characteristic: ENA-FIRST-PUBLIC

characteristic: External Id

text: Imperial College London

text: public

text: 12 to 14 week

text: ArrayExpress

text: house mouse

text: INS1-Cre_AMPK_WT_3 Protocols: Pancreatic islets (50-100) were extracted from Ins1LKB1KO mice or Ins1AMPKdKO and their wild type controls aging 12-14 weeks by pancreatic distension and digestion with collagenase. Islets were incubated in RPMI media containing 11 mM glucose, 10% FCS, 100 IU/mL penicillin, 100 ug/mL streptomycin, at 5% CO2 and 37 C for 24 h. RNA was extracted using RNAeasy kit according to the manufacturer's instructions (Qiagen) All libraries were prepared using the TruSeq RNA Sample Preparation Kits v2 (Illumina, San Diego, CA USA) according to the manufacturer's instructions. In brief, magnetic beads containing poly-dT molecules were first used to purify mRNA from 250 ng of total RNA. Second, samples were chemically fragmented and reverse transcribed into cDNA. Finally, end repair and A-base tailing was performed before Illumina adapters were ligated to the cDNA fragments. Purified samples were amplified by 15-cycle PCR. Amplified material was validated and quantified using an Agilent 2100 bioanalyzer and the DNA 1000 Nano Chip Kit (Agilent, Technologies, Santa Clara, CA, USA).

text: gene knock out

characteristic: genetic modification

text: floxed AMPK without Ins1-Cre

characteristic: genotype

text: Mus musculus

text: Mus musculus

text: islet of Langerhans

text: wild type

text: Mus musculus

characteristic: title


status: PUBLIC

tag: attribute

characteristic: ENA-CHECKLIST

characteristic: ENA-LAST-UPDATE

text: Imperial College London

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

tag: Namespace:Imperial College London

characteristic: Submitter Id

text: 12 to 14 week

characteristic: age

text: ArrayExpress

characteristic: broker name

text: house mouse

characteristic: common name

text: RIP-Cre_AMPK_dKO_1 Protocols: Pancreatic islets (50-100) were extracted from Ins1LKB1KO mice or Ins1AMPKdKO and their wild type controls aging 12-14 weeks by pancreatic distension and digestion with collagenase. Islets were incubated in RPMI media containing 11 mM glucose, 10% FCS, 100 IU/mL penicillin, 100 ug/mL streptomycin, at 5% CO2 and 37 C for 24 h. RNA was extracted using RNAeasy kit according to the manufacturer's instructions (Qiagen) All libraries were prepared using the TruSeq RNA Sample Preparation Kits v2 (Illumina, San Diego, CA USA) according to the manufacturer's instructions. In brief, magnetic beads containing poly-dT molecules were first used to purify mRNA from 250 ng of total RNA. Second, samples were chemically fragmented and reverse transcribed into cDNA. Finally, end repair and A-base tailing was performed before Illumina adapters were ligated to the cDNA fragments. Purified samples were amplified by 15-cycle PCR. Amplified material was validated and quantified using an Agilent 2100 bioanalyzer and the DNA 1000 Nano Chip Kit (Agilent, Technologies, Santa Clara, CA, USA).

characteristic: description

text: gene knock out

text: floxed AMPK alpha 1 and 2 with RIP-Cre

text: Mus musculus

characteristic: organism

text: Mus musculus

text: islet of Langerhans

characteristic: organism part

text: AMPK double knockout

characteristic: phenotype

text: Mus musculus

characteristic: strain

type: has member


characteristic: ENA-FIRST-PUBLIC

characteristic: External Id

text: Imperial College London

text: public

text: 12 to 14 week

text: ArrayExpress

text: house mouse

text: INS1-Cre_LKB1_WT_2 Protocols: Pancreatic islets (50-100) were extracted from Ins1LKB1KO mice or Ins1AMPKdKO and their wild type controls aging 12-14 weeks by pancreatic distension and digestion with collagenase. Islets were incubated in RPMI media containing 11 mM glucose, 10% FCS, 100 IU/mL penicillin, 100 ug/mL streptomycin, at 5% CO2 and 37 C for 24 h. RNA was extracted using RNAeasy kit according to the manufacturer's instructions (Qiagen) All libraries were prepared using the TruSeq RNA Sample Preparation Kits v2 (Illumina, San Diego, CA USA) according to the manufacturer's instructions. In brief, magnetic beads containing poly-dT molecules were first used to purify mRNA from 250 ng of total RNA. Second, samples were chemically fragmented and reverse transcribed into cDNA. Finally, end repair and A-base tailing was performed before Illumina adapters were ligated to the cDNA fragments. Purified samples were amplified by 15-cycle PCR. Amplified material was validated and quantified using an Agilent 2100 bioanalyzer and the DNA 1000 Nano Chip Kit (Agilent, Technologies, Santa Clara, CA, USA).

text: gene knock out

characteristic: genetic modification

text: floxed LKB1 without Ins1-Cre

characteristic: genotype

text: Mus musculus

text: Mus musculus

text: islet of Langerhans

text: wild type

text: Mus musculus

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-LAST-UPDATE

text: Imperial College London

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: 12 to 14 week

text: ArrayExpress

text: house mouse

text: INS1-Cre_LKB1_KO_4 Protocols: Pancreatic islets (50-100) were extracted from Ins1LKB1KO mice or Ins1AMPKdKO and their wild type controls aging 12-14 weeks by pancreatic distension and digestion with collagenase. Islets were incubated in RPMI media containing 11 mM glucose, 10% FCS, 100 IU/mL penicillin, 100 ug/mL streptomycin, at 5% CO2 and 37 C for 24 h. RNA was extracted using RNAeasy kit according to the manufacturer's instructions (Qiagen) All libraries were prepared using the TruSeq RNA Sample Preparation Kits v2 (Illumina, San Diego, CA USA) according to the manufacturer's instructions. In brief, magnetic beads containing poly-dT molecules were first used to purify mRNA from 250 ng of total RNA. Second, samples were chemically fragmented and reverse transcribed into cDNA. Finally, end repair and A-base tailing was performed before Illumina adapters were ligated to the cDNA fragments. Purified samples were amplified by 15-cycle PCR. Amplified material was validated and quantified using an Agilent 2100 bioanalyzer and the DNA 1000 Nano Chip Kit (Agilent, Technologies, Santa Clara, CA, USA).

text: gene knock out

text: floxed LKB1 with Ins1-Cre

text: Mus musculus

text: Mus musculus

text: islet of Langerhans

text: LKB1 knockout

text: Mus musculus


text: Imperial College London

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: 12 to 14 week

characteristic: age

text: ArrayExpress

characteristic: broker name

text: house mouse

text: INS1-Cre_AMPK_WT_5 Protocols: Pancreatic islets (50-100) were extracted from Ins1LKB1KO mice or Ins1AMPKdKO and their wild type controls aging 12-14 weeks by pancreatic distension and digestion with collagenase. Islets were incubated in RPMI media containing 11 mM glucose, 10% FCS, 100 IU/mL penicillin, 100 ug/mL streptomycin, at 5% CO2 and 37 C for 24 h. RNA was extracted using RNAeasy kit according to the manufacturer's instructions (Qiagen) All libraries were prepared using the TruSeq RNA Sample Preparation Kits v2 (Illumina, San Diego, CA USA) according to the manufacturer's instructions. In brief, magnetic beads containing poly-dT molecules were first used to purify mRNA from 250 ng of total RNA. Second, samples were chemically fragmented and reverse transcribed into cDNA. Finally, end repair and A-base tailing was performed before Illumina adapters were ligated to the cDNA fragments. Purified samples were amplified by 15-cycle PCR. Amplified material was validated and quantified using an Agilent 2100 bioanalyzer and the DNA 1000 Nano Chip Kit (Agilent, Technologies, Santa Clara, CA, USA).

text: gene knock out

text: floxed AMPK without Ins1-Cre

text: Mus musculus

text: Mus musculus

text: islet of Langerhans

text: wild type

text: Mus musculus


text: Imperial College London

text: public

text: 12 to 14 week

text: ArrayExpress

text: house mouse

characteristic: common name

text: INS1-Cre_LKB1_WT_4 Protocols: Pancreatic islets (50-100) were extracted from Ins1LKB1KO mice or Ins1AMPKdKO and their wild type controls aging 12-14 weeks by pancreatic distension and digestion with collagenase. Islets were incubated in RPMI media containing 11 mM glucose, 10% FCS, 100 IU/mL penicillin, 100 ug/mL streptomycin, at 5% CO2 and 37 C for 24 h. RNA was extracted using RNAeasy kit according to the manufacturer's instructions (Qiagen) All libraries were prepared using the TruSeq RNA Sample Preparation Kits v2 (Illumina, San Diego, CA USA) according to the manufacturer's instructions. In brief, magnetic beads containing poly-dT molecules were first used to purify mRNA from 250 ng of total RNA. Second, samples were chemically fragmented and reverse transcribed into cDNA. Finally, end repair and A-base tailing was performed before Illumina adapters were ligated to the cDNA fragments. Purified samples were amplified by 15-cycle PCR. Amplified material was validated and quantified using an Agilent 2100 bioanalyzer and the DNA 1000 Nano Chip Kit (Agilent, Technologies, Santa Clara, CA, USA).

characteristic: description

text: gene knock out

text: floxed LKB1 without Ins1-Cre

text: Mus musculus

characteristic: organism

text: Mus musculus

text: islet of Langerhans

characteristic: organism part

text: wild type

characteristic: phenotype

text: Mus musculus


characteristic: ENA-FIRST-PUBLIC

characteristic: External Id

text: Imperial College London

text: public

text: 12 to 14 week

text: ArrayExpress

text: house mouse

text: INS1-Cre_LKB1_WT_5 Protocols: Pancreatic islets (50-100) were extracted from Ins1LKB1KO mice or Ins1AMPKdKO and their wild type controls aging 12-14 weeks by pancreatic distension and digestion with collagenase. Islets were incubated in RPMI media containing 11 mM glucose, 10% FCS, 100 IU/mL penicillin, 100 ug/mL streptomycin, at 5% CO2 and 37 C for 24 h. RNA was extracted using RNAeasy kit according to the manufacturer's instructions (Qiagen) All libraries were prepared using the TruSeq RNA Sample Preparation Kits v2 (Illumina, San Diego, CA USA) according to the manufacturer's instructions. In brief, magnetic beads containing poly-dT molecules were first used to purify mRNA from 250 ng of total RNA. Second, samples were chemically fragmented and reverse transcribed into cDNA. Finally, end repair and A-base tailing was performed before Illumina adapters were ligated to the cDNA fragments. Purified samples were amplified by 15-cycle PCR. Amplified material was validated and quantified using an Agilent 2100 bioanalyzer and the DNA 1000 Nano Chip Kit (Agilent, Technologies, Santa Clara, CA, USA).

text: gene knock out

characteristic: genetic modification

text: floxed LKB1 without Ins1-Cre

characteristic: genotype

text: Mus musculus

text: Mus musculus

text: islet of Langerhans

text: wild type

text: Mus musculus

characteristic: strain


characteristic: ENA-CHECKLIST

characteristic: ENA-LAST-UPDATE

text: Imperial College London

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: 12 to 14 week

text: ArrayExpress

text: house mouse

text: INS1-Cre_LKB1_KO_2 Protocols: Pancreatic islets (50-100) were extracted from Ins1LKB1KO mice or Ins1AMPKdKO and their wild type controls aging 12-14 weeks by pancreatic distension and digestion with collagenase. Islets were incubated in RPMI media containing 11 mM glucose, 10% FCS, 100 IU/mL penicillin, 100 ug/mL streptomycin, at 5% CO2 and 37 C for 24 h. RNA was extracted using RNAeasy kit according to the manufacturer's instructions (Qiagen) All libraries were prepared using the TruSeq RNA Sample Preparation Kits v2 (Illumina, San Diego, CA USA) according to the manufacturer's instructions. In brief, magnetic beads containing poly-dT molecules were first used to purify mRNA from 250 ng of total RNA. Second, samples were chemically fragmented and reverse transcribed into cDNA. Finally, end repair and A-base tailing was performed before Illumina adapters were ligated to the cDNA fragments. Purified samples were amplified by 15-cycle PCR. Amplified material was validated and quantified using an Agilent 2100 bioanalyzer and the DNA 1000 Nano Chip Kit (Agilent, Technologies, Santa Clara, CA, USA).

