text: Whole embryo

text: Danio rerio

characteristic: ArrayExpress-Species

text: mixed

characteristic: ArrayExpress-StrainOrLine

text: SC

text: public

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from a single genotyped embryo wild type for tfap2a, allele sa24445 and heterozygous for tfap2c, allele sa18857 ZMP phenotype 192 clutch 1 plus ERCC spike mix 1 (Ambion). A 8 base indexing sequence (GTGTCCTT) is bases 13 to 20 of read 1 followed by CG and polyT. More information describing the mutant phenotype can be found at the Wellcome Trust Sanger Institute Zebrafish Mutation Project website http://www.sanger.ac.uk/sanger/Zebrafish_Zmpsearch/zmp_ph192.

text: Danio rerio

text: mixed


status: PUBLIC

text: Segmentation:1-4 somites - Segmentation:5-9 somites : ZFS:0000023 - ZFS:0000024

tag: attribute

characteristic: ArrayExpress-DevelopmentalStage

text: Whole embryo

characteristic: ArrayExpress-OrganismPart

text: Danio rerio

text: mixed

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: SC

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: zebrafish

characteristic: common name

text: Danio rerio

characteristic: organism

text: 3' end enriched mRNA from a single genotyped embryo wild type for tfap2a, allele sa24445 and heterozygous for tfap2c, allele sa18857 ZMP phenotype 192 clutch 1 plus ERCC spike mix 1 (Ambion). A 8 base indexing sequence (GACGGATT) is bases 13 to 20 of read 1 followed by CG and polyT. More information describing the mutant phenotype can be found at the Wellcome Trust Sanger Institute Zebrafish Mutation Project website http://www.sanger.ac.uk/sanger/Zebrafish_Zmpsearch/zmp_ph192.

characteristic: sample description

text: Danio rerio

text: mixed

characteristic: strain


text: Whole embryo

text: Danio rerio

characteristic: ArrayExpress-Species

text: mixed

characteristic: ArrayExpress-StrainOrLine

text: SC

text: public

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from a single genotyped embryo wild type for tfap2a, allele sa24445 and heterozygous for tfap2c, allele sa18857 ZMP phenotype 192 clutch 1 plus ERCC spike mix 1 (Ambion). A 8 base indexing sequence (GCAACATT) is bases 13 to 20 of read 1 followed by CG and polyT. More information describing the mutant phenotype can be found at the Wellcome Trust Sanger Institute Zebrafish Mutation Project website http://www.sanger.ac.uk/sanger/Zebrafish_Zmpsearch/zmp_ph192.

text: Danio rerio

text: mixed


characteristic: ArrayExpress-DevelopmentalStage

text: Whole embryo

characteristic: ArrayExpress-OrganismPart

text: Danio rerio

text: mixed

text: SC

text: public

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from a single genotyped embryo wild type for tfap2a, allele sa24445 and heterozygous for tfap2c, allele sa18857 ZMP phenotype 192 clutch 1 plus ERCC spike mix 1 (Ambion). A 8 base indexing sequence (GGTCGTGT) is bases 13 to 20 of read 1 followed by CG and polyT. More information describing the mutant phenotype can be found at the Wellcome Trust Sanger Institute Zebrafish Mutation Project website http://www.sanger.ac.uk/sanger/Zebrafish_Zmpsearch/zmp_ph192.

text: Danio rerio

text: mixed


text: Whole embryo

text: Danio rerio

text: mixed

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: SC

text: public

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from a single genotyped embryo wild type for tfap2a, allele sa24445 and heterozygous for tfap2c, allele sa18857 ZMP phenotype 192 clutch 1 plus ERCC spike mix 1 (Ambion). A 8 base indexing sequence (GAATCTGT) is bases 13 to 20 of read 1 followed by CG and polyT. More information describing the mutant phenotype can be found at the Wellcome Trust Sanger Institute Zebrafish Mutation Project website http://www.sanger.ac.uk/sanger/Zebrafish_Zmpsearch/zmp_ph192.

text: Danio rerio

text: mixed


text: Whole embryo

text: Danio rerio

text: mixed

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: SC

text: public

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from a single genotyped embryo wild type for tfap2a, allele sa24445 and heterozygous for tfap2c, allele sa18857 ZMP phenotype 192 clutch 1 plus ERCC spike mix 1 (Ambion). A 8 base indexing sequence (GAGGTGCT) is bases 13 to 20 of read 1 followed by CG and polyT. More information describing the mutant phenotype can be found at the Wellcome Trust Sanger Institute Zebrafish Mutation Project website http://www.sanger.ac.uk/sanger/Zebrafish_Zmpsearch/zmp_ph192.

text: Danio rerio

text: mixed


text: Whole embryo

text: Danio rerio

text: mixed

text: SC

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from a single genotyped embryo wild type for tfap2a, allele sa24445 and heterozygous for tfap2c, allele sa18857 ZMP phenotype 192 clutch 1 plus ERCC spike mix 1 (Ambion). A 8 base indexing sequence (GCATGGCT) is bases 13 to 20 of read 1 followed by CG and polyT. More information describing the mutant phenotype can be found at the Wellcome Trust Sanger Institute Zebrafish Mutation Project website http://www.sanger.ac.uk/sanger/Zebrafish_Zmpsearch/zmp_ph192.

text: Danio rerio

text: mixed


text: Whole embryo

text: Danio rerio

text: mixed

text: SC

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from a single genotyped embryo wild type for tfap2a, allele sa24445 and heterozygous for tfap2c, allele sa18857 ZMP phenotype 192 clutch 1 plus ERCC spike mix 1 (Ambion). A 8 base indexing sequence (GTTAGCCT) is bases 13 to 20 of read 1 followed by CG and polyT. More information describing the mutant phenotype can be found at the Wellcome Trust Sanger Institute Zebrafish Mutation Project website http://www.sanger.ac.uk/sanger/Zebrafish_Zmpsearch/zmp_ph192.

text: Danio rerio

text: mixed


text: Whole embryo

text: Danio rerio

text: mixed

text: SC

text: public

characteristic: SRA accession

characteristic: Submitter Id

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from a single genotyped embryo wild type for tfap2a, allele sa24445 and heterozygous for tfap2c, allele sa18857 ZMP phenotype 192 clutch 1 plus ERCC spike mix 1 (Ambion). A 8 base indexing sequence (GTCGCTAT) is bases 13 to 20 of read 1 followed by CG and polyT. More information describing the mutant phenotype can be found at the Wellcome Trust Sanger Institute Zebrafish Mutation Project website http://www.sanger.ac.uk/sanger/Zebrafish_Zmpsearch/zmp_ph192.

text: Danio rerio

text: mixed


text: Whole embryo

text: Danio rerio

text: mixed

text: SC

text: public

text: zebrafish

characteristic: common name

text: Danio rerio

characteristic: organism

text: 3' end enriched mRNA from a single genotyped embryo wild type for both tfap2a, allele sa24445 and tfap2c, allele sa18857 ZMP phenotype 192 clutch 1 plus ERCC spike mix 1 (Ambion). A 8 base indexing sequence (GGAATGAT) is bases 13 to 20 of read 1 followed by CG and polyT. More information describing the mutant phenotype can be found at the Wellcome Trust Sanger Institute Zebrafish Mutation Project website http://www.sanger.ac.uk/sanger/Zebrafish_Zmpsearch/zmp_ph192.

text: Danio rerio

text: mixed


text: Whole embryo

text: Danio rerio

text: mixed

text: SC

text: public

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from a single genotyped embryo wild type for both tfap2a, allele sa24445 and tfap2c, allele sa18857 ZMP phenotype 192 clutch 1 plus ERCC spike mix 1 (Ambion). A 8 base indexing sequence (GAGCCAAT) is bases 13 to 20 of read 1 followed by CG and polyT. More information describing the mutant phenotype can be found at the Wellcome Trust Sanger Institute Zebrafish Mutation Project website http://www.sanger.ac.uk/sanger/Zebrafish_Zmpsearch/zmp_ph192.

characteristic: sample description

text: Danio rerio

text: mixed

characteristic: strain


text: Whole embryo

text: Danio rerio

characteristic: ArrayExpress-Species

text: mixed

characteristic: ArrayExpress-StrainOrLine

text: SC

text: public

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from a single genotyped embryo wild type for both tfap2a, allele sa24445 and tfap2c, allele sa18857 ZMP phenotype 192 clutch 1 plus ERCC spike mix 1 (Ambion). A 8 base indexing sequence (GCTCCTTG) is bases 13 to 20 of read 1 followed by CG and polyT. More information describing the mutant phenotype can be found at the Wellcome Trust Sanger Institute Zebrafish Mutation Project website http://www.sanger.ac.uk/sanger/Zebrafish_Zmpsearch/zmp_ph192.

text: Danio rerio

text: mixed


characteristic: ArrayExpress-DevelopmentalStage

text: Whole embryo

characteristic: ArrayExpress-OrganismPart

text: Danio rerio

text: mixed

text: SC

text: public

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from a single genotyped embryo wild type for both tfap2a, allele sa24445 and tfap2c, allele sa18857 ZMP phenotype 192 clutch 1 plus ERCC spike mix 1 (Ambion). A 8 base indexing sequence (GTAAGGTG) is bases 13 to 20 of read 1 followed by CG and polyT. More information describing the mutant phenotype can be found at the Wellcome Trust Sanger Institute Zebrafish Mutation Project website http://www.sanger.ac.uk/sanger/Zebrafish_Zmpsearch/zmp_ph192.

text: Danio rerio

text: mixed


text: Whole embryo

text: Danio rerio

text: mixed

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: SC

text: public

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from a single genotyped embryo wild type for both tfap2a, allele sa24445 and tfap2c, allele sa18857 ZMP phenotype 192 clutch 1 plus ERCC spike mix 1 (Ambion). A 8 base indexing sequence (GAGGATGG) is bases 13 to 20 of read 1 followed by CG and polyT. More information describing the mutant phenotype can be found at the Wellcome Trust Sanger Institute Zebrafish Mutation Project website http://www.sanger.ac.uk/sanger/Zebrafish_Zmpsearch/zmp_ph192.

text: Danio rerio

text: mixed


text: Whole embryo

text: Danio rerio

text: mixed

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: SC

text: public

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from a single genotyped embryo wild type for both tfap2a, allele sa24445 and tfap2c, allele sa18857 ZMP phenotype 192 clutch 1 plus ERCC spike mix 1 (Ambion). A 8 base indexing sequence (GTTGTCGG) is bases 13 to 20 of read 1 followed by CG and polyT. More information describing the mutant phenotype can be found at the Wellcome Trust Sanger Institute Zebrafish Mutation Project website http://www.sanger.ac.uk/sanger/Zebrafish_Zmpsearch/zmp_ph192.

text: Danio rerio

text: mixed


text: Whole embryo

text: Danio rerio

text: mixed

text: SC

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from a single genotyped embryo wild type for both tfap2a, allele sa24445 and tfap2c, allele sa18857 ZMP phenotype 192 clutch 1 plus ERCC spike mix 1 (Ambion). A 8 base indexing sequence (GGATTAGG) is bases 13 to 20 of read 1 followed by CG and polyT. More information describing the mutant phenotype can be found at the Wellcome Trust Sanger Institute Zebrafish Mutation Project website http://www.sanger.ac.uk/sanger/Zebrafish_Zmpsearch/zmp_ph192.

text: Danio rerio

text: mixed


text: Whole embryo

text: Danio rerio

text: mixed

text: SC

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from a single genotyped embryo wild type for both tfap2a, allele sa24445 and tfap2c, allele sa18857 ZMP phenotype 192 clutch 1 plus ERCC spike mix 1 (Ambion). A 8 base indexing sequence (GATAGAGG) is bases 13 to 20 of read 1 followed by CG and polyT. More information describing the mutant phenotype can be found at the Wellcome Trust Sanger Institute Zebrafish Mutation Project website http://www.sanger.ac.uk/sanger/Zebrafish_Zmpsearch/zmp_ph192.

text: Danio rerio

text: mixed


text: Segmentation:1-4 somites - Segmentation:5-9 somites : ZFS:0000023 - ZFS:0000024

text: Whole embryo

text: Danio rerio

text: mixed

text: SC

text: public

characteristic: SRA accession

characteristic: Submitter Id

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from a single genotyped embryo wild type for both tfap2a, allele sa24445 and tfap2c, allele sa18857 ZMP phenotype 192 clutch 1 plus ERCC spike mix 1 (Ambion). A 8 base indexing sequence (GTGTGTCG) is bases 13 to 20 of read 1 followed by CG and polyT. More information describing the mutant phenotype can be found at the Wellcome Trust Sanger Institute Zebrafish Mutation Project website http://www.sanger.ac.uk/sanger/Zebrafish_Zmpsearch/zmp_ph192.

