text: European Molecular Biology Laboratory

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: ArrayExpress

text: baker's yeast

text: Protocols: Cells were grown in 50 mL YPD (1% yeast extract, 2% peptone, 2% glucose and 40 mg adenine) and harvested at an OD600 of ~1 Cross-linking was performed with 1% formaldehyde (final concentration) for 15 min at room temperature on a shaker plate. Fixation was quenched with the addition of Glycine to a final concentration of 0.135M. Cross-linked cells were washed three times in ice-cold TBS buffer (20 mM Tris pH 7.5, 0.146 M NaCl). Yeast pellets were resuspended in NP-S buffer (0.5 mM spermidine, 0.075% NP40, 10 mM Tris-HCl pH 7.4, 50 mM NaCl, 5 mM MgCl2, 1 mM CaCl2, and 1mM ??-mercaptoethanol) with Protease Inhibitor Cocktail (Roche) and lysed at 4??C with 2 volumes of glass beads in a FastPrep instrument (MP Biomedicals) using the following settings: 4 x 20 sec at 6.5 m/sec with 1 min pause between each pulse. Nucleosome fractions were isolated by incubating lysates with 80U of Micrococcal Nuclease (Worthington Biochemicals) for 45 min at 37??C. EGTA was added to samples at a final concentration of 0.01M for enzyme inactivation. Barcoding of nucleosome fractions was performed using 50 ??g of starting material as measured by absorbance at 260nm with Nanodrop. Chromatin fragments were end-repaired with 2 ??L of NEBNext End repair Enzyme Mix (New England BioLabs), dA-tailed with 2 mM dATP and 20U Klenow Fragment (Thermo Scientific) and ligated for 4 hrs at 16??C to paired-end adapters containing a 6-mer multiplex barcode with 1600U T4-DNA Ligase (New England BioLabs). Enzymes were heat-inactivated at 65??C-70??C between each step. Antibodies were diluted in PBS containing 5 mg/mL BSA (Sigma) and 10-30 microg of yeast tRNA (Ambion) and conjugated to 1.5 mg and 4.5 mg of protein A Dynabeads (Invitrogen) for classical ChIP and HT-ChIP respectively, for 4 hrs at 4C on a wheel. 50 microg of non-barcoded nucleosomes (classical ChIP) were diluted in lysis buffer (50 mM Hepes, 140 mM NaCl, 1 mM EDTA, 1% Triton, 0.1 % Sodium Deoxycholate, 1 mM Benzamidin and Protease Inhibitor Cocktail) and incubated with antibody-coated magnetic beads overnight at 4C on a wheel. Chromatin-antibody complexes were washed 8 times in RIPA buffer (0.05 M Hepes, 0.5 M LiCl, 1 mM EDTA, 1% NP-40 and 0.7% Sodium Deoxycholate) and chromatin was eluted from the antibody-coated beads by two 10 min-incubations in ChIP elution buffer (50 mM Tris pH 8.0, 10 mM EDTA and 1% SDS) at 68C with mixing. Formaldehyde crosslinking, Cell lysis using Fast-prep, Micrococcal nuclease digestion, Chromatin IP, Reverse crosslinking and library preparation 20 to 100 ng of IP- and input DNA were end-repaired, dA-tailed and ligated to paired-end adapters as described above. Purification of the newly barcoded DNA samples was performed using Ampure XP beads. 1 ng of barcoded IP- and input DNA from BAR- and classical ChIP experiments was amplified by PCR using 0.4 ??L of each Illumina Paired-End primers (at 10 ??M) and 20 ??L of 2X Phusion HF Master Mix (New England Biolabs) with the following program: 30 sec at 98 ??C for initial denaturation, 30 sec at 98??C, 30 sec at 65??C, 30 sec at 72??C for 18 cycles, followed by 5 min at 72??C for final extension

text: WT

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

text: mating type a


status: PUBLIC

tag: attribute

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: European Molecular Biology Laboratory

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

tag: Namespace:European Molecular Biology Laboratory

characteristic: Submitter Id

text: ArrayExpress

characteristic: broker name

text: baker's yeast

characteristic: common name

text: Protocols: Cells were grown in 50 mL YPD (1% yeast extract, 2% peptone, 2% glucose and 40 mg adenine) and harvested at an OD600 of ~1 Cross-linking was performed with 1% formaldehyde (final concentration) for 15 min at room temperature on a shaker plate. Fixation was quenched with the addition of Glycine to a final concentration of 0.135M. Cross-linked cells were washed three times in ice-cold TBS buffer (20 mM Tris pH 7.5, 0.146 M NaCl). Yeast pellets were resuspended in NP-S buffer (0.5 mM spermidine, 0.075% NP40, 10 mM Tris-HCl pH 7.4, 50 mM NaCl, 5 mM MgCl2, 1 mM CaCl2, and 1mM ??-mercaptoethanol) with Protease Inhibitor Cocktail (Roche) and lysed at 4??C with 2 volumes of glass beads in a FastPrep instrument (MP Biomedicals) using the following settings: 4 x 20 sec at 6.5 m/sec with 1 min pause between each pulse. Nucleosome fractions were isolated by incubating lysates with 80U of Micrococcal Nuclease (Worthington Biochemicals) for 45 min at 37??C. EGTA was added to samples at a final concentration of 0.01M for enzyme inactivation. Antibodies were diluted in PBS containing 5 mg/mL BSA (Sigma) and 10-30 microg of yeast tRNA (Ambion) and conjugated to 1.5 mg and 4.5 mg of protein A Dynabeads (Invitrogen) for classical ChIP and HT-ChIP respectively, for 4 hrs at 4C on a wheel. 50 microg of non-barcoded nucleosomes (classical ChIP) were diluted in lysis buffer (50 mM Hepes, 140 mM NaCl, 1 mM EDTA, 1% Triton, 0.1 % Sodium Deoxycholate, 1 mM Benzamidin and Protease Inhibitor Cocktail) and incubated with antibody-coated magnetic beads overnight at 4C on a wheel. Chromatin-antibody complexes were washed 8 times in RIPA buffer (0.05 M Hepes, 0.5 M LiCl, 1 mM EDTA, 1% NP-40 and 0.7% Sodium Deoxycholate) and chromatin was eluted from the antibody-coated beads by two 10 min-incubations in ChIP elution buffer (50 mM Tris pH 8.0, 10 mM EDTA and 1% SDS) at 68C with mixing. Formaldehyde crosslinking, Cell lysis using Fast-prep, Micrococcal nuclease digestion, Chromatin IP, Reverse crosslinking and library preparation 20 to 100 ng of IP- and input DNA were end-repaired, dA-tailed and ligated to paired-end adapters as described above. Purification of the newly barcoded DNA samples was performed using Ampure XP beads. 1 ng of barcoded IP- and input DNA from BAR- and classical ChIP experiments was amplified by PCR using 0.4 ??L of each Illumina Paired-End primers (at 10 ??M) and 20 ??L of 2X Phusion HF Master Mix (New England Biolabs) with the following program: 30 sec at 98 ??C for initial denaturation, 30 sec at 98??C, 30 sec at 65??C, 30 sec at 72??C for 18 cycles, followed by 5 min at 72??C for final extension

characteristic: description

text: gene knock out

characteristic: genetic modification

characteristic: genotype

text: Saccharomyces cerevisiae

characteristic: organism

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

text: mating type a

characteristic: sex

characteristic: strain

characteristic: title

type: has member


characteristic: ENA-CHECKLIST

text: European Molecular Biology Laboratory

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: E-MTAB-2945:sc_htchip_set2_confirm_K4me3_2

text: ArrayExpress

text: baker's yeast

text: gene knock out

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

text: mating type a


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: European Molecular Biology Laboratory

text: public

text: ArrayExpress

text: baker's yeast

text: gene knock out

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

text: mating type a


text: European Molecular Biology Laboratory

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-2945:sc_htchip_set2_confirm_WCE_1