text: gene knock out

text: floxed LKB1 with Ins1-Cre

text: Mus musculus

text: Mus musculus

text: islet of Langerhans

text: LKB1 knockout

text: Mus musculus

characteristic: title


text: Danio rerio

characteristic: ArrayExpress-Species

text: SC

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: zebrafish

text: Danio rerio

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

characteristic: sample description

text: Danio rerio


text: mus musculus

text: SC

text: public

text: house mouse

characteristic: common name

text: Mus musculus

characteristic: organism

text: Screen 2 Unstimulated Wild type Embryonic Stem Cell Derived Macrophages 24hr

text: Mus musculus


text: mus musculus

characteristic: ENA-FIRST-PUBLIC

characteristic: External Id

text: SC

text: public

text: house mouse

text: Mus musculus

text: Screen 2 Unstimulated Wild type Embryonic Stem Cell Derived Macrophages 4hr

text: Mus musculus


text: mus musculus

text: SC

text: public

text: house mouse

text: Mus musculus

text: Screen 2 Wild type Embryonic Stem Cell Derived Macrophages stimulated with Influenza 4 hr

text: Mus musculus


text: mus musculus

text: SC

text: public

text: house mouse

text: Mus musculus

text: Screen 2 Wild type Embryonic Stem Cell Derived Macrophages stimulated with Influenza 24 hr

text: Mus musculus


text: mus musculus

text: SC

text: public

text: house mouse

text: Mus musculus

text: Screen 2 Wild type Embryonic Stem Cell Derived Macrophages stimulated with Salmonella

text: Mus musculus


text: mus musculus

text: SC

text: public

text: house mouse

text: Mus musculus

text: Screen 2 Wild type Embryonic Stem Cell Derived Macrophages stimulated with LPS (Toll-like receptor agonist)

text: Mus musculus


text: mus musculus

text: SC

text: public

text: house mouse

text: Mus musculus

text: Screen 2 Wild type Embryonic Stem Cell Derived Macrophages stimulated with Poly I:C (Toll-like receptor agonist)

text: Mus musculus


text: mus musculus

text: SC

text: public

text: house mouse

text: Mus musculus

text: Screen 2 Wild type Embryonic Stem Cell Derived Macrophages stimulated with ODN 1826 (CpG)

text: Mus musculus


text: mus musculus

text: SC

text: public

text: house mouse

text: Mus musculus

text: Screen 2 Wild type Embryonic Stem Cell Derived Macrophages stimulated with M TRI-dap (NOD agonist)

text: Mus musculus


text: mus musculus

text: SC

text: public

text: house mouse

text: Mus musculus

text: Screen 2 Unstimulated IRAK-1 Knock-out Embryonic Stem Cell Derived Macrophages 24hr

text: Mus musculus


text: mus musculus

text: SC

text: public

text: house mouse

text: Mus musculus

text: Screen 2 Unstimulated IRAK-1 Knock-out Embryonic Stem Cell Derived Macrophages 4hr

text: Mus musculus


text: mus musculus

text: SC

text: public

text: house mouse

text: Mus musculus

text: Screen 2 IRAK-1 Knock-out Embryonic Stem Cell Derived Macrophages stimulated with Influenza 4 hr

text: Mus musculus


text: mus musculus

text: SC

text: public

text: house mouse

text: Mus musculus

text: Screen 2 IRAK-1 Knock-out Embryonic Stem Cell Derived Macrophages stimulated with Influenza 24 hr

text: Mus musculus


text: mus musculus

text: SC

text: public

text: house mouse

text: Mus musculus

text: Screen 2 IRAK-1 Knock-out Embryonic Stem Cell Derived Macrophages stimulated with Salmonella

text: Mus musculus


text: mus musculus

text: SC

text: public

text: house mouse

text: Mus musculus

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

text: Mus musculus


text: mus musculus

text: SC

text: public

text: house mouse

text: Mus musculus

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

text: Mus musculus


text: Danio rerio

text: SC

text: public

text: zebrafish

text: Danio rerio

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

text: Danio rerio


text: mus musculus

text: SC

text: public

text: house mouse

text: Mus musculus

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

text: Mus musculus


text: mus musculus

text: SC

text: public

text: house mouse

text: Mus musculus

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

text: Mus musculus


text: mus musculus

text: SC

text: public

text: house mouse

text: Mus musculus

text: Screen 2 Unstimulated BAP1 Knock-out Embryonic Stem Cell Derived Macrophages 24hr

text: Mus musculus


text: mus musculus

text: SC

text: public

text: house mouse

text: Mus musculus

text: Screen 2 Unstimulated BAP1 Knock-out Embryonic Stem Cell Derived Macrophages 4hr

text: Mus musculus


text: mus musculus

text: SC

text: public

text: house mouse

text: Mus musculus

text: Screen 2 BAP1 Knock-out Embryonic Stem Cell Derived Macrophages stimulated with Influenza 4 hr

text: Mus musculus


text: mus musculus

text: SC

text: public

text: house mouse

text: Mus musculus

text: Screen 2 BAP1 Knock-out Embryonic Stem Cell Derived Macrophages stimulated with Influenza 24 hr

text: Mus musculus


text: mus musculus

text: SC

text: public

text: house mouse

text: Mus musculus

text: Screen 2 BAP1 Knock-out Embryonic Stem Cell Derived Macrophages stimulated with Salmonella

text: Mus musculus


text: mus musculus

text: SC

text: public

text: house mouse

text: Mus musculus

text: Screen 2 BAP1 Knock-out Embryonic Stem Cell Derived Macrophages stimulated with LPS (Toll-like receptor agonist)

text: Mus musculus


text: mus musculus

text: SC

text: public

text: house mouse

text: Mus musculus

text: Screen 2 BAP1 Knock-out Embryonic Stem Cell Derived Macrophages stimulated with Poly I:C (Toll-like receptor agonist)

text: Mus musculus


text: mus musculus

text: SC

text: public

text: house mouse

text: Mus musculus

text: Screen 2 BAP1 Knock-out Embryonic Stem Cell Derived Macrophages stimulated with ODN 1826 (CpG)

text: Mus musculus


text: mus musculus

text: SC

text: public

text: house mouse

text: Mus musculus

text: Screen 2 BAP1 Knock-out Embryonic Stem Cell Derived Macrophages stimulated with M TRI-dap (NOD agonist)

text: Mus musculus


text: SCUOLA SUPERIORE SANT'ANNA

text: public

tag: Namespace:SCUOLA SUPERIORE SANT'ANNA

text: stiff brome

text: Brachypodium distachyon

text: Brachypodium distachyon

text: B. distachyon turkish germplasm


text: public

text: E-MTAB-2889:MED_D60_SCC_RNA.140508.HiSeq2000.FCB.lane7.R1.fastq.gz

tag: Namespace:Laboratory of Translational Genetics Vesalius Research Centre, VIB Department of Oncology , KU Leuven

text: ArrayExpress

characteristic: broker name

text: house mouse

text: Protocols: RNA libraries were created using the Illumina TruSeq RNA sample preparation kit V2 according to the manufacturers instructions.

characteristic: description

text: squamous cell carcinoma

characteristic: disease

characteristic: individual

text: Mus musculus

text: Mus musculus

text: Mus musculus


characteristic: ENA-CHECKLIST

characteristic: ENA-LAST-UPDATE

text: Laboratory of Translational Genetics Vesalius Research Centre, VIB Department of Oncology , KU Leuven

characteristic: INSDC center name

text: public

text: E-MTAB-2889:MED_D55_SCC_RNA.140508.HiSeq2000.FCB.lane5.R1.fastq.gz

text: ArrayExpress

text: house mouse

text: squamous cell carcinoma

text: Mus musculus

text: Mus musculus

text: Mus musculus


characteristic: INSDC first public

text: public

text: E-MTAB-2889:MED_D87_SCC_RNA.140508.HiSeq2000.FCB.lane3.R1.fastq.gz

text: ArrayExpress

text: house mouse

text: squamous cell carcinoma

text: Mus musculus

text: Mus musculus

text: Mus musculus

characteristic: title


characteristic: INSDC last update

text: public

characteristic: INSDC status

text: E-MTAB-2889:MED_D64_SCC_RNA.140508.HiSeq2000.FCB.lane2.R1.fastq.gz

text: ArrayExpress

text: house mouse

text: squamous cell carcinoma

text: Mus musculus

text: Mus musculus

text: Mus musculus


text: European Molecular Biology Laboratory

text: public

characteristic: SRA accession

tag: Namespace:European Molecular Biology Laboratory

characteristic: Submitter Id

text: ArrayExpress

characteristic: cell line

text: pluripotent stem cell

characteristic: cell type

text: human

text: Protocols: Cells were cultured in N2B27 medium (Ndiff227, StemCells Inc) supplemented with 1uM PD0325901 (PD03), 1uM CHIR99021 and human or murine LIF (according to species) (t2iL) + 5uM PKC inhibitor Go6983 (Sigma-Aldrich). piggyBac (PB) transposon vectors (2ug) carrying doxycycline-inducible KLF2 or NANOG coupled to Venus were co-transfected with an rtTA expression construct (2ug) and pBase helper plasmid (4ug) using the Neon Transfection System (Program 14; Invitrogen). Two days later, G418 was applied (100ug/ml). After selection for two weeks, Venus-negative cells were isolated by flow cytometry to remove cells with residual transgene expression. To induce resetting, transfected PSC were dissociated with trypsin and replated in the presence of Rho-associated kinase inhibitor (ROCKi) (Y-27632, Calbiochem). Doxycycline (DOX, 1uM) was added the following day and 24h later medium was changed to N2B27 medium (Ndiff227, StemCells Inc) with 1uM PD0325901 (PD03), human LIF (prepared in-house), 3uM CHIR99021 (2iL) or 1uM CHIR99021 (t2iL) and DOX. Medium was changed daily. Cells were split every five to seven days after dissociation with Accutase (Life Technologies). Total RNA was extracted with the TRIzol/chloroform method (Invitrogen), followed by resuspension in RNAsecure (Ambion), incubation with TURBO DNase (Ambion) at 37 C for 1 hour, further phenol/chloroform extraction and ethanol precipitation. RNA integrity was assessed with the RNA 6000 Nano assay on the 2100 Bioanalyzer (Agilent). Ribosomal RNA was depleted from 5ug of total RNA using Ribo-Zero capture probes (Epicentre). RNA samples were sheared by ultrasonication on a Covaris S2 for 90s set at Duty Cycle 10, Cycles per Burst 200 and Intensity 5. Fragmented RNA was reverse-transcribed with a combination of random hexamer and oligo-dT primers (New England Biolabs) by SuperScript III (Invitrogen) at 50 C for 2h in the presence of 6ug/ml actinomycin D (Sigma) to inhibit second-strand products. Second-strand cDNA was synthesized by DNA Polymerase I in the presence of RNase H with dUTPs substituted for dTTPs at 16 C for 2h. Sequential end repair and 3'-adenylation of cDNA products was carried out with T4 DNA polymerase and T4 polynucleotide kinase (20 C), and with exo- Klenow fragment (65 C) in the presence of dATPs (New England BioLabs). These were ligated to barcoded adapters (NEXTflex-96, Bioo Scientific) by T4 DNA ligase (New England BioLabs) at 20 C for 30min. Second-strand DNA was digested with uracil DNA glycosylase (UDG) and Endonuclease VIII at 37 C for 30min. PCR amplification of first-strand library constructs was carried out with KAPA HiFi DNA polymerase (Kapa Biosystems) for 13 cycles. Purification of reaction products at each step was performed with Ampure XP paramagnetic beads (Beckman Coulter). Library size distribution and molarity was assessed by the DNA 1000 assay on the 2100 Bioanalyzer (Agilent).

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens

text: fresh specimen

characteristic: specimen with known storage state


characteristic: ENA-FIRST-PUBLIC

characteristic: External Id

text: European Molecular Biology Laboratory

text: public

text: ArrayExpress

text: embryonic stem cell

text: house mouse

characteristic: common name

text: Protocols: Cells were cultured in N2B27 medium (Ndiff227, StemCells Inc) supplemented with 1uM PD0325901 (PD03), 1uM CHIR99021 and murine LIF (prepared in-house) (t2iL). Total RNA was extracted with the TRIzol/chloroform method (Invitrogen), followed by resuspension in RNAsecure (Ambion), incubation with TURBO DNase (Ambion) at 37 C for 1 hour, further phenol/chloroform extraction and ethanol precipitation. RNA integrity was assessed with the RNA 6000 Nano assay on the 2100 Bioanalyzer (Agilent). Ribosomal RNA was depleted from 5ug of total RNA using Ribo-Zero capture probes (Epicentre). RNA samples were sheared by ultrasonication on a Covaris S2 for 90s set at Duty Cycle 10, Cycles per Burst 200 and Intensity 5. Fragmented RNA was reverse-transcribed with a combination of random hexamer and oligo-dT primers (New England Biolabs) by SuperScript III (Invitrogen) at 50 C for 2h in the presence of 6ug/ml actinomycin D (Sigma) to inhibit second-strand products. Second-strand cDNA was synthesized by DNA Polymerase I in the presence of RNase H with dUTPs substituted for dTTPs at 16 C for 2h. Sequential end repair and 3'-adenylation of cDNA products was carried out with T4 DNA polymerase and T4 polynucleotide kinase (20 C), and with exo- Klenow fragment (65 C) in the presence of dATPs (New England BioLabs). These were ligated to barcoded adapters (NEXTflex-96, Bioo Scientific) by T4 DNA ligase (New England BioLabs) at 20 C for 30min. Second-strand DNA was digested with uracil DNA glycosylase (UDG) and Endonuclease VIII at 37 C for 30min. PCR amplification of first-strand library constructs was carried out with KAPA HiFi DNA polymerase (Kapa Biosystems) for 13 cycles. Purification of reaction products at each step was performed with Ampure XP paramagnetic beads (Beckman Coulter). Library size distribution and molarity was assessed by the DNA 1000 assay on the 2100 Bioanalyzer (Agilent).