text: Danio rerio

text: mixed


text: Whole embryo

text: Danio rerio

text: mixed

text: SC

text: public

text: zebrafish

characteristic: common name

text: Danio rerio

characteristic: organism

text: 3' end enriched mRNA from a single genotyped embryo wild type for both tfap2a, allele sa24445 and tfap2c, allele sa18857 ZMP phenotype 192 clutch 1 plus ERCC spike mix 1 (Ambion). A 8 base indexing sequence (GCAATCCG) is bases 13 to 20 of read 1 followed by CG and polyT. More information describing the mutant phenotype can be found at the Wellcome Trust Sanger Institute Zebrafish Mutation Project website http://www.sanger.ac.uk/sanger/Zebrafish_Zmpsearch/zmp_ph192.

text: Danio rerio

text: mixed


E-MTAB-3565:PD03 24h rep2

text: University of Cambridge

text: public

text: E-MTAB-3565:PD03 24h rep2

tag: Namespace:University of Cambridge

text: ArrayExpress

characteristic: broker name

text: trophoblast stem cells

characteristic: cell type

text: house mouse

text: Protocols: Mouse TSCs (blastocyst-derived TS EGFP line), proven to exhibit full developmental competence as the colonize all trophoblast layers in chimeras, were cultured as described previously. Transfections were performed for 6h in OptiMEM media supplemented with Fgf2 and heparin using 1% Lipofectamine 2000 (Life Technologies) on non-adherent dishes. After 24h cells were selected with 300ug ml-1 G418. Inhibitors used: 1uM LDN 193189 trihydrochloride (Axon, 1509); 2uM endo-IWR 1 (Tocris, 3532); 2uM PD0325901; 3uM CHIR99021; 50nM Gsk-Lsd1 (N-[(1R,2S)-2- phenylcyclopropyl]-4-piperidinamine, dihydrochloride), kindly provided by the Structural Genomics Consortium (http://www.thesgc.org); 10 uM SB431542; 15 uM diethylstilbestrol (DES) (Sigma). Total RNA prepared using RNeasy kit (Qiagen 74104) followed by DNase treatment using the TURBO DNA-free kit (Life Technologies AM1907), according to manufacturers’ 24 instructions. mRNA was isolated using the Dynabeads mRNA purification kit (Life Technologies 61006) and prepared into an indexed library using the ScriptSeq v2 RNA-Seq Library Preparation Kit (Epicentre SSV21106) according to manufacturers’ instructions. Libraries were quantified/assessed using both the KAPA Library Quantification Kit (KAPA Biosystems KK4824) and Bioanalyzer 2100 system (Agilent). Indexed libraries were pooled and sequenced with a 100bp single-end protocol.

characteristic: description

text: Mus musculus

text: Mus musculus

text: Mus musculus

text: PD03 24h rep2

characteristic: title


E-MTAB-3565:PD03 3h rep1

text: University of Cambridge

text: public

text: E-MTAB-3565:PD03 3h rep1

text: ArrayExpress

text: trophoblast stem cells

text: house mouse

text: Mus musculus

text: Mus musculus

text: Mus musculus

text: PD03 3h rep1


E-MTAB-3565:DES 24h rep4

text: University of Cambridge

text: public

text: E-MTAB-3565:DES 24h rep4

text: ArrayExpress

text: trophoblast stem cells

text: house mouse

text: Mus musculus

text: Mus musculus

text: Mus musculus

text: DES 24h rep4


E-MTAB-3565:Esrrb rep3

text: University of Cambridge

text: public

text: E-MTAB-3565:Esrrb rep3

text: ArrayExpress

text: trophoblast stem cells

text: house mouse

text: Protocols: Mouse TSCs (blastocyst-derived TS EGFP line), proven to exhibit full developmental competence as the colonize all trophoblast layers in chimeras, were cultured as described previously. Transfections were performed for 6h in OptiMEM media supplemented with Fgf2 and heparin using 1% Lipofectamine 2000 (Life Technologies) on non-adherent dishes. After 24h cells were selected with 300ug ml-1 G418. Inhibitors used: 1uM LDN 193189 trihydrochloride (Axon, 1509); 2uM endo-IWR 1 (Tocris, 3532); 2uM PD0325901; 3uM CHIR99021; 50nM Gsk-Lsd1 (N-[(1R,2S)-2- phenylcyclopropyl]-4-piperidinamine, dihydrochloride), kindly provided by the Structural Genomics Consortium (http://www.thesgc.org); 10 uM SB431542; 15 uM diethylstilbestrol (DES) (Sigma). Cells (1-2x108) were fixed in 2mM DSG (80424, Sigma) in PBS at room temperature (RT) for 45min. After washing in PBS, cells were fixed again in 1% formaldehyde in TS base media at RT for 12 min. Fixation was stopped by adding glycine to a final concentration 0.125M. Cells were washed twice in PBS and resuspended in wash buffer 1 (10 mM Hepes pH 7. 5, 10 mM EDTA, 0.5 mM EGTA, 0.75% Triton X-100) and incubated at 4C for 10min. After pelleting, cells were resuspended in wash buffer 2 (10 mM Hepes pH 7.5, 200 mM NaCl, 1 mM EDTA, 0.5 mM EGTA) and incubated at 4C for 10min. After pelleting cells were lysed in the lysis/sonication buffer (150 mM NaCl, 25 mM Tris pH 7.5, 5 mM EDTA, 0.1% Triton, 1% SDS, 0.5% Sodium Deoxycholate) with complete protease inhibitors (Roche) on ice for 30min. Chromatin was sonicated 30sec on/30off for 25-30 cycles using the BioRuptor (Diagenode) to the average 300-bp fragments. Chromatin was diluted 1/10 with the dilution buffer (150 mM NaCl, 25 mM Tris pH 7.5, 5 mM EDTA, 1% Triton-X 100, 0.1% SDS, 0.5% Sodium Deoxycholate) containing complete protease inhibitors. Protein G magnetic Dynabeads (10004D, Invitrogen) were blocked with 1mg ml-1 BSA and tRNA at 4C for 1h and washed with buffer A (150 mM NaCl, 25 mM Tris pH 7.5, 5 mM EDTA, 1% Triton-X 100, 0.1% SDS, 0.5% Sodium Deoxycholate). Chromatin was pre-cleared with pre-blocked beads at 4C for 1h. Three hundred and fifty micrograms of chromatin and 10ug of antibody were used per each IP. Immunoprecipitation was performed over night at 4C with rotation. Pre-blocked magnetic beads were added next morning for 7-8h. Beads were washed at 4C with buffer A (150 mM NaCl, 25 mM Tris pH 7.5, 5 mM EDTA, 1% Triton-X 100, 0.1% SDS, 0.5% Sodium Deoxycholate) three times, buffer B (50 mM Tris pH8.0, 500 mM NaCl, 0.1% SDS, 0.5% Sodium Deoxycholate, 1% NP40, 1 mM EDTA), buffer C (50 mM Tris pH8.0, 250 mM LiCl, 0.5% Sodium Deoxycholate, 1% NP40, 1 mM EDTA) and rinsed with TE buffer. DNA was eluted from beads in the elution buffer (1%SDS, 0.1M NaHCO3). Samples were treated with RNAse A and Proteinase K and reverse cross-linked overnight at 65C. DNA was phenol- chloroform extracted, chloroform extracted and purified on the PCR purification columns (Qiagen) (for ChIP-seq libraries). To generate a library, DNA from 4 IPs was pooled and the NEB Next DNA Library Prep Master Mix (NEB E6040) was used according to manufacturer’s instructions. Libraries were amplified using 18 PCR cycles, purified using Agencourt AMPure XP SPRI beads (Beckman Coulter, A63881) and size-selected on an agarose gel. The DNA was extracted using a Qiaquick gel extraction kit (Qiagen) and its concentration determined using the KAPA Illumina SYBR Universal Lid Q Kit (KAPA Biosystems KK4824) and Bioanalyzer 2100 system (Agilent).