text: ArrayExpress

text: baker's yeast

text: gene knock out

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

text: mating type a


text: European Molecular Biology Laboratory

text: public

characteristic: Submitter Id

text: ArrayExpress

characteristic: broker name

text: baker's yeast

characteristic: common name

text: Protocols: Cells were grown in 50 mL YPD (1% yeast extract, 2% peptone, 2% glucose and 40 mg adenine) and harvested at an OD600 of ~0.5. alpha-factor was added to reach a final concentration of 50ng/mL. Cells were then grown for two generations before harvest. Cross-linking was performed with 1% formaldehyde (final concentration) for 15 min at room temperature on a shaker plate. Fixation was quenched with the addition of Glycine to a final concentration of 0.135M. Cross-linked cells were washed three times in ice-cold TBS buffer (20 mM Tris pH 7.5, 0.146 M NaCl). Yeast pellets were resuspended in NP-S buffer (0.5 mM spermidine, 0.075% NP40, 10 mM Tris-HCl pH 7.4, 50 mM NaCl, 5 mM MgCl2, 1 mM CaCl2, and 1mM ??-mercaptoethanol) with Protease Inhibitor Cocktail (Roche) and lysed at 4??C with 2 volumes of glass beads in a FastPrep instrument (MP Biomedicals) using the following settings: 4 x 20 sec at 6.5 m/sec with 1 min pause between each pulse. Nucleosome fractions were isolated by incubating lysates with 80U of Micrococcal Nuclease (Worthington Biochemicals) for 45 min at 37??C. EGTA was added to samples at a final concentration of 0.01M for enzyme inactivation. Antibodies were diluted in PBS containing 5 mg/mL BSA (Sigma) and 10-30 microg of yeast tRNA (Ambion) and conjugated to 1.5 mg and 4.5 mg of protein A Dynabeads (Invitrogen) for classical ChIP and HT-ChIP respectively, for 4 hrs at 4C on a wheel. 50 microg of non-barcoded nucleosomes (classical ChIP) were diluted in lysis buffer (50 mM Hepes, 140 mM NaCl, 1 mM EDTA, 1% Triton, 0.1 % Sodium Deoxycholate, 1 mM Benzamidin and Protease Inhibitor Cocktail) and incubated with antibody-coated magnetic beads overnight at 4C on a wheel. Chromatin-antibody complexes were washed 8 times in RIPA buffer (0.05 M Hepes, 0.5 M LiCl, 1 mM EDTA, 1% NP-40 and 0.7% Sodium Deoxycholate) and chromatin was eluted from the antibody-coated beads by two 10 min-incubations in ChIP elution buffer (50 mM Tris pH 8.0, 10 mM EDTA and 1% SDS) at 68C with mixing. Formaldehyde crosslinking, Cell lysis using Fast-prep, Micrococcal nuclease digestion, Chromatin IP, Reverse crosslinking and library preparation 20 to 100 ng of IP- and input DNA were end-repaired, dA-tailed and ligated to paired-end adapters as described above. Purification of the newly barcoded DNA samples was performed using Ampure XP beads. 1 ng of barcoded IP- and input DNA from BAR- and classical ChIP experiments was amplified by PCR using 0.4 ??L of each Illumina Paired-End primers (at 10 ??M) and 20 ??L of 2X Phusion HF Master Mix (New England Biolabs) with the following program: 30 sec at 98 ??C for initial denaturation, 30 sec at 98??C, 30 sec at 65??C, 30 sec at 72??C for 18 cycles, followed by 5 min at 72??C for final extension

text: gene knock out

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

text: mating type a


text: European Molecular Biology Laboratory

text: public

text: ArrayExpress

text: baker's yeast

characteristic: description

text: WT

characteristic: genotype

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

text: mating type a


text: European Molecular Biology Laboratory

text: public

text: E-MTAB-2945:sc_htchip_set2rtt109_K14ac_3

text: ArrayExpress

text: baker's yeast

text: gene knock out

characteristic: genetic modification

text: Saccharomyces cerevisiae

characteristic: organism

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

text: mating type a

characteristic: sex


characteristic: ENA-CHECKLIST

text: European Molecular Biology Laboratory

text: public

text: E-MTAB-2945:sc_htchip_set2rtt109_K14ac_1

text: ArrayExpress

text: baker's yeast

text: gene knock out

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

text: mating type a

characteristic: strain

characteristic: title


characteristic: ENA-FIRST-PUBLIC

text: European Molecular Biology Laboratory

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: E-MTAB-2945:sc_htchip_set2rtt109_K14ac_2

text: ArrayExpress

text: baker's yeast

text: gene knock out

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

text: mating type a


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: European Molecular Biology Laboratory

characteristic: INSDC last update

text: public

text: E-MTAB-2945:sc_htchip_set2ada2sas3_WCE_2

text: ArrayExpress

text: baker's yeast

text: gene knock out

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

text: mating type a


text: European Molecular Biology Laboratory

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-2945:sc_htchip_set2ada2sas3_K4me2_3

characteristic: Submitter Id

text: ArrayExpress

text: baker's yeast

text: gene knock out

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

text: mating type a


text: European Molecular Biology Laboratory

text: public

text: E-MTAB-2945:sc_htchip_set2_confirm_WCE_2

text: ArrayExpress

characteristic: broker name

text: baker's yeast

characteristic: common name

characteristic: description

text: gene knock out

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

text: mating type a


text: European Molecular Biology Laboratory

text: public

text: E-MTAB-2945:sc_htchip_set2_confirm_K4me3_3

text: ArrayExpress

text: baker's yeast

text: gene knock out

characteristic: genetic modification

characteristic: genotype

text: Saccharomyces cerevisiae

characteristic: organism

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

text: mating type a


characteristic: ENA-CHECKLIST

text: European Molecular Biology Laboratory

text: public

text: E-MTAB-2945:sc_htchip_set2ada2sas3_WCE_3

text: ArrayExpress

text: baker's yeast

text: gene knock out

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

text: mating type a

characteristic: sex

characteristic: strain


text: 11 weeks

characteristic: ArrayExpress-Age

text: +/Mx1-Cre Dnmt3aR882H:+/+

characteristic: ArrayExpress-Genotype

text: Lin- bone marrow cells

characteristic: ArrayExpress-OrganismPart

text: female

characteristic: ArrayExpress-Sex

text: Mus Musculus

characteristic: ArrayExpress-Species

characteristic: ENA-FIRST-PUBLIC

text: SC

characteristic: INSDC center name

text: public

text: house mouse

text: Mus musculus

text: Lin- bone marrow cells

characteristic: sample description

text: Mus musculus


text: 11 weeks

text: +/Mx1-Cre Dnmt3aR882H/+

text: Lin- bone marrow cells

text: female

text: Mus Musculus

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: SC

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: house mouse

text: Mus musculus

text: Lin- bone marrow cells

text: Mus musculus


characteristic: ENA-CHECKLIST

text: public

tag: Namespace:Key Lab of Agricultural Animal Genetics and Breeding, Ministry of Education, College of Animal Science and Veterinary Medicine, Huazhong Agricultural University,

text: low residual feed intake

characteristic: behavior

text: ArrayExpress

characteristic: broker name

text: pig

characteristic: common name

text: Protocols: The castrated purebred Yorkshire boars from Hubei Jinlin Pedigree Seed Husbandry Ltd. were individually fed a commercial feedlot ration using ACEMA 64 automated individual feeding systems in Agricultural Ministry Breeding Swine Quality Supervision Inspecting and Testing Center (Wuhan). The recording of daily feed intake (DFI) were began when the pigs body weight reached 35 Kg and ended when the body weight reached 90 Kg. Every time, pigs were weighed after 24 hours of fasting. The average feed intake (ADG) were got by the total weight gain and the number of days on feed. Pigs with lower RFI (more efficiency) Total RNA was extracted with Trizol reagent (Invitrogen, USA), according to the product manufacturer's instructions. RNA sequencing libraries were prepared for each RNA-seq sample using TruSeq Stranded Total RNA Sample Preparation kit (Illumina) and all of the procedures and standards were performed according to the manual supplied with this kit.