text: Mus musculus

characteristic: organism

text: Mus musculus

text: Mus musculus

text: fresh specimen

characteristic: strain


characteristic: ENA-CHECKLIST

text: European Molecular Biology Laboratory

text: public

text: ArrayExpress

characteristic: broker name

text: pluripotent stem cell

text: human

text: Protocols: Conventional human pluripotent stem cell (PSC) medium (FGF/KSR) comprised DMEM/F12 (Sigma-Aldrich) with 10ng/ml bFGF (prepared in-house) and 20% KSR (Invitrogen) supplemented with 100mM 2-mercaptoethanol (Sigma-Aldrich, cat. M7522), MEM non-essential amino acids (Invitrogen, cat. 11140050) and 2 mM L-glutamine (Invitrogen, cat. 25030024). Cultures were passaged every five to seven days as small clumps by dissociation with 0.025% Trypsin, 1mg/ml Collagenase IV (Invitrogen17104-019), KSR (final 20%) and 1mM CaCl2. Cells were maintained on irradiated mouse embryonic fibroblasts (MEF) in 5% O2. Total RNA was extracted with the TRIzol/chloroform method (Invitrogen), followed by resuspension in RNAsecure (Ambion), incubation with TURBO DNase (Ambion) at 37 C for 1 hour, further phenol/chloroform extraction and ethanol precipitation. RNA integrity was assessed with the RNA 6000 Nano assay on the 2100 Bioanalyzer (Agilent). Ribosomal RNA was depleted from 5ug of total RNA using Ribo-Zero capture probes (Epicentre). RNA samples were sheared by ultrasonication on a Covaris S2 for 90s set at Duty Cycle 10, Cycles per Burst 200 and Intensity 5. Fragmented RNA was reverse-transcribed with a combination of random hexamer and oligo-dT primers (New England Biolabs) by SuperScript III (Invitrogen) at 50 C for 2h in the presence of 6ug/ml actinomycin D (Sigma) to inhibit second-strand products. Second-strand cDNA was synthesized by DNA Polymerase I in the presence of RNase H with dUTPs substituted for dTTPs at 16 C for 2h. Sequential end repair and 3'-adenylation of cDNA products was carried out with T4 DNA polymerase and T4 polynucleotide kinase (20 C), and with exo- Klenow fragment (65 C) in the presence of dATPs (New England BioLabs). These were ligated to barcoded adapters (NEXTflex-96, Bioo Scientific) by T4 DNA ligase (New England BioLabs) at 20 C for 30min. Second-strand DNA was digested with uracil DNA glycosylase (UDG) and Endonuclease VIII at 37 C for 30min. PCR amplification of first-strand library constructs was carried out with KAPA HiFi DNA polymerase (Kapa Biosystems) for 13 cycles. Purification of reaction products at each step was performed with Ampure XP paramagnetic beads (Beckman Coulter). Library size distribution and molarity was assessed by the DNA 1000 assay on the 2100 Bioanalyzer (Agilent).

characteristic: description

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens

text: fresh specimen


characteristic: ENA-LAST-UPDATE

text: European Molecular Biology Laboratory

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: ArrayExpress

text: embryonic stem cell

text: house mouse

text: Protocols: Cells were cultured in N2B27 medium (Ndiff227, StemCells Inc) supplemented with 1uM PD0325901 (PD03), 1uM CHIR99021 and human or murine LIF (according to species) (t2iL) + 5uM PKC inhibitor Go6983 (Sigma-Aldrich). Total RNA was extracted with the TRIzol/chloroform method (Invitrogen), followed by resuspension in RNAsecure (Ambion), incubation with TURBO DNase (Ambion) at 37 C for 1 hour, further phenol/chloroform extraction and ethanol precipitation. RNA integrity was assessed with the RNA 6000 Nano assay on the 2100 Bioanalyzer (Agilent). Ribosomal RNA was depleted from 5ug of total RNA using Ribo-Zero capture probes (Epicentre). RNA samples were sheared by ultrasonication on a Covaris S2 for 90s set at Duty Cycle 10, Cycles per Burst 200 and Intensity 5. Fragmented RNA was reverse-transcribed with a combination of random hexamer and oligo-dT primers (New England Biolabs) by SuperScript III (Invitrogen) at 50 C for 2h in the presence of 6ug/ml actinomycin D (Sigma) to inhibit second-strand products. Second-strand cDNA was synthesized by DNA Polymerase I in the presence of RNase H with dUTPs substituted for dTTPs at 16 C for 2h. Sequential end repair and 3'-adenylation of cDNA products was carried out with T4 DNA polymerase and T4 polynucleotide kinase (20 C), and with exo- Klenow fragment (65 C) in the presence of dATPs (New England BioLabs). These were ligated to barcoded adapters (NEXTflex-96, Bioo Scientific) by T4 DNA ligase (New England BioLabs) at 20 C for 30min. Second-strand DNA was digested with uracil DNA glycosylase (UDG) and Endonuclease VIII at 37 C for 30min. PCR amplification of first-strand library constructs was carried out with KAPA HiFi DNA polymerase (Kapa Biosystems) for 13 cycles. Purification of reaction products at each step was performed with Ampure XP paramagnetic beads (Beckman Coulter). Library size distribution and molarity was assessed by the DNA 1000 assay on the 2100 Bioanalyzer (Agilent).

text: Mus musculus

text: Mus musculus

text: Mus musculus

text: fresh specimen


text: European Molecular Biology Laboratory

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: ArrayExpress

text: embryonic stem cell

text: house mouse

text: Protocols: Cells were cultured in N2B27 medium (Ndiff227, StemCells Inc) supplemented with 1uM PD0325901 (PD03) and murine LIF (prepared in-house). Total RNA was extracted with the TRIzol/chloroform method (Invitrogen), followed by resuspension in RNAsecure (Ambion), incubation with TURBO DNase (Ambion) at 37 C for 1 hour, further phenol/chloroform extraction and ethanol precipitation. RNA integrity was assessed with the RNA 6000 Nano assay on the 2100 Bioanalyzer (Agilent). Ribosomal RNA was depleted from 5ug of total RNA using Ribo-Zero capture probes (Epicentre). RNA samples were sheared by ultrasonication on a Covaris S2 for 90s set at Duty Cycle 10, Cycles per Burst 200 and Intensity 5. Fragmented RNA was reverse-transcribed with a combination of random hexamer and oligo-dT primers (New England Biolabs) by SuperScript III (Invitrogen) at 50 C for 2h in the presence of 6ug/ml actinomycin D (Sigma) to inhibit second-strand products. Second-strand cDNA was synthesized by DNA Polymerase I in the presence of RNase H with dUTPs substituted for dTTPs at 16 C for 2h. Sequential end repair and 3'-adenylation of cDNA products was carried out with T4 DNA polymerase and T4 polynucleotide kinase (20 C), and with exo- Klenow fragment (65 C) in the presence of dATPs (New England BioLabs). These were ligated to barcoded adapters (NEXTflex-96, Bioo Scientific) by T4 DNA ligase (New England BioLabs) at 20 C for 30min. Second-strand DNA was digested with uracil DNA glycosylase (UDG) and Endonuclease VIII at 37 C for 30min. PCR amplification of first-strand library constructs was carried out with KAPA HiFi DNA polymerase (Kapa Biosystems) for 13 cycles. Purification of reaction products at each step was performed with Ampure XP paramagnetic beads (Beckman Coulter). Library size distribution and molarity was assessed by the DNA 1000 assay on the 2100 Bioanalyzer (Agilent).

text: Mus musculus

text: Mus musculus

text: Mus musculus

text: fresh specimen

characteristic: title


text: public

characteristic: SRA accession

text: E-MTAB-2888:ssMED001_D93_SCC1.140304.HiSeq2500.FCB.lane1.R1.fastq.gz

tag: Namespace:Laboratory of Translational Genetics Vesalius Research Centre, VIB Department of Oncology , KU Leuven,

characteristic: Submitter Id

text: ArrayExpress

text: house mouse

text: Protocols: DMBA/TPA-induced skin tumors. FVB/N mice were treated with DMBA (9,10-dimethyl-1,2-benzanthracene) and TPA (12-O-tetradecanoyl phorbol-13-acetate) as previously described 2. For the group of mice with single DMBA administration (n=14), DMBA (200 ul of 0.25 mg/ml solution in acetone) was applied on the shaved backskin of 28 days old mice, then TPA (200 ul of 0.02 mg/ml solution in acetone) was applied once weekly during 16 weeks. For the group of mice with multiple DMBA administration, DMBA was applied once weekly during 6 weeks, starting post natal day 28, and TPA was applied once weekly during 16 weeks. Whole genome DNA libraries were created using the Illumina TruSeq DNA sample preparation kit V2 according to the manufacturers instructions

text: squamous cell carcinoma

characteristic: disease

text: Mus musculus

text: Mus musculus

text: Mus musculus


characteristic: ENA-FIRST-PUBLIC

text: Laboratory of Translational Genetics Vesalius Research Centre, VIB Department of Oncology , KU Leuven,

text: public

text: E-MTAB-2888:ssMED001_D92_SCC1.140304.HiSeq2500.FCB.lane2.R1.fastq.gz

text: ArrayExpress

text: house mouse

text: squamous cell carcinoma

text: Mus musculus

text: Mus musculus

text: Mus musculus


characteristic: External Id

text: public

text: E-MTAB-2888:ssMED001_D87_SCC1.140304.HiSeq2500.FCB.lane1.R1.fastq.gz

text: ArrayExpress

text: house mouse

text: squamous cell carcinoma

text: Mus musculus

text: Mus musculus

text: Mus musculus


text: public

text: E-MTAB-2888:ssMED001_D17_SCC1.140304.HiSeq2500.FCB.lane1.R1.fastq.gz

text: ArrayExpress

text: house mouse

characteristic: common name

text: squamous cell carcinoma

text: Mus musculus

text: Mus musculus

text: Mus musculus


text: public

text: E-MTAB-2888:ssMED001_D55_SCC1.140304.HiSeq2500.FCB.lane2.R1.fastq.gz

text: ArrayExpress

text: house mouse

text: squamous cell carcinoma

text: Mus musculus

characteristic: organism

text: Mus musculus

text: Mus musculus


text: public

text: E-MTAB-2888:ssMED001_D87_SCC1.140304.HiSeq2500.FCB.lane2.R1.fastq.gz

text: ArrayExpress

text: house mouse

text: squamous cell carcinoma

text: Mus musculus

text: Mus musculus

text: Mus musculus


text: public

text: E-MTAB-2888:ssMED001_D94_SCC1.140304.HiSeq2500.FCB.lane1.R1.fastq.gz

text: ArrayExpress

text: house mouse

text: squamous cell carcinoma

text: Mus musculus

text: Mus musculus

text: Mus musculus


text: public

text: E-MTAB-2888:ssMED001_D76_SCC1.140304.HiSeq2500.FCB.lane2.R1.fastq.gz

text: ArrayExpress

text: house mouse

text: squamous cell carcinoma

text: Mus musculus

text: Mus musculus

text: Mus musculus


text: public

text: E-MTAB-2888:ssMED001_D93_SCC1.140304.HiSeq2500.FCB.lane2.R1.fastq.gz

text: ArrayExpress

text: house mouse

text: squamous cell carcinoma

text: Mus musculus

text: Mus musculus

text: Mus musculus


text: public

text: E-MTAB-2888:ssMED001_D33_SCC2.140304.HiSeq2500.FCB.lane1.R1.fastq.gz

text: ArrayExpress

text: house mouse

text: squamous cell carcinoma

text: Mus musculus

text: Mus musculus

text: Mus musculus


text: public

text: E-MTAB-2888:ssMED001_T2.140317.HiSeq2500.FCB.lane1.R1.fastq.gz

text: ArrayExpress

text: house mouse

text: squamous cell carcinoma

text: Mus musculus

text: Mus musculus

text: Mus musculus


text: public

text: E-MTAB-2888:ssMED001_D53_SCC1.140304.HiSeq2500.FCB.lane1.R1.fastq.gz

text: ArrayExpress

text: house mouse

text: squamous cell carcinoma

text: Mus musculus

text: Mus musculus

text: Mus musculus


text: public

text: E-MTAB-2888:ssMED001_T1.140317.HiSeq2500.FCB.lane2.R1.fastq.gz

text: ArrayExpress

text: house mouse

text: squamous cell carcinoma

text: Mus musculus

text: Mus musculus

text: Mus musculus


text: public

text: E-MTAB-2888:ssMED001_D32_SCC2.140304.HiSeq2500.FCB.lane2.R1.fastq.gz

text: ArrayExpress

text: house mouse

text: squamous cell carcinoma

text: Mus musculus

text: Mus musculus

text: Mus musculus


text: public

text: E-MTAB-2888:ssMED001_T1.140317.HiSeq2500.FCB.lane1.R1.fastq.gz

text: ArrayExpress

text: house mouse

text: squamous cell carcinoma

text: Mus musculus

text: Mus musculus

text: Mus musculus


text: public

text: E-MTAB-2888:ssMED001_D17_SCC1.140304.HiSeq2500.FCB.lane2.R1.fastq.gz

text: ArrayExpress

text: house mouse

text: squamous cell carcinoma

text: Mus musculus

text: Mus musculus

text: Mus musculus


text: public

text: E-MTAB-2888:ssMED001_D89_SCC1.140304.HiSeq2500.FCB.lane1.R1.fastq.gz

text: ArrayExpress

text: house mouse

text: Protocols: DMBA/TPA-induced skin tumors. FVB/N mice were treated with DMBA (9,10-dimethyl-1,2-benzanthracene) and TPA (12-O-tetradecanoyl phorbol-13-acetate) as previously described 2. For the group of mice with single DMBA administration (n=14), DMBA (200 ul of 0.25 mg/ml solution in acetone) was applied on the shaved backskin of 28 days old mice, then TPA (200 ul of 0.02 mg/ml solution in acetone) was applied once weekly during 16 weeks. For the group of mice with multiple DMBA administration, DMBA was applied once weekly during 6 weeks, starting post natal day 28, and TPA was applied once weekly during 16 weeks. Whole genome DNA libraries were created using the Illumina TruSeq DNA sample preparation kit V2 according to the manufacturers instructions