text: Mus musculus

text: Mus musculus

text: Mus musculus

text: Esrrb rep3


E-MTAB-3565:scr2 rep1

text: University of Cambridge

text: public

text: E-MTAB-3565:scr2 rep1

text: ArrayExpress

text: trophoblast stem cells

text: house mouse

text: Mus musculus

text: Mus musculus

text: Mus musculus

text: scr2 rep1


E-MTAB-3565:Dax1/Lsd1 igg control

text: University of Cambridge

text: public

text: E-MTAB-3565:Dax1/Lsd1 igg control

text: ArrayExpress

text: trophoblast stem cells

text: house mouse

text: Mus musculus

text: Mus musculus

text: Mus musculus

text: Dax1/Lsd1 igg control


E-MTAB-3565:PD03 ctrl 3h rep1

text: University of Cambridge

text: public

text: E-MTAB-3565:PD03 ctrl 3h rep1

text: ArrayExpress

text: trophoblast stem cells

text: house mouse

text: Mus musculus

text: Mus musculus

text: Mus musculus

text: PD03 ctrl 3h rep1


E-MTAB-3565:scr1 rep1

text: University of Cambridge

text: public

text: E-MTAB-3565:scr1 rep1

text: ArrayExpress

text: trophoblast stem cells

text: house mouse

text: Mus musculus

text: Mus musculus

text: Mus musculus

text: scr1 rep1


E-MTAB-3565:PD03 ctrl 3h rep2

text: University of Cambridge

text: public

text: E-MTAB-3565:PD03 ctrl 3h rep2

text: ArrayExpress

text: trophoblast stem cells

text: house mouse

text: Mus musculus

text: Mus musculus

text: Mus musculus

text: PD03 ctrl 3h rep2


E-MTAB-3565:Esrrb rep5

text: University of Cambridge

text: public

text: E-MTAB-3565:Esrrb rep5

text: ArrayExpress

text: trophoblast stem cells

text: house mouse

text: Mus musculus

text: Mus musculus

text: Mus musculus

text: Esrrb rep5


E-MTAB-3565:Esrrb rep2

text: University of Cambridge

text: public

text: E-MTAB-3565:Esrrb rep2

text: ArrayExpress

text: trophoblast stem cells

text: house mouse

text: Mus musculus

text: Mus musculus

text: Mus musculus

text: Esrrb rep2


E-MTAB-3565:PD03 24h rep1

text: University of Cambridge

text: public

text: E-MTAB-3565:PD03 24h rep1

text: ArrayExpress

text: trophoblast stem cells

text: house mouse

text: Mus musculus

text: Mus musculus

text: Mus musculus

text: PD03 24h rep1


E-MTAB-3565:KD2 rep2

text: University of Cambridge

text: public

text: E-MTAB-3565:KD2 rep2

text: ArrayExpress

text: trophoblast stem cells

text: house mouse

text: Mus musculus

text: Mus musculus

text: Mus musculus

text: KD2 rep2


E-MTAB-3565:DES 24h rep3

text: University of Cambridge

text: public

text: E-MTAB-3565:DES 24h rep3

text: ArrayExpress

text: trophoblast stem cells

text: house mouse

text: Mus musculus

text: Mus musculus

text: Mus musculus

text: DES 24h rep3


E-MTAB-3565:DES ctrl rep2

text: University of Cambridge

text: public

text: E-MTAB-3565:DES ctrl rep2

text: ArrayExpress

text: trophoblast stem cells

text: house mouse

text: Mus musculus

text: Mus musculus

text: Mus musculus

text: DES ctrl rep2


E-MTAB-3565:PD03 ctrl 24h rep1

text: University of Cambridge

text: public

text: E-MTAB-3565:PD03 ctrl 24h rep1

text: ArrayExpress

text: trophoblast stem cells

text: house mouse

text: Mus musculus

text: Mus musculus

text: Mus musculus

text: PD03 ctrl 24h rep1


E-MTAB-3565:Esrrb rep1

text: University of Cambridge

text: public

text: E-MTAB-3565:Esrrb rep1

text: ArrayExpress

text: trophoblast stem cells

text: house mouse

text: Mus musculus

text: Mus musculus

text: Mus musculus

text: Esrrb rep1


E-MTAB-3565:DES 4d rep3

text: University of Cambridge

text: public

text: E-MTAB-3565:DES 4d rep3

text: ArrayExpress

text: trophoblast stem cells

text: house mouse

text: Mus musculus

text: Mus musculus

text: Mus musculus

text: DES 4d rep3


E-MTAB-3565:KD2 rep1

text: University of Cambridge

text: public

text: E-MTAB-3565:KD2 rep1

text: ArrayExpress

text: trophoblast stem cells

text: house mouse

text: Mus musculus

text: Mus musculus

text: Mus musculus

text: KD2 rep1


E-MTAB-3565:Esrrb igg control rep2

text: University of Cambridge

text: public

text: E-MTAB-3565:Esrrb igg control rep2

text: ArrayExpress

text: trophoblast stem cells

text: house mouse

text: Mus musculus

text: Mus musculus

text: Mus musculus

text: Esrrb igg control rep2


E-MTAB-3565:DES 24h rep2

text: University of Cambridge

text: public

text: E-MTAB-3565:DES 24h rep2

text: ArrayExpress

text: trophoblast stem cells

text: house mouse

text: Mus musculus

text: Mus musculus

text: Mus musculus

text: DES 24h rep2


E-MTAB-3565:Dax1 rep1

text: University of Cambridge

text: public

text: E-MTAB-3565:Dax1 rep1

text: ArrayExpress

text: trophoblast stem cells

text: house mouse

text: Mus musculus

text: Mus musculus

text: Mus musculus

text: Dax1 rep1


E-MTAB-3565:DES 4d rep1

text: University of Cambridge

text: public

text: E-MTAB-3565:DES 4d rep1

text: ArrayExpress

text: trophoblast stem cells

text: house mouse

text: Mus musculus

text: Mus musculus

text: Mus musculus

text: DES 4d rep1


E-MTAB-3565:KD1 rep1

text: University of Cambridge

text: public

text: E-MTAB-3565:KD1 rep1

text: ArrayExpress

text: trophoblast stem cells

text: house mouse

text: Mus musculus

text: Mus musculus

text: Mus musculus

text: KD1 rep1


E-MTAB-3565:scr1 rep2

text: University of Cambridge

text: public

text: E-MTAB-3565:scr1 rep2

text: ArrayExpress

text: trophoblast stem cells

text: house mouse

text: Mus musculus

text: Mus musculus

text: Mus musculus

text: scr1 rep2


E-MTAB-3565:Esrrb igg control rep1

text: University of Cambridge

text: public

text: E-MTAB-3565:Esrrb igg control rep1

text: ArrayExpress

text: trophoblast stem cells

text: house mouse

text: Mus musculus

text: Mus musculus

text: Mus musculus

text: Esrrb igg control rep1


E-MTAB-3565:Esrrb rep4

text: University of Cambridge

text: public

text: E-MTAB-3565:Esrrb rep4

text: ArrayExpress

text: trophoblast stem cells

text: house mouse

text: Mus musculus

text: Mus musculus

text: Mus musculus

text: Esrrb rep4


E-MTAB-3565:DES ctrl rep1

text: University of Cambridge

text: public

text: E-MTAB-3565:DES ctrl rep1

text: ArrayExpress

text: trophoblast stem cells

text: house mouse

text: Mus musculus

text: Mus musculus

text: Mus musculus

text: DES ctrl rep1


E-MTAB-3565:DES 4d rep2

text: University of Cambridge

text: public

text: E-MTAB-3565:DES 4d rep2

text: ArrayExpress

text: trophoblast stem cells

text: house mouse

text: Mus musculus

text: Mus musculus

text: Mus musculus

text: DES 4d rep2


E-MTAB-3565:KD1 rep2

text: University of Cambridge

text: public

text: E-MTAB-3565:KD1 rep2

text: ArrayExpress

text: trophoblast stem cells

text: house mouse

text: Mus musculus

text: Mus musculus

text: Mus musculus

text: KD1 rep2


E-MTAB-3565:PD03 3h rep2

text: University of Cambridge

text: public

text: E-MTAB-3565:PD03 3h rep2

text: ArrayExpress

text: trophoblast stem cells

text: house mouse

text: Mus musculus

text: Mus musculus

text: Mus musculus

text: PD03 3h rep2


E-MTAB-3565:PD03 ctrl 24h rep2

text: University of Cambridge

text: public

text: E-MTAB-3565:PD03 ctrl 24h rep2

text: ArrayExpress

text: trophoblast stem cells

text: house mouse

text: Mus musculus

text: Mus musculus

text: Mus musculus

text: PD03 ctrl 24h rep2


E-MTAB-3565:DES ctrl rep3

text: University of Cambridge

text: public

text: E-MTAB-3565:DES ctrl rep3

text: ArrayExpress

text: trophoblast stem cells

text: house mouse

text: Mus musculus

text: Mus musculus

text: Mus musculus

text: DES ctrl rep3


E-MTAB-3565:Lsd1 rep1

text: University of Cambridge

text: public

text: E-MTAB-3565:Lsd1 rep1

text: ArrayExpress

text: trophoblast stem cells

text: house mouse

text: Mus musculus

text: Mus musculus

text: Mus musculus

text: Lsd1 rep1


E-MTAB-3565:DES 24h rep1

text: University of Cambridge

text: public

text: E-MTAB-3565:DES 24h rep1

text: ArrayExpress

text: trophoblast stem cells

text: house mouse

text: Mus musculus

text: Mus musculus

text: Mus musculus

text: DES 24h rep1


text: Homo sapiens

characteristic: ArrayExpress-Species

text: SC

text: public

text: human

text: Homo sapiens

text: Homo sapiens


text: Mus musculus

characteristic: ENA-CHECKLIST

text: SC

text: public

text: house mouse

text: Mus musculus

text: Mus musculus


text: Interneuron

characteristic: ArrayExpress-CellType

text: Wildtype

characteristic: ArrayExpress-Genotype

text: Interneuron

characteristic: ArrayExpress-OrganismPart

text: Wildtype

characteristic: ArrayExpress-Phenotype

text: female

characteristic: ArrayExpress-Sex

text: Mus musculus

text: Mixed

characteristic: ArrayExpress-StrainOrLine

text: vehicle

characteristic: ArrayExpress-Treatment

characteristic: ENA-FIRST-PUBLIC

text: SC

text: public

text: house mouse

text: Mus musculus

text: cDNA from sham-treated interneurons

characteristic: sample description

text: Mus musculus

text: Mixed

characteristic: strain


text: Interneuron

text: Wildtype

text: Interneuron

text: Wildtype

text: male

text: Mus musculus

text: Mixed

text: pentylenetetrazol

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: SC

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: house mouse

characteristic: common name

text: Mus musculus

characteristic: organism

text: cDNA from PTZ-treated interneurons

text: Mus musculus

text: Mixed


text: Interneuron

characteristic: ArrayExpress-CellType

text: Wildtype

characteristic: ArrayExpress-Genotype

text: Interneuron

characteristic: ArrayExpress-OrganismPart

text: Wildtype

characteristic: ArrayExpress-Phenotype

text: female

text: Mus musculus

characteristic: ArrayExpress-Species

text: Mixed

text: pentylenetetrazol

characteristic: ENA-CHECKLIST

text: SC

text: public

text: house mouse

text: Mus musculus

text: cDNA from PTZ-treated interneurons

text: Mus musculus

text: Mixed


text: Interneuron

text: Wildtype

text: Interneuron

text: Wildtype

text: male

characteristic: ArrayExpress-Sex

text: Mus musculus

text: Mixed

characteristic: ArrayExpress-StrainOrLine

text: vehicle

characteristic: ArrayExpress-Treatment

characteristic: ENA-FIRST-PUBLIC

text: SC

text: public

text: house mouse

text: Mus musculus

text: cDNA from sham-treated interneurons

characteristic: sample description

text: Mus musculus

text: Mixed

characteristic: strain


text: Plasmodium falciparum

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: SC

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: malaria parasite P. falciparum

text: Plasmodium falciparum

text: Plasmodium falciparum


text: Yeast

text: Schizosaccharomyces pombe

text: SC

text: public

characteristic: SRA accession

characteristic: Submitter Id

text: fission yeast

characteristic: common name

text: Schizosaccharomyces pombe

characteristic: organism

text: Schizosaccharomyces pombe


characteristic: ENA-CHECKLIST

text: IPK-Gatersleben

text: public

text: domesticated barley

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

characteristic: description

text: Hordeum vulgare subsp. vulgare

text: Hordeum vulgare subsp. vulgare

characteristic: title


text: mouse ESC

characteristic: ArrayExpress-CellType

text: cell line

characteristic: ArrayExpress-OrganismPart

text: mus musculus

characteristic: ArrayExpress-Species

text: SC

text: public

text: house mouse

text: Mus musculus

text: MuERVL+ Zscan4+ replicate A

text: Mus musculus


text: mouse ESC

text: cell line

text: mus musculus

characteristic: ENA-FIRST-PUBLIC

text: SC

text: public

text: house mouse

text: Mus musculus

text: MuERVL- Zscan4- replicate A

characteristic: sample description

text: Mus musculus


text: mouse ESC

text: cell line

text: mus musculus

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: SC

text: public

text: house mouse

text: Mus musculus

text: MuERVL+ Zscan4+ replicate B

text: Mus musculus


text: mouse ESC

text: cell line

text: mus musculus

text: SC

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: house mouse

text: Mus musculus

text: MuERVL- Zscan4- replicate B

text: Mus musculus


text: mouse ESC

text: cell line

text: mus musculus

text: SC

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: house mouse

text: Mus musculus

text: MuERVL+ Zscan4+ replicate C

text: Mus musculus


text: mouse ESC

text: cell line

text: mus musculus

text: SC

text: public

characteristic: SRA accession

characteristic: Submitter Id

text: house mouse

text: Mus musculus

text: MuERVL- Zscan4- replicate C

text: Mus musculus


text: mouse ESC

text: cell line

text: mus musculus

text: SC

text: public

text: house mouse

characteristic: common name

text: Mus musculus

characteristic: organism

text: MuERVL+ Zscan4+ replicate D

text: Mus musculus


text: mouse ESC

text: cell line

text: mus musculus

characteristic: ENA-CHECKLIST

text: SC

text: public

text: house mouse

text: Mus musculus

text: MuERVL- Zscan4- replicate D

text: Mus musculus


text: mouse ESC

text: cell line

text: mus musculus

text: SC

text: public

text: house mouse

text: Mus musculus

text: pIG4M34 GFP+ rep 3

text: Mus musculus


text: mouse ESC

text: cell line

text: mus musculus

text: SC

text: public

text: house mouse

text: Mus musculus

text: pIG4M34 GFP- rep 3

text: Mus musculus


text: male

characteristic: ArrayExpress-Sex

text: Homo Sapien

text: SC

text: public

text: human

text: Homo sapiens

text: Amplicon library

text: Homo sapiens


text: Homo Sapien

text: SC

text: public

text: human

text: Homo sapiens

text: Amplicon library

text: Homo sapiens


text: Melanoma

characteristic: ArrayExpress-Phenotype

text: Mus musculus

text: SC

text: public

text: house mouse

text: Mus musculus

text: Mus musculus


E-MTAB-3588:WT Sample 3

text: public

text: E-MTAB-3588:WT Sample 3

tag: Namespace:International Institute of Molecular and Cell Biology in Warsaw

text: ArrayExpress

characteristic: broker name

text: baker's yeast

text: Protocols: Yeast cells (3 X10 power of 8) were isolated by centrifugation at 4500 x g, 19 degree C for 5 min. Cell pellets were resuspended with RNAlater solution (Ambion) and stored at -80 degree C before RNA extraction. Yeast cells were grown in the liquid culture at 19 degree C in the YPG media (3% [v/v] glycerol) till the mid-logarithmic phase (OD600 of approx 0.65) RNA was extracted from frozen material using MagNA Lyser with MagNA Pure Compact RNA Isolation Kit (Roche), according to manufacturer's protocol. Genomic DNA remaining after isolation has been digested with TURBO DNA-freeKit (Life Technologies) according to manufacturer's protocol for standard digestion. To ensure that no gDNA contamination was present, each RNA sample has been used as a template for PCR reaction with primers specific to genomic loci (ERV1 gene). Samples were run on Agilent 2100 Bioanalyzer to ensure that high-quality RNA was used. Accurate RNA concentrations were measured with Qubit RNA BR Assay (Life Technologies). 1.5 ug of RNA from each sample was spiked with 3 ul of 100x diluted ERCC RNA Spike-In Mix (Life Technologies) and rRNA depleted with Ribo-Zero Gold rRNA Removal Kit (Yeast) (Illumina) according to manufacturer's protocol. RNA was validated on Agilent 2100 Bioanalyzer and Qubit and the depletion levels (95%-96%) were estimated . RNA-seq libraries were then prepared with Ion Total RNA-Seq Kit v2 (Life technologies) according to manufacturer's manual with slight modifications. Briefly, RNA was fragmented with RNase III, purified with magnetic beads and validated on Agilent 2100 Bioanalyzer. Fragmented RNA was hybridized and ligated with adapters and reverse transcribed. cDNA was purified with the same magnetic beads and amplified (2 + 10 cycles instead of 2 + 16 cycles in the manual) using barcoded primers. Amplified cDNA was purified and molar concentrations were measured with Agilent 2100 Bioanalyzer. Equal molar concentrations of each sample were pooled to prepare library mix for sequencing.

