text: public

characteristic: INSDC status

tag: Namespace:Molecular BioSciences Goethe University of Frankfurt a.M.

text: ArrayExpress

text: human

text: Protocols: Tissue samples were obtained from six patients with PDAC who underwent resection at the Department of Surgery, Technical University of Munich, Germany. Normal pancreatic tissue samples from five patients without pancreatic ductal adenocarcinoma were used as controls. Tissue collection was approved by the Ethics Committee of the Technical University of Munich and informed consent was obtained from all patients. Tissue were collected directly in the operating theatre and were immediately stored at -80 degree C until analysis. 20 mg of frozen tissue were disrupted and homogenized (TissueLyser, Qiagen) and RNA was isolated (NucleoSpin miRNA Kit, Macherey-Nagel) in two fractions (small RNA < 200 nt and large RNA > 200 nt). For preparation of small RNA libraries, 5 ug RNA (small RNA fraction) was size-selected (< 40 nt) by polyacrylamide gel electrophoresis (FlashPAGE, Life Technologies) and precipitated. About 30 ng small RNA (< 40 nt) was successive ligated (T4 RNA Ligase 1 and T4 RNA Ligase 2, NEB) to modified 3 prime and 5 prime adapters (TrueQuant RNA adapters, GenXPro). Adapter-ligated RNA was reverse transcribed (SuperScript III, Life Technologies) and amplified by PCR (KAPA HiFi Hot-Start Polymerase, KAPA Biosystems). Amplified libraries were size-selected by polyacrylamide gel electrophoresis (PAGE) .

text: pancreatic ductal adenocarcinoma

characteristic: disease

text: Homo sapiens

text: Homo sapiens

text: pancreas

characteristic: organism part

text: Homo sapiens


status: PUBLIC

tag: attribute

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Molecular BioSciences Goethe University of Frankfurt a.M.

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: SRA accession

characteristic: Submitter Id

text: ArrayExpress

characteristic: broker name

text: human

characteristic: common name

characteristic: description

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: pancreas

text: Homo sapiens

characteristic: title

type: has member


text: public

characteristic: INSDC status

text: ArrayExpress

text: human

text: pancreatic ductal adenocarcinoma

text: Homo sapiens

text: Homo sapiens

text: pancreas

text: Homo sapiens


text: public

text: E-MTAB-2888_2:sMED001_D75_PAP3.150208.HiSeq2000.FCB.lane2.R1.fastq.gz

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

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 μl of 0,25 mg/ml solution in acetone) was applied on the shaved backskin of 28 days old mice, then TPA (200 μl 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 manufacturer’s instructions

text: squamous cell carcinoma

characteristic: disease

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_2:sMED001_D71_PAP4.150208.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: public

text: E-MTAB-2888_2:sMED003_T1.150203.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: public

text: E-MTAB-2888_2:sMED004_T1.150203.HiSeq2000.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_2:sMED001_D69_PAP1.150208.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: public

text: E-MTAB-2888_2:sMED001_D76_PAP1.150208.HiSeq2000.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_2:sMED001_D75_PAP2.150208.HiSeq2000.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_2:MED006_T1.150201.HiSeq2000.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_2:sMED001_D69_PAP2.150208.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: public

text: E-MTAB-2888_2:sMED001_D75_PAP4.150208.HiSeq2000.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_2:MED002_T2.150201.HiSeq2000.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_2:sMED001_D71_PAP4.150208.HiSeq2000.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_2:sMED001_D73_PAP3.150208.HiSeq2000.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_2:sMED005_T1.150203.HiSeq2000.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_2:sMED001_D73_PAP2.150208.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: public

text: E-MTAB-2888_2:sMED005_T1.150203.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: public

text: E-MTAB-2888_2:sMED001_D75_PAP4.150208.HiSeq2000.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 μl of 0,25 mg/ml solution in acetone) was applied on the shaved backskin of 28 days old mice, then TPA (200 μl 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 manufacturer’s 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_2:sMED002_T1.150203.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: public

text: E-MTAB-2888_2:sMED001_D75_PAP3.150208.HiSeq2000.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_2:MED002_T2.150201.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: public

text: E-MTAB-2888_2:sMED001_D73_PAP3.150208.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: public

text: E-MTAB-2888_2:sMED001_D69_PAP1.150208.HiSeq2000.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_2:sMED002_T1.150203.HiSeq2000.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_2:sMED001_D75_PAP2.150208.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: public

text: E-MTAB-2888_2:sMED003_T1.150203.HiSeq2000.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_2:sMED001_D73_PAP2.150208.HiSeq2000.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_2:sMED001_D76_PAP1.150208.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: public

text: E-MTAB-2888_2:sMED004_T1.150203.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: public

text: E-MTAB-2888_2:MED006_T1.150201.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: public

text: E-MTAB-2888_2:sMED001_D69_PAP2.150208.HiSeq2000.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

tag: Namespace:IHSM-UMA-CSIC Universidad de Malaga. Dep. de Biologia Molecular y Bioquimica

text: ArrayExpress

text: strawberry

text: Biological Replicate 3 Protocols: Red ripped strawberry fruits RNA extraction 2-Butoxyetanol Osorio Illumina Protocol

text: ripening

characteristic: developmental stage

text: Fragaria x ananassa

text: Fragaria x ananassa

text: fruit

characteristic: organism part

text: Fragaria x ananassa

text: Camarosa'

characteristic: strain


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: IHSM-UMA-CSIC Universidad de Malaga. Dep. de Biologia Molecular y Bioquimica

text: public

text: ArrayExpress

text: strawberry

text: Biological Replicate 1 Protocols: Red ripped strawberry fruits RNA extraction 2-Butoxyetanol Osorio Illumina Protocol

text: ripening

text: Fragaria x ananassa

text: Fragaria x ananassa

text: fruit

text: Fragaria x ananassa

text: Camarosa'


characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: ArrayExpress

text: strawberry

text: Biological Replicate 2 Protocols: Red ripped strawberry fruits RNA extraction 2-Butoxyetanol Osorio Illumina Protocol

text: ripening

text: FaGAMYB silenced

characteristic: genotype

text: Fragaria x ananassa

text: Fragaria x ananassa

text: fruit

text: Fragaria x ananassa

text: Camarosa'


characteristic: INSDC last update

text: public

characteristic: SRA accession

characteristic: Submitter Id

text: ArrayExpress

characteristic: broker name

text: strawberry

text: ripening

text: FaGAMYB silenced

text: Fragaria x ananassa

text: Fragaria x ananassa

text: fruit

text: Fragaria x ananassa

text: Camarosa'


text: public

text: ArrayExpress

text: strawberry

characteristic: common name

characteristic: description

text: ripening

text: Fragaria x ananassa

characteristic: organism

text: Fragaria x ananassa

text: fruit

text: Fragaria x ananassa

text: Camarosa'

characteristic: title


text: public

characteristic: INSDC status

text: ArrayExpress

text: strawberry

text: ripening

characteristic: developmental stage

text: FaGAMYB silenced

text: Fragaria x ananassa

text: Fragaria x ananassa

text: fruit

characteristic: organism part

text: Fragaria x ananassa

text: Camarosa'


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: IPK-Gatersleben

text: public

text: domesticated barley

text: Sequencing of barley BACs, that constitute the MTP of chromosome 3H

text: Hordeum vulgare subsp. vulgare

text: Hordeum vulgare subsp. vulgare


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: public

tag: Namespace:Genome Organization & Function (B066) German Cancer Research Center and BioQuant

text: ArrayExpress

characteristic: cell line

text: human

text: Protocols: Cells were grown in DMEM medium containing 10% FCS, at 37 degree C and 5% CO2 supply. Cells were transfected for 14 hours with transfection reagent only (Mock), with a control antisense oligonucleotide (ControlASO) or with an antisense oligonucleotide targeting alu-repeat containing RNA transcripts (AluASO). RNA was extracted from whole cells or cellular fractions (nucleoplasmic = nuclear minus nucleoli; nucleoli = isolated nucleoli) using the RNeasy Mini Kit from Qiagen. Libraries were prepared using the NEB library prep kit for long RNAs.

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens

text: AluASO

characteristic: treatment


text: Genome Organization & Function (B066) German Cancer Research Center and BioQuant

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: ArrayExpress

text: human

text: Protocols: Cells were grown in DMEM medium containing 10% FCS, at 37 degree C and 5% CO2 supply. no treatment RNA was extracted from whole cells or cellular fractions (nucleoplasmic = nuclear minus nucleoli; nucleoli = isolated nucleoli) using the RNeasy Mini Kit from Qiagen. Libraries were prepared using the NEB library prep kit for long RNAs.

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens


text: public

characteristic: SRA accession

characteristic: Submitter Id

text: ArrayExpress

characteristic: broker name

text: human

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens

text: ControlASO

text: control antisense oligonucleotide


text: public

text: ArrayExpress

text: human

characteristic: common name

characteristic: description

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: Homo sapiens

text: Mock

text: transfection reagent only (mock RNAi)


text: public

characteristic: INSDC status

text: ArrayExpress

text: human

text: Protocols: Cells were grown in DMEM medium containing 10% FCS, at 37 degree C and 5% CO2 supply. Cells were incubated 5 hours with ML-60218 (200 uM) to specifically inhibit RNA polymerase III. RNA was extracted from whole cells or cellular fractions (nucleoplasmic = nuclear minus nucleoli; nucleoli = isolated nucleoli) using the RNeasy Mini Kit from Qiagen. Libraries were prepared using the NEB library prep kit for long RNAs.

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens

characteristic: title

text: ML60218 (RNA pol III inhibitor)


characteristic: ENA-CHECKLIST

text: public

text: ArrayExpress

text: human

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens

text: Nucleoplasmic-RNA


characteristic: ENA-FIRST-PUBLIC

text: public

text: ArrayExpress

text: human

text: Protocols: Cells were grown in DMEM medium containing 10% FCS, at 37 degree C and 5% CO2 supply. Cell were incubated 5 hours with alpha-amanitin (50 ug/ml) to specifically inhibit RNA polymerase II. RNA was extracted from whole cells or cellular fractions (nucleoplasmic = nuclear minus nucleoli; nucleoli = isolated nucleoli) using the RNeasy Mini Kit from Qiagen. Libraries were prepared using the NEB library prep kit for long RNAs.