characteristic: description

characteristic: individual

text: Sus scrofa

characteristic: organism

text: Sus scrofa

text: longissimus dorsi muscle

characteristic: organism part

text: Sus scrofa

text: male

characteristic: sex

characteristic: title


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: Key Lab of Agricultural Animal Genetics and Breeding, Ministry of Education, College of Animal Science and Veterinary Medicine, Huazhong Agricultural University,

characteristic: INSDC center name

text: public

text: high residual feed intake

text: ArrayExpress

text: pig

text: Protocols: The castrated purebred Yorkshire boars from Hubei Jinlin Pedigree Seed Husbandry Ltd. were individually fed a commercial feedlot ration using ACEMA 64 automated individual feeding systems in Agricultural Ministry Breeding Swine Quality Supervision Inspecting and Testing Center (Wuhan). The recording of daily feed intake (DFI) were began when the pigs body weight reached 35 Kg and ended when the body weight reached 90 Kg. Every time, pigs were weighed after 24 hours of fasting. The average feed intake (ADG) were got by the total weight gain and the number of days on feed. Pigs with higher RFI (less efficiency) Total RNA was extracted with Trizol reagent (Invitrogen, USA), according to the product manufacturer's instructions. RNA sequencing libraries were prepared for each RNA-seq sample using TruSeq Stranded Total RNA Sample Preparation kit (Illumina) and all of the procedures and standards were performed according to the manual supplied with this kit.

text: Sus scrofa

text: Sus scrofa

text: longissimus dorsi muscle

text: Sus scrofa

text: male


characteristic: External Id

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: low residual feed intake

text: ArrayExpress

text: pig

text: Sus scrofa

text: Sus scrofa

text: longissimus dorsi muscle

text: Sus scrofa

text: male


text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: low residual feed intake

text: ArrayExpress

text: pig

text: Protocols: The castrated purebred Yorkshire boars from Hubei Jinlin Pedigree Seed Husbandry Ltd. were individually fed a commercial feedlot ration using ACEMA 64 automated individual feeding systems in Agricultural Ministry Breeding Swine Quality Supervision Inspecting and Testing Center (Wuhan). The recording of daily feed intake (DFI) were began when the pigs body weight reached 35 Kg and ended when the body weight reached 90 Kg. Every time, pigs were weighed after 24 hours of fasting. The average feed intake (ADG) were got by the total weight gain and the number of days on feed. Total RNA was extracted with Trizol reagent (Invitrogen, USA), according to the product manufacturer's instructions. RNA sequencing libraries were prepared for each RNA-seq sample using TruSeq Stranded Total RNA Sample Preparation kit (Illumina) and all of the procedures and standards were performed according to the manual supplied with this kit.

text: pooled 5 individuals

text: Sus scrofa

text: Sus scrofa

text: longissimus dorsi muscle

text: Sus scrofa

text: male


characteristic: ENA-CHECKLIST

text: public

text: high residual feed intake

characteristic: behavior

text: ArrayExpress

characteristic: broker name

text: pig

text: pooled 5 individuals

text: Sus scrofa

text: Sus scrofa

text: longissimus dorsi muscle

text: Sus scrofa

text: male


text: public

tag: Namespace:Faculty of Science, University of Zagreb

text: ArrayExpress

text: house mouse

characteristic: common name

text: Protocols: Growing oocytes were obtained from 12-14-day-old B6D2F1 mice (SLC Japan). The ovaries were transferred to HEPES-buffered KSOM and punctured with a 30-gauge needle. Liberated oocytes with attached follicle cells were harvested and the follicle cells were gently removed using a narrow-bore glass pipette. The oocytes were then transferred into alpha-minimal essential medium (alpha-MEM; Life Technologies, Inc., Grand Island, NY) containing 5% fetal bovine serum and 10 ng/ml epidermal growth factor (both from Sigma-Aldrich). Total RNA was extracted from 3000, 3000, 4500, 2800, 1400 and 700 MII eggs, 1-, 2-, and 4-cell embryos, morulae and blastocysts obtained from C57BL6/J mice, respectively, using Isogen (Nippon Gene, Tokyo, Japan), according to the manufacturers instructions. In the second trials for MII eggs and 1-cell embryos, similar numbers of cells used for the first trials were used for RNA extraction. RNA quality analysis and size-selection (>200 tn) were performed on the Bioanalyzer RNA Pico Chip (Agilent Technologies, Santa Clara, CA). RNA-Seq libraries were constructed using the mRNA-Seq Sample Preparation Kit (Illumina, San Diego, CA) without selection of polyadenylated RNA. Briefly, size-selected total RNA was fragmented to 40~900 nt fragments in fragmentation buffer at 94 oC for 5 min, reverse transcribed with random primers and ligated with adaptors. cDNA templates were amplified by PCR in the conditions as follows: the initial heat treatment at 98oC for 30 s followed by 15 cycles of 98oC for 10 s, 65oC for 30 s, 72oC for 30 s, and final treatment of 72 oC for 5 min. RNA-seq libraries were subjected to 76-nt paired-end-sequencing.

characteristic: description

text: blastocyst

characteristic: developmental stage

text: Mus musculus

text: Mus musculus

text: Mus musculus

characteristic: strain


text: Faculty of Science, University of Zagreb

text: public

text: ArrayExpress

text: house mouse

text: Protocols: Growing oocytes were obtained from 12-14-day-old B6D2F1 mice (SLC Japan). The ovaries were transferred to HEPES-buffered KSOM and punctured with a 30-gauge needle. Liberated oocytes with attached follicle cells were harvested and the follicle cells were gently removed using a narrow-bore glass pipette. The oocytes were then transferred into alpha-minimal essential medium (alpha-MEM; Life Technologies, Inc., Grand Island, NY) containing 5% fetal bovine serum and 10 ng/ml epidermal growth factor (both from Sigma-Aldrich). For DRB treatment, 1-cell embryos were transferred into KSOM containing 120 uM DRB (Sigma-Aldrich) or 3 ug/ml aphidicolin (Sigma-Aldrich) at 4 (before initiation of transcription (Aoki et al., 1997)) or 16 h post-insemination ( embryos enter M phase at 16 h after insemination), Total RNA was extracted from 3000, 3000, 4500, 2800, 1400 and 700 MII eggs, 1-, 2-, and 4-cell embryos, morulae and blastocysts obtained from C57BL6/J mice, respectively, using Isogen (Nippon Gene, Tokyo, Japan), according to the manufacturers instructions. In the second trials for MII eggs and 1-cell embryos, similar numbers of cells used for the first trials were used for RNA extraction. RNA quality analysis and size-selection (>200 tn) were performed on the Bioanalyzer RNA Pico Chip (Agilent Technologies, Santa Clara, CA). RNA-Seq libraries were constructed using the mRNA-Seq Sample Preparation Kit (Illumina, San Diego, CA) without selection of polyadenylated RNA. Briefly, size-selected total RNA was fragmented to 40~900 nt fragments in fragmentation buffer at 94 oC for 5 min, reverse transcribed with random primers and ligated with adaptors. cDNA templates were amplified by PCR in the conditions as follows: the initial heat treatment at 98oC for 30 s followed by 15 cycles of 98oC for 10 s, 65oC for 30 s, 72oC for 30 s, and final treatment of 72 oC for 5 min. RNA-seq libraries were subjected to 76-nt paired-end-sequencing.