characteristic: description

text: wild type genotype

characteristic: genotype

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

characteristic: strain

text: WT Sample 3

characteristic: title

type: has member


E-MTAB-3588:WT Sample 1

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: International Institute of Molecular and Cell Biology in Warsaw

text: public

text: E-MTAB-3588:WT Sample 1

text: ArrayExpress

text: baker's yeast

text: wild type genotype

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

text: WT Sample 1


E-MTAB-3588:mia40-4int Sample 3

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: E-MTAB-3588:mia40-4int Sample 3

text: ArrayExpress

text: baker's yeast

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

text: mia40-4int Sample 3


E-MTAB-3588:WT Sample 2

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-3588:WT Sample 2

characteristic: Submitter Id

text: ArrayExpress

text: baker's yeast

text: wild type genotype

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

text: WT Sample 2


E-MTAB-3588:mia40-4int Sample 1

characteristic: ENA-CHECKLIST

text: public

text: E-MTAB-3588:mia40-4int Sample 1

text: ArrayExpress

text: baker's yeast

characteristic: common name

text: Saccharomyces cerevisiae

characteristic: organism

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

text: mia40-4int Sample 1


E-MTAB-3588:mia40-4int Sample 2

text: public

text: E-MTAB-3588:mia40-4int Sample 2

text: ArrayExpress

characteristic: broker name

text: baker's yeast

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

text: mia40-4int Sample 2


E-MTAB-3569:Nubbin-GAL4 1

text: Brighton and Sussex Medical School

text: public

text: E-MTAB-3569:Nubbin-GAL4 1

tag: Namespace:Brighton and Sussex Medical School

text: ArrayExpress

text: fruit fly

text: Protocols: 60 wing imaginal discs per sample were dissected from wandering 3rd instar larvae. Nubbin-Gal4 homozygous females were crossed to homozygous UAS-Dis3RNAi males at 25 degrees C.All offspring were of knockdown (nubbin-Gal4/UAS-Dis3RNAi) genotype. RNA was extracted from each sample of 60 wing discs using a miRNeasy kit. RNA was size selected (18-22nt) then libraries were constructed using illumina TruSeq Small RNA sample preparation protocol.

characteristic: description

text: third instar larva stage

characteristic: developmental stage

text: Drosophila melanogaster

text: Drosophila melanogaster

text: Wild type

characteristic: phenotype

text: Control construct - nubbin-AC-62 from Bloomington Drosophila stock center (stock number BL25754)t

characteristic: rna interference

text: Drosophila melanogaster

text: Nubbin-GAL4 1


E-MTAB-3569:UAS-Dis3RNAi 1

characteristic: ENA-FIRST-PUBLIC

text: Brighton and Sussex Medical School

text: public

text: E-MTAB-3569:UAS-Dis3RNAi 1

text: ArrayExpress

text: fruit fly

text: third instar larva stage

text: Drosophila melanogaster

text: Drosophila melanogaster

text: Wild type

text: Control construct - v35090 from Vienna Drosophila RNAi centrer

text: Drosophila melanogaster

text: UAS-Dis3RNAi 1

characteristic: title


E-MTAB-3569:Nubbin-GAL4 2

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Brighton and Sussex Medical School

text: public

text: E-MTAB-3569:Nubbin-GAL4 2

text: ArrayExpress

text: fruit fly

text: third instar larva stage

text: Drosophila melanogaster

text: Drosophila melanogaster

text: Wild type

text: Control construct - nubbin-AC-62 from Bloomington Drosophila stock center (stock number BL25754)

text: Drosophila melanogaster

text: Nubbin-GAL4 2


E-MTAB-3569:UAS-Dis3RNAi 2

text: Brighton and Sussex Medical School

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: E-MTAB-3569:UAS-Dis3RNAi 2

text: ArrayExpress

text: fruit fly

text: third instar larva stage

text: Drosophila melanogaster

text: Drosophila melanogaster

text: Wild type

text: Drosophila melanogaster

text: UAS-Dis3RNAi 2


E-MTAB-3569:Knockdown 2

text: Brighton and Sussex Medical School

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: E-MTAB-3569:Knockdown 2

text: ArrayExpress

text: fruit fly

text: third instar larva stage

text: Drosophila melanogaster

text: Drosophila melanogaster

text: Knockdown

text: Knockdown - contains both Nubbin-Gal4 and UAS-Dis3RNAi constructs

text: Drosophila melanogaster

text: Knockdown 2


E-MTAB-3569:Knockdown 1

text: Brighton and Sussex Medical School

text: public

characteristic: SRA accession

text: E-MTAB-3569:Knockdown 1

characteristic: Submitter Id

text: ArrayExpress

text: fruit fly

text: third instar larva stage

text: Drosophila melanogaster

text: Drosophila melanogaster

text: Knockdown

text: Drosophila melanogaster

text: Knockdown 1


characteristic: ENA-CHECKLIST

text: Leibniz Institute on Aging - Fritz Lipmann Institute (FLI)

text: public

tag: Namespace:Leibniz Institute on Aging – Fritz Lipmann Institute (FLI)

unit: hpf

characteristic: age

text: turquoise killifish

characteristic: common name

text: Nothobranchius furzeri

text: pool of individuals

characteristic: sample composition

text: Nothobranchius furzeri

characteristic: strain

text: embryo

characteristic: tissue

text: Nothobranchius furzeri MZM-0403 121025_cDNA_MZM0403_24hpf_embryo, 24 hpf old, embryo


text: public

text: turquoise killifish

text: Nothobranchius furzeri

characteristic: organism

text: pool of individuals

text: Nothobranchius furzeri

text: embryo

text: Nothobranchius furzeri MZM-0403 121025_cDNA_MZM0403_somite_embryo, embryo


characteristic: ENA-FIRST-PUBLIC

text: public

text: turquoise killifish

characteristic: individual name

text: Nothobranchius furzeri

text: Nothobranchius furzeri

text: kidney

text: Nothobranchius furzeri MZM-0703 s_17alt_42_6_dpi2, kidney


characteristic: ENA-LAST-UPDATE

text: public

text: turquoise killifish

text: Nothobranchius furzeri

text: Nothobranchius furzeri

text: kidney

text: Nothobranchius furzeri MZCS-08122 s_1jung_36_PBS, kidney

characteristic: title


characteristic: External Id

characteristic: INSDC center name

text: public

text: turquoise killifish

text: Nothobranchius furzeri

text: Nothobranchius furzeri

text: kidney

text: Nothobranchius furzeri MZM-0403 s_20alt_42_2_dpiPBS, kidney


characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: turquoise killifish

text: Nothobranchius furzeri

text: Nothobranchius furzeri

text: kidney

text: Nothobranchius furzeri MZM-0403 s_21alt_42_3_dpiPBS, kidney


text: public

characteristic: INSDC status

characteristic: SRA accession

text: turquoise killifish

text: Nothobranchius furzeri

text: Nothobranchius furzeri

text: kidney

text: Nothobranchius furzeri MZCS-08122 s_3jung_40_PBS, kidney


characteristic: ENA-CHECKLIST

text: public

characteristic: Submitter Id

text: turquoise killifish

text: Nothobranchius furzeri

text: Nothobranchius furzeri

text: kidney

text: Nothobranchius furzeri MZCS-08122 s_4jung_27_dpi2, kidney


text: mus musculus

characteristic: ArrayExpress-Species

text: SC

text: public

text: house mouse

characteristic: common name

text: Mus musculus

text: Screen 11 Unstimulated Wild Type Knock-out Embryonic Stem Cell Derived Macrophages 4hr

characteristic: sample description

text: Mus musculus


text: mus musculus

text: SC

text: public

text: house mouse

text: Mus musculus

text: Screen 11 Wild Type Knock-out Embryonic Stem Cell Derived Macrophages stimulated with Poly I:C (Toll-like receptor agonist)

text: Mus musculus


text: mus musculus

text: SC

text: public

text: house mouse

text: Mus musculus

text: Screen 11 Wild Type Knock-out Embryonic Stem Cell Derived Macrophages stimulated with ODN 1826 (CpG)

text: Mus musculus


text: mus musculus

text: SC

text: public

text: house mouse

text: Mus musculus

text: Screen 11 Wild Type Knock-out Embryonic Stem Cell Derived Macrophages stimulated with M TRI-dap (NOD agonist)

text: Mus musculus


text: mus musculus

text: SC

text: public

text: house mouse

text: Mus musculus

text: Screen 11 Wild Type Knock-out Embryonic Stem Cell Derived Macrophages stimulated with LPS (Toll-like receptor agonist)

text: Mus musculus


text: mus musculus

text: SC

text: public

text: house mouse

text: Mus musculus

text: Screen 11 Wild Type Knock-out Embryonic Stem Cell Derived Macrophages stimulated with Salmonella

text: Mus musculus


text: mus musculus

text: SC

text: public

text: house mouse

text: Mus musculus

text: Screen 11 Wild Type Knock-out Embryonic Stem Cell Derived Macrophages stimulated with Influenza 6 hr

text: Mus musculus


text: mus musculus

text: SC

text: public

text: house mouse

text: Mus musculus

text: Screen 11 Wild Type Knock-out Embryonic Stem Cell Derived Macrophages stimulated with Influenza 24 hr

text: Mus musculus


text: mus musculus

text: SC

text: public

text: house mouse

text: Mus musculus

text: Screen 11 Unstimulated Wild Type Knock-out Embryonic Stem Cell Derived Macrophages 24hr

text: Mus musculus


text: mus musculus

text: SC

text: public

text: house mouse

text: Mus musculus

text: Screen 11 Unstimulated Irf1 Knock-out Embryonic Stem Cell Derived Macrophages 4hr

text: Mus musculus


text: mus musculus

text: SC

text: public

text: house mouse

text: Mus musculus

text: Screen 11 Irf1 Knock-out Embryonic Stem Cell Derived Macrophages stimulated with Poly I:C (Toll-like receptor agonist)

text: Mus musculus


text: mus musculus

text: SC

text: public

text: house mouse

text: Mus musculus

text: Screen 11 Irf1 Knock-out Embryonic Stem Cell Derived Macrophages stimulated with ODN 1826 (CpG)

text: Mus musculus


text: mus musculus

text: SC

text: public

text: house mouse

text: Mus musculus

text: Screen 11 Irf1 Knock-out Embryonic Stem Cell Derived Macrophages stimulated with M TRI-dap (NOD agonist)

text: Mus musculus


text: mus musculus

text: SC

text: public

text: house mouse

text: Mus musculus

text: Screen 11 Irf1 Knock-out Embryonic Stem Cell Derived Macrophages stimulated with LPS (Toll-like receptor agonist)

text: Mus musculus


text: mus musculus

text: SC

text: public

text: house mouse

text: Mus musculus

text: Screen 11 Irf1 Knock-out Embryonic Stem Cell Derived Macrophages stimulated with Salmonella

text: Mus musculus


text: mus musculus

text: SC

text: public

text: house mouse

text: Mus musculus

text: Screen 11 Irf1 Knock-out Embryonic Stem Cell Derived Macrophages stimulated with Influenza 6 hr

text: Mus musculus


text: mus musculus

text: SC

text: public

text: house mouse

text: Mus musculus

text: Screen 11 Irf1 Knock-out Embryonic Stem Cell Derived Macrophages stimulated with Influenza 24 hr

text: Mus musculus


text: mus musculus

text: SC

text: public

text: house mouse

text: Mus musculus

text: Screen 11 Unstimulated Irf1 Knock-out Embryonic Stem Cell Derived Macrophages 24hr

text: Mus musculus


text: mus musculus

text: SC

text: public

text: house mouse

text: Mus musculus

text: Screen 11 Unstimulated Mapk14 Knock-out Embryonic Stem Cell Derived Macrophages 4hr

text: Mus musculus


text: mus musculus

text: SC

text: public

text: house mouse

text: Mus musculus

text: Screen 11 Mapk14 Knock-out Embryonic Stem Cell Derived Macrophages stimulated with Poly I:C (Toll-like receptor agonist)

text: Mus musculus


text: mus musculus

text: SC

text: public

text: house mouse

text: Mus musculus

text: Screen 11 Mapk14 Knock-out Embryonic Stem Cell Derived Macrophages stimulated with ODN 1826 (CpG)

text: Mus musculus


text: mus musculus

text: SC

text: public

text: house mouse

text: Mus musculus

text: Screen 11 Mapk14 Knock-out Embryonic Stem Cell Derived Macrophages stimulated with M TRI-dap (NOD agonist)

text: Mus musculus


text: mus musculus

text: SC

text: public

text: house mouse

text: Mus musculus

text: Screen 11 Mapk14 Knock-out Embryonic Stem Cell Derived Macrophages stimulated with LPS (Toll-like receptor agonist)