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens

text: Amanitin (RNA pol II inhibitor)


characteristic: ENA-LAST-UPDATE

text: EMBL

text: public

text: ArrayExpress

text: mouse embryonic stem cell

characteristic: cell type

text: house mouse

text: Protocols: Chromosome conformation capture was performed starting from 1x107 cells, cross-linked in 2% formaldehyde. Inducible RsCre Rif1 ES cells have been cultured for two and four days in presence of tamoxifen Primary restriction digest was performed by incubation with HindIII, while for the secondary digest we have chosen the 4-bp cutter DpnII.

characteristic: genotype

text: Mus musculus

text: Mus musculus

text: Mus musculus

text: LL

characteristic: viewpoint


characteristic: External Id

text: EMBL

characteristic: INSDC center name

text: public

text: ArrayExpress

text: mouse embryonic stem cell

text: house mouse

text: Mus musculus

text: Mus musculus

text: Mus musculus


E-MTAB-3502:Rif1FH ESC clone FH12in

text: EMBL

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: E-MTAB-3502:Rif1FH ESC clone FH12in

text: ArrayExpress

text: mouse embryonic stem cell

text: house mouse

text: Protocols: 3 independent embryonic stem cells (ESCs) lines carrying an homozygous allele encoding for an N-terminal FLAG-HA2 Rif1 were used for ChIP seq to determine the genome-wide Ri1f occupancy. Littermate wild type cells were used as negative controls. ChIP-seq libraries were prepared with NEBNext ChIP-Seq Library Prep Master Mix Set for Illumina (NEB#E6240S/L), except that bead purification was employed (Agencourt AMPure XP beads, Beckman Coulter A63881). Size selection was performed on 2% agarose gels (E-Gel Invitrogen G6610-02). Generally 13 PCR cycles for 10ng starting material were applied. Libraries were barcoded with the NEBNext Multiplex Oligos for Illumina (Index Primers Set 1, NEB#E7335S/L).

text: Mus musculus

text: Mus musculus

text: Mus musculus

text: Rif1FH ESC clone FH12in


E-MTAB-3502:Rif1FH ESC clone FH11

text: EMBL

text: public

characteristic: SRA accession

text: E-MTAB-3502:Rif1FH ESC clone FH11

characteristic: Submitter Id

text: ArrayExpress

text: mouse embryonic stem cell

text: house mouse

text: Mus musculus

text: Mus musculus

text: Mus musculus

text: Rif1FH ESC clone FH11


E-MTAB-3502:Rif1FH ESC clone FH11in

text: EMBL

text: public

text: E-MTAB-3502:Rif1FH ESC clone FH11in

text: ArrayExpress

characteristic: broker name

text: mouse embryonic stem cell

text: house mouse

characteristic: common name

text: Mus musculus

text: Mus musculus

text: Mus musculus

text: Rif1FH ESC clone FH11in


E-MTAB-3502:Rif1FH ESC clone FH16in

text: EMBL

text: public

text: E-MTAB-3502:Rif1FH ESC clone FH16in

text: ArrayExpress

text: mouse embryonic stem cell

text: house mouse

characteristic: description

text: Mus musculus

characteristic: organism

text: Mus musculus

text: Mus musculus

text: Rif1FH ESC clone FH16in


E-MTAB-3502:Rif1FH ESC clone FH16

text: EMBL

text: public

characteristic: INSDC status

text: E-MTAB-3502:Rif1FH ESC clone FH16

text: ArrayExpress

text: mouse embryonic stem cell

text: house mouse

text: Mus musculus

text: Mus musculus

text: Mus musculus

text: Rif1FH ESC clone FH16

characteristic: title


E-MTAB-3502:Rif1FH ESC clone FH12

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: EMBL

text: public

text: E-MTAB-3502:Rif1FH ESC clone FH12

text: ArrayExpress

text: mouse embryonic stem cell

text: house mouse

text: Mus musculus

text: Mus musculus

text: Mus musculus

text: Rif1FH ESC clone FH12


characteristic: ENA-LAST-UPDATE

text: NCGR

text: public

text: Japanese rice

text: ssRNA-seq of cDNA sample from wide-type rice leaf

text: Oryza sativa Japonica Group

text: Oryza sativa Japonica Group


text: NCGR

text: public

text: Japanese rice

text: ssRNA-seq of cDNA sample from transgenic line of rice leaf

text: Oryza sativa Japonica Group

text: Oryza sativa Japonica Group


text: NCGR

text: public

text: Japanese rice

text: ssRNA-seq of cDNA sample from wide-type rice panicle

text: Oryza sativa Japonica Group

text: Oryza sativa Japonica Group


text: NCGR

text: public

text: Japanese rice

text: ssRNA-seq of cDNA sample from transgenic line of rice panicle

text: Oryza sativa Japonica Group

text: Oryza sativa Japonica Group


text: EMBL

text: public

text: ArrayExpress

text: primary mouse embryonic fibroblast

characteristic: cell type

text: house mouse

text: Protocols: Chromosome conformation capture was performed starting from 1x107 cells, cross-linked in 2% formaldehyde. Rif1F/F Rosa26Cre-ERT2 pMEF synchronized in G1 have been treated with tamoxifen to activate the Cre and induce the deletion (pMEF_Rif1 ko). Rif1+/+ Rosa26Cre-ERT2 pMEF were treated in parallel (pMEF_Rif1wt) Primary restriction digest was performed by incubation with HindIII, while for the secondary digest we have chosen the 4-bp cutter DpnII.

characteristic: genotype

text: Mus musculus

text: Mus musculus

text: Mus musculus

text: EE


characteristic: External Id

text: EMBL

text: public

text: ArrayExpress

text: primary mouse embryonic fibroblast

text: house mouse

text: Mus musculus

text: Mus musculus

text: Mus musculus

characteristic: viewpoint


text: EMBL

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: ArrayExpress

text: primary mouse embryonic fibroblast

text: house mouse

text: Mus musculus

text: Mus musculus

text: Mus musculus

text: LL


characteristic: INSDC last update

text: public

characteristic: SRA accession

text: E-MTAB-2889_2:MED_D86_SCC_RNA.150203.HiSeq2000.FCB.lane1.R1.fastq.gz

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

text: ArrayExpress

text: house mouse

text: Protocols: Collection of murine skin or mSCC. Samples with names starting with “MED_skin” are those of normal skin, of the same mouse colony which developed mouse squamous cell carcinoma at a later stage RNA libraries were created using the Illumina TruSeq RNA sample preparation kit V2 according to the manufacturer’s instructions.

text: squamous cell carcinoma

characteristic: disease

characteristic: individual

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-2889_2:MED_SkinB2_SCC_RNA.150301.HiSeq2000.FCB.lane2.R1.fastq.gz

characteristic: Submitter Id

text: ArrayExpress

characteristic: broker name

text: house mouse

characteristic: common name

characteristic: description

text: normal

text: Mus musculus

text: Mus musculus

text: skin

characteristic: organism part

text: Mus musculus


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: public

characteristic: INSDC status

text: E-MTAB-2889_2:MED_D81_SCC_RNA.150203.HiSeq2000.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

characteristic: title


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: public

text: E-MTAB-2889_2:MED_SkinB2_SCC_RNA.150301.HiSeq2000.FCB.lane1.R1.fastq.gz

text: ArrayExpress

text: house mouse

text: normal

text: Mus musculus

text: Mus musculus

text: skin

text: Mus musculus


characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: E-MTAB-2889_2:MED_D86_SCC_RNA.150203.HiSeq2000.FCB.lane2.R1.fastq.gz

text: ArrayExpress

text: house mouse

text: squamous cell carcinoma

text: Mus musculus

text: Mus musculus

text: Mus musculus


characteristic: INSDC last update

text: public

characteristic: SRA accession

text: E-MTAB-2889_2:MED_SkinB4_SCC_RNA.150301.HiSeq2000.FCB.lane2.R1.fastq.gz

text: ArrayExpress

text: house mouse

text: normal

text: Mus musculus

text: Mus musculus

text: skin

text: Mus musculus


text: public

text: E-MTAB-2889_2:MED_SkinB1_SCC_RNA.150301.HiSeq2000.FCB.lane2.R1.fastq.gz

text: ArrayExpress

text: house mouse

text: normal

characteristic: disease

text: Mus musculus

text: Mus musculus

text: skin

text: Mus musculus


text: public

text: E-MTAB-2889_2:MED_Skin2_SCC_RNA.150203.HiSeq2000.FCB.lane1.R1.fastq.gz

characteristic: Submitter Id

text: ArrayExpress

text: house mouse

text: normal

text: Mus musculus

text: Mus musculus

text: skin

text: Mus musculus


text: public

text: E-MTAB-2889_2:MED_Skin2_SCC_RNA.150203.HiSeq2000.FCB.lane2.R1.fastq.gz

text: ArrayExpress

characteristic: broker name

text: house mouse

text: normal

text: Mus musculus

text: Mus musculus

text: skin

text: Mus musculus


text: public

text: E-MTAB-2889_2:MED_SkinB3_SCC_RNA.150301.HiSeq2000.FCB.lane1.R1.fastq.gz

text: ArrayExpress

text: house mouse

characteristic: common name

text: normal

text: Mus musculus

text: Mus musculus

text: skin

text: Mus musculus


text: public

text: E-MTAB-2889_2:MED_SkinB4_SCC_RNA.150301.HiSeq2000.FCB.lane1.R1.fastq.gz

text: ArrayExpress

text: house mouse

characteristic: description

text: normal

text: Mus musculus

text: Mus musculus

text: skin

text: Mus musculus


text: public

text: E-MTAB-2889_2:MED_SkinB1_SCC_RNA.150301.HiSeq2000.FCB.lane1.R1.fastq.gz

text: ArrayExpress

text: house mouse

text: normal

text: Mus musculus

text: Mus musculus

text: skin

characteristic: organism part

text: Mus musculus


characteristic: ENA-CHECKLIST

text: public

text: E-MTAB-2889_2:MED_SkinB3_SCC_RNA.150301.HiSeq2000.FCB.lane2.R1.fastq.gz

text: ArrayExpress

text: house mouse

text: normal

text: Mus musculus

text: Mus musculus

text: skin

text: Mus musculus


characteristic: ENA-FIRST-PUBLIC

text: public

text: E-MTAB-2889_2:MED_D81_SCC_RNA.150203.HiSeq2000.FCB.lane1.R1.fastq.gz

text: ArrayExpress

text: house mouse

text: squamous cell carcinoma

characteristic: individual

text: Mus musculus

text: Mus musculus

text: Mus musculus


text: Plasmodium falciparum

characteristic: ArrayExpress-Species

text: SC

text: public

characteristic: INSDC status

text: malaria parasite P. falciparum

text: Plasmodium falciparum

characteristic: organism

text: Plasmodium falciparum


text: Danio rerio

characteristic: ENA-LAST-UPDATE

characteristic: External Id

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.

characteristic: sample description

text: Danio rerio


E-MTAB-3515:Sample 17

text: Ospedale Pediatrico Bambino Gesu

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: E-MTAB-3515:Sample 17

tag: Namespace:Ospedale Pediatrico Bambino Gesu

text: ArrayExpress

text: human

text: Protocols: Genomic DNA was extracted from peripheral blood with Qiagen columns (QIAamp DNA minikit; Qiagen, Hilden, Germany) according to the manufacturer's instructions Library preparation and sequencing runs have been performed according to the manufacturer's procedure (Illumina, San Diego, CA).