text: zygote

text: Mus musculus

characteristic: organism

text: Mus musculus

text: Mus musculus

characteristic: title


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: public

text: ArrayExpress

text: house mouse

text: MII oocyte

text: Mus musculus

text: Mus musculus

text: Mus musculus


characteristic: External Id

characteristic: INSDC center name

text: public

text: ArrayExpress

text: house mouse

text: cleavage 4-cell

text: Mus musculus

text: Mus musculus

text: Mus musculus


characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: ArrayExpress

text: house mouse

text: cleavage 2-cell

text: Mus musculus

text: Mus musculus

text: Mus musculus


text: public

characteristic: INSDC status

characteristic: SRA accession

text: ArrayExpress

text: house mouse

text: cleavage 2-cell

text: Mus musculus

text: Mus musculus

text: Mus musculus


characteristic: ENA-CHECKLIST

text: public

characteristic: Submitter Id

text: ArrayExpress

text: house mouse

text: morula

text: Mus musculus

text: Mus musculus

text: Mus musculus


text: public

text: ArrayExpress

characteristic: broker name

text: house mouse

text: zygote

text: Mus musculus

text: Mus musculus

text: Mus musculus


text: Mus musculus

characteristic: ArrayExpress-Species

text: SC

text: public

text: house mouse

characteristic: common name

text: Mus musculus

text: Mus musculus


text: Homo sapiens

text: SC

text: public

text: human

text: Homo sapiens

text: Homo sapiens


text: Plasmodium falciparum

text: SC

text: public

text: malaria parasite P. falciparum

text: Plasmodium falciparum

text: Plasmodium falciparum


text: female

characteristic: ArrayExpress-Sex

text: Mouse

text: SC

text: public

text: house mouse

text: Mus musculus

text: Epiblast stem cell line (EpiSC)

characteristic: sample description

text: Mus musculus


text: female

text: Mouse

text: SC

text: public

text: house mouse

text: Mus musculus

characteristic: organism

text: EpiSC expressing TET2

text: Mus musculus


text: female

text: Mouse

text: SC

text: public

text: house mouse

text: Mus musculus

text: EpiSC expressing Tet1-CD

text: Mus musculus


text: female

text: Mouse

text: SC

text: public

text: house mouse

text: Mus musculus

text: EpiSC expressing TET1

text: Mus musculus


text: female

text: Mouse

text: SC

text: public

text: house mouse

text: Mus musculus

text: EpiSC expressing TET1-Mut

text: Mus musculus


text: female

text: Mouse

text: SC

text: public

text: house mouse

text: Mus musculus

text: EpiSC Empty Vector

text: Mus musculus


E-MTAB-2953:Sample 1

text: public

text: E-MTAB-2953:Sample 1

tag: Namespace:Swedish University of Agricultural Sciences, SLU

text: ArrayExpress

text: black nightshade

text: Leaves were collected before infection and at 24 and 48 hours after infection by P. infestans (isolate SE-03058). Samples were pooled for each species. Protocols: RNA was isolated by RNeasy Plant Mini Kit (Qiagen) Beads with oligo(dT) were used to isolate poly(A) mRNA. Fragmentation buffer was added for interrupting mRNA to short fragments. Taking these short fragments as templates, Random hexamerprimer were used to synthesize the first-strand cDNA. The second-strand cDNA was synthesized using buffer, dNTPs, RNase H and DNA polymerase I, respectively. Short fragments were purified with QiaQuick PCR extraction kit and resolved with EB buffer for end reparation and adding poly(A). After that, the short fragments were connected with sequencing adaptors. And, for amplification with PCR, we selected suitable fragments, as templates, with respect to the result of agarose gel electrophoresis.

characteristic: description

text: Solanum nigrum

text: Solanum nigrum

text: detached leaves

characteristic: organism part

text: Solanum nigrum

text: Sample 1

characteristic: title


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: GSC

text: public

text: bread wheat

text: Triticum aestivum

text: Triticum aestivum


characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

tag: Namespace:Institut de Biologie de l'Ecole Normale Superieure

text: ArrayExpress

characteristic: cell line

text: human

text: glucocorticoid treated Protocols: For ChIP-exo experiments, approximately 15 million cells were treated with dexamethasone and chromatin was sheared essentially as described for ChIP-seq experiment. The resulting sheared and cross-linked chromatin along with GR-antibody (N499) was sent to Peconic (PA, USA) for further processing.

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens


characteristic: ENA-CHECKLIST

text: Institut de Biologie de l'Ecole Normale Superieure

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: ArrayExpress

text: human

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens


text: Larval:Day 5 - ZFS:0000037

characteristic: ArrayExpress-DevelopmentalStage

text: Whole embryo

characteristic: ArrayExpress-OrganismPart

text: Danio rerio

characteristic: ArrayExpress-Species

text: mixed

characteristic: ArrayExpress-StrainOrLine

text: SC

text: public

text: zebrafish

characteristic: common name

text: Danio rerio

text: 3' end enriched mRNA from a single 5 dpf genotyped homozygous mutant embryo for kdm2aa, allele sa9360,ZMP phenotype 98 clutch 1 plus ERCC spike mix 1 (Ambion). A 8 base indexing sequence (TGTCTATC) 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/cgi-bin/Projects/D_rerio/zmp/search.pl?q=zmp_ph98

text: Danio rerio

text: mixed

characteristic: strain


text: Larval:Day 5 - ZFS:0000037

text: Whole embryo

text: Danio rerio

text: mixed

characteristic: ENA-FIRST-PUBLIC

text: SC

text: public

text: zebrafish

text: Danio rerio

characteristic: organism

text: 3' end enriched mRNA from a single 5 dpf genotyped homozygous mutant embryo for kdm2aa, allele sa9360,ZMP phenotype 98 clutch 1 plus ERCC spike mix 1 (Ambion). A 8 base indexing sequence (TATGTGGC) 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/cgi-bin/Projects/D_rerio/zmp/search.pl?q=zmp_ph98

characteristic: sample description

text: Danio rerio

text: mixed


text: Larval:Day 5 - ZFS:0000037

text: Whole embryo

text: Danio rerio

text: mixed

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: SC

characteristic: INSDC center name

text: public

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from a single 5 dpf genotyped homozygous mutant embryo for kdm2aa, allele sa9360,ZMP phenotype 98 clutch 1 plus ERCC spike mix 1 (Ambion). A 8 base indexing sequence (TTACTCGC) 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/cgi-bin/Projects/D_rerio/zmp/search.pl?q=zmp_ph98

text: Danio rerio

text: mixed


text: Larval:Day 5 - ZFS:0000037

text: Whole embryo

text: Danio rerio

text: mixed

text: SC

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from a single 5 dpf genotyped homozygous mutant embryo for kdm2aa, allele sa9360,ZMP phenotype 98 clutch 1 plus ERCC spike mix 1 (Ambion). A 8 base indexing sequence (TCGTTAGC) 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/cgi-bin/Projects/D_rerio/zmp/search.pl?q=zmp_ph98

text: Danio rerio

text: mixed


text: Larval:Day 5 - ZFS:0000037

text: Whole embryo

text: Danio rerio

text: mixed

characteristic: ENA-CHECKLIST

text: SC

text: public

characteristic: INSDC status

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from a single 5 dpf genotyped homozygous mutant embryo for kdm2aa, allele sa9360,ZMP phenotype 98 clutch 1 plus ERCC spike mix 1 (Ambion). A 8 base indexing sequence (TACCGAGC) 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/cgi-bin/Projects/D_rerio/zmp/search.pl?q=zmp_ph98

text: Danio rerio

text: mixed


text: Larval:Day 5 - ZFS:0000037

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 5 dpf genotyped homozygous mutant embryo for kdm2aa, allele sa9360,ZMP phenotype 98 clutch 1 plus ERCC spike mix 1 (Ambion). A 8 base indexing sequence (TGTTCTCC) 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/cgi-bin/Projects/D_rerio/zmp/search.pl?q=zmp_ph98