text: Mus musculus


text: mus musculus

text: SC

text: public

text: house mouse

text: Mus musculus

text: Screen 11 Mapk14 Knock-out Embryonic Stem Cell Derived Macrophages stimulated with Salmonella

text: Mus musculus


text: mus musculus

text: SC

text: public

text: house mouse

text: Mus musculus

text: Screen 11 Mapk14 Knock-out Embryonic Stem Cell Derived Macrophages stimulated with Influenza 6 hr

text: Mus musculus


text: mus musculus

text: SC

text: public

text: house mouse

text: Mus musculus

text: Screen 11 Mapk14 Knock-out Embryonic Stem Cell Derived Macrophages stimulated with Influenza 24 hr

text: Mus musculus


text: mus musculus

text: SC

text: public

text: house mouse

text: Mus musculus

text: Screen 11 Unstimulated Mapk14 Knock-out Embryonic Stem Cell Derived Macrophages 24hr

text: Mus musculus


text: mus musculus

text: SC

text: public

text: house mouse

text: Mus musculus

text: Screen 11 Unstimulated Lmnb2 Knock-out Embryonic Stem Cell Derived Macrophages 4hr

text: Mus musculus


text: mus musculus

text: SC

text: public

text: house mouse

text: Mus musculus

text: Screen 11 Lmnb2 Knock-out Embryonic Stem Cell Derived Macrophages stimulated with Poly I:C (Toll-like receptor agonist)

text: Mus musculus


text: mus musculus

text: SC

text: public

text: house mouse

text: Mus musculus

text: Screen 11 Lmnb2 Knock-out Embryonic Stem Cell Derived Macrophages stimulated with ODN 1826 (CpG)

text: Mus musculus


text: mus musculus

text: SC

text: public

text: house mouse

text: Mus musculus

text: Screen 11 Lmnb2 Knock-out Embryonic Stem Cell Derived Macrophages stimulated with M TRI-dap (NOD agonist)

text: Mus musculus


text: mus musculus

text: SC

text: public

text: house mouse

text: Mus musculus

text: Screen 11 Lmnb2 Knock-out Embryonic Stem Cell Derived Macrophages stimulated with LPS (Toll-like receptor agonist)

text: Mus musculus


text: mus musculus

text: SC

text: public

text: house mouse

text: Mus musculus

text: Screen 11 Lmnb2 Knock-out Embryonic Stem Cell Derived Macrophages stimulated with Salmonella

text: Mus musculus


text: public

tag: Namespace:All India Institute of Medical Sciences (AIIMS)

text: ArrayExpress

characteristic: broker name

text: sorghum

text: Protocols: Sorghum (Sorghum bicolor (L.) Moench) seeds of genotypes M35-1 (drought tolerant/DT) (Jogeswar, et al., 2006) was obtained from Directorate of Sorghum Research, Hyderabad, India. Seeds were grown at 28-32 degrees C day/night temperature with 12/12 h light/dark period in the phytotron glass house. Plants were irrigated alternately with water and Hoagland's solution at 3 days interval. Thirty days after sowing, drought stress was imposed by withholding irrigation to one set of plants (documented as treated with drought stressed; Sample 3 and 4) until the leaf relative water content reached to about 60-65%. The fully opened uppermost leaves from control and drought stressed seedlings were sampled and stored at -80 degrees C. For RNA-Seq libraries, one microgram of total RNA was extracted with Trizol reagent (Invitrogen, USA) and mRNA libraries were produced using the TruSeq mRNA-Seq library kit (Illumina) according to manufacturer's instructions.

characteristic: description

text: Seedlings

characteristic: developmental stage

text: Drought tolerant (M35-1)

characteristic: genotype

characteristic: growth condition

text: Sorghum bicolor

text: Sorghum bicolor

text: Leaves

characteristic: organism part

text: Sorghum bicolor

text: Drought stress

characteristic: stimulus

text: sampleB

text: Drought stress

characteristic: treatment


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: All India Institute of Medical Sciences (AIIMS)

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: ArrayExpress

text: sorghum

text: Seedlings

text: Drought tolerant (M35-1)

text: 28-32 degrees C day/night temperature with 12/12 h light/dark period in the phytotron glass house

text: Sorghum bicolor

characteristic: organism

text: Sorghum bicolor

text: Leaves

text: Sorghum bicolor

text: No stress (control)

text: sampleA

characteristic: title

text: No treatment


text: Danio rerio

characteristic: ArrayExpress-Species

characteristic: ENA-CHECKLIST

text: SC

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: zebrafish

characteristic: common name

text: Danio rerio

text: Danio rerio


text: public

tag: Namespace:Department of Plant Sciences University of Cambridge

text: ArrayExpress

characteristic: broker name

text: house mouse

text: Protocols: Murine 17 clone 1 cells were maintained in Dulbecco’s modification of Eagle’s medium supplemented with 10% (vol/vol) fetal calf serum. Cells (107) were plated in a 10 cm dish and upon reaching 100% confluence, cycloheximide (Sigma-Aldrich) was added to 100 µg/ml. After 2 min, cells were rinsed with 5 ml of ice-cold PBS, the dishes submerged in a reservoir of liquid nitrogen for 10 sec, transferred to dry ice and 400 µl of lysis buffer (20 mM Tris-HCl pH 7.5, 150 mM NaCl, 5 mM MgCl2, 1 mM DTT, 1% Triton X-100, 100 µg/ml cycloheximide and 25 U/ml TURBO™ DNase (Life Technologies) dripped on. The cells were scraped extensively to ensure lysis, collected and triturated with a 26-G needle ten times. Lysates were clarified by centrifugation for 20 min at 13,000 g at 4 ºC, the supernatants recovered and stored in liquid nitrogen. For mouse samples, lysates were slowly thawed on ice and 300 µl treated with 7.5 µl RNase 1 followed by incubation for 45 min at room temperature on a rotating wheel. 10 µl of SUPERase-In RNase inhibitor was added, the sample layered onto a 1M sucrose cushion in mammalian polysome buffer (20 mM Tris-HCl pH 7.5, 150 mM NaCl, 5 mM MgCl2, 1 mM DTT, 100 µg/ml cycloheximide) and ultracentrifuged at 28,000 rpm (16 hr, 4 ºC) in a Beckman SW55Ti rotor. Subsequently, all ribosome pellets were resuspended in 200 µl of the corresponding polysome buffer and digested with proteinase K (10 mM Tris-HCl pH 7.5, 10% SDS, 200 µg/ml Proteinase K [New England Biolabs]) for 30 min at 42 ºC. RPFs were recovered by extracting twice with pre-warmed (65 ºC) acidic phenol:chloroform (Life Technologies) and once with chloroform (1:1, vol/vol, buffered with 10 mM Tris pH 7.5, 0.1 mM EDTA), followed by ethanol precipitation. RPFs were resuspended in 10 mM Tris-HCl pH 7.5 and quantified by spectrophotometry. The RNA samples from above were heated at 80 ºC for 2 min, cooled and the 3’ phosphate group removed using T4 polynucleotide kinase (T4 PNK, New England Biolabs) at 37 ºC for 2 hrs in a 20 µl reaction lacking ATP. The RNA was concentrated by ethanol precipitation, resuspended in 10 mM Tris-HCl pH 7.5 and ligated in a 20 µl reaction overnight at 14 ºC to a preadenylated 3’-adaptor (5’ rATGGAATTCTCGGGTGCCAAGG 3’) using T4 RNA Ligase 2 truncated K227Q (New England Biolabs). This 3’ adaptor was adenylated using a 5’ DNA adenylation kit (New England Biolabs) following the manufacturer’s instructions. RNA was precipitated, loaded into a 15% (wt/vol) denaturing polyacrylamide gel and ligated RNA fragments migrating between 49 nt and 53 nt excised. The RNA was eluted, precipitated, resuspended as above and 5’ phosphorylated using T4 PNK in the presence of 1mM ATP for 2 hrs at 37 ºC. RNA was concentrated by ethanol precipitation, resuspended in 10mM Tris-HCl pH 7.5 and ligated to a 5’ RNA adaptor (5’ rGrUrUrCrArGrArGrUrUrCrUrArCrArGrUrCrCrGrArCrGrArUrC 3’) in a 20 µl reaction overnight at 14 ºC using T4 RNA Ligase (Promega). The fully adapted RNAs were recovered by ethanol precipitation, dissolved in 6 µl 10mM Tris-HCl pH 7.5 and 3 µl of this ligated product annealed to an RT primer (5' GCCTTGGCACCCGAGAATTCCA, 50 pmol) at 65 ºC for 5 min. The RNA was subsequently reverse transcribed at 55 ºC for 50 min in a 20 µl reaction following addition of first strand buffer (Invitrogen, to 1X), 2.5 mM MgCl2, 10 mM DTT, 0.5 µl SUPERase-In and 1 µl SuperScript III (Invitrogen), followed by heat inactivation at 85 ˚C for 5 min. For PCR and ribosomal depletion steps, see referenced manuscript.

characteristic: description

text: Mus musculus

text: Mus musculus

text: Mus musculus

text: rRNA depletion by RiboZero

characteristic: transcriptome


characteristic: ENA-FIRST-PUBLIC

text: Department of Plant Sciences University of Cambridge

text: public

text: ArrayExpress

text: house mouse

text: Mus musculus

text: Mus musculus

text: Mus musculus

text: rRNA depletion by duplex-specific nuclease (two cycle)


characteristic: ENA-LAST-UPDATE

text: public

text: ArrayExpress

text: house mouse

text: Mus musculus

text: Mus musculus

text: Mus musculus

text: No rRNA depletion


characteristic: External Id

text: public

text: ArrayExpress

text: house mouse

text: Mus musculus

text: Mus musculus

text: Mus musculus

text: rRNA depletion by duplex-specific nuclease (one cycle)


characteristic: INSDC center name

text: public

text: ArrayExpress

text: house mouse

text: Mus musculus

text: Mus musculus

text: Mus musculus

text: rRNA depletion by antisense oligonucleotide


text: Shanghai Jiao Tong university

characteristic: INSDC first public

text: public

tag: Namespace:Shanghai Jiao Tong university

text: ArrayExpress

characteristic: cell line

text: lung cancer cell

characteristic: cell type

text: human

text: Protocols: RPMI 1640 supplemented with 10% fetal bovine serum (FBS) and penicillin/streptomycin with final concentration is 100U/ml JFK group was treated with JFK extract (0.054mg/ml) 10 μg of total RNA were puriﬁed using Oligotex mRNA Mini Kit (70022, QIAGEN) according to manufacturer’s instructions.

text: non-small cell lung carcinoma

characteristic: disease

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens

text: Control


characteristic: ENA-CHECKLIST

text: Shanghai Jiao Tong university

text: public

text: ArrayExpress

text: lung cancer cell

text: human

text: non-small cell lung carcinoma

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: Homo sapiens

text: JFK

characteristic: title


text: Inserm U938

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

tag: Namespace:Inserm U938

text: human

text: Homo sapiens

text: Homo sapiens


text: bone marrow

characteristic: ArrayExpress-CellType

text: leukeamia

characteristic: ArrayExpress-DiseaseState

text: Homo Sapien

characteristic: ArrayExpress-Species

characteristic: ArrayExpress-StrainOrLine

text: SC

text: public

characteristic: Submitter Id

text: human

characteristic: common name

text: Homo sapiens

text: cell DNA

characteristic: sample description

text: Homo sapiens

characteristic: strain


text: myeloid cell line

text: leukeamia

text: Homo Sapien

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: SC

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: human

text: Homo sapiens

text: cell DNA

text: Homo sapiens


text: Plasmodium falciparum

characteristic: ENA-CHECKLIST

text: SC

text: public

text: malaria parasite P. falciparum

text: Plasmodium falciparum

characteristic: organism

text: Plasmodium falciparum


characteristic: INSDC last update

text: public

characteristic: INSDC status

tag: Namespace:Kennedy Institute of Rheumatology, University of Oxford

text: 8 week

characteristic: age

characteristic: biological replicate

text: ArrayExpress

characteristic: broker name

text: house mouse

text: Protocols: oral gavage of helicobacter hepaticus at 1E8 bacterium on days 0,1 and 2 intraperitoneal injection of anti-IL10 receptor antibody at days 0 and 7 For simultaneous DNA and RNA extraction, pellets were dissolved in 500 ul extraction buffer (200 mM NaCl, 20 mM EDTA, 4 M guanidine thiocyanate, 1 % (v/v) β-mercaptoethanol) and 210 ul 20 % (w/v) SDS and lysed with a bead beater twice for 2 minutes employing Lysing Matrix E tubes (MP Biomedicals). Samples were centrifuged at 8000 g for 5 minutes and the supernatant was diluted with 3 volumes of lysing buffer (ZR-Duet DNA/RNA Miniprep Kit, Zymo Research). DNA and RNA were further extracted employing the ZR-Duet DNA/RNA Miniprep Kit according to the manufacturer’s instructions. Libraries were prepared using the PrepX ILM 32i DNA Library Kit

characteristic: description

text: colitis

characteristic: disease

text: Mus musculus

text: Mus musculus

text: Mus musculus

text: male

characteristic: sex

text: Faeces

characteristic: starting material

characteristic: title

text: Helicobacter hepaticus gavage (10E8 bacteria) with Intraperitoneal injection of 10mg anti-IL10R antibody on days 0 and 7

characteristic: treatment


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: Kennedy Institute of Rheumatology, University of Oxford

text: public

characteristic: SRA accession

characteristic: Submitter Id

text: 8 week

text: ArrayExpress

text: house mouse

characteristic: common name

text: Protocols: Steady state mice not treated For simultaneous DNA and RNA extraction, pellets were dissolved in 500 ul extraction buffer (200 mM NaCl, 20 mM EDTA, 4 M guanidine thiocyanate, 1 % (v/v) β-mercaptoethanol) and 210 ul 20 % (w/v) SDS and lysed with a bead beater twice for 2 minutes employing Lysing Matrix E tubes (MP Biomedicals). Samples were centrifuged at 8000 g for 5 minutes and the supernatant was diluted with 3 volumes of lysing buffer (ZR-Duet DNA/RNA Miniprep Kit, Zymo Research). DNA and RNA were further extracted employing the ZR-Duet DNA/RNA Miniprep Kit according to the manufacturer’s instructions. Total RNA was depleted of ribosomal RNA using Epibio’s universal bacteria ribo-zero kit, single version. Libraries were constructed using the NEBNext Ultra directional RNA Library Prep Kit (E7420L).