text: Retinoblastoma

text: Homo sapiens

text: Homo sapiens

text: peripheral blood

text: Homo sapiens

text: Sample 17

characteristic: title


E-MTAB-3515:Sample 15

text: Ospedale Pediatrico Bambino Gesu

text: public

characteristic: SRA accession

text: E-MTAB-3515:Sample 15

characteristic: Submitter Id

text: ArrayExpress

characteristic: broker name

text: human

text: Unilateral retinoblastoma

characteristic: disease

text: Homo sapiens

text: Homo sapiens

text: peripheral blood

text: Homo sapiens

text: Sample 15


E-MTAB-3515:Sample 7

characteristic: ENA-CHECKLIST

text: Ospedale Pediatrico Bambino Gesu

text: public

text: E-MTAB-3515:Sample 7

text: ArrayExpress

text: human

characteristic: common name

characteristic: description

text: Retinoblastoma

text: Homo sapiens

text: Homo sapiens

text: peripheral blood

characteristic: organism part

text: Homo sapiens

text: Sample 7


E-MTAB-3515:Sample 6

characteristic: ENA-FIRST-PUBLIC

text: Ospedale Pediatrico Bambino Gesu

text: public

characteristic: INSDC status

text: E-MTAB-3515:Sample 6

text: ArrayExpress

text: human

text: Retinoblastoma

text: Homo sapiens

text: Homo sapiens

text: peripheral blood

text: Homo sapiens

text: Sample 6


E-MTAB-3515:Sample 12

characteristic: ENA-LAST-UPDATE

text: Ospedale Pediatrico Bambino Gesu

text: public

text: E-MTAB-3515:Sample 12

text: ArrayExpress

text: human

text: Retinoblastoma

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: peripheral blood

text: Homo sapiens

text: Sample 12


E-MTAB-3515:Sample 1

characteristic: External Id

text: Ospedale Pediatrico Bambino Gesu

text: public

text: E-MTAB-3515:Sample 1

text: ArrayExpress

text: human

text: Retinoblastoma

text: Homo sapiens

text: Homo sapiens

text: peripheral blood

text: Homo sapiens

text: Sample 1


E-MTAB-3515:Sample 19

text: Ospedale Pediatrico Bambino Gesu

characteristic: INSDC center name

text: public

text: E-MTAB-3515:Sample 19

text: ArrayExpress

text: human

text: Retinoblastoma

text: Homo sapiens

text: Homo sapiens

text: peripheral blood

text: Homo sapiens

text: Sample 19


E-MTAB-3515:Sample 16

text: Ospedale Pediatrico Bambino Gesu

characteristic: INSDC first public

text: public

text: E-MTAB-3515:Sample 16

text: ArrayExpress

text: human

text: Retinoblastoma

text: Homo sapiens

text: Homo sapiens

text: peripheral blood

text: Homo sapiens

text: Sample 16


E-MTAB-3515:Sample 21

text: Ospedale Pediatrico Bambino Gesu

characteristic: INSDC last update

text: public

text: E-MTAB-3515:Sample 21

text: ArrayExpress

text: human

text: Retinoblastoma

text: Homo sapiens

text: Homo sapiens

text: peripheral blood

text: Homo sapiens

text: Sample 21


E-MTAB-3515:Sample 11

text: Ospedale Pediatrico Bambino Gesu

text: public

text: E-MTAB-3515:Sample 11

text: ArrayExpress

text: human

text: Retinoblastoma

text: Homo sapiens

text: Homo sapiens

text: peripheral blood

text: Homo sapiens

text: Sample 11

characteristic: title


E-MTAB-3515:Sample 13

text: Ospedale Pediatrico Bambino Gesu

text: public

characteristic: SRA accession

text: E-MTAB-3515:Sample 13

text: ArrayExpress

text: human

text: Retinoblastoma

text: Homo sapiens

text: Homo sapiens

text: peripheral blood

text: Homo sapiens

text: Sample 13


E-MTAB-3515:Sample 8

text: Ospedale Pediatrico Bambino Gesu

text: public

text: E-MTAB-3515:Sample 8

characteristic: Submitter Id

text: ArrayExpress

text: human

text: Retinoblastoma

text: Homo sapiens

text: Homo sapiens

text: peripheral blood

text: Homo sapiens

text: Sample 8


E-MTAB-3515:Sample 9

text: Ospedale Pediatrico Bambino Gesu

text: public

text: E-MTAB-3515:Sample 9

text: ArrayExpress

characteristic: broker name

text: human

text: Retinoblastoma

text: Homo sapiens

text: Homo sapiens

text: peripheral blood

text: Homo sapiens

text: Sample 9


E-MTAB-3515:Sample 4

text: Ospedale Pediatrico Bambino Gesu

text: public

text: E-MTAB-3515:Sample 4

text: ArrayExpress

text: human

text: Retinoblastoma

characteristic: disease

text: Homo sapiens

text: Homo sapiens

text: peripheral blood

text: Homo sapiens

text: Sample 4


E-MTAB-3515:Sample 2

characteristic: ENA-CHECKLIST

text: Ospedale Pediatrico Bambino Gesu

text: public

text: E-MTAB-3515:Sample 2

text: ArrayExpress

text: human

text: Retinoblastoma

text: Homo sapiens

text: Homo sapiens

text: peripheral blood

text: Homo sapiens

text: Sample 2


E-MTAB-3515:Sample 5

text: Ospedale Pediatrico Bambino Gesu

text: public

text: E-MTAB-3515:Sample 5

text: ArrayExpress

text: human

characteristic: common name

text: Retinoblastoma

text: Homo sapiens

text: Homo sapiens

text: peripheral blood

text: Homo sapiens

text: Sample 5


E-MTAB-3515:Sample 10

text: Ospedale Pediatrico Bambino Gesu

text: public

text: E-MTAB-3515:Sample 10

text: ArrayExpress

text: human

characteristic: description

text: Retinoblastoma

text: Homo sapiens

text: Homo sapiens

text: peripheral blood

text: Homo sapiens

text: Sample 10


E-MTAB-3515:Sample 3

text: Ospedale Pediatrico Bambino Gesu

text: public

text: E-MTAB-3515:Sample 3

text: ArrayExpress

text: human

text: Retinoblastoma

text: Homo sapiens

text: Homo sapiens

text: peripheral blood

characteristic: organism part

text: Homo sapiens

text: Sample 3


E-MTAB-3515:Sample 20

characteristic: ENA-FIRST-PUBLIC

text: Ospedale Pediatrico Bambino Gesu

text: public

text: E-MTAB-3515:Sample 20

text: ArrayExpress

text: human

text: Retinoblastoma

text: Homo sapiens

text: Homo sapiens

text: peripheral blood

text: Homo sapiens

text: Sample 20


E-MTAB-3515:Sample 23

text: Ospedale Pediatrico Bambino Gesu

text: public

characteristic: INSDC status

text: E-MTAB-3515:Sample 23

text: ArrayExpress

text: human

text: Retinoblastoma

text: Homo sapiens

text: Homo sapiens

text: peripheral blood

text: Homo sapiens

text: Sample 23


E-MTAB-3515:Sample 22

characteristic: ENA-LAST-UPDATE

text: Ospedale Pediatrico Bambino Gesu

text: public

text: E-MTAB-3515:Sample 22

text: ArrayExpress

text: human

text: Retinoblastoma

text: Homo sapiens

text: Homo sapiens

text: peripheral blood

text: Homo sapiens

text: Sample 22


E-MTAB-3515:Sample 14

text: Ospedale Pediatrico Bambino Gesu

text: public

text: E-MTAB-3515:Sample 14

text: ArrayExpress

text: human

text: Retinoblastoma

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: peripheral blood

text: Homo sapiens

text: Sample 14


E-MTAB-3515:Sample 18

characteristic: External Id

text: Ospedale Pediatrico Bambino Gesu

text: public

text: E-MTAB-3515:Sample 18

text: ArrayExpress

text: human

text: Retinoblastoma

text: Homo sapiens

text: Homo sapiens

text: peripheral blood

text: Homo sapiens

text: Sample 18


E-MTAB-3520:mouse 4

text: Oregon Health and Science University

characteristic: INSDC center name

text: public

text: E-MTAB-3520:mouse 4

tag: Namespace:Oregon Health and Science University

text: ArrayExpress

text: house mouse

text: Protocols: NA

text: adult

characteristic: developmental stage

text: Mus musculus

text: Mus musculus

text: Mus musculus

text: male

characteristic: sex

text: NOD-SCID

characteristic: strain or line

text: mouse 4


E-MTAB-3520:mouse 2

text: Oregon Health and Science University

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: SRA accession

text: E-MTAB-3520:mouse 2

text: 8 to 12 week

characteristic: age

text: ArrayExpress

text: house mouse

text: Protocols: Gall bladders (GBs) were removed by a surgical incision and bile released by making a single cut in the wall. GBs were rinsed twice in DPBS (Life Technologies, Grand Island, Ca) and then cut into several pieces. This material was then incubated at 37ﾰC with 0.25% Trypsin/EDTA (Life Technologies, Grand Island, Ca) for 45 minutes to obtain a cell suspension. Cells were cultured using a modified protocol to that previously described (Manohar, R. & Lagasse, E. Transdetermination: A New Trend in Cellular Reprogramming. Mol Ther 17, 936-938, 2009). Briefly, cells were plated on a 70-80% confluent irradiated LA7 rat epithelial feeder layer that had been previously irradiated at 60 Gy. Cells were cultured in DMEM/F12 (Life Technologies, Grand Island, Ca) supplemented with 0.5% FBS (Thermo Fisher Scientific, Cambridge, MA), 1% insulin-transferrin-selenium (Roche, Indianapolis, IN), 15mM HEPES (Thermo Fisher Scientific, Cambridge, MA) and antimicrobials (100U/ml penicillin, 100mg/ml streptomycin and 0.25mg/ml Amphotericin B; Cellgro, Manassas, VA) in a 37ﾰC incubator with 5% CO2. Media was changed every two to three days. When GBCs were 70-90% confluent, they were passaged by incubation with 0.05% trypsin/EDTA (Life Technologies, Grand Island, Ca) at 37ﾰC, followed by incubation with DNaseI at 37ﾰC for 10 minutes to obtain a single cell suspension.