text: squamous cell carcinoma

text: Mus musculus

text: Mus musculus

text: Mus musculus


text: Laboratory of Translational Genetics Vesalius Research Centre, VIB Department of Oncology , KU Leuven,

text: public

text: E-MTAB-2888:ssMED001_D32_SCC2.140304.HiSeq2500.FCB.lane1.R1.fastq.gz

text: ArrayExpress

text: house mouse

text: squamous cell carcinoma

text: Mus musculus

text: Mus musculus

text: Mus musculus


text: public

text: E-MTAB-2888:ssMED001_D60_SCC1.140304.HiSeq2500.FCB.lane2.R1.fastq.gz

text: ArrayExpress

text: house mouse

text: squamous cell carcinoma

text: Mus musculus

text: Mus musculus

text: Mus musculus


text: public

text: E-MTAB-2888:ssMED001_D33_SCC2.140304.HiSeq2500.FCB.lane2.R1.fastq.gz

text: ArrayExpress

text: house mouse

text: squamous cell carcinoma

text: Mus musculus

text: Mus musculus

text: Mus musculus


text: public

text: E-MTAB-2888:ssMED001_D64_SCC1.140304.HiSeq2500.FCB.lane2.R1.fastq.gz

text: ArrayExpress

text: house mouse

text: squamous cell carcinoma

text: Mus musculus

text: Mus musculus

text: Mus musculus


text: public

text: E-MTAB-2888:ssMED001_D64_SCC1.140304.HiSeq2500.FCB.lane1.R1.fastq.gz

text: ArrayExpress

text: house mouse

text: squamous cell carcinoma

text: Mus musculus

text: Mus musculus

text: Mus musculus


text: public

text: E-MTAB-2888:ssMED001_D53_SCC1.140304.HiSeq2500.FCB.lane2.R1.fastq.gz

text: ArrayExpress

text: house mouse

text: squamous cell carcinoma

text: Mus musculus

text: Mus musculus

text: Mus musculus


text: public

text: E-MTAB-2888:ssMED001_D76_SCC1.140304.HiSeq2500.FCB.lane1.R1.fastq.gz

text: ArrayExpress

text: house mouse

text: squamous cell carcinoma

text: Mus musculus

text: Mus musculus

text: Mus musculus


text: public

text: E-MTAB-2888:ssMED001_D91_SCC1.140304.HiSeq2500.FCB.lane1.R1.fastq.gz

text: ArrayExpress

text: house mouse

text: squamous cell carcinoma

text: Mus musculus

text: Mus musculus

text: Mus musculus


text: public

text: E-MTAB-2888:ssMED001_D92_SCC1.140304.HiSeq2500.FCB.lane1.R1.fastq.gz

text: ArrayExpress

text: house mouse

text: squamous cell carcinoma

text: Mus musculus

text: Mus musculus

text: Mus musculus


text: public

text: E-MTAB-2888:ssMED001_D88_SCC1.140304.HiSeq2500.FCB.lane2.R1.fastq.gz

text: ArrayExpress

text: house mouse

text: squamous cell carcinoma

text: Mus musculus

text: Mus musculus

text: Mus musculus


text: public

text: E-MTAB-2888:ssMED001_D60_SCC1.140304.HiSeq2500.FCB.lane1.R1.fastq.gz

text: ArrayExpress

text: house mouse

text: squamous cell carcinoma

text: Mus musculus

text: Mus musculus

text: Mus musculus


text: public

text: E-MTAB-2888:ssMED001_T2.140317.HiSeq2500.FCB.lane2.R1.fastq.gz

text: ArrayExpress

text: house mouse

text: squamous cell carcinoma

text: Mus musculus

text: Mus musculus

text: Mus musculus


text: public

text: E-MTAB-2888:ssMED001_D94_SCC1.140304.HiSeq2500.FCB.lane2.R1.fastq.gz

text: ArrayExpress

text: house mouse

text: squamous cell carcinoma

text: Mus musculus

text: Mus musculus

text: Mus musculus


text: public

text: E-MTAB-2888:ssMED001_D89_SCC1.140304.HiSeq2500.FCB.lane2.R1.fastq.gz

text: ArrayExpress

text: house mouse

text: squamous cell carcinoma

text: Mus musculus

text: Mus musculus

text: Mus musculus


text: public

text: E-MTAB-2888:ssMED001_D88_SCC1.140304.HiSeq2500.FCB.lane1.R1.fastq.gz

text: ArrayExpress

text: house mouse

text: squamous cell carcinoma

text: Mus musculus

text: Mus musculus

text: Mus musculus


text: public

text: E-MTAB-2888:ssMED001_D91_SCC1.140304.HiSeq2500.FCB.lane2.R1.fastq.gz

text: ArrayExpress

text: house mouse

text: Protocols: DMBA/TPA-induced skin tumors. FVB/N mice were treated with DMBA (9,10-dimethyl-1,2-benzanthracene) and TPA (12-O-tetradecanoyl phorbol-13-acetate) as previously described 2. For the group of mice with single DMBA administration (n=14), DMBA (200 ul of 0.25 mg/ml solution in acetone) was applied on the shaved backskin of 28 days old mice, then TPA (200 ul of 0.02 mg/ml solution in acetone) was applied once weekly during 16 weeks. For the group of mice with multiple DMBA administration, DMBA was applied once weekly during 6 weeks, starting post natal day 28, and TPA was applied once weekly during 16 weeks. Whole genome DNA libraries were created using the Illumina TruSeq DNA sample preparation kit V2 according to the manufacturers instructions

text: squamous cell carcinoma

text: Mus musculus

text: Mus musculus

text: Mus musculus


text: Laboratory of Translational Genetics Vesalius Research Centre, VIB Department of Oncology , KU Leuven,

text: public

text: E-MTAB-2888:ssMED001_D55_SCC1.140304.HiSeq2500.FCB.lane1.R1.fastq.gz

text: ArrayExpress

text: house mouse

text: squamous cell carcinoma

text: Mus musculus

text: Mus musculus

text: Mus musculus


text: Mouse

characteristic: ArrayExpress-Species

text: SC

text: public

text: house mouse

text: Mus musculus

text: mRNAseq Nextera library made from RNA extracted from haemopoetic stem and progenitor cells

characteristic: sample description

text: Mus musculus


characteristic: ArrayExpress-DevelopmentalStage

text: Wildtype

characteristic: ArrayExpress-Genotype

text: Mus Musculus

characteristic: ENA-CHECKLIST

text: SC

text: public

text: house mouse

text: Mus musculus

text: RNA from mouse embryo

text: Mus musculus


characteristic: ENA-LAST-UPDATE

text: The Pirbright Institute

characteristic: INSDC center name

text: public

tag: Namespace:The Pirbright Institute

text: 24 hour

characteristic: age

text: ArrayExpress

characteristic: broker name

text: African malaria mosquito

text: 15-20 4th instar larvae collected 22-24 h after ecdysis constituted the sample Protocols: Three days post-blood feeding females were allowed to lay eggs for 10-15 min, after which the egg dish was removed and kept at standard insectary conditions (27 C and 12h light/12h dark cycle). Individual embryos were sexed by PCR using a combination of primers targeting the Y chromosome-specific and the non-Y chromosome repetitive markers (Krzywinski et al. 2004, Genetics 166: 1291; Krzywinski et al. 2005, Genetics 169: 185). Larvae were reared at low density in pans with de-ionized water and fed daily with ground Tetramin fish food. Larvae were collected from progeny of a cross between Pimperena strain females and males of a transgenic strain with an X-linked GFP/dsRED marker on a Pimperena genetic background. Pans containing fully grown 2nd or 3rd instar larvae were inspected every two hours, and newly moulted 3rd or 4th instar individuals were transferred into marked pans for subsequent sample collection. Similarly, pans with fully grown 4th instar larvae were inspected every hour and newly pupated individuals were transferred into marked pans with clean de-ionized water. Transferred individuals were sexed and then collected at required time intervals. Larvae were sexed under a fluorescence microscope based on the principle of inheritance of the fluorescently labelled X chromosome by F1 females from transgenic fathers and lack of fluorescent markers in F1 males. Pupae were sexed based on morphological characters. Individual embryo samples of the same sex (determined by PCR) were combined prior to RNA extraction. Total RNA was isolated using PureLink RNA Mini Kit (Ambion) with an on-column DNase treatment step according to the manufacturer's protocol. Ribo-Zero, Magnetic Gold Kit was used to deplete rRNAs from total RNA prior to library construction. The libraries were constructed using a modified TruSeq RNA protocol (Illumina). The total RNA was fragmented and the first-strand cDNA synthesized. During the second-strand synthesis, dDUTP was incorporated instead of dTTP. The double-stranded cDNA fragments were blunt-ended and their 3-prime ends adenylated to prevent formation of chimeric molecules during the adapter ligation. After adapter ligation, the fragments were treated with Uracil-N-Glycosylase to selectively degrade the second-strand of cDNA. Then, the fragments were subjected to a bead-based size selection using AMPure XP beads. Prior to hybridisation to the flow cell, the cDNA constructs were amplified by PCR to selectively enrich fragments with adapter molecules on both ends. The concentration of the libraries was determined by using a Qubit dsDNA HS Assay (Life Technologies).

characteristic: description

text: 4th instar larvae

characteristic: developmental stage

text: Anopheles gambiae

text: Anopheles gambiae

text: Anopheles gambiae

text: male

characteristic: sex

text: fresh specimen

characteristic: specimen with known storage state

text: Pimperena

characteristic: strain


characteristic: ENA-FIRST-PUBLIC

characteristic: External Id

text: The Pirbright Institute

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: 12 hour

text: ArrayExpress

text: African malaria mosquito

text: 45-50 3rd instar larvae collected 12-14 h after ecdysis constituted the sample Protocols: Three days post-blood feeding females were allowed to lay eggs for 10-15 min, after which the egg dish was removed and kept at standard insectary conditions (27 C and 12h light/12h dark cycle). Individual embryos were sexed by PCR using a combination of primers targeting the Y chromosome-specific and the non-Y chromosome repetitive markers (Krzywinski et al. 2004, Genetics 166: 1291; Krzywinski et al. 2005, Genetics 169: 185). Larvae were reared at low density in pans with de-ionized water and fed daily with ground Tetramin fish food. Larvae were collected from progeny of a cross between Pimperena strain females and males of a transgenic strain with an X-linked GFP/dsRED marker on a Pimperena genetic background. Pans containing fully grown 2nd or 3rd instar larvae were inspected every two hours, and newly moulted 3rd or 4th instar individuals were transferred into marked pans for subsequent sample collection. Similarly, pans with fully grown 4th instar larvae were inspected every hour and newly pupated individuals were transferred into marked pans with clean de-ionized water. Transferred individuals were sexed and then collected at required time intervals. Larvae were sexed under a fluorescence microscope based on the principle of inheritance of the fluorescently labelled X chromosome by F1 females from transgenic fathers and lack of fluorescent markers in F1 males. Pupae were sexed based on morphological characters. Individual embryo samples of the same sex (determined by PCR) were combined prior to RNA extraction. Total RNA was isolated using PureLink RNA Mini Kit (Ambion) with an on-column DNase treatment step according to the manufacturer's protocol. Ribo-Zero, Magnetic Gold Kit was used to deplete rRNAs from total RNA prior to library construction. The libraries were constructed using a modified TruSeq RNA protocol (Illumina). The total RNA was fragmented and the first-strand cDNA synthesized. During the second-strand synthesis, dDUTP was incorporated instead of dTTP. The double-stranded cDNA fragments were blunt-ended and their 3-prime ends adenylated to prevent formation of chimeric molecules during the adapter ligation. After adapter ligation, the fragments were treated with Uracil-N-Glycosylase to selectively degrade the second-strand of cDNA. Then, the fragments were subjected to a bead-based size selection using AMPure XP beads. Prior to hybridisation to the flow cell, the cDNA constructs were amplified by PCR to selectively enrich fragments with adapter molecules on both ends. The concentration of the libraries was determined by using a Qubit dsDNA HS Assay (Life Technologies).