text: Danio rerio

text: mixed


text: Larval:Day 5 - ZFS:0000037

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 5 dpf genotyped homozygous mutant embryo for kdm2aa, allele sa9360,ZMP phenotype 98 clutch 1 plus ERCC spike mix 1 (Ambion). A 8 base indexing sequence (TTCGCACC) 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/cgi-bin/Projects/D_rerio/zmp/search.pl?q=zmp_ph98

text: Danio rerio

text: mixed


text: Larval:Day 5 - ZFS:0000037

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 5 dpf genotyped homozygous mutant embryo for kdm2aa, allele sa9360,ZMP phenotype 98 clutch 1 plus ERCC spike mix 1 (Ambion). A 8 base indexing sequence (TTGCGTAC) 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/cgi-bin/Projects/D_rerio/zmp/search.pl?q=zmp_ph98

text: Danio rerio

text: mixed


text: Larval:Day 5 - ZFS:0000037

text: Whole embryo

text: Danio rerio

text: mixed

text: SC

text: public

text: zebrafish

characteristic: common name

text: Danio rerio

text: 3' end enriched mRNA from a single 5 dpf genotyped homozygous mutant embryo for kdm2aa, allele sa9360,ZMP phenotype 98 clutch 1 plus ERCC spike mix 1 (Ambion). A 8 base indexing sequence (TCTACGAC) 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/cgi-bin/Projects/D_rerio/zmp/search.pl?q=zmp_ph98

text: Danio rerio

text: mixed

characteristic: strain


text: Larval:Day 5 - ZFS:0000037

text: Whole embryo

text: Danio rerio

text: mixed

characteristic: ENA-FIRST-PUBLIC

text: SC

text: public

text: zebrafish

text: Danio rerio

characteristic: organism

text: 3' end enriched mRNA from a single 5 dpf genotyped homozygous mutant embryo for kdm2aa, allele sa9360,ZMP phenotype 98 clutch 1 plus ERCC spike mix 1 (Ambion). A 8 base indexing sequence (TGACAGAC) 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/cgi-bin/Projects/D_rerio/zmp/search.pl?q=zmp_ph98

text: Danio rerio

text: mixed


text: Larval:Day 5 - ZFS:0000037

text: Whole embryo

text: Danio rerio

text: mixed

characteristic: ENA-LAST-UPDATE

text: SC

text: public

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from a single 5 dpf genotyped heterozygous embryo for kdm2aa, allele sa9360,ZMP phenotype 98 clutch 1 plus ERCC spike mix 1 (Ambion). A 8 base indexing sequence (TGCTGATA) 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/cgi-bin/Projects/D_rerio/zmp/search.pl?q=zmp_ph98

characteristic: sample description

text: Danio rerio

text: mixed


text: Larval:Day 5 - ZFS:0000037

text: Whole embryo

text: Danio rerio

text: mixed

characteristic: External Id

text: SC

characteristic: INSDC center name

text: public

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from a single 5 dpf genotyped heterozygous embryo for kdm2aa, allele sa9360,ZMP phenotype 98 clutch 1 plus ERCC spike mix 1 (Ambion). A 8 base indexing sequence (TAGACGGA) 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/cgi-bin/Projects/D_rerio/zmp/search.pl?q=zmp_ph98

text: Danio rerio

text: mixed


text: Larval:Day 5 - ZFS:0000037

text: Whole embryo

text: Danio rerio

text: mixed

text: SC

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from a single 5 dpf genotyped heterozygous embryo for kdm2aa, allele sa9360,ZMP phenotype 98 clutch 1 plus ERCC spike mix 1 (Ambion). A 8 base indexing sequence (TGTGAAGA) 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/cgi-bin/Projects/D_rerio/zmp/search.pl?q=zmp_ph98

text: Danio rerio

text: mixed


text: Larval:Day 5 - ZFS:0000037

text: Whole embryo

text: Danio rerio

text: mixed

characteristic: ENA-CHECKLIST

text: SC

text: public

characteristic: INSDC status

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from a single 5 dpf genotyped heterozygous embryo for kdm2aa, allele sa9360,ZMP phenotype 98 clutch 1 plus ERCC spike mix 1 (Ambion). A 8 base indexing sequence (TCTCTTCA) 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/cgi-bin/Projects/D_rerio/zmp/search.pl?q=zmp_ph98

text: Danio rerio

text: mixed


text: Larval:Day 5 - ZFS:0000037

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 5 dpf genotyped heterozygous embryo for kdm2aa, allele sa9360,ZMP phenotype 98 clutch 1 plus ERCC spike mix 1 (Ambion). A 8 base indexing sequence (TTGTTCCA) 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/cgi-bin/Projects/D_rerio/zmp/search.pl?q=zmp_ph98

text: Danio rerio

text: mixed


text: Larval:Day 5 - ZFS:0000037

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 5 dpf genotyped heterozygous embryo for kdm2aa, allele sa9360,ZMP phenotype 98 clutch 1 plus ERCC spike mix 1 (Ambion). A 8 base indexing sequence (TGAAGCCA) 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/cgi-bin/Projects/D_rerio/zmp/search.pl?q=zmp_ph98

text: Danio rerio

text: mixed


text: Larval:Day 5 - ZFS:0000037

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 5 dpf genotyped wild type embryo for kdm2aa, allele sa9360,ZMP phenotype 98 clutch 1 plus ERCC spike mix 1 (Ambion). A 8 base indexing sequence (TACCACCA) 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/cgi-bin/Projects/D_rerio/zmp/search.pl?q=zmp_ph98

text: Danio rerio

text: mixed


text: Larval:Day 5 - ZFS:0000037

text: Whole embryo

text: Danio rerio

text: mixed

text: SC

text: public

text: zebrafish

characteristic: common name

text: Danio rerio

text: 3' end enriched mRNA from a single 5 dpf genotyped wild type embryo for kdm2aa, allele sa9360,ZMP phenotype 98 clutch 1 plus ERCC spike mix 1 (Ambion). A 8 base indexing sequence (TGCGTGAA) 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/cgi-bin/Projects/D_rerio/zmp/search.pl?q=zmp_ph98

text: Danio rerio

text: mixed

characteristic: strain


text: Larval:Day 5 - ZFS:0000037

text: Whole embryo

text: Danio rerio

text: mixed

characteristic: ENA-FIRST-PUBLIC

text: SC

text: public

text: zebrafish

text: Danio rerio

characteristic: organism

text: 3' end enriched mRNA from a single 5 dpf genotyped wild type embryo for kdm2aa, allele sa9360,ZMP phenotype 98 clutch 1 plus ERCC spike mix 1 (Ambion). A 8 base indexing sequence (GGTGAGTT) 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/cgi-bin/Projects/D_rerio/zmp/search.pl?q=zmp_ph98

text: Danio rerio

text: mixed


text: Larval:Day 5 - ZFS:0000037

text: Whole embryo

text: Danio rerio

text: mixed

characteristic: ENA-LAST-UPDATE

text: SC

text: public

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from a single 5 dpf genotyped wild type embryo for kdm2aa, allele sa9360,ZMP phenotype 98 clutch 1 plus ERCC spike mix 1 (Ambion). A 8 base indexing sequence (GATCTCTT) 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/cgi-bin/Projects/D_rerio/zmp/search.pl?q=zmp_ph98

characteristic: sample description

text: Danio rerio

text: mixed


text: Larval:Day 5 - ZFS:0000037

text: Whole embryo

text: Danio rerio

text: mixed

characteristic: External Id

text: SC

characteristic: INSDC center name

text: public

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from a single 5 dpf genotyped wild type embryo for kdm2aa, allele sa9360,ZMP phenotype 98 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/cgi-bin/Projects/D_rerio/zmp/search.pl?q=zmp_ph98

text: Danio rerio

text: mixed


text: Larval:Day 5 - ZFS:0000037

text: Whole embryo

text: Danio rerio

text: mixed

text: SC

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from a single 5 dpf genotyped wild type embryo for kdm2aa, allele sa9360,ZMP phenotype 98 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/cgi-bin/Projects/D_rerio/zmp/search.pl?q=zmp_ph98