text: adult

text: Mus musculus

text: Mus musculus

text: Mus musculus

text: male

text: mouse 2

characteristic: title


E-MTAB-3520:mouse 1

characteristic: ENA-CHECKLIST

text: Oregon Health and Science University

text: public

text: E-MTAB-3520:mouse 1

characteristic: Submitter Id

text: 8 to 12 week

text: ArrayExpress

characteristic: broker name

text: house mouse

characteristic: common name

text: adult

text: Mus musculus

text: Mus musculus

text: Mus musculus

text: male

text: mouse 1


E-MTAB-3520:mouse 3

characteristic: ENA-FIRST-PUBLIC

text: Oregon Health and Science University

text: public

characteristic: INSDC status

text: E-MTAB-3520:mouse 3

text: ArrayExpress

text: house mouse

text: Protocols: NA

characteristic: description

text: adult

text: Mus musculus

text: Mus musculus

text: Mus musculus

text: female

text: NOD-SCID

text: mouse 3


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: KAROLINSKA INSITUTET

text: public

tag: Namespace:KAROLINSKA INSITUTET

text: sensory neurons

characteristic: cell type

text: house mouse

text: adult

characteristic: dev stage

text: Mus musculus

characteristic: organism

text: Mus musculus

text: dorsal root ganglion

characteristic: tissue type

text: batch 130717, control, replica 1


text: KAROLINSKA INSITUTET

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: sensory neurons

text: house mouse

text: adult

text: Mus musculus

text: Mus musculus

text: dorsal root ganglion

text: batch 130729, control, replica 1


text: KAROLINSKA INSITUTET

text: public

characteristic: SRA accession

text: sensory neurons

text: house mouse

text: adult

text: Mus musculus

text: Mus musculus

text: dorsal root ganglion

text: batch 130814, control, replica 1

characteristic: title


characteristic: ENA-CHECKLIST

text: KAROLINSKA INSITUTET

text: public

characteristic: Submitter Id

text: sensory neurons

text: house mouse

text: adult

text: Mus musculus

text: Mus musculus

text: dorsal root ganglion

text: batch 130717, control, replica 2


text: KAROLINSKA INSITUTET

text: public

text: sensory neurons

text: house mouse

characteristic: common name

text: adult

text: Mus musculus

text: Mus musculus

text: dorsal root ganglion

text: batch 130729, control, replica 2


characteristic: ENA-FIRST-PUBLIC

text: KAROLINSKA INSITUTET

text: public

text: sensory neurons

text: house mouse

text: adult

text: Mus musculus

text: Mus musculus

text: dorsal root ganglion

text: batch 130814, control, replica 2


text: KAROLINSKA INSITUTET

text: public

characteristic: INSDC status

text: sensory neurons

text: house mouse

text: adult

text: Mus musculus

text: Mus musculus

text: dorsal root ganglion

text: batch 130717, control, replica 3


text: KAROLINSKA INSITUTET

text: public

text: sensory neurons

text: house mouse

text: adult

text: Mus musculus

text: Mus musculus

text: dorsal root ganglion

text: batch 130729, control, replica 3


text: KAROLINSKA INSITUTET

text: public

text: sensory neurons

text: house mouse

text: adult

text: Mus musculus

text: Mus musculus

text: dorsal root ganglion

text: batch 130814, control, replica 3


text: KAROLINSKA INSITUTET

text: public

text: sensory neurons

text: house mouse

text: adult

text: Mus musculus

text: Mus musculus

text: dorsal root ganglion

text: batch 130717, control, replica 4


text: KAROLINSKA INSITUTET

text: public

text: sensory neurons

text: house mouse

text: adult

text: Mus musculus

text: Mus musculus

text: dorsal root ganglion

text: batch 130729, control, replica 4


text: KAROLINSKA INSITUTET

text: public

text: sensory neurons

text: house mouse

text: adult

text: Mus musculus

text: Mus musculus

text: dorsal root ganglion

text: batch 130814, control, replica 4


text: KAROLINSKA INSITUTET

text: public

text: sensory neurons

text: house mouse

text: adult

text: Mus musculus

text: Mus musculus

text: dorsal root ganglion

text: batch 130717, stimulated with IL31, replica 1


text: KAROLINSKA INSITUTET

text: public

text: sensory neurons

text: house mouse

text: adult

text: Mus musculus

text: Mus musculus

text: dorsal root ganglion

text: batch 130729, stimulated with IL31, replica 1


text: KAROLINSKA INSITUTET

text: public

text: sensory neurons

text: house mouse

text: adult

text: Mus musculus

text: Mus musculus

text: dorsal root ganglion

text: batch 130814, stimulated with IL31, replica 1


text: KAROLINSKA INSITUTET

text: public

text: sensory neurons

text: house mouse

text: adult

text: Mus musculus

text: Mus musculus

text: dorsal root ganglion

text: batch 130717, stimulated with IL31, replica 2


text: KAROLINSKA INSITUTET

text: public

text: sensory neurons

text: house mouse

text: adult

text: Mus musculus

text: Mus musculus

text: dorsal root ganglion

text: batch 130729, stimulated with IL31, replica 2


text: KAROLINSKA INSITUTET

text: public

text: sensory neurons

text: house mouse

text: adult

text: Mus musculus

text: Mus musculus

text: dorsal root ganglion

text: batch 130814, stimulated with IL31, replica 2


text: KAROLINSKA INSITUTET

text: public

text: sensory neurons

text: house mouse

text: adult

text: Mus musculus

text: Mus musculus

text: dorsal root ganglion

text: batch 130717, stimulated with IL31, replica 3


text: KAROLINSKA INSITUTET

text: public

text: sensory neurons

text: house mouse

text: adult

text: Mus musculus

text: Mus musculus

text: dorsal root ganglion

text: batch 130729, stimulated with IL31, replica 3


text: KAROLINSKA INSITUTET

text: public

text: sensory neurons

text: house mouse

text: adult

text: Mus musculus

text: Mus musculus

text: dorsal root ganglion

text: batch 130814, stimulated with IL31, replica 3


text: KAROLINSKA INSITUTET

text: public

text: sensory neurons

text: house mouse

text: adult

text: Mus musculus

text: Mus musculus

text: dorsal root ganglion

text: batch 130717, stimulated with IL31, replica 4


text: KAROLINSKA INSITUTET

text: public

text: sensory neurons

text: house mouse

text: adult

text: Mus musculus

text: Mus musculus

text: dorsal root ganglion

text: batch 130729, stimulated with IL31, replica 4


text: KAROLINSKA INSITUTET

text: public

text: sensory neurons

text: house mouse

text: adult

text: Mus musculus

text: Mus musculus

text: dorsal root ganglion

text: batch 130814, stimulated with IL31, replica 4


text: KAROLINSKA INSITUTET

text: public

text: sensory neurons

text: house mouse

text: adult

text: Mus musculus

text: Mus musculus

text: dorsal root ganglion

text: batch 130717, stimulated with NGF, replica 1


text: KAROLINSKA INSITUTET

text: public

text: sensory neurons

text: house mouse

text: adult

text: Mus musculus

text: Mus musculus

text: dorsal root ganglion

text: batch 130729, stimulated with NGF, replica 1


text: KAROLINSKA INSITUTET

text: public

text: sensory neurons

text: house mouse

text: adult

text: Mus musculus

text: Mus musculus

text: dorsal root ganglion

text: batch 130814, stimulated with NGF, replica 1


text: KAROLINSKA INSITUTET

text: public

text: sensory neurons

text: house mouse

text: adult

text: Mus musculus

text: Mus musculus

text: dorsal root ganglion

text: batch 130717, stimulated with NGF, replica 2


text: KAROLINSKA INSITUTET

text: public

text: sensory neurons

text: house mouse

text: adult

text: Mus musculus

text: Mus musculus

text: dorsal root ganglion

text: batch 130729, stimulated with NGF, replica 2


text: KAROLINSKA INSITUTET

text: public

text: sensory neurons

text: house mouse

text: adult

text: Mus musculus

text: Mus musculus

text: dorsal root ganglion

text: batch 130814, stimulated with NGF, replica 2


text: KAROLINSKA INSITUTET

text: public

text: sensory neurons

text: house mouse

text: adult

text: Mus musculus

text: Mus musculus

text: dorsal root ganglion

text: batch 130717, stimulated with NGF, replica 3


text: KAROLINSKA INSITUTET

text: public

text: sensory neurons

text: house mouse

text: adult

text: Mus musculus

text: Mus musculus

text: dorsal root ganglion

text: batch 130729, stimulated with NGF, replica 3


text: KAROLINSKA INSITUTET

text: public

text: sensory neurons

text: house mouse

text: adult

text: Mus musculus

text: Mus musculus

text: dorsal root ganglion

text: batch 130814, stimulated with NGF, replica 3


text: KAROLINSKA INSITUTET

text: public

text: sensory neurons

text: house mouse

text: adult

text: Mus musculus

text: Mus musculus

text: dorsal root ganglion

text: batch 130717, stimulated with NGF, replica 4


text: KAROLINSKA INSITUTET

text: public

text: sensory neurons

text: house mouse

text: adult

text: Mus musculus

text: Mus musculus

text: dorsal root ganglion

text: batch 130729, stimulated with NGF, replica 4


text: KAROLINSKA INSITUTET

text: public

text: sensory neurons

text: house mouse

text: adult

text: Mus musculus

text: Mus musculus

text: dorsal root ganglion

text: batch 130814, stimulated with NGF, replica 4


text: Dracunculus medinensis

characteristic: ArrayExpress-Species

text: Chad

characteristic: ArrayExpress-StrainOrLine

text: SC

text: public

text: Guinea worm

text: Dracunculus medinensis

text: Dracunculus medinensis

text: Chad

characteristic: strain


text: Plasmodium falciparum

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: SC

text: public

text: malaria parasite P. falciparum

text: Plasmodium falciparum

text: Plasmodium falciparum


text: IPK-Gatersleben

text: public

text: domesticated barley

text: Sequencing of barley BACs, that constitute the MTP of chromosome 3H

characteristic: description

text: Hordeum vulgare subsp. vulgare

characteristic: organism

text: Hordeum vulgare subsp. vulgare


text: EMBL

characteristic: INSDC center name

text: public

text: ArrayExpress

characteristic: broker name

text: primary mouse embryonic fibroblast

characteristic: cell type

text: house mouse

text: Protocols: Chromosome conformation capture was performed starting from 1x107 cells, cross-linked in 2% formaldehyde. Rif1F/F Rosa26Cre-ERT2 pMEF synchronized in G1 have been treated with tamoxifen to activate the Cre and induce the deletion (pMEF_Rif1 ko). Rif1+/+ Rosa26Cre-ERT2 pMEF were treated in parallel (pMEF_Rif1wt) Primary restriction digest was performed by incubation with HindIII, while for the secondary digest we have chosen the 4-bp cutter DpnII.

characteristic: genotype

text: Mus musculus

text: Mus musculus

text: Mus musculus

characteristic: viewpoint


text: Danio rerio

text: mixed

characteristic: ENA-CHECKLIST

text: SC

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: SRA accession

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from morphologically normal zebrafish embryos for protocol development. A 8 base indexing sequence (ATCACGTT) is bases 13 to 20 of read 1 followed by CG and polyT. 10uM 8mers used. Spike dilution of 1/10x used.

characteristic: sample description

text: Danio rerio

text: mixed


text: Danio rerio

characteristic: ArrayExpress-Species

text: mixed

characteristic: ENA-FIRST-PUBLIC

text: SC

text: public

characteristic: INSDC status

characteristic: Submitter Id

text: zebrafish

characteristic: common name

text: Danio rerio

text: 3' end enriched mRNA from morphologically normal zebrafish embryos for protocol development. A 8 base indexing sequence (CGATGTTT) is bases 13 to 20 of read 1 followed by CG and polyT. 10uM 8mers used. Spike dilution of 1/10x used.