text: 3rd instar larvae

text: Anopheles gambiae

text: Anopheles gambiae

text: Anopheles gambiae

text: female

text: fresh specimen

text: Pimperena

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-LAST-UPDATE

text: The Pirbright Institute

text: public

text: 20 hour

text: ArrayExpress

text: African malaria mosquito

characteristic: common name

text: Approximately 300 20-22 h old embryos constituted the sample Protocols: Three days post-blood feeding females were allowed to lay eggs for 10-15 min, after which the egg dish was removed and kept at standard insectary conditions (27 C and 12h light/12h dark cycle). Individual embryos were sexed by PCR using a combination of primers targeting the Y chromosome-specific and the non-Y chromosome repetitive markers (Krzywinski et al. 2004, Genetics 166: 1291; Krzywinski et al. 2005, Genetics 169: 185). Larvae were reared at low density in pans with de-ionized water and fed daily with ground Tetramin fish food. Larvae were collected from progeny of a cross between Pimperena strain females and males of a transgenic strain with an X-linked GFP/dsRED marker on a Pimperena genetic background. Pans containing fully grown 2nd or 3rd instar larvae were inspected every two hours, and newly moulted 3rd or 4th instar individuals were transferred into marked pans for subsequent sample collection. Similarly, pans with fully grown 4th instar larvae were inspected every hour and newly pupated individuals were transferred into marked pans with clean de-ionized water. Transferred individuals were sexed and then collected at required time intervals. Larvae were sexed under a fluorescence microscope based on the principle of inheritance of the fluorescently labelled X chromosome by F1 females from transgenic fathers and lack of fluorescent markers in F1 males. Pupae were sexed based on morphological characters. Individual embryo samples of the same sex (determined by PCR) were combined prior to RNA extraction. Total RNA was isolated using PureLink RNA Mini Kit (Ambion) with an on-column DNase treatment step according to the manufacturer's protocol. Ribo-Zero, Magnetic Gold Kit was used to deplete rRNAs from total RNA prior to library construction. The libraries were constructed using a modified TruSeq RNA protocol (Illumina). The total RNA was fragmented and the first-strand cDNA synthesized. During the second-strand synthesis, dDUTP was incorporated instead of dTTP. The double-stranded cDNA fragments were blunt-ended and their 3-prime ends adenylated to prevent formation of chimeric molecules during the adapter ligation. After adapter ligation, the fragments were treated with Uracil-N-Glycosylase to selectively degrade the second-strand of cDNA. Then, the fragments were subjected to a bead-based size selection using AMPure XP beads. Prior to hybridisation to the flow cell, the cDNA constructs were amplified by PCR to selectively enrich fragments with adapter molecules on both ends. The concentration of the libraries was determined by using a Qubit dsDNA HS Assay (Life Technologies).

text: embryo stage

text: Anopheles gambiae

characteristic: organism

text: Anopheles gambiae

text: Anopheles gambiae

text: male

text: fresh specimen

text: Pimperena


text: The Pirbright Institute

characteristic: INSDC center name

text: public

text: 10 hour

characteristic: age

text: ArrayExpress

characteristic: broker name

text: African malaria mosquito

text: 12-15 10 h old pupae constituted the sample Protocols: Three days post-blood feeding females were allowed to lay eggs for 10-15 min, after which the egg dish was removed and kept at standard insectary conditions (27 C and 12h light/12h dark cycle). Individual embryos were sexed by PCR using a combination of primers targeting the Y chromosome-specific and the non-Y chromosome repetitive markers (Krzywinski et al. 2004, Genetics 166: 1291; Krzywinski et al. 2005, Genetics 169: 185). Larvae were reared at low density in pans with de-ionized water and fed daily with ground Tetramin fish food. Larvae were collected from progeny of a cross between Pimperena strain females and males of a transgenic strain with an X-linked GFP/dsRED marker on a Pimperena genetic background. Pans containing fully grown 2nd or 3rd instar larvae were inspected every two hours, and newly moulted 3rd or 4th instar individuals were transferred into marked pans for subsequent sample collection. Similarly, pans with fully grown 4th instar larvae were inspected every hour and newly pupated individuals were transferred into marked pans with clean de-ionized water. Transferred individuals were sexed and then collected at required time intervals. Larvae were sexed under a fluorescence microscope based on the principle of inheritance of the fluorescently labelled X chromosome by F1 females from transgenic fathers and lack of fluorescent markers in F1 males. Pupae were sexed based on morphological characters. Individual embryo samples of the same sex (determined by PCR) were combined prior to RNA extraction. Total RNA was isolated using PureLink RNA Mini Kit (Ambion) with an on-column DNase treatment step according to the manufacturer's protocol. Ribo-Zero, Magnetic Gold Kit was used to deplete rRNAs from total RNA prior to library construction. The libraries were constructed using a modified TruSeq RNA protocol (Illumina). The total RNA was fragmented and the first-strand cDNA synthesized. During the second-strand synthesis, dDUTP was incorporated instead of dTTP. The double-stranded cDNA fragments were blunt-ended and their 3-prime ends adenylated to prevent formation of chimeric molecules during the adapter ligation. After adapter ligation, the fragments were treated with Uracil-N-Glycosylase to selectively degrade the second-strand of cDNA. Then, the fragments were subjected to a bead-based size selection using AMPure XP beads. Prior to hybridisation to the flow cell, the cDNA constructs were amplified by PCR to selectively enrich fragments with adapter molecules on both ends. The concentration of the libraries was determined by using a Qubit dsDNA HS Assay (Life Technologies).

characteristic: description

text: pupae

text: Anopheles gambiae

text: Anopheles gambiae

text: Anopheles gambiae

text: male

text: fresh specimen

text: Pimperena


text: The Pirbright Institute

text: public

text: 20 hour

text: ArrayExpress

text: African malaria mosquito

text: embryo stage

characteristic: developmental stage

text: Anopheles gambiae

text: Anopheles gambiae

text: Anopheles gambiae

text: female

characteristic: sex

text: fresh specimen

characteristic: specimen with known storage state

text: Pimperena

characteristic: strain


characteristic: ENA-FIRST-PUBLIC

characteristic: External Id

text: The Pirbright Institute

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: 12 hour

text: ArrayExpress

text: African malaria mosquito

text: 3rd instar larvae

text: Anopheles gambiae

text: Anopheles gambiae

text: Anopheles gambiae

text: male

text: fresh specimen

text: Pimperena


text: The Pirbright Institute

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: 24 hour

text: ArrayExpress

text: African malaria mosquito

text: 4th instar larvae

text: Anopheles gambiae

text: Anopheles gambiae

text: Anopheles gambiae

text: female

text: fresh specimen

text: Pimperena

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-LAST-UPDATE

text: The Pirbright Institute

text: public

text: 10 hour

text: ArrayExpress

text: African malaria mosquito

characteristic: common name

text: pupae

text: Anopheles gambiae

characteristic: organism

text: Anopheles gambiae

text: Anopheles gambiae

text: female

text: fresh specimen

text: Pimperena


E-MTAB-2879:equine tissue pool

text: KU Leuven

characteristic: INSDC center name

text: public

text: E-MTAB-2879:equine tissue pool

tag: Namespace:KU Leuven

text: mixed age

characteristic: age

text: ArrayExpress

characteristic: broker name

text: horse

text: Protocols: RNA was isolated using variations of guanidinium-based protocols, MacLeod JN et al. (1996) J Biol Chem 271: 18954-18960.and Chomczynski P, and Sacchi N (1987) Anal Biochem 162: 156-159 messenger RNA was isolated from total RNA with the Oligotex kit (Qiagen, Valencia, CA). Primary cDNA library with adaptors compatible with the 454 system constructed as previously published Lambert JD et al (2010) Integr Comp Biol 50: 768-777.

characteristic: description

text: mixed developmental stage

text: Equus caballus

text: Equus caballus

text: mixed tissues

characteristic: organism part

text: Equus caballus

text: mixed sex

text: fresh specimen

text: light breed horse (primarily Thoroughbred)

text: equine tissue pool


text: 8.8 weeks

characteristic: ArrayExpress-Age

text: Lin- bone marrow cells

characteristic: ArrayExpress-CellType

text: KO

characteristic: ArrayExpress-Genotype

text: wild type

characteristic: ArrayExpress-Phenotype

text: female

characteristic: ArrayExpress-Sex

text: Mus Musculus

characteristic: ArrayExpress-Species

characteristic: ENA-FIRST-PUBLIC

text: SC

text: public

text: house mouse

text: Mus musculus

text: Lin- bone marrow cells

characteristic: sample description

text: Mus musculus


text: 8.8 weeks

text: Lin- bone marrow cells

text: WT

text: wild type

text: female

text: Mus Musculus

characteristic: ENA-CHECKLIST

characteristic: External Id

text: SC

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: house mouse

text: Mus musculus

text: Lin- bone marrow cells

text: Mus musculus


text: Danio rerio

characteristic: ENA-LAST-UPDATE

text: SC

characteristic: INSDC center name

text: public

text: zebrafish

characteristic: common name

text: Danio rerio

characteristic: organism

text: Danio rerio


text: Mus musculus

text: SC

text: public

text: house mouse

text: Mus musculus

text: Mus musculus


text: Homo Sapien

text: SC

text: public

text: human

text: Homo sapiens

text: Homo sapiens


E-MTAB-2886:MM01 T

text: Iowa State University

text: public

text: E-MTAB-2886:MM01 T

tag: Namespace:Iowa State University

text: ArrayExpress

characteristic: broker name

text: zebrafish

text: Protocols: isolation and care of zebrafish transgenic line Tg(flk1:RFP)is18 Tissues for isolation of total RNA for RNA-Seq libraries were dissected from three age-matched genotypes. Total RNA was isolated using Qiagen RNeasy RNA Isolation Kit (Qiagen). The first sample, “Wild Type”, contained three pooled retinas from 6-month-old wild type adults. The second sample, “Pretumor”, consisted of three pooled retinas from age-matched heterozygous Tg(flk1:RFP)is18/+ adults that did not show obvious gross ocular tumors. The third sample, “Tumor”, consisted of tumor tissue dissected from the eyes of two age-matched heterozygous Tg(flk1:RFP)is18/+ adults that had advanced, large tumors that filled the vitreous and distorted the ocular cavity. RNA-Seq libraries were prepared from each sample and 100 bp paired-end sequenced in individual lanes on an Illumina HiSeq 2000 instrument at the Genome Sequencing and Analysis Core Resource, Duke Institute for Genome Sciences and Policy, Duke University.

characteristic: description

characteristic: genotype

text: Danio rerio

text: Danio rerio

text: retinal tumor

characteristic: organism part

text: Danio rerio

text: MM01 T

characteristic: title


E-MTAB-2886:MM02 PT

characteristic: ENA-FIRST-PUBLIC

text: Iowa State University

text: public

text: E-MTAB-2886:MM02 PT

text: ArrayExpress

text: zebrafish

text: Danio rerio

text: Danio rerio

text: retina

text: Danio rerio

text: MM02 PT


E-MTAB-2886:MM03 WT

characteristic: ENA-CHECKLIST

text: Iowa State University

text: public

text: E-MTAB-2886:MM03 WT

text: ArrayExpress

text: zebrafish

text: wild type genotype

text: Danio rerio

text: Danio rerio

text: retina

text: Danio rerio

text: MM03 WT


E-MTAB-2755:Bovine Pregnancy MG 134

characteristic: External Id

text: public

text: E-MTAB-2755:Bovine Pregnancy MG 134

tag: Namespace:INRA, UMR1313 Genetique Animale et Biologie Integrative

text: ArrayExpress

text: cattle

text: biopsies Protocols: Total RNA was extracted from a 50 mg specimen using 750 ul Trizol LS reagent (Invitrogen, Cat. N. 10296-010), treated with DNase I (QIAGEN, Cat. N. 79254) and then purified using NucleoSpin RNA Clean-up (Macherey-Nagel, Cat. N. 740948.50). Total RNA was eluted with 50 ul DNase I-free water. Approximately 20 to 30 ug were recovered per biopsy. RiboMinus RNA (ribosomal RNA-depleted RNA) was purified from 5 ug total RNA using the RiboMinus Eukaryote Kit for RNA-Seq (Invitrogen, Cat. N. A10837-08). RNA Integrity was assessed using an Agilent Bioanalyzer. Strand orientated libraries were prepared with the Truseq Small RNA sample prep Kit (Illumina), the final gel purification step being replaced by a PCR cleanup with AMPureXP beads (Beckman-Coulter).