text: Mus musculus

text: Mus musculus

text: Mus musculus

text: male

text: Faeces

characteristic: strain


characteristic: ENA-CHECKLIST

characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: 8 week

text: ArrayExpress

text: house mouse

text: Protocols: intraperitoneal injection of anti-IL10 receptor antibody at days 0 and 7 For simultaneous DNA and RNA extraction, pellets were dissolved in 500 ul extraction buffer (200 mM NaCl, 20 mM EDTA, 4 M guanidine thiocyanate, 1 % (v/v) β-mercaptoethanol) and 210 ul 20 % (w/v) SDS and lysed with a bead beater twice for 2 minutes employing Lysing Matrix E tubes (MP Biomedicals). Samples were centrifuged at 8000 g for 5 minutes and the supernatant was diluted with 3 volumes of lysing buffer (ZR-Duet DNA/RNA Miniprep Kit, Zymo Research). DNA and RNA were further extracted employing the ZR-Duet DNA/RNA Miniprep Kit according to the manufacturer’s instructions. Total RNA was depleted of ribosomal RNA using Epibio’s universal bacteria ribo-zero kit, single version. Libraries were constructed using the NEBNext Ultra directional RNA Library Prep Kit (E7420L).

text: Mus musculus

characteristic: organism

text: Mus musculus

text: Mus musculus

text: male

text: Faeces

text: Intraperitoneal injection of 10mg anti-IL10R antibody on days 0 and 7


text: public

characteristic: INSDC status

text: 8 week

characteristic: age

characteristic: biological replicate

text: ArrayExpress

characteristic: broker name

text: house mouse

text: Protocols: oral gavage of helicobacter hepaticus at 1E8 bacterium on days 0,1 and 2 intraperitoneal injection of anti-IL10 receptor antibody at days 0 and 7 For simultaneous DNA and RNA extraction, pellets were dissolved in 500 ul extraction buffer (200 mM NaCl, 20 mM EDTA, 4 M guanidine thiocyanate, 1 % (v/v) β-mercaptoethanol) and 210 ul 20 % (w/v) SDS and lysed with a bead beater twice for 2 minutes employing Lysing Matrix E tubes (MP Biomedicals). Samples were centrifuged at 8000 g for 5 minutes and the supernatant was diluted with 3 volumes of lysing buffer (ZR-Duet DNA/RNA Miniprep Kit, Zymo Research). DNA and RNA were further extracted employing the ZR-Duet DNA/RNA Miniprep Kit according to the manufacturer’s instructions. Total RNA was depleted of ribosomal RNA using Epibio’s universal bacteria ribo-zero kit, single version. Libraries were constructed using the NEBNext Ultra directional RNA Library Prep Kit (E7420L).

characteristic: description

text: colitis

characteristic: disease

text: Mus musculus

text: Mus musculus

text: Mus musculus

text: male

text: Faeces


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: public

text: 8 week

text: ArrayExpress

text: house mouse

text: Protocols: Steady state mice not treated For simultaneous DNA and RNA extraction, pellets were dissolved in 500 ul extraction buffer (200 mM NaCl, 20 mM EDTA, 4 M guanidine thiocyanate, 1 % (v/v) β-mercaptoethanol) and 210 ul 20 % (w/v) SDS and lysed with a bead beater twice for 2 minutes employing Lysing Matrix E tubes (MP Biomedicals). Samples were centrifuged at 8000 g for 5 minutes and the supernatant was diluted with 3 volumes of lysing buffer (ZR-Duet DNA/RNA Miniprep Kit, Zymo Research). DNA and RNA were further extracted employing the ZR-Duet DNA/RNA Miniprep Kit according to the manufacturer’s instructions. Libraries were prepared using the PrepX ILM 32i DNA Library Kit

text: Mus musculus

text: Mus musculus

text: Mus musculus

text: male

characteristic: sex

text: Faeces

characteristic: starting material

characteristic: title


characteristic: ENA-CHECKLIST

text: public

characteristic: SRA accession

characteristic: Submitter Id

text: 8 week

text: ArrayExpress

text: house mouse

characteristic: common name

text: Protocols: oral gavage of helicobacter hepaticus at 1E8 bacterium on days 0,1 and 2 For simultaneous DNA and RNA extraction, pellets were dissolved in 500 ul extraction buffer (200 mM NaCl, 20 mM EDTA, 4 M guanidine thiocyanate, 1 % (v/v) β-mercaptoethanol) and 210 ul 20 % (w/v) SDS and lysed with a bead beater twice for 2 minutes employing Lysing Matrix E tubes (MP Biomedicals). Samples were centrifuged at 8000 g for 5 minutes and the supernatant was diluted with 3 volumes of lysing buffer (ZR-Duet DNA/RNA Miniprep Kit, Zymo Research). DNA and RNA were further extracted employing the ZR-Duet DNA/RNA Miniprep Kit according to the manufacturer’s instructions. Total RNA was depleted of ribosomal RNA using Epibio’s universal bacteria ribo-zero kit, single version. Libraries were constructed using the NEBNext Ultra directional RNA Library Prep Kit (E7420L).

text: Mus musculus

text: Mus musculus

text: Mus musculus

text: male

text: Faeces

characteristic: strain

text: Helicobacter hepaticus gavage (10E8 bacteria)

characteristic: treatment


characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: 8 week

text: ArrayExpress

text: house mouse

text: Protocols: intraperitoneal injection of anti-IL10 receptor antibody at days 0 and 7 For simultaneous DNA and RNA extraction, pellets were dissolved in 500 ul extraction buffer (200 mM NaCl, 20 mM EDTA, 4 M guanidine thiocyanate, 1 % (v/v) β-mercaptoethanol) and 210 ul 20 % (w/v) SDS and lysed with a bead beater twice for 2 minutes employing Lysing Matrix E tubes (MP Biomedicals). Samples were centrifuged at 8000 g for 5 minutes and the supernatant was diluted with 3 volumes of lysing buffer (ZR-Duet DNA/RNA Miniprep Kit, Zymo Research). DNA and RNA were further extracted employing the ZR-Duet DNA/RNA Miniprep Kit according to the manufacturer’s instructions. Libraries were prepared using the PrepX ILM 32i DNA Library Kit

text: Mus musculus

characteristic: organism

text: Mus musculus

text: Mus musculus

text: male

text: Faeces


characteristic: ENA-FIRST-PUBLIC

text: public

text: 8 week

characteristic: age

characteristic: biological replicate

text: ArrayExpress

characteristic: broker name

text: house mouse

characteristic: description

text: colitis

characteristic: disease

text: Mus musculus

text: Mus musculus

text: Mus musculus

text: male

text: Faeces


characteristic: ENA-CHECKLIST

characteristic: ENA-LAST-UPDATE

text: public

characteristic: SRA accession

text: 8 week

text: ArrayExpress

text: house mouse

text: Protocols: oral gavage of helicobacter hepaticus at 1E8 bacterium on days 0,1 and 2 For simultaneous DNA and RNA extraction, pellets were dissolved in 500 ul extraction buffer (200 mM NaCl, 20 mM EDTA, 4 M guanidine thiocyanate, 1 % (v/v) β-mercaptoethanol) and 210 ul 20 % (w/v) SDS and lysed with a bead beater twice for 2 minutes employing Lysing Matrix E tubes (MP Biomedicals). Samples were centrifuged at 8000 g for 5 minutes and the supernatant was diluted with 3 volumes of lysing buffer (ZR-Duet DNA/RNA Miniprep Kit, Zymo Research). DNA and RNA were further extracted employing the ZR-Duet DNA/RNA Miniprep Kit according to the manufacturer’s instructions. Libraries were prepared using the PrepX ILM 32i DNA Library Kit

text: Mus musculus

text: Mus musculus

text: Mus musculus

text: male

characteristic: sex

text: Faeces

characteristic: starting material

characteristic: title

text: Helicobacter hepaticus oral gavage (1E8 bacteria on days 0,1 and 2)


characteristic: External Id

characteristic: INSDC center name

text: public

characteristic: Submitter Id

text: 8 week

text: ArrayExpress

text: house mouse

characteristic: common name

text: Mus musculus

text: Mus musculus

text: Mus musculus

text: male

text: Faeces

characteristic: strain

text: Helicobacter hepaticus oral gavage (10E8 bacteria on days 0,1 and 2)

characteristic: treatment


characteristic: ENA-FIRST-PUBLIC

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: 8 week

characteristic: age

text: ArrayExpress

text: house mouse

text: Mus musculus

characteristic: organism

text: Mus musculus

text: Mus musculus

text: male

text: Faeces


characteristic: ENA-CHECKLIST

characteristic: ENA-LAST-UPDATE

text: public

text: 8 week

characteristic: biological replicate

text: ArrayExpress

characteristic: broker name

text: house mouse

characteristic: description

text: Mus musculus

text: Mus musculus

text: Mus musculus

text: male

text: Faeces

text: Helicobacter hepaticus oral gavage (1E8 bacteria on days 0, 1 and 2)


characteristic: External Id

text: public

characteristic: SRA accession

tag: Namespace:SickKids Research Institute Genetics & Genome Biology Program  and  Department of Molecular Genetics, University of Toronto