text: Danio rerio

text: mixed


text: Danio rerio

text: mixed

characteristic: ArrayExpress-StrainOrLine

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: SC

text: public

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from morphologically normal zebrafish embryos for protocol development. A 8 base indexing sequence (TTAGGCAT) is bases 13 to 20 of read 1 followed by CG and polyT. 10uM 8mers used. Spike dilution of 1/10x used.

text: Danio rerio

text: mixed

characteristic: strain


text: Danio rerio

text: mixed

text: SC

characteristic: INSDC center name

text: public

text: zebrafish

text: Danio rerio

characteristic: organism

text: 3' end enriched mRNA from morphologically normal zebrafish embryos for protocol development.. A 8 base indexing sequence (TGACCACT) is bases 13 to 20 of read 1 followed by CG and polyT. 10uM 8mers used. Spike dilution of 1/5x used.

text: Danio rerio

text: mixed


text: Danio rerio

text: mixed

text: SC

text: public

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from morphologically normal zebrafish embryos for protocol development. A 8 base indexing sequence (ACAGTGGT) is bases 13 to 20 of read 1 followed by CG and polyT. 10uM 8mers used. Spike dilution of 1/5x used.

text: Danio rerio

text: mixed


text: Danio rerio

text: mixed

text: SC

text: public

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from morphologically normal zebrafish embryos for protocol development. A 8 base indexing sequence (GCCAATGT) is bases 13 to 20 of read 1 followed by CG and polyT. 10uM 8mers used. Spike dilution of 1/5x used.

text: Danio rerio

text: mixed


text: Danio rerio

text: mixed

text: SC

text: public

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from morphologically normal zebrafish embryos for protocol development. A 8 base indexing sequence (CAGATCTG) is bases 13 to 20 of read 1 followed by CG and polyT. 10uM 8mers used. Spike dilution of 1x used.

text: Danio rerio

text: mixed


text: Danio rerio

text: mixed

text: SC

text: public

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from morphologically normal zebrafish embryos for protocol development.. A 8 base indexing sequence (ACTTGATG) is bases 13 to 20 of read 1 followed by CG and polyT. 10uM 8mers used. Spike dilution of 1x used.

text: Danio rerio

text: mixed


text: Danio rerio

text: mixed

text: SC

text: public

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from morphologically normal zebrafish embryos for protocol development. A 8 base indexing sequence (GATCAGCG) is bases 13 to 20 of read 1 followed by CG and polyT. 10uM 8mers used. Spike dilution of 1x used.

text: Danio rerio

text: mixed


text: Danio rerio

text: mixed

text: SC

text: public

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from morphologically normal zebrafish embryos for protocol development.. A 8 base indexing sequence (TAGCTTGT) is bases 13 to 20 of read 1 followed by CG and polyT. 10uM 8mers used. Spike dilution of 5x used.

text: Danio rerio

text: mixed


text: Danio rerio

text: mixed

text: SC

text: public

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from morphologically normal zebrafish embryos for protocol development. A 8 base indexing sequence (GGCTACAG) is bases 13 to 20 of read 1 followed by CG and polyT. 10uM 8mers used. Spike dilution of 5x used.

text: Danio rerio

text: mixed


text: Danio rerio

text: mixed

text: SC

text: public

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from morphologically normal zebrafish embryos for protocol development. A 8 base indexing sequence (CTTGTACT) is bases 13 to 20 of read 1 followed by CG and polyT. 10uM 8mers used. Spike dilution of 5x used.

text: Danio rerio

text: mixed


text: IPK-Gatersleben

text: public

text: domesticated barley

text: Sequencing of barley BACs that could not yet be assigned to a barley chromosome

characteristic: description

text: Hordeum vulgare subsp. vulgare

text: Hordeum vulgare subsp. vulgare

characteristic: title


characteristic: ENA-CHECKLIST

text: IPK-Gatersleben

characteristic: INSDC first public

text: public

text: domesticated barley

text: Sequencing of barley BACs, that constitute the MTP of chromosome 1H

text: Hordeum vulgare subsp. vulgare

text: Hordeum vulgare subsp. vulgare


text: IPK-Gatersleben

characteristic: INSDC last update

text: public

characteristic: SRA accession

text: domesticated barley

text: Sequencing of barley BACs, that constitute the MTP of chromosome 2H

text: Hordeum vulgare subsp. vulgare

text: Hordeum vulgare subsp. vulgare


text: IPK-Gatersleben

text: public

text: domesticated barley

text: Sequencing of barley BACs, that constitute the MTP of chromosome 4H

text: Hordeum vulgare subsp. vulgare

text: Hordeum vulgare subsp. vulgare


text: Mus musculus

characteristic: ArrayExpress-Species

text: SC

text: public

text: house mouse

text: Mus musculus

text: PBAT bisulfite library

characteristic: sample description

text: Mus musculus


text: Homo Sapien

text: Bisulphite methylation

characteristic: ArrayExpress-Treatment

characteristic: ENA-FIRST-PUBLIC

text: SC

text: public

characteristic: INSDC status

text: human

text: Homo sapiens

text: Bisulphite library

text: Homo sapiens


text: Mus musculus

text: Bisulphite methylation

text: SC

text: public

characteristic: Submitter Id

text: house mouse

characteristic: common name

text: Mus musculus

text: Bisulphite library

text: Mus musculus


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: public

text: E-MTAB-2887_2:eMED001_G187_SCC3.MED.150130.HiSeq2500.FCB.lane5.R1

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

text: ArrayExpress

characteristic: broker name

text: house mouse

text: Protocols: DMBA/TPA-induced skin tumors. FVB/N mice were treated with DMBA and TPA. DMBA (200 μl of 0,25 mg/ml solution in acetone) was applied on the shaved backskin of 28 days old mice, when hair follicles are in their regenerative stage (anagen), as administration of DMBA during anagen promote tumor development . TPA (200 μl of 0,02 mg/ml solution in acetone) was then applied once weekly during 16 weeks. Mouse skin squamous cell carcinomas (msSCCs), paired lung or lymph node metastases and premalignant tumors (also called papillomas) were included in this study. Since all used mice for DMBA carcinogenesis were from FVBN/N inbred strain, whole exome sequencing (WES) was performed on 6 bone marrow (BM) samples from 6 different FVB/N mice as a germline DNA to eliminate eventual SNPs. Tamoxifen administration for genetic KrasLSL-G12D/p53fl/fl model. Lgr5CREER/KrasLSL-G12D/ p53fl/fl/Rosa-YFP 2 were treated with 4 times 2.5 mg of tamoxifen from days 28 to 31 after birth. Carcinomas were harvested 2 months after tamoxifen administration. In total 11 SCCs from 7 different mice were included in WES and low-depth whole genome sequencing (Shallow WGS). Since these were outbred strains, WES was performed on the BM of each mouse (n=7) as a germline DNA to eliminate SNPs. 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_2:eMED001_G188_BM.MED.150130.HiSeq2500.FCB.lane4.R1

text: ArrayExpress

text: house mouse

characteristic: description

text: normal

text: Mus musculus

characteristic: organism

text: Mus musculus

text: bone marrow

characteristic: organism part

text: Mus musculus


characteristic: ENA-CHECKLIST

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: E-MTAB-2887_2:eMED001_D81_1.MED.150130.HiSeq2500.FCB.lane5.R1

text: ArrayExpress

text: house mouse

text: squamous cell carcinoma

text: Mus musculus

text: Mus musculus

text: Mus musculus

characteristic: title


text: public

characteristic: SRA accession

text: E-MTAB-2887_2:MED.MED006_N1.130118.FCA.lane5.R1

text: ArrayExpress

text: house mouse

text: normal

text: Mus musculus

text: Mus musculus

text: bone marrow

text: Mus musculus


characteristic: ENA-FIRST-PUBLIC

text: public

text: E-MTAB-2887_2:MED.MED006_T1.130118.FCA.lane5.R1

text: ArrayExpress

text: house mouse

text: squamous cell carcinoma

text: Mus musculus

text: Mus musculus

text: Mus musculus


text: public

characteristic: INSDC status

text: E-MTAB-2887_2:eMED001_D78_1.MED.150130.HiSeq2500.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_2:eMED001_G187_SCC5.MED.150130.HiSeq2500.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_2:eMED001_D80_1.MED.150130.HiSeq2500.FCB.lane7.R1

text: ArrayExpress

text: house mouse

characteristic: common name

text: squamous cell carcinoma

text: Mus musculus

text: Mus musculus

text: Mus musculus


characteristic: ENA-LAST-UPDATE

text: public

text: E-MTAB-2887_2:eMED001_D103_LN_UNST.MED.150313.HiSeq2500.FCB.lane2.R1

text: ArrayExpress

text: house mouse

text: metastasis

text: Mus musculus

text: Mus musculus

text: Mus musculus


characteristic: External Id

text: public

text: E-MTAB-2887_2:MED.MED002_N1.130118.FCA.lane7.R1

text: ArrayExpress

text: house mouse

text: normal

text: Mus musculus

text: Mus musculus

text: bone marrow

text: Mus musculus


text: public

text: E-MTAB-2887_2:eMED001_G188_SCC7.MED.150130.HiSeq2500.FCB.lane6.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_2:MED.MED005_N1.130118.FCA.lane5.R1

text: ArrayExpress

text: house mouse

text: normal

characteristic: disease

text: Mus musculus

text: Mus musculus

text: bone marrow

text: Mus musculus


characteristic: INSDC center name

text: public

text: E-MTAB-2887_2:eMED001_D81_1.MED.150130.HiSeq2500.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_2:eMED001_G187_SCC2.MED.150130.HiSeq2500.FCB.lane6.R1

text: ArrayExpress

text: house mouse

characteristic: description

text: squamous cell carcinoma

text: Mus musculus

text: Mus musculus

text: Mus musculus


text: public

text: E-MTAB-2887_2:MED.MED002_T2.130118.FCA.lane7.R1

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-2887_2:MED.MED003_N1.130118.FCA.lane2.R1

text: ArrayExpress

text: house mouse

text: normal

text: Mus musculus

text: Mus musculus

text: bone marrow

characteristic: organism part

text: Mus musculus


characteristic: ENA-CHECKLIST

text: public

text: E-MTAB-2887_2:eMED001_D100_Lung_UNST.MED.150313.HiSeq2500.FCB.lane2.R1

text: ArrayExpress

text: house mouse

text: Protocols: DMBA/TPA-induced skin tumors. FVB/N mice were treated with DMBA and TPA. DMBA (200 μl of 0,25 mg/ml solution in acetone) was applied on the shaved backskin of 28 days old mice, when hair follicles are in their regenerative stage (anagen), as administration of DMBA during anagen promote tumor development . TPA (200 μl of 0,02 mg/ml solution in acetone) was then applied once weekly during 16 weeks. Mouse skin squamous cell carcinomas (msSCCs), paired lung or lymph node metastases and premalignant tumors (also called papillomas) were included in this study. Since all used mice for DMBA carcinogenesis were from FVBN/N inbred strain, whole exome sequencing (WES) was performed on 6 bone marrow (BM) samples from 6 different FVB/N mice as a germline DNA to eliminate eventual SNPs. Tamoxifen administration for genetic KrasLSL-G12D/p53fl/fl model. Lgr5CREER/KrasLSL-G12D/ p53fl/fl/Rosa-YFP 2 were treated with 4 times 2.5 mg of tamoxifen from days 28 to 31 after birth. Carcinomas were harvested 2 months after tamoxifen administration. In total 11 SCCs from 7 different mice were included in WES and low-depth whole genome sequencing (Shallow WGS). Since these were outbred strains, WES was performed on the BM of each mouse (n=7) as a germline DNA to eliminate SNPs. 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: metastasis