text: pregnancy day 60

characteristic: developmental stage

text: Bos taurus

text: Bos taurus

text: mammary gland

text: Bos taurus

text: female

characteristic: sex

text: Bovine Pregnancy MG 134


E-MTAB-2755:Bovine Pregnancy MG 840

text: INRA, UMR1313 Genetique Animale et Biologie Integrative

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: E-MTAB-2755:Bovine Pregnancy MG 840

text: ArrayExpress

text: cattle

text: pregnancy day 60

text: Bos taurus

text: Bos taurus

text: mammary gland

text: Bos taurus

text: female

text: Bovine Pregnancy MG 840


name: E-MTAB-2755:Bovine Lactation MG ODM Pool 1

characteristic: ENA-LAST-UPDATE

text: public

characteristic: SRA accession

characteristic: Submitter Id

text: ArrayExpress

text: cattle

text: Lactation day 53-74

text: Bos taurus

text: Bos taurus

text: mammary gland

text: Bos taurus

text: female

text: Bovine Lactation MG ODM Pool 1


E-MTAB-2755:Bovine Pregnancy MG 838

characteristic: INSDC center name

text: public

text: E-MTAB-2755:Bovine Pregnancy MG 838

text: ArrayExpress

text: cattle

characteristic: common name

text: pregnancy day 60

text: Bos taurus

characteristic: organism

text: Bos taurus

text: mammary gland

text: Bos taurus

text: female

text: Bovine Pregnancy MG 838


name: E-MTAB-2755:Bovine Lactation MG TDM Pool 3

text: public

text: ArrayExpress

characteristic: broker name

text: cattle

characteristic: description

text: Lactation day 53-74

text: Bos taurus

text: Bos taurus

text: mammary gland

text: Bos taurus

text: female

text: Bovine Lactation MG TDM Pool 3


name: E-MTAB-2755:Bovine Lactation MG ODM Pool 2

text: public

text: ArrayExpress

text: cattle

text: Lactation day 53-74

text: Bos taurus

text: Bos taurus

text: mammary gland

characteristic: organism part

text: Bos taurus

text: female

text: Bovine Lactation MG ODM Pool 2

characteristic: title


name: E-MTAB-2755:Bovine Lactation MG TDM Pool 4

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: public

text: ArrayExpress

text: cattle

text: Lactation day 53-74

text: Bos taurus

text: Bos taurus

text: mammary gland

text: Bos taurus

text: female

text: Bovine Lactation MG TDM Pool 4


E-MTAB-2755:Bovine Pregnancy MG 68

characteristic: External Id

text: public

text: E-MTAB-2755:Bovine Pregnancy MG 68

text: ArrayExpress

text: cattle

text: pregnancy day 60

characteristic: developmental stage

text: Bos taurus

text: Bos taurus

text: mammary gland

text: Bos taurus

text: female

text: Bovine Pregnancy MG 68


E-MTAB-2885:hGO 1

characteristic: INSDC first public

text: public

text: E-MTAB-2885:hGO 1

tag: Namespace:Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA

text: ArrayExpress

text: human

text: human gastric organoid Protocols: hGOs were generated through a 34-day step-wise directed differentiation protocol of pluripotent stem cells. The cells were differentiated through normal embryonic stages, including endoderm formation, foregut specification and patterning, antrum specification, and growth and maturation. Total RNA was isolated from gastric organoids using the NucleoSpin RNA II kit (Macherey-Nagel 740955) RNA libraries were prepared for sequencing using standard Illumina protocols

text: day 34

characteristic: individual

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens

text: hGO 1


E-MTAB-2885:hGO 2

text: Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: E-MTAB-2885:hGO 2

text: ArrayExpress

text: human

text: day 34

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens

text: hGO 2


characteristic: ENA-LAST-UPDATE

text: The University of Manchester

text: public

characteristic: SRA accession

tag: Namespace:The University of Manchester

text: ArrayExpress

text: baker's yeast

text: Protocols: Grown in SCD media lacking uracil at 30C to exponential phase (OD600 ~0.6), pelleted by centrifugation and snap frozen into liquid nitrogen. Samples lysed in Buffer A using a 6870 Freezer Mill (Spex). Lysates cleared by centrifuging twice at 15000 g. Nucleic acids extracted using Trizol Reagent. rRNA was depleted from samples using Ribo-ZeroTM Magnetic Gold Kit for RNA-Seq. Depleted samples were precipitated with ethanol, and re-suspended in 10ul DEPC water. Sequencing libraries were then generated using the TruSeq Stranded mRNA sample preparation guide from ilumina from the Incubate RFP step, with 5ul of the ribosome depleted RNA added to 13ul of the fragment prime and finish mix.

text: his3delta1; leu2delta0; met15delta0; ura3delta0; caf20::G418; pCAF20-FLAG::URA3

characteristic: genotype

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

text: Mat a

characteristic: sex

text: fresh specimen

characteristic: specimen with known storage state

characteristic: strain


text: The University of Manchester

characteristic: INSDC center name

text: public

characteristic: Submitter Id

text: ArrayExpress

characteristic: broker name

text: baker's yeast

characteristic: common name

characteristic: description

text: targeted mutation

characteristic: genetic modification

text: his3delta1; leu2delta0; met15delta0; ura3delta0; caf20::G418; pCAF20m2-FLAG::URA3

text: Saccharomyces cerevisiae

characteristic: organism

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

text: Mat a

text: fresh specimen


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: External Id

text: The University of Manchester

characteristic: INSDC first public

text: public

text: ArrayExpress

text: baker's yeast

text: Protocols: Grown in SCD media lacking uracil at 30C to exponential phase (OD600 ~0.6), pelleted by centrifugation and snap frozen into liquid nitrogen. Samples lysed in Buffer A using a 6870 Freezer Mill (Spex). Lysates cleared by centrifuging twice at 15000 g. Nucleic acids extracted using Trizol Reagent. Caf20p-FLAGged samples were immunoprecipitated for 2 hours at 4 C and washed five times with Buffer A (3 x 1 minute washes followed by 2 x 15 minute washes). For RNA isolation after the final wash, the beads were resuspended in 270 ul Buffer A, and 250 ul were treated with Trizol for RNA extraction. Proteins were eluted by incubation for 2 hours in Buffer A 200 ug 3xFLAG Peptide. rRNA was depleted from samples using Ribo-ZeroTM Magnetic Gold Kit for RNA-Seq. Depleted samples were precipitated with ethanol, and re-suspended in 10 ul DEPC water. Sequencing libraries were then generated using the TruSeq Stranded mRNA sample preparation guide from ilumina from the Incubate RFP step, with 5ul of the ribosome depleted RNA added to 13ul of the fragment prime and finish mix.

text: targeted mutation

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

text: Mat a

text: fresh specimen

characteristic: title


characteristic: ENA-LAST-UPDATE

text: The University of Manchester

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: ArrayExpress

text: baker's yeast

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

text: Mat a

text: fresh specimen


text: public

text: E-MTAB-2887:eMED001_D88_SCC1.MED.131211.HiSeq2000.FCB.lane4.R1

tag: Namespace:Laboratory Translational Genetics Vesalius research Centre, VIB Department of Oncology, KU Leuven

text: ArrayExpress

text: house mouse

text: Protocols: Whole genome DNA libraries were created using the Illumina TruSeq DNA sample preparation kit V2 according to the manufacturers instructions and whole-exome capture was performed using the Nimblegen SeqCap EZ Developer Library kit (110624_MM9_Exome L2R_D02_EZ_HX1_9999042611).

text: squamous cell carcinoma

characteristic: disease

text: Mus musculus

text: Mus musculus

text: Mus musculus


text: Laboratory Translational Genetics Vesalius research Centre, VIB Department of Oncology, KU Leuven

characteristic: INSDC center name

text: public

text: E-MTAB-2887:eMED001_D64_SCC1.MED.131211.HiSeq2000.FCB.lane6.R1

text: ArrayExpress

text: house mouse

text: squamous cell carcinoma

text: Mus musculus

text: Mus musculus

text: Mus musculus


text: public

text: E-MTAB-2887:eMED001_D60_SCC1.MED.131211.HiSeq2000.FCB.lane7.R1

characteristic: Submitter Id

text: ArrayExpress

text: house mouse

text: squamous cell carcinoma

text: Mus musculus

text: Mus musculus

text: Mus musculus


text: public

text: E-MTAB-2887:eMED001_D87_SCC1.MED.131211.HiSeq2000.FCB.lane3.R1

text: ArrayExpress

characteristic: broker name

text: house mouse

text: squamous cell carcinoma

text: Mus musculus

text: Mus musculus

text: Mus musculus


text: public

text: E-MTAB-2887:eMED001_D64_BM.MED.131211.HiSeq2000.FCB.lane3.R1

text: ArrayExpress

text: house mouse

characteristic: common name

text: BM

text: Mus musculus

text: Mus musculus

text: Mus musculus


text: public

text: E-MTAB-2887:eMED001_D94_BM.MED.131211.HiSeq2000.FCB.lane7.R1

text: ArrayExpress

text: house mouse

characteristic: description

text: BM

text: Mus musculus

text: Mus musculus

text: Mus musculus


text: public

text: E-MTAB-2887:eMED.MED001_N1.130118.FCA.lane1.R1

text: ArrayExpress

text: house mouse

text: BM

text: Mus musculus

text: Mus musculus

text: Mus musculus


text: public

text: E-MTAB-2887:eMED001_D87_BM.MED.131211.HiSeq2000.FCB.lane6.R1

text: ArrayExpress

text: house mouse

text: BM

text: Mus musculus

text: Mus musculus

text: Mus musculus


text: public

text: E-MTAB-2887:eMED001_T2_R1.MED.lane8.121019FCA.R1

text: ArrayExpress

text: house mouse

text: squamous cell carcinoma

text: Mus musculus

text: Mus musculus

text: Mus musculus


text: public

text: E-MTAB-2887:eMED001_D87_SCC1.MED.131211.HiSeq2000.FCB.lane7.R1

text: ArrayExpress

text: house mouse

text: squamous cell carcinoma

text: Mus musculus

text: Mus musculus

text: Mus musculus


text: public

text: E-MTAB-2887:eMED001_D89_SCC1.MED.131211.HiSeq2000.FCB.lane7.R1

text: ArrayExpress

text: house mouse

text: squamous cell carcinoma

text: Mus musculus

text: Mus musculus

text: Mus musculus


text: public

text: E-MTAB-2887:eMED001_D33_SCC2.MED.131211.HiSeq2000.FCB.lane7.R1

text: ArrayExpress

text: house mouse

text: squamous cell carcinoma

text: Mus musculus

text: Mus musculus

text: Mus musculus


text: public

text: E-MTAB-2887:eMED001_D93_SCC1.MED.131211.HiSeq2000.FCB.lane4.R1

text: ArrayExpress

text: house mouse

text: squamous cell carcinoma

text: Mus musculus

text: Mus musculus

text: Mus musculus


text: public

text: E-MTAB-2887:eMED001_D87_BM.MED.131211.HiSeq2000.FCB.lane3.R1

text: ArrayExpress

text: house mouse

text: BM

text: Mus musculus

text: Mus musculus

text: Mus musculus


text: public

text: E-MTAB-2887:eMED001_D17_SCC1.MED.131211.HiSeq2000.FCB.lane5.R1

text: ArrayExpress

text: house mouse

text: squamous cell carcinoma

text: Mus musculus

text: Mus musculus

text: Mus musculus


text: public

text: E-MTAB-2887:eMED001_D87_SCC1.MED.131211.HiSeq2000.FCB.lane5.R1

text: ArrayExpress

text: house mouse

text: squamous cell carcinoma

text: Mus musculus

text: Mus musculus

text: Mus musculus


text: public

text: E-MTAB-2887:eMED001_D89_SCC1.MED.131211.HiSeq2000.FCB.lane5.R1

text: ArrayExpress

text: house mouse

text: Protocols: Whole genome DNA libraries were created using the Illumina TruSeq DNA sample preparation kit V2 according to the manufacturers instructions and whole-exome capture was performed using the Nimblegen SeqCap EZ Developer Library kit (110624_MM9_Exome L2R_D02_EZ_HX1_9999042611).

text: squamous cell carcinoma

text: Mus musculus

text: Mus musculus

text: Mus musculus


text: Laboratory Translational Genetics Vesalius research Centre, VIB Department of Oncology, KU Leuven