text: 2 to 4 month

characteristic: antibody part number

text: ArrayExpress

text: house mouse

text: Protocols: Samples were prepared as previously described (doi:10.1016/j.ymeth.2009.03.001). Liver material was crosslinked in 1% formaldehyde for 20 minutes followed by a 10 minute incubation in 500 mM glycine buffer to neutralize the formaldehyde. Samples were rinsed with PBS and frozen at -80 Celsius until use. Chromatin immunoprecipitation was performed as previously described (doi:10.1016/j.ymeth.2009.03.001). Chromatin from a mass equivalent of at least 1/4 mouse liver was used for each ChIP experiment. Crosslinked tissues were dounce homogenized into a single cell suspension and rinsed with ice-cold PBS. Each pellet of crosslinked material was resuspended in 10 ml of LB1 (50 mM Hepes-KOH, pH 7.5; 140 mM NaCl; 1mM EDTA; 10% Glycerol; 0.5% NP-40 or Igepal CA-630; 0.25% Triton X-100), rocked at 4 degrees C for 10 minutes, and pelleted by centrifugation at 2,000 x rcf for 4 minutes at 4 degrees C. Pellets were then resuspended in 10 ml of LB2 (10 mM Tris-HCL, pH8.0; 200 mM NaCl; 1 mM EDTA; 0.5 mM EGTA), rocked gently at 4 degrees C for 5 minutes, and pelleted again by centrifugation at 2,000 x rcf for 4 minutes at 4 degrees C. Finally each pellet was resuspended in 3 ml of LB3 (10 mM Tris-HCl, pH 8; 100 mM NaCl; 1 mM EDTA; 0.5 mM EGTA; 0.1% Na-Deoxycholate; 0.5% N-lauroylsarcosine). Chromatin from the nuclei fraction was fragmented to an average length of 300 bp by sonication. Sonicated lysates were treated with 150uL of 20% triton X-100, and sonication debris was removed by centrifugation at 20,000 x rcf for 10 minutes at 4 degrees C. 150uL of whole cell extract (WCE) was taken as the input control. 100uL of magnetic protein-G Dynabeads (LifeTechnologies, cat. no. 10004D) was washed three times and pre-blocked with 0.5% BSA (Sigma, cat. no. A8412) w/v in PBS. 5-10 ug of antibody was incubated with pre-blocked Dynabeads for at least 6 hours, rotating at 4 degrees C, then washed three times with blocking solution to remove excess unbound antibody. Antibodies used were: Rad21 (Abcam, ab992), Top2b (Santa Cruz Biotech, sc13059), H3K4me3 (Abcam, ab8580), H3K36me3 (clone 13C9 from Hitoshi Kimura), Ctcf (Millipore, mp07-729), H3K4me2 (Millipore, mp07-030). Lysates were added to protein-G bound antibodies and incubated overnight at 4 degrees C. ChIP DNA was prepared for Illumina sequencing by blunt-end repair, dA-tailing, and ligating Illumina adaptors using NEBNext DNA library preparation kit (New England Biolabs, cat. no. E6040L). ChIP DNA and 220ng of WCE were end repaired for 30 minutes at room temperature, and purified using either DNA Clean and Concentrator kit (Zymogen, cat. no. D4014) or PCR column purification kit (Qiagen, cat. no. 28106) following manufacturers protocols. Blunt-end repaired DNA was dA-tailed for 40 minutes at 37 degrees C, then column purified. dA-tailed DNA was ligated to Illumina adaptors (final concentration 6.67 nM) that have a T-overhang and a proprietary uracil hairpin. USER enzyme was used to cleave the uracil hairpin, and adaptor-ligated DNA was column purified. The library was PCR amplified for 16-18 cycles using a universal primer and a barcoded primers (New England Biolabs, cat. no. E7335L) in order to multiplex the libraries for sequencing. PCR-amplified DNA was purified using PCR column purification and eluted in 20uL of elution buffer for gel extraction, or 30uL of TE for the Pippin Prep size selection. Size selection was performed in one of two ways: (i) 200-300bp region was gel purified by casting a 2% ultra-pure ChIP-grade agarose gel and MinElute Gel Extraction Kit, or (ii) samples were size selected from 200-350bp using a 2% agarose dye-free automated size selection cassettes from Pippin Prep (Sage Sciences, cat. no. CDF2010).

characteristic: individual

text: ChIP-seq

characteristic: method

text: Mus musculus

text: Mus musculus

text: liver

characteristic: organism part

text: Mus musculus

text: male

characteristic: sex

characteristic: title


characteristic: ENA-FIRST-PUBLIC

text: SickKids Research Institute Genetics & Genome Biology Program and Department of Molecular Genetics, University of Toronto

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: Submitter Id

text: 2 to 4 month

text: ArrayExpress

text: house mouse

characteristic: common name

text: ChIP-seq

text: Mus musculus

text: Mus musculus

text: liver

text: Mus musculus

text: male

characteristic: strain


characteristic: ENA-CHECKLIST

characteristic: ENA-LAST-UPDATE

text: public

characteristic: INSDC status

text: 2 to 4 month

characteristic: age

text: ArrayExpress

characteristic: broker name

text: house mouse

text: Protocols: Samples were prepared as previously described (doi:10.1016/j.ymeth.2009.03.001). Liver material was crosslinked in 1% formaldehyde for 20 minutes followed by a 10 minute incubation in 500 mM glycine buffer to neutralize the formaldehyde. Samples were rinsed with PBS and frozen at -80 Celsius until use. Chromatin immunoprecipitation was performed as previously described (doi:10.1016/j.ymeth.2009.03.001). Chromatin from a mass equivalent of at least 1/4 mouse liver was used for each ChIP experiment. Crosslinked tissues were dounce homogenized into a single cell suspension and rinsed with ice-cold PBS. Each pellet of crosslinked material was resuspended in 10 ml of LB1 (50 mM Hepes-KOH, pH 7.5; 140 mM NaCl; 1mM EDTA; 10% Glycerol; 0.5% NP-40 or Igepal CA-630; 0.25% Triton X-100), rocked at 4 degrees C for 10 minutes, and pelleted by centrifugation at 2,000 x rcf for 4 minutes at 4 degrees C. Pellets were then resuspended in 10 ml of LB2 (10 mM Tris-HCL, pH8.0; 200 mM NaCl; 1 mM EDTA; 0.5 mM EGTA), rocked gently at 4 degrees C for 5 minutes, and pelleted again by centrifugation at 2,000 x rcf for 4 minutes at 4 degrees C. Finally each pellet was resuspended in 3 ml of LB3 (10 mM Tris-HCl, pH 8; 100 mM NaCl; 1 mM EDTA; 0.5 mM EGTA; 0.1% Na-Deoxycholate; 0.5% N-lauroylsarcosine). Chromatin from the nuclei fraction was fragmented to an average length of 300 bp by sonication. Sonicated lysates were treated with 150uL of 20% triton X-100, and sonication debris was removed by centrifugation at 20,000 x rcf for 10 minutes at 4 degrees C. 150uL of whole cell extract (WCE) was taken as the input control. 100uL of magnetic protein-G Dynabeads (LifeTechnologies, cat. no. 10004D) was washed three times and pre-blocked with 0.5% BSA (Sigma, cat. no. A8412) w/v in PBS. 5-10 ug of antibody was incubated with pre-blocked Dynabeads for at least 6 hours, rotating at 4 degrees C, then washed three times with blocking solution to remove excess unbound antibody. Antibodies used were: Rad21 (Abcam, ab992), Top2b (Santa Cruz Biotech, sc13059), H3K4me3 (Abcam, ab8580), H3K36me3 (clone 13C9 from Hitoshi Kimura), Ctcf (Millipore, mp07-729), H3K4me2 (Millipore, mp07-030). Lysates were added to protein-G bound antibodies and incubated overnight at 4 degrees C. ChIP-exo was performed as previously described (doi: 10.1093/nar/gku846). Livers from wildtype C57BL6/J male mice (~3 months old) were obtained post mortem. Approximately 1/3 of each liver was utilized per ChIP-exo experiment. 7 ug of antibody against the Top2b (Santa Cruz Biotech, sc13059), Ctcf (Millipore, mp07-729), and Rad21 (Abcam, ab992) were used for each biological replicate. Individual livers were cross-linked in 1% formaldehyde and chromatin immunoprecipitation (ChIP) was performed as previously described up until and including the RIPA buffer washes (step 38 from (doi:10.1016/j.ymeth.2009.03.001)). The ChIP-exo portion of the protocol was performed as previously described (doi: 10.1016/j.cell.2011.11.013) with modifications making the assay compatible with the Illumina sequencing platform. Briefly, while still on the magnetic beads (Invitrogen, Dynabeads), the immunoprecipitated DNA was end-repaired (NebNext End Repair Module, New England Biolabs (NEB)). The P7 adapter was designed based on the adapter sequence provided by NEB: 5'-Phos-TGACTGGAGTTCAGACGTGTGCTCTTCCGATCT-3' and 5'-AGATCGGAAGAGCACACGTCTGAACTCC-3'. After ligation, the DNA was nick-repaired with phi29 polymerase, and digested by lambda and RecJf exonucleases (NEB). DNA samples were eluted from the beads by performing reverse crosslinking overnight at 65 degrees C, followed by RNaseA (Ambion) and ProteinaseK (Invitrogen) treatments. DNA was extracted using phenol-chloroform-isoamyl protocol and ethanol precipitation. DNA was denatured at 95 degrees C, 3' ends were primer-extended with a P7 fill-in primer (5'-TGACTGGAGTTCAGACGTGTGCTCTTCCGATCT-3'), and phi29 polymerase. A second adaptor ligation to only lambda exonuclease-digested ends of double stranded DNA was performed using 15 pmol of P5 adapter (sequence provided by NEB: 5'-AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTG-3' and 5'-TCTACACTCTTTCCCTACACGACGCTCTTCCGATCT-3'). The resulting DNA samples were PCR-amplified using multiplexing index primers (NEBNext DNA Library Prep Master Mix Set for Illumina). Libraries were size selected from 180-300bp using a 2% agarose dye-free automated size selection cassettes from Pippin Prep (Sage Sciences, cat. no. CDF2010), and quantified with 2100 Bioanalyzer (Agilent).

text: ChIP-exo

text: Mus musculus

characteristic: organism

text: Mus musculus

text: liver

text: Mus musculus

text: male


characteristic: External Id

text: public

characteristic: SRA accession

text: 2 to 4 month

text: clone 13C9 (H. Kimura)

characteristic: antibody part number

text: ArrayExpress

text: house mouse

text: Protocols: Samples were prepared as previously described (doi:10.1016/j.ymeth.2009.03.001). Liver material was crosslinked in 1% formaldehyde for 20 minutes followed by a 10 minute incubation in 500 mM glycine buffer to neutralize the formaldehyde. Samples were rinsed with PBS and frozen at -80 Celsius until use. Chromatin immunoprecipitation was performed as previously described (doi:10.1016/j.ymeth.2009.03.001). Chromatin from a mass equivalent of at least 1/4 mouse liver was used for each ChIP experiment. Crosslinked tissues were dounce homogenized into a single cell suspension and rinsed with ice-cold PBS. Each pellet of crosslinked material was resuspended in 10 ml of LB1 (50 mM Hepes-KOH, pH 7.5; 140 mM NaCl; 1mM EDTA; 10% Glycerol; 0.5% NP-40 or Igepal CA-630; 0.25% Triton X-100), rocked at 4 degrees C for 10 minutes, and pelleted by centrifugation at 2,000 x rcf for 4 minutes at 4 degrees C. Pellets were then resuspended in 10 ml of LB2 (10 mM Tris-HCL, pH8.0; 200 mM NaCl; 1 mM EDTA; 0.5 mM EGTA), rocked gently at 4 degrees C for 5 minutes, and pelleted again by centrifugation at 2,000 x rcf for 4 minutes at 4 degrees C. Finally each pellet was resuspended in 3 ml of LB3 (10 mM Tris-HCl, pH 8; 100 mM NaCl; 1 mM EDTA; 0.5 mM EGTA; 0.1% Na-Deoxycholate; 0.5% N-lauroylsarcosine). Chromatin from the nuclei fraction was fragmented to an average length of 300 bp by sonication. Sonicated lysates were treated with 150uL of 20% triton X-100, and sonication debris was removed by centrifugation at 20,000 x rcf for 10 minutes at 4 degrees C. 150uL of whole cell extract (WCE) was taken as the input control. 100uL of magnetic protein-G Dynabeads (LifeTechnologies, cat. no. 10004D) was washed three times and pre-blocked with 0.5% BSA (Sigma, cat. no. A8412) w/v in PBS. 5-10 ug of antibody was incubated with pre-blocked Dynabeads for at least 6 hours, rotating at 4 degrees C, then washed three times with blocking solution to remove excess unbound antibody. Antibodies used were: Rad21 (Abcam, ab992), Top2b (Santa Cruz Biotech, sc13059), H3K4me3 (Abcam, ab8580), H3K36me3 (clone 13C9 from Hitoshi Kimura), Ctcf (Millipore, mp07-729), H3K4me2 (Millipore, mp07-030). Lysates were added to protein-G bound antibodies and incubated overnight at 4 degrees C. ChIP libraries were made as previously described protocol (doi:10.1016/j.ymeth.2009.03.001). 50 µl of cell lysate from each sonication was removed as the input control DNA that was processed. Libraries were prepared following the instructions of Illumina (Sample preparation for genomic DNA - version 2.2) with the following modifications: The ChIP-enriched DNA and input DNA were not further fragmented. After end-repair and addition of an 'A' base to the 3' ends, the adapters were ligated to the ends of the DNA fragments using 2 µl of forty-fold diluted 'Adapter oligo mix'’ in a total reaction volume of 25 µl. Between these steps, the DNA was purified using the DNA Clean-and-Concentrator-5 kit (Zymo Research). Subsequently, the DNA was amplified by 18 cycles of PCR, purified with QIAquick PCR purification Kit, and eluted with 33.5 µl of 10 mM Tris buffer at pH7.0. The PCR product was sized selected on 2% agarose gel and a gel slice containing the 200-300 bp fragments was excised.