text: Mus musculus

text: Mus musculus

text: Mus musculus


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

characteristic: INSDC first public

text: public

text: E-MTAB-2887_2:eMED001_D103_SCC1_UNST.MED.150130.HiSeq2500.FCB.lane5.R1

text: ArrayExpress

text: house mouse

text: squamous cell carcinoma

text: Mus musculus

text: Mus musculus

text: Mus musculus


characteristic: INSDC last update

text: public

text: E-MTAB-2887_2:eMED001_D100_LN_UNST.MED.150130.HiSeq2500.FCB.lane4.R1

text: ArrayExpress

text: house mouse

text: metastasis

text: Mus musculus

text: Mus musculus

text: Mus musculus


text: public

text: E-MTAB-2887_2:eMED001_D103_LN_UNST.MED.150130.HiSeq2500.FCB.lane5.R1

text: ArrayExpress

text: house mouse

text: metastasis

text: Mus musculus

text: Mus musculus

text: Mus musculus

characteristic: title


text: public

characteristic: SRA accession

text: E-MTAB-2887_2:eMED001_D102_SCC1.MED.150130.HiSeq2500.FCB.lane8.R1

text: ArrayExpress

text: house mouse

text: squamous cell carcinoma

text: Mus musculus

text: Mus musculus

text: Mus musculus


characteristic: ENA-FIRST-PUBLIC

text: public

text: E-MTAB-2887_2:MED.MED002_T2.130118.FCA.lane6.R1

text: ArrayExpress

text: house mouse

text: squamous cell carcinoma

text: Mus musculus

text: Mus musculus

text: Mus musculus


text: public

characteristic: INSDC status

text: E-MTAB-2887_2:MED.MED003_T1.130118.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_2:eMED001_G188_BM.MED.150130.HiSeq2500.FCB.lane5.R1

characteristic: Submitter Id

text: ArrayExpress

text: house mouse

text: normal

text: Mus musculus

text: Mus musculus

text: bone marrow

text: Mus musculus


text: public

text: E-MTAB-2887_2:eMED001_G187_SCC3.MED.150130.HiSeq2500.FCB.lane4.R1

text: ArrayExpress

text: house mouse

characteristic: common name

text: squamous cell carcinoma

text: Mus musculus

text: Mus musculus

text: Mus musculus


characteristic: ENA-LAST-UPDATE

text: public

text: E-MTAB-2887_2:eMED001_D86_1.MED.150130.HiSeq2500.FCB.lane6.R1

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-2887_2:eMED001_D100_LN_UNST.MED.150313.HiSeq2500.FCB.lane2.R1

text: ArrayExpress

text: house mouse

text: metastasis

text: Mus musculus

text: Mus musculus

text: Mus musculus


text: public

text: E-MTAB-2887_2:MED.MED005_T1.130118.FCA.lane5.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_2:eMED001_D100_Lung_UNST.MED.150130.HiSeq2500.FCB.lane4.R1

text: ArrayExpress

text: house mouse

text: metastasis

characteristic: disease

text: Mus musculus

text: Mus musculus

text: Mus musculus


characteristic: INSDC center name

text: public

text: E-MTAB-2887_2:eMED001_D78_Lung_UNST.MED.150130.HiSeq2500.FCB.lane5.R1

text: ArrayExpress

text: house mouse

text: metastasis

text: Mus musculus

text: Mus musculus

text: Mus musculus


text: public

text: E-MTAB-2887_2:eMED001_D100_SCC_UNST.MED.150130.HiSeq2500.FCB.lane4.R1

text: ArrayExpress

text: house mouse

characteristic: description

text: squamous cell carcinoma

text: Mus musculus

text: Mus musculus

text: Mus musculus


text: public

text: E-MTAB-2887_2:MED.MED004_T1.130118.FCA.lane2.R1

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-2887_2:MED.MED003_T1.130118.FCA.lane2.R1

text: ArrayExpress

text: house mouse

text: Protocols: DMBA/TPA-induced skin tumors. FVB/N mice were treated with DMBA and TPA. DMBA (200 μl of 0,25 mg/ml solution in acetone) was applied on the shaved backskin of 28 days old mice, when hair follicles are in their regenerative stage (anagen), as administration of DMBA during anagen promote tumor development . TPA (200 μl of 0,02 mg/ml solution in acetone) was then applied once weekly during 16 weeks. Mouse skin squamous cell carcinomas (msSCCs), paired lung or lymph node metastases and premalignant tumors (also called papillomas) were included in this study. Since all used mice for DMBA carcinogenesis were from FVBN/N inbred strain, whole exome sequencing (WES) was performed on 6 bone marrow (BM) samples from 6 different FVB/N mice as a germline DNA to eliminate eventual SNPs. Tamoxifen administration for genetic KrasLSL-G12D/p53fl/fl model. Lgr5CREER/KrasLSL-G12D/ p53fl/fl/Rosa-YFP 2 were treated with 4 times 2.5 mg of tamoxifen from days 28 to 31 after birth. Carcinomas were harvested 2 months after tamoxifen administration. In total 11 SCCs from 7 different mice were included in WES and low-depth whole genome sequencing (Shallow WGS). Since these were outbred strains, WES was performed on the BM of each mouse (n=7) as a germline DNA to eliminate SNPs. 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_2:MED.MED004_N1.130118.FCA.lane2.R1

text: ArrayExpress

text: house mouse

text: normal

text: Mus musculus

text: Mus musculus

text: bone marrow

characteristic: organism part

text: Mus musculus


characteristic: ENA-CHECKLIST

text: public

text: E-MTAB-2887_2:MED.MED002_N1.130118.FCA.lane6.R1

text: ArrayExpress

text: house mouse

text: normal

text: Mus musculus

text: Mus musculus

text: bone marrow

text: Mus musculus


characteristic: INSDC first public

text: public

text: E-MTAB-2887_2:eMED001_G187_SCC1.MED.150130.HiSeq2500.FCB.lane6.R1

text: ArrayExpress

text: house mouse

text: squamous cell carcinoma

text: Mus musculus

text: Mus musculus

text: Mus musculus


characteristic: INSDC last update

text: public

text: E-MTAB-2887_2:MED.MED004_N1.130118.FCA.lane1.R1

text: ArrayExpress

text: house mouse

text: normal

text: Mus musculus

text: Mus musculus

text: bone marrow

text: Mus musculus


text: public

text: E-MTAB-2887_2:MED.MED002_T1.130118.FCA.lane7.R1

text: ArrayExpress

text: house mouse

text: squamous cell carcinoma

text: Mus musculus

text: Mus musculus

text: Mus musculus

characteristic: title


text: public

characteristic: SRA accession

text: E-MTAB-2887_2:MED.MED004_T1.130118.FCA.lane1.R1

text: ArrayExpress

text: house mouse

text: squamous cell carcinoma

text: Mus musculus

text: Mus musculus

text: Mus musculus


characteristic: ENA-FIRST-PUBLIC

text: public

text: E-MTAB-2887_2:MED.MED003_N1.130118.FCA.lane1.R1

text: ArrayExpress

text: house mouse

text: normal

text: Mus musculus

text: Mus musculus

text: bone marrow

text: Mus musculus


text: public

characteristic: INSDC status

text: E-MTAB-2887_2:eMED001_G187_BM.MED.150130.HiSeq2500.FCB.lane6.R1

text: ArrayExpress

text: house mouse

text: normal

text: Mus musculus

text: Mus musculus

text: bone marrow

text: Mus musculus


E-MTAB-3491:eNSC Bmi1-2

text: public

text: E-MTAB-3491:eNSC Bmi1-2

tag: Namespace:Wadsworth Center, NY State Dept of Health

characteristic: Submitter Id

text: ArrayExpress

text: neural stem cell

characteristic: cell type

text: house mouse

text: Protocols: Isolated neural stem cells from E18.5 or adult Swiss Webster mice were grown under non-adherent conditions for three weeks/two passages (eNSCs) or four weeks/three passages (aNSCs) prior to RNA isolation Embryonic NSCs were acutely transduced with empty vector (EV) or Bmi1-overexpressing lentiviral vector; adult NSCs were allowed to recover overnight prior to transduction Total RNA was isolated using RNAeasy Plus Micro kit (Qiagen) 150-250 ng RNA was used for library construction. Ribosomal RNA was removed using the Ribo-Zero Magnetic Kit (Epicentre), and libraries prepared using the ScripSeq V2 RNA-seq Kit (Epicentre), using the low input protocol.

text: embryonic day 18.5

characteristic: developmental stage

text: Bmi1-overexpressing lentiviral vector

characteristic: genetic modification

text: neurospheres

characteristic: growth condition

text: Mus musculus

text: Mus musculus

text: Mus musculus

text: eNSC Bmi1-2


E-MTAB-3491:aNSC EV-2

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Wadsworth Center, NY State Dept of Health