text: public

text: E-MTAB-2887:eMED001_D64_BM.MED.131211.HiSeq2000.FCB.lane7.R1

text: ArrayExpress

text: house mouse

text: BM

text: Mus musculus

text: Mus musculus

text: Mus musculus


text: public

text: E-MTAB-2887:eMED001_D93_SCC1.MED.131211.HiSeq2000.FCB.lane5.R1

text: ArrayExpress

text: house mouse

text: squamous cell carcinoma

text: Mus musculus

text: Mus musculus

text: Mus musculus


text: public

text: E-MTAB-2887:eMED001_D76_SCC1.MED.131211.HiSeq2000.FCB.lane5.R1

text: ArrayExpress

text: house mouse

text: squamous cell carcinoma

text: Mus musculus

text: Mus musculus

text: Mus musculus


text: public

text: E-MTAB-2887:eMED001_D60_SCC1.MED.131211.HiSeq2000.FCB.lane5.R1

text: ArrayExpress

text: house mouse

text: squamous cell carcinoma

text: Mus musculus

text: Mus musculus

text: Mus musculus


text: public

text: E-MTAB-2887:eMED001_D94_SCC1.MED.131211.HiSeq2000.FCB.lane5.R1

text: ArrayExpress

text: house mouse

text: squamous cell carcinoma

text: Mus musculus

text: Mus musculus

text: Mus musculus


text: public

text: E-MTAB-2887:eMED001_D88_SCC1.MED.131211.HiSeq2000.FCB.lane3.R1

text: ArrayExpress

text: house mouse

text: squamous cell carcinoma

text: Mus musculus

text: Mus musculus

text: Mus musculus


text: public

text: E-MTAB-2887:eMED001_D64_SCC1.MED.131211.HiSeq2000.FCB.lane5.R1

text: ArrayExpress

text: house mouse

text: squamous cell carcinoma

text: Mus musculus

text: Mus musculus

text: Mus musculus


text: public

text: E-MTAB-2887:eMED001_D89_SCC1.MED.131211.HiSeq2000.FCB.lane3.R1

text: ArrayExpress

text: house mouse

text: squamous cell carcinoma

text: Mus musculus

text: Mus musculus

text: Mus musculus


text: public

text: E-MTAB-2887:eMED001_D17_SCC1.MED.131211.HiSeq2000.FCB.lane6.R1

text: ArrayExpress

text: house mouse

text: squamous cell carcinoma

text: Mus musculus

text: Mus musculus

text: Mus musculus


text: public

text: E-MTAB-2887:eMED001_D92_SCC1.MED.131211.HiSeq2000.FCB.lane5.R1

text: ArrayExpress

text: house mouse

text: squamous cell carcinoma

text: Mus musculus

text: Mus musculus

text: Mus musculus


text: public

text: E-MTAB-2887:eMED001_D32_SCC2.MED.131211.HiSeq2000.FCB.lane5.R1

text: ArrayExpress

text: house mouse

text: squamous cell carcinoma

text: Mus musculus

text: Mus musculus

text: Mus musculus


text: public

text: E-MTAB-2887:eMED001_D88_SCC1.MED.131211.HiSeq2000.FCB.lane7.R1

text: ArrayExpress

text: house mouse

text: squamous cell carcinoma

text: Mus musculus

text: Mus musculus

text: Mus musculus


text: public

text: E-MTAB-2887:eMED001_D17_BM.MED.131211.HiSeq2000.FCB.lane4.R1

text: ArrayExpress

text: house mouse

text: BM

text: Mus musculus

text: Mus musculus

text: Mus musculus


text: public

text: E-MTAB-2887:eMED001_D93_SCC1.MED.131211.HiSeq2000.FCB.lane7.R1

text: ArrayExpress

text: house mouse

text: squamous cell carcinoma

text: Mus musculus

text: Mus musculus

text: Mus musculus


text: public

text: E-MTAB-2887:eMED001_D87_BM.MED.131211.HiSeq2000.FCB.lane4.R1

text: ArrayExpress

text: house mouse

text: BM

text: Mus musculus

text: Mus musculus

text: Mus musculus


text: public

text: E-MTAB-2887:eMED001_D76_SCC1.MED.131211.HiSeq2000.FCB.lane6.R1

text: ArrayExpress

text: house mouse

text: Protocols: Whole genome DNA libraries were created using the Illumina TruSeq DNA sample preparation kit V2 according to the manufacturers instructions and whole-exome capture was performed using the Nimblegen SeqCap EZ Developer Library kit (110624_MM9_Exome L2R_D02_EZ_HX1_9999042611).

text: squamous cell carcinoma

text: Mus musculus

text: Mus musculus

text: Mus musculus


text: Laboratory Translational Genetics Vesalius research Centre, VIB Department of Oncology, KU Leuven

text: public

text: E-MTAB-2887:eMED001_D91_SCC1.MED.131211.HiSeq2000.FCB.lane4.R1

text: ArrayExpress

text: house mouse

text: squamous cell carcinoma

text: Mus musculus

text: Mus musculus

text: Mus musculus


text: public

text: E-MTAB-2887:eMED001_D64_BM.MED.131211.HiSeq2000.FCB.lane4.R1

text: ArrayExpress

text: house mouse

text: BM

text: Mus musculus

text: Mus musculus

text: Mus musculus


text: public

text: E-MTAB-2887:eMED001_D60_SCC1.MED.131211.HiSeq2000.FCB.lane6.R1

text: ArrayExpress

text: house mouse

text: squamous cell carcinoma

text: Mus musculus

text: Mus musculus

text: Mus musculus


text: public

text: E-MTAB-2887:eMED001_D87_SCC1.MED.131211.HiSeq2000.FCB.lane4.R1

text: ArrayExpress

text: house mouse

text: squamous cell carcinoma

text: Mus musculus

text: Mus musculus

text: Mus musculus


text: public

text: E-MTAB-2887:eMED001_D53_SCC1.MED.131211.HiSeq2000.FCB.lane6.R1

text: ArrayExpress

text: house mouse

text: squamous cell carcinoma

text: Mus musculus

text: Mus musculus

text: Mus musculus


text: public

text: E-MTAB-2887:eMED001_D88_SCC1.MED.131211.HiSeq2000.FCB.lane5.R1

text: ArrayExpress

text: house mouse

text: squamous cell carcinoma

text: Mus musculus

text: Mus musculus

text: Mus musculus


text: public

text: E-MTAB-2887:eMED001_D60_BM.MED.131211.HiSeq2000.FCB.lane4.R1

text: ArrayExpress

text: house mouse

text: BM

text: Mus musculus

text: Mus musculus

text: Mus musculus


text: public

text: E-MTAB-2887:eMED001_D53_SCC1.MED.131211.HiSeq2000.FCB.lane4.R1

text: ArrayExpress

text: house mouse

text: squamous cell carcinoma

text: Mus musculus

text: Mus musculus

text: Mus musculus


text: public

text: E-MTAB-2887:eMED001_D53_SCC1.MED.131211.HiSeq2000.FCB.lane7.R1

text: ArrayExpress

text: house mouse

text: squamous cell carcinoma

text: Mus musculus

text: Mus musculus

text: Mus musculus


text: public

text: E-MTAB-2887:eMED001_D32_SCC2.MED.131211.HiSeq2000.FCB.lane4.R1

text: ArrayExpress

text: house mouse

text: squamous cell carcinoma

text: Mus musculus

text: Mus musculus

text: Mus musculus


text: public

text: E-MTAB-2887:eMED001_D32_SCC2.MED.131211.HiSeq2000.FCB.lane3.R1

text: ArrayExpress

text: house mouse

text: squamous cell carcinoma

text: Mus musculus

text: Mus musculus

text: Mus musculus


text: public

text: E-MTAB-2887:eMED001_D60_BM.MED.131211.HiSeq2000.FCB.lane7.R1

text: ArrayExpress

text: house mouse

text: BM

text: Mus musculus

text: Mus musculus

text: Mus musculus


text: public

text: E-MTAB-2887:eMED001_D91_SCC1.MED.131211.HiSeq2000.FCB.lane6.R1

text: ArrayExpress

text: house mouse

text: squamous cell carcinoma

text: Mus musculus

text: Mus musculus

text: Mus musculus


text: public

text: E-MTAB-2887:eMED001_D60_BM.MED.131211.HiSeq2000.FCB.lane3.R1

text: ArrayExpress

text: house mouse

text: BM

text: Mus musculus

text: Mus musculus

text: Mus musculus


text: public

text: E-MTAB-2887:eMED001_D91_SCC1.MED.131211.HiSeq2000.FCB.lane7.R1

text: ArrayExpress

text: house mouse

text: squamous cell carcinoma

text: Mus musculus

text: Mus musculus

text: Mus musculus


text: public

text: E-MTAB-2887:eMED001_D33_SCC2.MED.131211.HiSeq2000.FCB.lane4.R1

text: ArrayExpress

text: house mouse

text: Protocols: Whole genome DNA libraries were created using the Illumina TruSeq DNA sample preparation kit V2 according to the manufacturers instructions and whole-exome capture was performed using the Nimblegen SeqCap EZ Developer Library kit (110624_MM9_Exome L2R_D02_EZ_HX1_9999042611).

text: squamous cell carcinoma

text: Mus musculus

text: Mus musculus

text: Mus musculus


text: Laboratory Translational Genetics Vesalius research Centre, VIB Department of Oncology, KU Leuven

text: public

text: E-MTAB-2887:eMED001_D55_SCC1.MED.131211.HiSeq2000.FCB.lane6.R1

text: ArrayExpress

text: house mouse

text: squamous cell carcinoma

text: Mus musculus

text: Mus musculus

text: Mus musculus


text: public

text: E-MTAB-2887:eMED001_D17_SCC1.MED.131211.HiSeq2000.FCB.lane7.R1

text: ArrayExpress

text: house mouse

text: squamous cell carcinoma

text: Mus musculus

text: Mus musculus

text: Mus musculus


text: public

text: E-MTAB-2887:eMED001_D32_SCC2.MED.131211.HiSeq2000.FCB.lane6.R1

text: ArrayExpress

text: house mouse

text: squamous cell carcinoma

text: Mus musculus

text: Mus musculus

text: Mus musculus


text: public

text: E-MTAB-2887:eMED001_D17_SCC1.MED.131211.HiSeq2000.FCB.lane4.R1

text: ArrayExpress

text: house mouse

text: squamous cell carcinoma

text: Mus musculus

text: Mus musculus

text: Mus musculus


text: public

text: E-MTAB-2887:eMED001_D87_SCC1.MED.131211.HiSeq2000.FCB.lane6.R1

text: ArrayExpress

text: house mouse

text: squamous cell carcinoma

text: Mus musculus

text: Mus musculus

text: Mus musculus


text: public

text: E-MTAB-2887:eMED001_D60_SCC1.MED.131211.HiSeq2000.FCB.lane3.R1

text: ArrayExpress

text: house mouse

text: squamous cell carcinoma

text: Mus musculus

text: Mus musculus

text: Mus musculus


text: public

text: E-MTAB-2887:eMED001_D87_BM.MED.131211.HiSeq2000.FCB.lane5.R1

text: ArrayExpress

text: house mouse

text: BM

text: Mus musculus

text: Mus musculus

text: Mus musculus


text: public

text: E-MTAB-2887:eMED.MED001_T5.130118.FCA.lane1.R1

text: ArrayExpress

text: house mouse

text: squamous cell carcinoma

text: Mus musculus

text: Mus musculus

text: Mus musculus


text: public

text: E-MTAB-2887:eMED001_D32_SCC2.MED.131211.HiSeq2000.FCB.lane7.R1

text: ArrayExpress

text: house mouse

text: squamous cell carcinoma

text: Mus musculus

text: Mus musculus

text: Mus musculus


text: public

text: E-MTAB-2887:eMED001_D88_SCC1.MED.131211.HiSeq2000.FCB.lane6.R1

text: ArrayExpress

text: house mouse

text: squamous cell carcinoma

text: Mus musculus

text: Mus musculus

text: Mus musculus


text: public

text: E-MTAB-2887:eMED001_D55_SCC1.MED.131211.HiSeq2000.FCB.lane5.R1

text: ArrayExpress

text: house mouse

text: squamous cell carcinoma

text: Mus musculus

text: Mus musculus

text: Mus musculus


text: public

text: E-MTAB-2887:eMED001_D92_SCC1.MED.131211.HiSeq2000.FCB.lane3.R1

text: ArrayExpress

text: house mouse

text: squamous cell carcinoma

text: Mus musculus

text: Mus musculus

text: Mus musculus


text: public

text: E-MTAB-2887:eMED001_D17_BM.MED.131211.HiSeq2000.FCB.lane6.R1

text: ArrayExpress

text: house mouse

text: BM

text: Mus musculus

text: Mus musculus

text: Mus musculus


text: public

text: E-MTAB-2887:eMED001_D33_SCC2.MED.131211.HiSeq2000.FCB.lane5.R1

text: ArrayExpress

text: house mouse

text: squamous cell carcinoma

text: Mus musculus

text: Mus musculus

text: Mus musculus


text: public

text: E-MTAB-2887:eMED001_D53_SCC1.MED.131211.HiSeq2000.FCB.lane5.R1

text: ArrayExpress

text: house mouse

text: squamous cell carcinoma

text: Mus musculus

text: Mus musculus

text: Mus musculus


text: public

text: E-MTAB-2887:eMED001_T3_R1.MED.lane8.121019FCA.R1

text: ArrayExpress

text: house mouse

text: Protocols: Whole genome DNA libraries were created using the Illumina TruSeq DNA sample preparation kit V2 according to the manufacturers instructions and whole-exome capture was performed using the Nimblegen SeqCap EZ Developer Library kit (110624_MM9_Exome L2R_D02_EZ_HX1_9999042611).