characteristic: description

characteristic: individual

text: ChIP-seq

characteristic: method

text: Mus musculus

text: Mus musculus

text: liver

text: Mus musculus

text: male

text: C57BL/6J x A/J


characteristic: ENA-FIRST-PUBLIC

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: 2 to 4 month

text: ArrayExpress

text: house mouse

text: ChIP-seq

text: Mus musculus

text: Mus musculus

text: liver

characteristic: organism part

text: Mus musculus

text: male

characteristic: sex

text: C57BL/6J x A/J

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-LAST-UPDATE

characteristic: INSDC last update

text: public

characteristic: Submitter Id

text: 2 to 4 month

text: ArrayExpress

text: house mouse

characteristic: common name

text: ChIP-seq

text: Mus musculus

text: Mus musculus

text: liver

text: Mus musculus

text: male

characteristic: strain


characteristic: External Id

text: public

characteristic: INSDC status

characteristic: SRA accession

text: 2 to 4 month

characteristic: age

text: ArrayExpress

characteristic: broker name

text: house mouse

text: ChIP-seq

text: Mus musculus

characteristic: organism

text: Mus musculus

text: liver

text: Mus musculus

text: male


E-MTAB-3591:Sample 4

characteristic: ENA-FIRST-PUBLIC

text: FAU Erlangen, Division of Genetics

characteristic: INSDC center name

text: public

text: E-MTAB-3591:Sample 4

tag: Namespace:FAU Erlangen, Division of Genetics

text: ArrayExpress

text: CD117-positive primary hematopoietic precursor cell

characteristic: cell type

text: house mouse

text: Protocols: For generation of Meer cells primary hematopoietic precursor cells were isolated from the bone marrow of Meer mice that carry a knock-in of an ENL-ER (mutant estrogen receptor ligand binding domain) portion into the mouse Mll locus 22. CD117 (c-kit) positive cells were isolated by magnetic enrichment according to the instructions of the manufacturer (CD117 enrichment kit, Miltenyi Biotech, Bergisch-Gladbach, Germany) and initially plated in methocel (MethoCult M3234, StemCellTechnologies, Koln, Germany) to purge residual stroma cells that cannot grow in semisolid media. After two rounds of growth in methylcellulose cells were expanded in RPMI1640 supplemented with 10% FCS. All media contained 50ng/ml recombinant murine (rm) SCF, 10ng/ml of rm-IL3, IL6, GM-CSF (cytokines were bought from Miltenyi Biotech, Bergisch-Gladbach, Germany) and for activation of the estrogen receptor 100nM 4-hydroxytamoxifen (TAM, Sigma, Taufkirchen, Germany). Inactivation of MLL-ENL was achieved by washing out TAM keeping other media composition constant. Generation and purification of nascent RNA To determine RNA synthesis rates, newly transcribed RNA was labeled by addition of 100uM 4-thio-uridine (Sigma, Taufkirchen, Germany) directly to the cell culture medium. After 1h total RNA was isolated by RNeasy spin column purification according to the instructions of the manufacturer (Quiagen, Hilden, Germany). 100 ug of RNA were biotinylated with 200ug/ml EZ-Link HPDP Biotin (Pierce-Thermo, Rockford, IL) in 1ml of 10mM Tris-HCl pH7.4, 1mM EDTA. Biotinylated nucleic acid was bound to uMACS streptavidin magnetic beads and washed as recommended by the manufacturer (Miltenyi, Bergisch-Gladbach, Germany). Elution of retained material was done with 100mM DTT. After a final purification on RNeasy columns nascent RNA was subjected to standard reverse transcription and qPCR. random primed library using nascent RNA as input

characteristic: description

text: gene knock in

characteristic: genetic modification

text: ENL-ER knock in Mll locus 22

characteristic: genotype

text: cell suspension culture

characteristic: growth condition

text: Mus musculus

text: Mus musculus

text: Mus musculus

text: Meer

text: 24 hour

characteristic: time

text: Sample 4


E-MTAB-3591:Sample 3

characteristic: ENA-CHECKLIST

characteristic: ENA-LAST-UPDATE

text: FAU Erlangen, Division of Genetics

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: E-MTAB-3591:Sample 3

characteristic: Submitter Id

text: ArrayExpress

text: house mouse

text: gene knock in

text: ENL-ER knock in Mll locus 22

text: cell suspension culture

text: Mus musculus

text: Mus musculus

text: Mus musculus

text: Meer

text: 16 hour

text: Sample 3

characteristic: title


E-MTAB-3591:Sample 1

characteristic: External Id

text: FAU Erlangen, Division of Genetics

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-3591:Sample 1

text: ArrayExpress

text: house mouse

characteristic: common name

text: gene knock in

text: ENL-ER knock in Mll locus 22

text: cell suspension culture

text: Mus musculus

text: Mus musculus

text: Mus musculus

text: Meer

characteristic: strain

text: 0 hour

text: Sample 1


E-MTAB-3591:Sample 5

characteristic: ENA-FIRST-PUBLIC

text: FAU Erlangen, Division of Genetics

characteristic: INSDC center name

text: public

text: E-MTAB-3591:Sample 5

text: ArrayExpress

characteristic: broker name

characteristic: cell type

text: house mouse

text: gene knock in

text: ENL-ER knock in Mll locus 22

text: cell suspension culture

text: Mus musculus

characteristic: organism

text: Mus musculus

text: Mus musculus

text: Meer

text: 48 hour

text: Sample 5


E-MTAB-3591:Sample 2

text: FAU Erlangen, Division of Genetics

text: public

text: E-MTAB-3591:Sample 2

text: ArrayExpress

text: house mouse

characteristic: description

text: gene knock in

characteristic: genetic modification

text: ENL-ER knock in Mll locus 22

characteristic: genotype

text: cell suspension culture

characteristic: growth condition

text: Mus musculus

text: Mus musculus

text: Mus musculus

text: Meer

text: 8 hour

characteristic: time

text: Sample 2


E-MTAB-3591:Sample 6

characteristic: ENA-CHECKLIST

characteristic: ENA-LAST-UPDATE

text: FAU Erlangen, Division of Genetics

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: E-MTAB-3591:Sample 6

characteristic: Submitter Id

text: ArrayExpress

text: house mouse

text: gene knock in

text: ENL-ER knock in Mll locus 22

text: cell suspension culture

text: Mus musculus

text: Mus musculus

text: Mus musculus

text: Meer

text: 72 hour

text: Sample 6


characteristic: External Id

text: European Molecular Biology Laboratory

text: public

characteristic: INSDC status

characteristic: SRA accession

tag: Namespace:European Molecular Biology Laboratory

text: ArrayExpress

text: hek t293

characteristic: cell line

text: human

characteristic: common name

text: Protocols: Cells were seeded 48 hours prior to treatment. DMSO was subsequently added to cells as a solvent control. Cells were harvested in PBS 3 hours later. Total RNA was extracted using Trizol LS. Cells were fractionated and cytoplasmic RNA was extracted using the Paris Kit (Life technologies) according to the manufacturer's instructions. 3'T-fill libraries were created as described in Wilkening S, et al. An efficient method for genome-wide polyadenylation site mapping and RNA quantification. Nucleic Acids Research. 2013;41(5):e65. doi:10.1093/nar/gks1249.

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens

text: cytRNA-DMSO-R-II

characteristic: title


characteristic: ENA-FIRST-PUBLIC

text: European Molecular Biology Laboratory

characteristic: INSDC center name

text: public

text: ArrayExpress

characteristic: broker name

text: hek t293

text: human

text: Protocols: Cells were seeded 48 hours prior to treatment. DMSO was subsequently added to cells as a solvent control. Cells were harvested in PBS 3 hours later. Total RNA was extracted using Trizol LS. Cells were fractionated and nuclear RNA was extracted using the Paris Kit (Life technologies) according to the manufacturer's instructions. mRNA-Seq libraries (from polyA+ cytoplasmic RNA) were created according to the standard Illumina TruSeq protocol.

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: Homo sapiens


text: European Molecular Biology Laboratory

text: public

text: ArrayExpress

text: hek t293

text: human

characteristic: description

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens

text: cytRNA-DMSO-R-I


text: European Molecular Biology Laboratory

text: public

text: ArrayExpress

text: hek t293

text: human

text: Protocols: Cells were seeded 48 hours prior to stress treatment. Cells were subsequently treated with 5 ??g/ml Anisomycin for 3 hours and harvested in PBS. Total RNA was extracted using Trizol LS. Cells were fractionated and cytoplasmic RNA was extracted using the Paris Kit (Life technologies) according to the manufacturer's instructions. 3'T-fill libraries were created as described in Wilkening S, et al. An efficient method for genome-wide polyadenylation site mapping and RNA quantification. Nucleic Acids Research. 2013;41(5):e65. doi:10.1093/nar/gks1249.

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens

text: cytRNA-Aniso-RII


text: European Molecular Biology Laboratory

text: public

text: ArrayExpress

text: hek t293

text: human

text: Protocols: Cells were seeded 48 hours prior to stress treatment. Cells were subsequently treated with 5 ??g/ml Anisomycin for 3 hours and harvested in PBS. Total RNA was extracted using Trizol LS. Cells were fractionated and nuclear RNA was extracted using the Paris Kit (Life technologies) according to the manufacturer's instructions. mRNA-Seq libraries (from polyA+ cytoplasmic RNA) were created according to the standard Illumina TruSeq protocol.

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens


text: European Molecular Biology Laboratory

text: public

text: ArrayExpress

text: hek t293

text: human

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens

text: cytRNA-Aniso-R-I


text: European Molecular Biology Laboratory

text: public

text: ArrayExpress

text: hek t293

text: human

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens

text: cytRNA-Aniso-RIII


text: European Molecular Biology Laboratory

text: public

text: ArrayExpress

text: hek t293

text: human

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens

text: cytRNA-DMSO-RIII


E-MTAB-3600:Sample 4

text: public

text: E-MTAB-3600:Sample 4

tag: Namespace:Laboratory of Molecular Cytogenetics, Institute of Experimental Biology, Faculty of Science, Masaryk University, Brno, Czech Republic 2Babak Myeloma Group, Department of Pathological Physiology, Faculty of Medicine, Masaryk University, Brno, Czech Republic

text: ArrayExpress

text: human

text: Protocols: Female patient was diagnosed with MM in the Department of Internal Medicine - Hematooncology (IHOK), University Hospital Brno, in 11/2007. Patient's biological material was obtained after she signed the informed consent form approved by the Ethical committee of the hospital Plasma cells (CD138+) a were obtained from the bone marrow of multiple myeloma patients during routine clinical procedure. Plasma cells (CD138+) in mononuclear cell fraction were enriched by anti-CD138 immunomagnetic beads and sorted using magnetic activated cell sorting, MACS (AutoMACS, Miltenyi Biotec). Purity of CD138+ fraction was measured by flowcytometry. genomic_DNA was extracted from sorted cells sing the Puregene Core kit according to manufacturer's protocol. Extracted gDNA was diluted in TE buffer and stored in -20C. Targeted resequencing of TP53 was made with SeqPlate TP53 system. The SeqPlate TP53 enablesd sequencing of exons 4 to 11 of the human TP53 gene where single nucleotide polymorphisms (SNPs) associated with hematological malignancies have been found. The SeqPlate TP53 was used to generate 8 amplicons with emulsion PCR (emPCR)

text: multiple myeloma

characteristic: disease

text: extarmedullary myeloma

characteristic: disease staging

text: non-hyperdiploid

characteristic: karyotype

characteristic: mutation type

text: Homo sapiens

text: Homo sapiens

text: extramedullar tissue

characteristic: organism part

text: Homo sapiens

text: Sample 4


E-MTAB-3600:Sample 1

characteristic: ENA-CHECKLIST

characteristic: ENA-LAST-UPDATE

text: Laboratory of Molecular Cytogenetics, Institute of Experimental Biology, Faculty of Science, Masaryk University, Brno, Czech Republic 2Babak Myeloma Group, Department of Pathological Physiology, Faculty of Medicine, Masaryk University, Brno, Czech Republic

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: E-MTAB-3600:Sample 1

characteristic: Submitter Id

text: ArrayExpress

characteristic: cell type

text: human

text: multiple myeloma

text: new diagnosis

text: hyperdiploid

text: c.632C->T; c.700T->C

text: Homo sapiens

text: Homo sapiens

text: bone marrow

text: Homo sapiens

text: Sample 1


E-MTAB-3600:Sample 2

characteristic: External Id

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-3600:Sample 2

text: ArrayExpress

text: human

characteristic: common name

text: multiple myeloma

text: 2nd relapse

text: hyperdiploid

text: c.632C->T; c.700T->C

text: Homo sapiens

text: Homo sapiens

text: bone marrow

text: Homo sapiens

text: Sample 2

characteristic: title


E-MTAB-3600:Sample 3

characteristic: ENA-FIRST-PUBLIC

characteristic: INSDC center name

text: public

text: E-MTAB-3600:Sample 3

text: ArrayExpress

characteristic: broker name

text: human

characteristic: description

text: multiple myeloma

text: progression

text: non-hyperdiploid

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: bone marrow

text: Homo sapiens

text: Sample 3