text: public

text: E-MTAB-3491:aNSC EV-2

text: ArrayExpress

characteristic: broker name

text: neural stem cell

text: house mouse

characteristic: common name

text: adult

text: empty vector control

text: neurospheres

text: Mus musculus

text: Mus musculus

text: Mus musculus

text: aNSC EV-2


E-MTAB-3491:eNSC H1-2

characteristic: INSDC center name

text: public

text: E-MTAB-3491:eNSC H1-2

text: ArrayExpress

text: neural stem cell

text: house mouse

characteristic: description

text: embryonic day 18.5

text: empty vector control

text: neurospheres

text: Mus musculus

characteristic: organism

text: Mus musculus

text: Mus musculus

text: eNSC H1-2


E-MTAB-3491:aNSC Bmi1-1

characteristic: ENA-CHECKLIST

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: E-MTAB-3491:aNSC Bmi1-1

text: ArrayExpress

text: neural stem cell

text: house mouse

text: adult

text: Bmi1-overexpressing lentiviral vector

text: neurospheres

text: Mus musculus

text: Mus musculus

text: Mus musculus

text: aNSC Bmi1-1


E-MTAB-3491:aNSC EV-1

characteristic: ENA-FIRST-PUBLIC

text: public

characteristic: SRA accession

text: E-MTAB-3491:aNSC EV-1

text: ArrayExpress

text: neural stem cell

text: house mouse

text: adult

text: empty vector control

text: neurospheres

text: Mus musculus

text: Mus musculus

text: Mus musculus

text: aNSC EV-1

characteristic: title


E-MTAB-3491:aNSC Bmi1-2

text: public

characteristic: INSDC status

text: E-MTAB-3491:aNSC Bmi1-2

characteristic: Submitter Id

text: ArrayExpress

text: neural stem cell

characteristic: cell type

text: house mouse

text: adult

text: Bmi1-overexpressing lentiviral vector

text: neurospheres

text: Mus musculus

text: Mus musculus

text: Mus musculus

text: aNSC Bmi1-2


E-MTAB-3491:eNSC H1-1

text: public

text: E-MTAB-3491:eNSC H1-1

text: ArrayExpress

text: neural stem cell

text: house mouse

text: embryonic day 18.5

characteristic: developmental stage

text: empty vector control

characteristic: genetic modification

text: neurospheres

characteristic: growth condition

text: Mus musculus

text: Mus musculus

text: Mus musculus

text: eNSC H1-1


E-MTAB-3491:eNSC Bmi1-1

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: public

text: E-MTAB-3491:eNSC Bmi1-1

text: ArrayExpress

characteristic: broker name

text: neural stem cell

text: house mouse

text: embryonic day 18.5

text: Bmi1-overexpressing lentiviral vector

text: neurospheres

text: Mus musculus

text: Mus musculus

text: Mus musculus

text: eNSC Bmi1-1


text: IPK-Gatersleben

characteristic: INSDC center name

text: public

text: domesticated barley

characteristic: common name

text: Sequencing of barley BACs, that constitute the MTP of chromosome 5H

characteristic: description

text: Hordeum vulgare subsp. vulgare

text: Hordeum vulgare subsp. vulgare


characteristic: ENA-CHECKLIST

text: IPK-Gatersleben

characteristic: INSDC first public

text: public

text: domesticated barley

text: Sequencing of barley BACs, that constitute the MTP of chromosome 6H

text: Hordeum vulgare subsp. vulgare

characteristic: organism

text: Hordeum vulgare subsp. vulgare


characteristic: ENA-FIRST-PUBLIC

text: IPK-Gatersleben

characteristic: INSDC last update

text: public

characteristic: SRA accession

text: domesticated barley

text: Sequencing of barley BACs, that constitute the MTP of chromosome 7H

text: Hordeum vulgare subsp. vulgare

text: Hordeum vulgare subsp. vulgare


text: public

characteristic: INSDC status

text: E-MTAB-2887_2:MED.MED002_T1.130118.FCA.lane6.R1

characteristic: Submitter Id

text: ArrayExpress

text: house mouse

text: squamous cell carcinoma

characteristic: disease

text: Mus musculus

text: Mus musculus

text: Mus musculus

characteristic: title


text: Plasmodium falciparum

characteristic: ArrayExpress-Species

characteristic: ArrayExpress-StrainOrLine

text: SC

text: public

text: malaria parasite P. falciparum

text: Plasmodium falciparum

text: Plasmodium falciparum

characteristic: strain


text: Homo sapiens

characteristic: ENA-LAST-UPDATE

characteristic: External Id

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text: public

text: human

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text: Homo sapiens


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characteristic: INSDC center name

text: public

tag: Namespace:Salk Institute for Biological Studies

text: ArrayExpress

characteristic: broker name

text: human

characteristic: common name

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

characteristic: individual

text: Homo sapiens

text: Homo sapiens

text: hippocampus

characteristic: organism part

text: Alu

characteristic: retrotransposon

text: Homo sapiens


text: single cell

characteristic: ENA-CHECKLIST

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text: single cell

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text: human

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text: low input

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text: Salk Institute for Biological Studies

characteristic: INSDC first public

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text: public

text: ArrayExpress

text: human

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text: liver

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text: human

characteristic: description

text: NeuN+

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text: Homo sapiens

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text: single cell

characteristic: ENA-LAST-UPDATE

text: Salk Institute for Biological Studies

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text: ArrayExpress

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characteristic: title


text: single cell

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text: Salk Institute for Biological Studies

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characteristic: broker name

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text: Homo sapiens

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text: bulk tissue

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text: human

characteristic: common name

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text: Homo sapiens

text: hippocampus

characteristic: organism part

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text: Homo sapiens


text: bulk tissue

characteristic: ENA-CHECKLIST

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text: Salk Institute for Biological Studies

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text: public

text: ArrayExpress

text: human

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text: Homo sapiens

text: heart

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text: single cell

text: Salk Institute for Biological Studies

text: public

characteristic: SRA accession

text: ArrayExpress

text: human

characteristic: description

text: NeuN-

characteristic: neun staining

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: hippocampus

text: Homo sapiens


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characteristic: ENA-LAST-UPDATE

text: Salk Institute for Biological Studies

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text: Salk Institute for Biological Studies

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text: public

text: ArrayExpress

characteristic: broker name

text: human

text: Homo sapiens

text: Homo sapiens

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text: single cell

text: Salk Institute for Biological Studies

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text: ArrayExpress

text: human

characteristic: common name

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text: Homo sapiens

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text: Alu

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text: bulk tissue

characteristic: ENA-CHECKLIST

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text: Salk Institute for Biological Studies

characteristic: INSDC first public

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text: public

text: ArrayExpress

text: human

text: Homo sapiens

text: Homo sapiens

text: cerebellum

text: Alu

text: Homo sapiens


text: low input

text: Salk Institute for Biological Studies

text: public

characteristic: SRA accession

text: ArrayExpress

text: human

characteristic: description

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: liver

text: Homo sapiens


text: bulk tissue

characteristic: ENA-LAST-UPDATE

text: Salk Institute for Biological Studies

text: public

characteristic: INSDC status

characteristic: Submitter Id

text: ArrayExpress

text: human

text: Homo sapiens

text: Homo sapiens

text: cerebellum

text: Homo sapiens


text: bulk tissue

characteristic: DNA source

characteristic: External Id

text: Salk Institute for Biological Studies

text: public

text: ArrayExpress

text: human

text: Homo sapiens

text: Homo sapiens

text: hippocampus

text: Alu

text: Homo sapiens

characteristic: title


text: single cell

text: Salk Institute for Biological Studies

characteristic: INSDC center name

text: public

text: ArrayExpress

characteristic: broker name

text: human

characteristic: common name

text: NeuN-

characteristic: neun staining

text: Homo sapiens

text: Homo sapiens

text: cortex

text: Alu

text: Homo sapiens


text: single cell

characteristic: ENA-CHECKLIST

text: Salk Institute for Biological Studies

text: public

text: ArrayExpress

text: human

characteristic: individual

text: NeuN+

text: Homo sapiens

text: Homo sapiens

text: cortex

characteristic: organism part

characteristic: retrotransposon

text: Homo sapiens


text: single cell

characteristic: ENA-FIRST-PUBLIC

text: Salk Institute for Biological Studies

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: SRA accession

text: ArrayExpress

text: human

text: NeuN-

text: Homo sapiens

text: Homo sapiens

text: hippocampus

text: Alu

text: Homo sapiens


text: single cell

characteristic: ENA-LAST-UPDATE

text: Salk Institute for Biological Studies

text: public

characteristic: INSDC status

text: ArrayExpress

text: human

characteristic: description

text: NeuN+

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: hippocampus

text: Homo sapiens


text: single cell

characteristic: DNA source

characteristic: External Id

text: Salk Institute for Biological Studies

text: public

characteristic: Submitter Id

text: ArrayExpress

text: human

text: NeuN+

text: Homo sapiens

text: Homo sapiens

text: hippocampus

text: Alu

text: Homo sapiens

characteristic: title


text: bulk tissue

text: Salk Institute for Biological Studies

characteristic: INSDC center name

text: public

text: ArrayExpress

characteristic: broker name

text: human

characteristic: common name

text: Homo sapiens

text: Homo sapiens

text: cortex

text: Homo sapiens


text: low input

characteristic: ENA-CHECKLIST

text: Salk Institute for Biological Studies

text: public

text: ArrayExpress

text: human

characteristic: individual

text: Homo sapiens

text: Homo sapiens

text: liver

characteristic: organism part

text: Alu

text: Homo sapiens


text: bulk tissue

characteristic: ENA-FIRST-PUBLIC

text: Salk Institute for Biological Studies

characteristic: INSDC first public

text: public

text: ArrayExpress

text: human

text: Homo sapiens

text: Homo sapiens

text: heart

characteristic: retrotransposon

text: Homo sapiens


text: bulk tissue

characteristic: ENA-LAST-UPDATE

text: Salk Institute for Biological Studies

characteristic: INSDC last update

text: public

characteristic: SRA accession

text: ArrayExpress

text: human

text: Homo sapiens

text: Homo sapiens

text: liver

text: Homo sapiens


text: bulk tissue

text: Salk Institute for Biological Studies

text: public

characteristic: INSDC status

text: ArrayExpress

text: human

characteristic: description

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: hippocampus

text: Homo sapiens


text: single cell

characteristic: DNA source

characteristic: External Id

text: Salk Institute for Biological Studies

text: public

characteristic: Submitter Id

text: ArrayExpress

text: human

text: NeuN-

characteristic: neun staining

text: Homo sapiens

text: Homo sapiens

text: cortex

text: Homo sapiens


text: bulk tissue

text: Salk Institute for Biological Studies

characteristic: INSDC center name

text: public

text: ArrayExpress

characteristic: broker name

text: human

characteristic: common name

text: Homo sapiens

text: Homo sapiens

text: liver

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text: Homo sapiens

characteristic: title


text: bulk tissue

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: Salk Institute for Biological Studies

text: public

text: ArrayExpress

text: human

characteristic: individual

text: Homo sapiens

text: Homo sapiens

text: heart

characteristic: organism part

text: Alu

text: Homo sapiens


text: single cell

characteristic: ENA-LAST-UPDATE

text: Salk Institute for Biological Studies

characteristic: INSDC first public

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text: public

text: ArrayExpress

text: human

text: NeuN-

text: Homo sapiens

text: Homo sapiens

text: hippocampus

characteristic: retrotransposon

text: Homo sapiens


text: low input

text: Salk Institute for Biological Studies

text: public

characteristic: INSDC status

characteristic: SRA accession

text: ArrayExpress

text: human

characteristic: description

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: liver

text: Homo sapiens


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characteristic: External Id

text: Salk Institute for Biological Studies

text: public

characteristic: Submitter Id

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text: Homo sapiens

text: cerebellum

text: Homo sapiens


text: bulk tissue

text: Salk Institute for Biological Studies

characteristic: INSDC center name

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characteristic: common name

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text: Homo sapiens

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characteristic: ENA-CHECKLIST

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text: Salk Institute for Biological Studies

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characteristic: title


text: single cell

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text: Salk Institute for Biological Studies

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text: Homo sapiens

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characteristic: organism part

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text: single cell

text: Salk Institute for Biological Studies

characteristic: INSDC first public

characteristic: INSDC last update

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text: NeuN+

characteristic: neun staining

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text: Homo sapiens

text: cortex

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characteristic: retrotransposon

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text: single cell

text: Salk Institute for Biological Studies

text: public

characteristic: INSDC status

characteristic: SRA accession

text: ArrayExpress

text: human

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text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: hippocampus

text: Homo sapiens


text: single cell

characteristic: DNA source

characteristic: External Id

text: Salk Institute for Biological Studies

characteristic: INSDC center name

text: public

characteristic: Submitter Id

text: ArrayExpress

text: human

text: NeuN-

text: Homo sapiens

text: Homo sapiens

text: cortex

text: Alu

text: Homo sapiens


text: single cell

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: Salk Institute for Biological Studies

text: public

text: ArrayExpress

characteristic: broker name

text: human

characteristic: common name

text: NeuN+

text: Homo sapiens

text: Homo sapiens

text: cortex

text: Homo sapiens


text: single cell

characteristic: ENA-LAST-UPDATE

text: Salk Institute for Biological Studies

text: public

text: ArrayExpress

text: human

characteristic: individual

text: NeuN+

text: Homo sapiens

text: Homo sapiens

text: hippocampus

characteristic: organism part

text: Alu

text: Homo sapiens

characteristic: title


text: single cell

text: Salk Institute for Biological Studies

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: ArrayExpress

text: human

text: NeuN-

characteristic: neun staining

text: Homo sapiens

text: Homo sapiens

text: hippocampus

text: Alu

characteristic: retrotransposon

text: Homo sapiens


text: low input

text: Salk Institute for Biological Studies

text: public

characteristic: INSDC status

characteristic: SRA accession

text: ArrayExpress

text: human

characteristic: description

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: liver

text: Alu

text: Homo sapiens


text: bulk tissue

characteristic: DNA source

characteristic: External Id

text: Salk Institute for Biological Studies

characteristic: INSDC center name

text: public

characteristic: Submitter Id

text: ArrayExpress

text: human

text: Homo sapiens

text: Homo sapiens

text: cortex

text: Homo sapiens


text: bulk tissue

characteristic: ENA-CHECKLIST

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text: Salk Institute for Biological Studies

text: public

text: ArrayExpress

characteristic: broker name

text: human

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text: Homo sapiens

text: Homo sapiens

text: hippocampus

text: Homo sapiens


text: bulk tissue

characteristic: ENA-LAST-UPDATE

text: Salk Institute for Biological Studies

text: public

text: ArrayExpress

text: human

characteristic: individual

text: Homo sapiens

text: Homo sapiens

text: liver

characteristic: organism part

text: Alu

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text: single cell

text: Salk Institute for Biological Studies

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: ArrayExpress

text: human

text: NeuN-

characteristic: neun staining

text: Homo sapiens

text: Homo sapiens

text: cortex

characteristic: retrotransposon

text: Homo sapiens


text: single cell

text: Salk Institute for Biological Studies

text: public

characteristic: INSDC status

characteristic: SRA accession

text: ArrayExpress

text: human

characteristic: description

text: NeuN-

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: hippocampus

text: Homo sapiens


text: low input

characteristic: DNA source

characteristic: External Id

text: Salk Institute for Biological Studies

characteristic: INSDC center name

text: public

characteristic: Submitter Id

text: ArrayExpress

text: human

text: Homo sapiens

text: Homo sapiens

text: liver

text: Homo sapiens


text: bulk tissue

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: Salk Institute for Biological Studies

text: public

text: ArrayExpress

characteristic: broker name

text: human

characteristic: common name

text: Homo sapiens

text: Homo sapiens

text: cerebellum

text: Homo sapiens


E-MTAB-3532:TSAR1 OE 1

characteristic: ENA-LAST-UPDATE

text: public

text: E-MTAB-3532:TSAR1 OE 1

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

text: ArrayExpress

text: Hairy root

characteristic: cell type

text: barrel medic

text: Protocols: Sterilization of M. truncatula seeds (ecotype Jemalong J5), transformation of seedlings by Agrobacterium rhizogenes (strain LBA 9402/12) and generation of hairy roots was carried out as described (Pollier et al. 2011, J Nat Prod 74: 1462-1476). Hairy roots were grown for 21 days in liquid medium. About 100 mg of frozen ground root material was used. 450 μl Buffer RLT (supplemented with 10 μl β-ME per ml Buffer RLT) was added and the mixture was vortexed vigorously. The lysate was transferred to a QIAshredder spin column placed in a 2 ml collection tube and centrifuged for 2 min at full speed. The supernatant was mixed with half a volume of ethanol and transferred to a an RNeasy spin column placed in a 2 ml collection tube followed by centrifugation for 15 seconds at full speed. 350 μl RW1 buffer was added and the column was centrifuged for 15s at max speed. Next an on column DNase digestion was performed and the column was washed again with 350 μl RW1 buffer. Next, the column was washed twice with 500 μl Buffer RPE. The RNA was eluated in a clean 1.5 mL eppendorf by adding 40 μl RNase-free water and centrifuging at maximum speed for 1 minute. Library construction: Random primed cDNA library: Purification of poly-A containing mRNA molecules - mRNA fragmentation - Random primed cDNA synthesis - Adapter ligation and adapter specific PCR amplification

text: TSAR1 over expression

characteristic: genotype

text: Medicago truncatula

text: Medicago truncatula

text: Medicago truncatula

text: Jemalong J5

characteristic: strain

text: TSAR1 OE 1

characteristic: title


E-MTAB-3532:TSAR1 OE 3

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

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: E-MTAB-3532:TSAR1 OE 3

text: ArrayExpress

text: Hairy root

text: barrel medic

text: TSAR1 over expression

text: Medicago truncatula

text: Medicago truncatula

text: Medicago truncatula

text: Jemalong J5

text: TSAR1 OE 3


E-MTAB-3532:TSAR2 OE 2

text: public

characteristic: SRA accession

text: E-MTAB-3532:TSAR2 OE 2

text: ArrayExpress

text: Hairy root

text: barrel medic

characteristic: description

text: TSAR2 over expression

text: Medicago truncatula

characteristic: organism

text: Medicago truncatula

text: Medicago truncatula

text: Jemalong J5

text: TSAR2 OE 2


E-MTAB-3532:CONTROL 3

characteristic: External Id

characteristic: INSDC center name

text: public

text: E-MTAB-3532:CONTROL 3

text: ArrayExpress

text: Hairy root

text: barrel medic

text: CONTROL

text: Medicago truncatula

text: Medicago truncatula

text: Medicago truncatula

text: Jemalong J5

text: CONTROL 3


E-MTAB-3532:CONTROL 2

characteristic: ENA-CHECKLIST

text: public

text: E-MTAB-3532:CONTROL 2

characteristic: Submitter Id

text: ArrayExpress

text: Hairy root

text: barrel medic

text: CONTROL

text: Medicago truncatula

text: Medicago truncatula

text: Medicago truncatula

text: Jemalong J5

text: CONTROL 2


E-MTAB-3532:TSAR1 OE 2

characteristic: ENA-FIRST-PUBLIC

text: public

text: E-MTAB-3532:TSAR1 OE 2

text: ArrayExpress

characteristic: broker name

text: Hairy root

text: barrel medic

text: TSAR1 over expression

text: Medicago truncatula

text: Medicago truncatula

text: Medicago truncatula

text: Jemalong J5

text: TSAR1 OE 2


E-MTAB-3532:TSAR2 OE 3

characteristic: ENA-LAST-UPDATE

text: public

text: E-MTAB-3532:TSAR2 OE 3

text: ArrayExpress

text: Hairy root

text: barrel medic

characteristic: common name

text: TSAR1 over expression

text: Medicago truncatula

text: Medicago truncatula

text: Medicago truncatula

text: Jemalong J5

text: TSAR2 OE 3


E-MTAB-3532:CONTROL 1

text: public

text: E-MTAB-3532:CONTROL 1

text: ArrayExpress

text: Hairy root

characteristic: cell type

text: barrel medic

text: CONTROL

characteristic: genotype

text: Medicago truncatula

text: Medicago truncatula

text: Medicago truncatula

text: Jemalong J5

text: CONTROL 1


E-MTAB-3532:TSAR2 OE1

text: public

text: E-MTAB-3532:TSAR2 OE1

text: ArrayExpress

text: Hairy root

text: barrel medic

text: TSAR2 over expression

text: Medicago truncatula

text: Medicago truncatula

text: Medicago truncatula

text: Jemalong J5

characteristic: strain

text: TSAR2 OE1

characteristic: title


text: Skin

characteristic: ArrayExpress-CellType

text: Mus musculus

characteristic: ArrayExpress-Species

characteristic: ArrayExpress-StrainOrLine

text: SC

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: house mouse

text: Mus musculus

text: PCR from earclip

characteristic: sample description

text: Mus musculus


text: Skin

text: Mus musculus

characteristic: External Id

text: SC

characteristic: INSDC center name

text: public

characteristic: INSDC status

characteristic: SRA accession

text: house mouse

text: Mus musculus

characteristic: organism

text: PCR from blastocyst

text: Mus musculus


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: public

tag: Namespace:Karolinska Institutet Department of Biosciences and Nutrition

characteristic: Submitter Id

text: 21 day

characteristic: age

text: ArrayExpress

characteristic: broker name

text: Lgr6-negative hair follicle/sebaceous gland cell

text: house mouse

text: Protocols: Keratinocytes were isolated from three-week-old Lgr6-EGFP-CreETR2 mice as described previously (Jaks et al., 2008). Briefly, dorsal skin was harvested, cut in strips and digested in trypsin. Epidermal cells were peeled off the dermis and singularized by magnetic stirring. Cells from 2 - 3 mice were pooled per experiment. The collected cells were stained with AlexaFluor647-conjugated anti-CD49f antibody and PE-Cy7-conjugated anti-Sca-1 antibody (both from BD Biosciences), and filtered before sorting. Keratinocytes stained for CD49f, Sca-1 and 7-AAD were live sorted using a FACSAria (BD). Lgr6+ IFE cells were defined as the CD49fhigh, Sca-1high and EGFPhigh fraction. Lgr6+ HF cells were defined as the CD49fhigh+dim, Sca-1neg and EGFPhigh fraction. One hundred thousand cells were collected for each population. RNA was isolated from sorted keratinocytes by combining the RNA-containing aqueous phase extract using RNA-Bee (Amsbio) with the RNAaqueous-Micro Kit (Ambion). RNA integrity was measured using an Agilent 2100 Bioanalyzer Pico Chip or a 2200 TapeStation High Sensitivity R6K Screen Tape. The RNA integrity number of the used samples was higher than 8.5. The sequencing library was generated according to the STRT protocol, described in (Islam et al., 2012), using 1 ng total RNA as input for each sample. For each sample two technical replicates were sequenced (suffix _1 and _2). Islam, S., Kjällquist, U., Moliner, A., Zajac, P., Fan, J.B., Lönnerberg, P. and Linnarsson, S. (2012). Highly multiplexed and strand-specific single-cell RNA 5' end sequencing. Nat Protoc 7, 813-828.

characteristic: description

text: Lgr6cre-EGFP-IRES-CreERT2 heterozygous

text: Mus musculus

text: Mus musculus

text: dorsal skin

characteristic: organism part

text: CD49f hi/Sca1 neg/EGFP neg

characteristic: phenotype

text: Mus musculus

text: male

characteristic: sex