text: squamous cell carcinoma

text: Mus musculus

text: Mus musculus

text: Mus musculus


text: Laboratory Translational Genetics Vesalius research Centre, VIB Department of Oncology, KU Leuven

text: public

text: E-MTAB-2887:eMED001_D91_SCC1.MED.131211.HiSeq2000.FCB.lane5.R1

text: ArrayExpress

text: house mouse

text: squamous cell carcinoma

text: Mus musculus

text: Mus musculus

text: Mus musculus


text: public

text: E-MTAB-2887:eMED.MED001_T5.130118.FCA.lane2.R1

text: ArrayExpress

text: house mouse

text: squamous cell carcinoma

text: Mus musculus

text: Mus musculus

text: Mus musculus


text: public

text: E-MTAB-2887:eMED001_D94_SCC1.MED.131211.HiSeq2000.FCB.lane4.R1

text: ArrayExpress

text: house mouse

text: squamous cell carcinoma

text: Mus musculus

text: Mus musculus

text: Mus musculus


text: public

text: E-MTAB-2887:eMED001_D93_SCC1.MED.131211.HiSeq2000.FCB.lane3.R1

text: ArrayExpress

text: house mouse

text: squamous cell carcinoma

text: Mus musculus

text: Mus musculus

text: Mus musculus


text: public

text: E-MTAB-2887:eMED001_D60_SCC1.MED.131211.HiSeq2000.FCB.lane4.R1

text: ArrayExpress

text: house mouse

text: squamous cell carcinoma

text: Mus musculus

text: Mus musculus

text: Mus musculus


text: public

text: E-MTAB-2887:eMED001_D64_SCC1.MED.131211.HiSeq2000.FCB.lane7.R1

text: ArrayExpress

text: house mouse

text: squamous cell carcinoma

text: Mus musculus

text: Mus musculus

text: Mus musculus


text: public

text: E-MTAB-2887:eMED001_D55_SCC1.MED.131211.HiSeq2000.FCB.lane7.R1

text: ArrayExpress

text: house mouse

text: squamous cell carcinoma

text: Mus musculus

text: Mus musculus

text: Mus musculus


text: public

text: E-MTAB-2887:eMED001_D76_SCC1.MED.131211.HiSeq2000.FCB.lane4.R1

text: ArrayExpress

text: house mouse

text: squamous cell carcinoma

text: Mus musculus

text: Mus musculus

text: Mus musculus


text: public

text: E-MTAB-2887:eMED001_D93_SCC1.MED.131211.HiSeq2000.FCB.lane6.R1

text: ArrayExpress

text: house mouse

text: squamous cell carcinoma

text: Mus musculus

text: Mus musculus

text: Mus musculus


text: public

text: E-MTAB-2887:eMED001_D92_SCC1.MED.131211.HiSeq2000.FCB.lane6.R1

text: ArrayExpress

text: house mouse

text: squamous cell carcinoma

text: Mus musculus

text: Mus musculus

text: Mus musculus


text: public

text: E-MTAB-2887:eMED001_D64_SCC1.MED.131211.HiSeq2000.FCB.lane3.R1

text: ArrayExpress

text: house mouse

text: squamous cell carcinoma

text: Mus musculus

text: Mus musculus

text: Mus musculus


text: public

text: E-MTAB-2887:eMED001_D17_BM.MED.131211.HiSeq2000.FCB.lane7.R1

text: ArrayExpress

text: house mouse

text: BM

text: Mus musculus

text: Mus musculus

text: Mus musculus


text: public

text: E-MTAB-2887:eMED001_D94_BM.MED.131211.HiSeq2000.FCB.lane3.R1

text: ArrayExpress

text: house mouse

text: BM

text: Mus musculus

text: Mus musculus

text: Mus musculus


text: public

text: E-MTAB-2887:eMED001_D89_SCC1.MED.131211.HiSeq2000.FCB.lane6.R1

text: ArrayExpress

text: house mouse

text: squamous cell carcinoma

text: Mus musculus

text: Mus musculus

text: Mus musculus


text: public

text: E-MTAB-2887:eMED001_D60_BM.MED.131211.HiSeq2000.FCB.lane5.R1

text: ArrayExpress

text: house mouse

text: BM

text: Mus musculus

text: Mus musculus

text: Mus musculus


text: public

text: E-MTAB-2887:eMED001_D64_BM.MED.131211.HiSeq2000.FCB.lane6.R1

text: ArrayExpress

text: house mouse

text: Protocols: Whole genome DNA libraries were created using the Illumina TruSeq DNA sample preparation kit V2 according to the manufacturers instructions and whole-exome capture was performed using the Nimblegen SeqCap EZ Developer Library kit (110624_MM9_Exome L2R_D02_EZ_HX1_9999042611).

text: BM

text: Mus musculus

text: Mus musculus

text: Mus musculus


text: Laboratory Translational Genetics Vesalius research Centre, VIB Department of Oncology, KU Leuven

text: public

text: E-MTAB-2887:eMED001_D76_SCC1.MED.131211.HiSeq2000.FCB.lane7.R1

text: ArrayExpress

text: house mouse

text: squamous cell carcinoma

text: Mus musculus

text: Mus musculus

text: Mus musculus


text: public

text: E-MTAB-2887:eMED001_D94_BM.MED.131211.HiSeq2000.FCB.lane5.R1

text: ArrayExpress

text: house mouse

text: BM

text: Mus musculus

text: Mus musculus

text: Mus musculus


text: public

text: E-MTAB-2887:eMED001_D94_SCC1.MED.131211.HiSeq2000.FCB.lane7.R1

text: ArrayExpress

text: house mouse

text: squamous cell carcinoma

text: Mus musculus

text: Mus musculus

text: Mus musculus


text: public

text: E-MTAB-2887:eMED001_D53_SCC1.MED.131211.HiSeq2000.FCB.lane3.R1

text: ArrayExpress

text: house mouse

text: squamous cell carcinoma

text: Mus musculus

text: Mus musculus

text: Mus musculus


text: public

text: E-MTAB-2887:eMED001_D94_BM.MED.131211.HiSeq2000.FCB.lane6.R1

text: ArrayExpress

text: house mouse

text: BM

text: Mus musculus

text: Mus musculus

text: Mus musculus


text: public

text: E-MTAB-2887:eMED001_D60_BM.MED.131211.HiSeq2000.FCB.lane6.R1

text: ArrayExpress

text: house mouse

text: BM

text: Mus musculus

text: Mus musculus

text: Mus musculus


text: public

text: E-MTAB-2887:eMED001_D33_SCC2.MED.131211.HiSeq2000.FCB.lane6.R1

text: ArrayExpress

text: house mouse

text: squamous cell carcinoma

text: Mus musculus

text: Mus musculus

text: Mus musculus


text: public

text: E-MTAB-2887:eMED001_D91_SCC1.MED.131211.HiSeq2000.FCB.lane3.R1

text: ArrayExpress

text: house mouse

text: squamous cell carcinoma

text: Mus musculus

text: Mus musculus

text: Mus musculus


text: public

text: E-MTAB-2887:eMED001_D89_SCC1.MED.131211.HiSeq2000.FCB.lane4.R1

text: ArrayExpress

text: house mouse

text: squamous cell carcinoma

text: Mus musculus

text: Mus musculus

text: Mus musculus


text: public

text: E-MTAB-2887:eMED001_D64_BM.MED.131211.HiSeq2000.FCB.lane5.R1

text: ArrayExpress

text: house mouse

text: BM

text: Mus musculus

text: Mus musculus

text: Mus musculus


text: public

text: E-MTAB-2887:eMED001_D55_SCC1.MED.131211.HiSeq2000.FCB.lane4.R1

text: ArrayExpress

text: house mouse

text: squamous cell carcinoma

text: Mus musculus

text: Mus musculus

text: Mus musculus


text: public

text: E-MTAB-2887:eMED001_D17_BM.MED.131211.HiSeq2000.FCB.lane5.R1

text: ArrayExpress

text: house mouse

text: BM

text: Mus musculus

text: Mus musculus

text: Mus musculus


text: public

text: E-MTAB-2887:eMED001_D55_SCC1.MED.131211.HiSeq2000.FCB.lane3.R1

text: ArrayExpress

text: house mouse

text: squamous cell carcinoma

text: Mus musculus

text: Mus musculus

text: Mus musculus


text: public

text: E-MTAB-2887:eMED001_D94_BM.MED.131211.HiSeq2000.FCB.lane4.R1

text: ArrayExpress

text: house mouse

text: BM

text: Mus musculus

text: Mus musculus

text: Mus musculus


text: public

text: E-MTAB-2887:eMED001_D33_SCC2.MED.131211.HiSeq2000.FCB.lane3.R1

text: ArrayExpress

text: house mouse

text: squamous cell carcinoma

text: Mus musculus

text: Mus musculus

text: Mus musculus


text: public

text: E-MTAB-2887:eMED001_D64_SCC1.MED.131211.HiSeq2000.FCB.lane4.R1

text: ArrayExpress

text: house mouse

text: Protocols: Whole genome DNA libraries were created using the Illumina TruSeq DNA sample preparation kit V2 according to the manufacturers instructions and whole-exome capture was performed using the Nimblegen SeqCap EZ Developer Library kit (110624_MM9_Exome L2R_D02_EZ_HX1_9999042611).

text: squamous cell carcinoma

text: Mus musculus

text: Mus musculus

text: Mus musculus


text: Laboratory Translational Genetics Vesalius research Centre, VIB Department of Oncology, KU Leuven

text: public

text: E-MTAB-2887:eMED001_D76_SCC1.MED.131211.HiSeq2000.FCB.lane3.R1

text: ArrayExpress

text: house mouse

text: squamous cell carcinoma

text: Mus musculus

text: Mus musculus

text: Mus musculus


text: public

text: E-MTAB-2887:eMED001_D92_SCC1.MED.131211.HiSeq2000.FCB.lane7.R1

text: ArrayExpress

text: house mouse

text: squamous cell carcinoma

text: Mus musculus

text: Mus musculus

text: Mus musculus


text: public

text: E-MTAB-2887:eMED001_T1_R1.MED.lane8.121019FCA.R1

text: ArrayExpress

text: house mouse

text: squamous cell carcinoma

text: Mus musculus

text: Mus musculus

text: Mus musculus


text: public

text: E-MTAB-2887:eMED001_D94_SCC1.MED.131211.HiSeq2000.FCB.lane3.R1

text: ArrayExpress

text: house mouse

text: squamous cell carcinoma

text: Mus musculus

text: Mus musculus

text: Mus musculus


text: public

text: E-MTAB-2887:eMED.MED001_N1.130118.FCA.lane2.R1

text: ArrayExpress

text: house mouse

text: BM

text: Mus musculus

text: Mus musculus

text: Mus musculus


text: public

text: E-MTAB-2887:eMED001_D92_SCC1.MED.131211.HiSeq2000.FCB.lane4.R1

text: ArrayExpress

text: house mouse

text: squamous cell carcinoma

text: Mus musculus

text: Mus musculus

text: Mus musculus


text: public

text: E-MTAB-2887:eMED001_T4_R1.MED.lane8.121019FCA.R1

text: ArrayExpress

text: house mouse

text: squamous cell carcinoma

text: Mus musculus

text: Mus musculus

text: Mus musculus


text: public

text: E-MTAB-2887:eMED001_D17_BM.MED.131211.HiSeq2000.FCB.lane3.R1

text: ArrayExpress

text: house mouse

text: BM

text: Mus musculus

text: Mus musculus

text: Mus musculus


text: public

text: E-MTAB-2887:eMED001_D87_BM.MED.131211.HiSeq2000.FCB.lane7.R1

text: ArrayExpress

text: house mouse

text: BM

text: Mus musculus

text: Mus musculus

text: Mus musculus


text: public

text: E-MTAB-2887:eMED001_D94_SCC1.MED.131211.HiSeq2000.FCB.lane6.R1

text: ArrayExpress

text: house mouse

text: squamous cell carcinoma

text: Mus musculus

text: Mus musculus

text: Mus musculus


text: public

text: E-MTAB-2887:eMED001_D17_SCC1.MED.131211.HiSeq2000.FCB.lane3.R1

text: ArrayExpress

text: house mouse

text: squamous cell carcinoma

text: Mus musculus

text: Mus musculus

text: Mus musculus


text: IOA

text: public

text: Slovenia

text: Mediterranean mussel

text: Mytilus galloprovincialis

text: Mytilus galloprovincialis


text: IOA

text: public

text: Canada

text: common blue mussel

text: Mytilus trossulus

text: Mytilus trossulus


text: public

tag: Namespace:Institute for Genetics University of Cologne

text: ArrayExpress

text: HeLa

characteristic: cell line

text: human

text: Protocols: Standard lab conditions were used to grow the HeLa cells used for these experiments HeLa cells were grown over night in 6 cm plates and transiently transfected with 300 pmol siRNA using Lipofectamine RNAiMAX (Life Technologies). 24 h post transfection the cells were split 1:2 in 10 cm plates and the day after transfected again with 600 pmol siRNA. RNA samples were obtained from XRN1 knockdown HeLa cells transfected with the indicated reporter mRNA expressing plasmids (TPI-WT or -PTCs). Total RNA was extracted using Isol-RNA-Lysis Reagent. 3' fragments were linker ligated, reverse transcribed and specific PCR products were amplified with gene specific primers.

text: Endo SMG5

characteristic: fraction

text: XRN1 siRNA-mediated knockdown

characteristic: genotype

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: Institute for Genetics University of Cologne

text: public

text: ArrayExpress

text: HeLa

text: human

text: Endo SMG5

text: XRN1 siRNA-mediated knockdown

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: Homo sapiens


characteristic: External Id

characteristic: INSDC first public

text: public

text: ArrayExpress

text: HeLa

text: human

text: TPI PTC48

text: XRN1 siRNA-mediated knockdown

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens

characteristic: title


characteristic: ENA-LAST-UPDATE

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: ArrayExpress

text: HeLa

text: human

text: TPI WT

text: XRN1 siRNA-mediated knockdown

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens


characteristic: INSDC center name

text: public

characteristic: SRA accession

text: ArrayExpress

text: HeLa

text: human

text: TPI PTC100

text: XRN1 siRNA-mediated knockdown

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens


text: public

characteristic: Submitter Id

text: ArrayExpress

characteristic: broker name

text: HeLa

text: human

text: TPI PTC189

text: XRN1 siRNA-mediated knockdown

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens


text: public

text: ArrayExpress

text: HeLa

text: human

characteristic: common name

characteristic: description

text: TPI PTC120

text: XRN1 siRNA-mediated knockdown

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens