 mg) of each leaf in three biological replicates for inoculated and not inoculated shoots, 12 samples for each time points (72 and 96 hpi), 24 in total. Total RNA was extracted using SV Total RNA Isolation System (Promega Corporation, USA) with column purification Complementary DNA (cDNA) libraries were constructed, starting from 1 ug of total RNA, at the Functional Genomic Center Zurich (FGCZ) following the TruSeq RNA Sample preparation protocol v. 2 instructions (Low Throughput protocol, Illumina, Inc.).

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

characteristic: developmental stage

text: mock inoculation

characteristic: infect

text: Malus domestica

text: Malus domestica

text: leaf

characteristic: organism part

text: Malus domestica

text: fresh specimen

text: 17 +/- 2 degree celsius

characteristic: temperature

text: 72 hour

characteristic: time post inoculation


text: Danio rerio

characteristic: ArrayExpress-Species

characteristic: ENA-FIRST-PUBLIC

characteristic: External Id

text: SC

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: zFOS_896C12-sc-2013-07-05T13:37:01Z-1660358

text: zebrafish

characteristic: common name

text: Danio rerio

text: Danio rerio


characteristic: ENA-LAST-UPDATE

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

text: public

text: ArrayExpress

characteristic: broker name

text: bread wheat

characteristic: cultivar

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

characteristic: description

text: anthesis

text: mock inoculation

text: Triticum aestivum

characteristic: organism

text: Triticum aestivum

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

text: Triticum aestivum

text: frozen specimen

characteristic: specimen with known storage state

characteristic: title


text: Mus Musculus

characteristic: ENA-CHECKLIST

text: SC

text: public

characteristic: INSDC status

characteristic: SRA accession

text: mES_lif_s1_cell20-sc-2013-07-11T08:56:40Z-1661117

characteristic: Submitter Id

text: house mouse

text: Mus musculus

text: mRNA-seq Nextera library

characteristic: sample description

text: Mus musculus


text: Danio rerio

characteristic: ArrayExpress-Species

characteristic: ENA-FIRST-PUBLIC

characteristic: External Id

text: SC

text: public

text: zFOS_1410B11-sc-2013-07-05T13:36:38Z-1660333

text: zebrafish

text: Danio rerio

text: Danio rerio


text: Plasmodium falciparum

text: SC

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: malaria parasite P. falciparum

text: Plasmodium falciparum

text: Plasmodium falciparum


text: Danio rerio

characteristic: ENA-LAST-UPDATE

text: SC

text: public

text: CH1073_422A21-sc-2013-07-05T13:37:40Z-1660401

text: zebrafish

characteristic: common name

text: Danio rerio

text: Danio rerio


text: SRA-Webin

characteristic: ENA-SUBMISSION-TOOL

text: ISB-USA

text: public

text: baker's yeast

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

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


text: Mus Musculus

text: SC

text: public

text: mES_lif_s1_cell35-sc-2013-07-11T08:56:55Z-1661132

text: house mouse

text: Mus musculus

characteristic: organism

text: mRNA-seq Nextera library

text: Mus musculus


text: Danio rerio

text: SC

text: public

text: CH1073_151C21-sc-2013-07-05T13:36:24Z-1660319

text: zebrafish

text: Danio rerio

text: Danio rerio


text: male

characteristic: ArrayExpress-Sex

text: Mus musculus

text: SC

text: public

text: 6TGR_3_3-sc-2013-06-26T16:20:20Z-1654038

text: house mouse

text: Mus musculus

text: PCR products

text: Mus musculus


text: Danio rerio

text: SC

text: public

text: CH1073_20K9-sc-2013-07-05T13:38:47Z-1660478

text: zebrafish

text: Danio rerio

text: Danio rerio


text: Danio rerio

text: SC

text: public

text: CH73_345G4-sc-2013-07-05T13:38:36Z-1660465

text: zebrafish

text: Danio rerio

text: Danio rerio


text: Danio rerio

text: SC

text: public

text: zFOS_1286A4-sc-2013-07-05T13:36:22Z-1660317

text: zebrafish

text: Danio rerio

text: Danio rerio


text: public

tag: Namespace:Cancer Research UK, Cambridge Research Institute, Robinson Way, Cambridge, UK

text: 2 to 6 month

characteristic: age

text: ArrayExpress

characteristic: broker name

text: house mouse

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

characteristic: description

text: adult

characteristic: developmental stage

characteristic: genotype

characteristic: individual

text: Mus musculus

text: Mus musculus

text: liver

characteristic: organism part

text: Mus musculus

text: male

characteristic: sex

characteristic: title


text: Danio rerio

characteristic: ArrayExpress-Species

characteristic: ENA-FIRST-PUBLIC

characteristic: External Id

text: SC

characteristic: INSDC center name

text: public

characteristic: INSDC status

characteristic: SRA accession

text: CH1073_118G16-sc-2013-07-05T13:37:37Z-1660398

characteristic: Submitter Id

text: zebrafish

text: Danio rerio

text: Danio rerio


text: Danio rerio

characteristic: ENA-LAST-UPDATE

text: SC

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: CH1073_140I5-sc-2013-07-05T13:37:44Z-1660406

text: zebrafish

characteristic: common name

text: Danio rerio

characteristic: organism

text: Danio rerio


text: Mus Musculus

characteristic: ENA-CHECKLIST

text: SC

text: public

text: mES_lif_s1_cell2-sc-2013-07-11T08:56:21Z-1661099

text: house mouse

text: Mus musculus

text: mRNA-seq Nextera library

characteristic: sample description

text: Mus musculus


text: Glia

characteristic: ArrayExpress-CellType

text: Adult

characteristic: ArrayExpress-DevelopmentalStage

text: MeCP2 GFP tagged

characteristic: ArrayExpress-Genotype

text: Chromotek GFP trap Agarose

characteristic: ArrayExpress-Immunoprecipitate

text: Brain

characteristic: ArrayExpress-OrganismPart

text: wildtype

characteristic: ArrayExpress-Phenotype

text: male

characteristic: ArrayExpress-Sex

text: Mus musculus

text: Bl6 MeCP2 GFP

characteristic: ArrayExpress-StrainOrLine

text: SC

text: public

text: m_Input_G1-sc-2013-07-18T13:26:46Z-1669278

text: house mouse

text: Mus musculus

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

text: Mus musculus

text: Bl6 MeCP2 GFP

characteristic: strain


text: adult

text: female

text: Dracunculus medinensis

characteristic: ArrayExpress-Species

characteristic: ENA-FIRST-PUBLIC

characteristic: External Id

text: SC

characteristic: INSDC center name

text: public

characteristic: INSDC status

characteristic: SRA accession

text: Dracunculus_medinensis-sc-2013-07-15T15:11:13Z-1667991

characteristic: Submitter Id

text: Guinea worm

text: Dracunculus medinensis

text: section of adult female worm

text: Dracunculus medinensis


text: Danio rerio

characteristic: ENA-LAST-UPDATE

text: SC

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: CH1073_109I6-sc-2013-07-05T13:38:39Z-1660469

text: zebrafish

characteristic: common name

text: Danio rerio

characteristic: organism

text: Danio rerio


text: University College London

text: public

text: ArrayExpress

characteristic: broker name

text: HEKn

characteristic: cell line

text: keratinocyte

characteristic: cell type

text: human

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

characteristic: description

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens

text: fresh specimen

characteristic: specimen with known storage state

characteristic: title