text: Danio rerio

text: mixed


text: Larval:Day 5 - ZFS:0000037

text: Whole embryo

text: Danio rerio

text: mixed

characteristic: ENA-CHECKLIST

text: SC

text: public

characteristic: INSDC status

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from a single 5 dpf genotyped homozygous mutant embryo for kdm2aa, allele sa898,ZMP phenotype 108 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/cgi-bin/Projects/D_rerio/zmp/search.pl?q=zmp_ph108

text: Danio rerio

text: mixed


text: Larval:Day 5 - ZFS:0000037

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 5 dpf genotyped homozygous mutant embryo for kdm2aa, allele sa898,ZMP phenotype 108 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/cgi-bin/Projects/D_rerio/zmp/search.pl?q=zmp_ph108

text: Danio rerio

text: mixed


text: Larval:Day 5 - ZFS:0000037

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 5 dpf genotyped homozygous mutant embryo for kdm2aa, allele sa898,ZMP phenotype 108 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/cgi-bin/Projects/D_rerio/zmp/search.pl?q=zmp_ph108

text: Danio rerio

text: mixed


text: Larval:Day 5 - ZFS:0000037

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 5 dpf genotyped homozygous mutant embryo for kdm2aa, allele sa898,ZMP phenotype 108 clutch 1 plus ERCC spike mix 1 (Ambion). A 8 base indexing sequence (GTACATCT) 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/cgi-bin/Projects/D_rerio/zmp/search.pl?q=zmp_ph108

text: Danio rerio

text: mixed


text: Larval:Day 5 - ZFS:0000037

text: Whole embryo

text: Danio rerio

text: mixed

text: SC

text: public

text: zebrafish

characteristic: common name

text: Danio rerio

text: 3' end enriched mRNA from a single 5 dpf genotyped homozygous mutant embryo for kdm2aa, allele sa898,ZMP phenotype 108 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/cgi-bin/Projects/D_rerio/zmp/search.pl?q=zmp_ph108

text: Danio rerio

text: mixed

characteristic: strain


text: Larval:Day 5 - ZFS:0000037

text: Whole embryo

text: Danio rerio

text: mixed

characteristic: ENA-FIRST-PUBLIC

text: SC

text: public

text: zebrafish

text: Danio rerio

characteristic: organism

text: 3' end enriched mRNA from a single 5 dpf genotyped homozygous mutant embryo for kdm2aa, allele sa898,ZMP phenotype 108 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/cgi-bin/Projects/D_rerio/zmp/search.pl?q=zmp_ph108

text: Danio rerio

text: mixed


text: Larval:Day 5 - ZFS:0000037

text: Whole embryo

text: Danio rerio

text: mixed

characteristic: ENA-LAST-UPDATE

text: SC

text: public

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from a single 5 dpf genotyped homozygous mutant embryo for kdm2aa, allele sa898,ZMP phenotype 108 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/cgi-bin/Projects/D_rerio/zmp/search.pl?q=zmp_ph108

characteristic: sample description

text: Danio rerio

text: mixed


text: Larval:Day 5 - ZFS:0000037

text: Whole embryo

text: Danio rerio

text: mixed

characteristic: External Id

text: SC

characteristic: INSDC center name

text: public

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from a single 5 dpf genotyped homozygous mutant embryo for kdm2aa, allele sa898,ZMP phenotype 108 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/cgi-bin/Projects/D_rerio/zmp/search.pl?q=zmp_ph108

text: Danio rerio

text: mixed


text: Larval:Day 5 - ZFS:0000037

text: Whole embryo

text: Danio rerio

text: mixed

text: SC

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from a single 5 dpf genotyped homozygous mutant embryo for kdm2aa, allele sa898,ZMP phenotype 108 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/cgi-bin/Projects/D_rerio/zmp/search.pl?q=zmp_ph108

text: Danio rerio

text: mixed


text: Larval:Day 5 - ZFS:0000037

text: Whole embryo

text: Danio rerio

text: mixed

characteristic: ENA-CHECKLIST

text: SC

text: public

characteristic: INSDC status

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from a single 5 dpf genotyped homozygous mutant embryo for kdm2aa, allele sa898,ZMP phenotype 108 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/cgi-bin/Projects/D_rerio/zmp/search.pl?q=zmp_ph108

text: Danio rerio

text: mixed


text: Larval:Day 5 - ZFS:0000037

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 5 dpf genotyped homozygous mutant embryo for kdm2aa, allele sa898,ZMP phenotype 108 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/cgi-bin/Projects/D_rerio/zmp/search.pl?q=zmp_ph108

text: Danio rerio

text: mixed


text: Larval:Day 5 - ZFS:0000037

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 5 dpf genotyped homozygous mutant embryo for kdm2aa, allele sa898,ZMP phenotype 108 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/cgi-bin/Projects/D_rerio/zmp/search.pl?q=zmp_ph108

text: Danio rerio

text: mixed


text: Larval:Day 5 - ZFS:0000037

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 5 dpf genotyped heterozygous embryo for kdm2aa, allele sa898,ZMP phenotype 108 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/cgi-bin/Projects/D_rerio/zmp/search.pl?q=zmp_ph108

text: Danio rerio

text: mixed


text: Larval:Day 5 - ZFS:0000037

text: Whole embryo

text: Danio rerio

text: mixed

text: SC

text: public

text: zebrafish

characteristic: common name

text: Danio rerio

text: 3' end enriched mRNA from a single 5 dpf genotyped heterozygous embryo for kdm2aa, allele sa898,ZMP phenotype 108 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/cgi-bin/Projects/D_rerio/zmp/search.pl?q=zmp_ph108

text: Danio rerio

text: mixed

characteristic: strain


text: Larval:Day 5 - ZFS:0000037

text: Whole embryo

text: Danio rerio

text: mixed

characteristic: ENA-FIRST-PUBLIC

text: SC

text: public

text: zebrafish

text: Danio rerio

characteristic: organism

text: 3' end enriched mRNA from a single 5 dpf genotyped heterozygous embryo for kdm2aa, allele sa898,ZMP phenotype 108 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/cgi-bin/Projects/D_rerio/zmp/search.pl?q=zmp_ph108

text: Danio rerio

text: mixed


text: Larval:Day 5 - ZFS:0000037

text: Whole embryo

text: Danio rerio

text: mixed

characteristic: ENA-LAST-UPDATE

text: SC

text: public

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from a single 5 dpf genotyped heterozygous embryo for kdm2aa, allele sa898,ZMP phenotype 108 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/cgi-bin/Projects/D_rerio/zmp/search.pl?q=zmp_ph108

characteristic: sample description

text: Danio rerio

text: mixed


text: Larval:Day 5 - ZFS:0000037

text: Whole embryo

text: Danio rerio

text: mixed

characteristic: External Id

text: SC

characteristic: INSDC center name

text: public

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from a single 5 dpf genotyped heterozygous embryo for kdm2aa, allele sa898,ZMP phenotype 108 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/cgi-bin/Projects/D_rerio/zmp/search.pl?q=zmp_ph108

text: Danio rerio

text: mixed


text: Larval:Day 5 - ZFS:0000037

text: Whole embryo

text: Danio rerio

text: mixed

text: SC

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from a single 5 dpf genotyped heterozygous embryo for kdm2aa, allele sa898,ZMP phenotype 108 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/cgi-bin/Projects/D_rerio/zmp/search.pl?q=zmp_ph108

text: Danio rerio

text: mixed


text: Larval:Day 5 - ZFS:0000037

text: Whole embryo

text: Danio rerio

text: mixed

characteristic: ENA-CHECKLIST

text: SC

text: public

characteristic: INSDC status

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from a single 5 dpf genotyped wild type embryo for kdm2aa, allele sa898,ZMP phenotype 108 clutch 1 plus ERCC spike mix 1 (Ambion). A 8 base indexing sequence (GACCTTAG) 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/cgi-bin/Projects/D_rerio/zmp/search.pl?q=zmp_ph108

text: Danio rerio

text: mixed


text: Larval:Day 5 - ZFS:0000037

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 5 dpf genotyped wild type embryo for kdm2aa, allele sa898,ZMP phenotype 108 clutch 1 plus ERCC spike mix 1 (Ambion). A 8 base indexing sequence (GCCTGTTC) 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/cgi-bin/Projects/D_rerio/zmp/search.pl?q=zmp_ph108

text: Danio rerio

text: mixed


text: Larval:Day 5 - ZFS:0000037

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 5 dpf genotyped wild type embryo for kdm2aa, allele sa898,ZMP phenotype 108 clutch 1 plus ERCC spike mix 1 (Ambion). A 8 base indexing sequence (GCACTGTC) 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/cgi-bin/Projects/D_rerio/zmp/search.pl?q=zmp_ph108

text: Danio rerio

text: mixed


text: Larval:Day 5 - ZFS:0000037

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 5 dpf genotyped wild type embryo for kdm2aa, allele sa898,ZMP phenotype 108 clutch 1 plus ERCC spike mix 1 (Ambion). A 8 base indexing sequence (GCTAACTC) 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/cgi-bin/Projects/D_rerio/zmp/search.pl?q=zmp_ph108

text: Danio rerio

text: mixed


text: Larval:Day 5 - ZFS:0000037

text: Whole embryo

text: Danio rerio

text: mixed

text: SC

text: public

text: zebrafish

characteristic: common name

text: Danio rerio

text: 3' end enriched mRNA from a single 5 dpf genotyped wild type embryo for kdm2aa, allele sa898,ZMP phenotype 108 clutch 1 plus ERCC spike mix 1 (Ambion). A 8 base indexing sequence (GATTCATC) 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/cgi-bin/Projects/D_rerio/zmp/search.pl?q=zmp_ph108

text: Danio rerio

text: mixed

characteristic: strain


text: Larval:Day 5 - ZFS:0000037

text: Whole embryo

text: Danio rerio

text: mixed

characteristic: ENA-FIRST-PUBLIC

text: SC

text: public

text: zebrafish

text: Danio rerio

characteristic: organism

text: 3' end enriched mRNA from a single 5 dpf genotyped wild type embryo for kdm2aa, allele sa898,ZMP phenotype 108 clutch 1 plus ERCC spike mix 1 (Ambion). A 8 base indexing sequence (GTCTTGGC) 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/cgi-bin/Projects/D_rerio/zmp/search.pl?q=zmp_ph108

text: Danio rerio

text: mixed


text: Larval:Day 5 - ZFS:0000037

text: Whole embryo

text: Danio rerio

text: mixed

characteristic: ENA-LAST-UPDATE

text: SC

text: public

text: zebrafish

text: Danio rerio

text: mRNA from a single 5 dpf genotyped homozygous mutant embryo for kdm2aa, allele sa9360,ZMP phenotype 97 clutch 1 plus ERCC spike mix 1 (Ambion).

characteristic: sample description

text: Danio rerio

text: mixed


text: Larval:Day 5 - ZFS:0000037

text: Whole embryo

text: Danio rerio

text: mixed

characteristic: External Id

text: SC

characteristic: INSDC center name

text: public

text: zebrafish

text: Danio rerio

text: mRNA from a single 5 dpf genotyped heterozygous embryo for kdm2aa, allele sa9360,ZMP phenotype 97 clutch 1 plus ERCC spike mix 1 (Ambion).

text: Danio rerio

text: mixed


text: Larval:Day 5 - ZFS:0000037

text: Whole embryo

text: Danio rerio

text: mixed

text: SC

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: zebrafish

text: Danio rerio

text: mRNA from a single 5 dpf genotyped wild type embryo for kdm2aa, allele sa9360,ZMP phenotype 97 clutch 1 plus ERCC spike mix 1 (Ambion).

text: Danio rerio

text: mixed


text: Larval:Day 5 - ZFS:0000037

text: Whole embryo

text: Danio rerio

text: mixed

characteristic: ENA-CHECKLIST

text: SC

text: public

characteristic: INSDC status

text: zebrafish

text: Danio rerio

text: mRNA from a single 5 dpf genotyped homozygous mutant embryo for kdm2aa, allele sa898,ZMP phenotype 108 clutch 1 plus ERCC spike mix 1 (Ambion).

text: Danio rerio

text: mixed


text: Larval:Day 5 - ZFS:0000037

text: Whole embryo

text: Danio rerio

text: mixed

text: SC

text: public

characteristic: SRA accession

characteristic: Submitter Id

text: zebrafish

text: Danio rerio

text: mRNA from a single 5 dpf genotyped heterozygous embryo for kdm2aa, allele sa898,ZMP phenotype 108 clutch 1 plus ERCC spike mix 1 (Ambion).

text: Danio rerio

text: mixed


text: Larval:Day 5 - ZFS:0000037

characteristic: ArrayExpress-DevelopmentalStage

text: Whole embryo

characteristic: ArrayExpress-OrganismPart

text: Danio rerio

text: mixed

text: SC

text: public

text: zebrafish

text: Danio rerio

text: mRNA from a single 5 dpf genotyped wild type embryo for kdm2aa, allele sa898,ZMP phenotype 108 clutch 1 plus ERCC spike mix 1 (Ambion).

text: Danio rerio

text: mixed


text: Larval:Day 5 - ZFS:0000037

text: Whole embryo

text: Danio rerio

characteristic: ArrayExpress-Species

text: mixed

characteristic: ArrayExpress-StrainOrLine

text: SC

text: public

text: ZMP_phenotype_108_1_RNASeq_10-sc-2133703

text: zebrafish

text: Danio rerio

text: Danio rerio

text: mixed


text: Larval:Day 5 - ZFS:0000037

text: Whole embryo

text: Danio rerio

text: mixed

text: SC

text: public

text: ZMP_phenotype_108_1_RNASeq_11-sc-2133704

text: zebrafish

characteristic: common name

text: Danio rerio

text: Danio rerio

text: mixed

characteristic: strain


text: Larval:Day 5 - ZFS:0000037

text: Whole embryo

text: Danio rerio

text: mixed

characteristic: ENA-FIRST-PUBLIC

text: SC

text: public

text: ZMP_phenotype_108_1_RNASeq_12-sc-2133705

text: zebrafish

text: Danio rerio

characteristic: organism

text: Danio rerio

text: mixed


text: Larval:Day 12 - ZFS:0000039

text: Whole larva

text: Danio rerio

text: mixed

characteristic: ENA-LAST-UPDATE

text: SC

text: public

text: zebrafish

text: Danio rerio

text: mRNA from a single 12 dpf genotyped homozygous mutant larva for kdm2aa, allele sa898,ZMP phenotype 111 clutch 1 plus ERCC spike mix 1 (Ambion).

characteristic: sample description

text: Danio rerio

text: mixed


text: Larval:Day 12 - ZFS:0000039

text: Whole larva

text: Danio rerio

text: mixed

characteristic: External Id

text: SC

characteristic: INSDC center name

text: public

text: zebrafish

text: Danio rerio

text: mRNA from a single 12 dpf genotyped heterozygous larva for kdm2aa, allele sa898,ZMP phenotype 111 clutch 1 plus ERCC spike mix 1 (Ambion).

text: Danio rerio

text: mixed


text: Larval:Day 12 - ZFS:0000039

text: Whole larva

text: Danio rerio

text: mixed

text: SC

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: zebrafish

text: Danio rerio

text: mRNA from a single 12 dpf genotyped wild type larva for kdm2aa, allele sa898,ZMP phenotype 111 clutch 1 plus ERCC spike mix 1 (Ambion).

text: Danio rerio

text: mixed


text: Larval:Day 12 - ZFS:0000039

text: Whole larva

text: Danio rerio

text: mixed

characteristic: ENA-CHECKLIST

text: SC

text: public

characteristic: INSDC status

text: ZMP_phenotype_111_1_RNASeq_10-sc-2133715

text: zebrafish

text: Danio rerio

text: Danio rerio

text: mixed


text: Larval:Day 12 - ZFS:0000039

text: Whole larva

text: Danio rerio

text: mixed

text: SC

text: public

characteristic: SRA accession

text: ZMP_phenotype_111_1_RNASeq_11-sc-2133716

characteristic: Submitter Id

text: zebrafish

text: Danio rerio

text: Danio rerio

text: mixed


text: Larval:Day 12 - ZFS:0000039

characteristic: ArrayExpress-DevelopmentalStage

text: Whole larva

characteristic: ArrayExpress-OrganismPart

text: Danio rerio

text: mixed

text: SC

text: public

text: ZMP_phenotype_111_1_RNASeq_12-sc-2133717

text: zebrafish

text: Danio rerio

text: Danio rerio

text: mixed


text: Larval:Day 12 - ZFS:0000039

text: Whole larva

text: Danio rerio

characteristic: ArrayExpress-Species

text: mixed

characteristic: ArrayExpress-StrainOrLine

text: SC

text: public

text: zebrafish

text: Danio rerio

text: mRNA from a single 12 dpf genotyped homozygous mutant larva for kdm2aa, allele sa9360,ZMP phenotype 114 clutch 1 plus ERCC spike mix 1 (Ambion).

text: Danio rerio

text: mixed


text: Larval:Day 12 - ZFS:0000039

text: Whole larva

text: Danio rerio

text: mixed

text: SC

text: public

text: zebrafish

characteristic: common name

text: Danio rerio

text: mRNA from a single 12 dpf genotyped heterozygous larva for kdm2aa, allele sa9360,ZMP phenotype 114 clutch 1 plus ERCC spike mix 1 (Ambion).

text: Danio rerio

text: mixed

characteristic: strain


text: Larval:Day 12 - ZFS:0000039

text: Whole larva

text: Danio rerio

text: mixed

characteristic: ENA-FIRST-PUBLIC

text: SC

text: public

text: zebrafish

text: Danio rerio

characteristic: organism

text: mRNA from a single 12 dpf genotyped wild type larva for kdm2aa, allele sa9360,ZMP phenotype 114 clutch 1 plus ERCC spike mix 1 (Ambion).

text: Danio rerio

text: mixed


text: Larval:Day 12 - ZFS:0000039

text: Whole larva

text: Danio rerio

text: mixed

characteristic: ENA-LAST-UPDATE

text: SC

text: public

text: ZMP_phenotype_114_1_RNASeq_10-sc-2133727

text: zebrafish

text: Danio rerio

characteristic: sample description

text: Danio rerio

text: mixed


text: Larval:Day 12 - ZFS:0000039

text: Whole larva

text: Danio rerio

text: mixed

characteristic: External Id

text: SC

characteristic: INSDC center name

text: public

text: ZMP_phenotype_114_1_RNASeq_11-sc-2133728

text: zebrafish

text: Danio rerio

text: Danio rerio

text: mixed


text: Homo sapiens

text: SC

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: human

text: Homo sapiens

text: Homo sapiens


text: mus musculus

characteristic: ENA-CHECKLIST

text: SC

text: public

characteristic: INSDC status

text: house mouse

text: Mus musculus

text: Screen 3 BAP1 Knock-out Embryonic Stem Cell Derived Macrophages stimulated with ODN 1826 (CpG)

text: Mus musculus


text: mus musculus

text: SC

text: public

characteristic: SRA accession

characteristic: Submitter Id

text: house mouse

text: Mus musculus

text: Screen 3 BAP1 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 3 BAP1 Knock-out Embryonic Stem Cell Derived Macrophages stimulated with LPS (Toll-like receptor agonist)

text: Mus musculus


text: mus musculus

text: SC

text: public

text: house mouse

text: Mus musculus

text: Screen 3 BAP1 Knock-out Embryonic Stem Cell Derived Macrophages stimulated with Poly I:C (Toll-like receptor agonist)

text: Mus musculus


text: mus musculus

text: SC

text: public

text: house mouse

text: Mus musculus

text: Screen 3 BAP1 Knock-out Embryonic Stem Cell Derived Macrophages stimulated with Influenza 24 hr

text: Mus musculus


text: mus musculus

text: SC

text: public

text: house mouse

text: Mus musculus

text: Screen 3 BAP1 Knock-out Embryonic Stem Cell Derived Macrophages stimulated with Influenza 4 hr

text: Mus musculus


text: mus musculus

text: SC

text: public

text: house mouse

text: Mus musculus

text: Screen 3 BAP1 Knock-out Embryonic Stem Cell Derived Macrophages stimulated with Salmonella

text: Mus musculus


text: mus musculus

text: SC

text: public

text: house mouse

text: Mus musculus

text: Mus musculus


text: mus musculus

text: SC

text: public

text: house mouse

text: Mus musculus

text: Screen 3 Unstimulated BAP1 Knock-out Embryonic Stem Cell Derived Macrophages 24hr

text: Mus musculus


text: mus musculus

text: SC

text: public

text: house mouse

text: Mus musculus

text: Screen 3 Wild Type Embryonic Stem Cell Derived Macrophages stimulated with ODN 1826 (CpG)

text: Mus musculus


text: mus musculus

text: SC

text: public

text: house mouse

text: Mus musculus

text: Screen 3 Wild Type Embryonic Stem Cell Derived Macrophages stimulated with M TRI-dap (NOD agonist)

text: Mus musculus


text: mus musculus

text: SC

text: public

text: house mouse

text: Mus musculus

text: Screen 3 Wild Type Embryonic Stem Cell Derived Macrophages stimulated with LPS (Toll-like receptor agonist)

text: Mus musculus


text: mus musculus

text: SC

text: public

text: house mouse

text: Mus musculus

text: Screen 3 Wild Type Embryonic Stem Cell Derived Macrophages stimulated with Poly I:C (Toll-like receptor agonist)

text: Mus musculus


text: mus musculus

text: SC

text: public

text: house mouse

text: Mus musculus

text: Screen 3 Wild Type Embryonic Stem Cell Derived Macrophages stimulated with Influenza 24 hr

text: Mus musculus


text: mus musculus

text: SC

text: public

text: house mouse

text: Mus musculus

text: Screen 3 Wild Type Embryonic Stem Cell Derived Macrophages stimulated with Influenza 4 hr

text: Mus musculus


text: mus musculus

text: SC

text: public

text: house mouse

text: Mus musculus

text: Screen 3 Wild Type Embryonic Stem Cell Derived Macrophages stimulated with Salmonella

text: Mus musculus


text: mus musculus

text: SC

text: public

text: house mouse

text: Mus musculus

text: Screen 3 Unstimulated Wild Type Embryonic Stem Cell Derived Macrophages 4hr

text: Mus musculus


text: mus musculus

text: SC

text: public

text: house mouse

text: Mus musculus

text: Screen 3 Unstimulated Wild Type Embryonic Stem Cell Derived Macrophages 24hr

text: Mus musculus


text: mus musculus

text: SC

text: public

text: house mouse

text: Mus musculus

text: Screen 3 IRAK-1 Kock-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 3 IRAK-1 Knock-out Embryonic Stem Cell Derived Macrophages stimulated with M TRI-dap (NOD agonist)

text: Mus musculus


text: mus musculus

text: SC

text: public

text: house mouse

text: Mus musculus

text: Screen 3 IRAK-1 Knock-out Embryonic Stem Cell Derived Macrophages stimulated with LPS (Toll-like receptor agonist)

text: Mus musculus


text: mus musculus

text: SC

text: public

text: house mouse

text: Mus musculus

text: Screen 3 IRAK-1 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 3 IRAK-1 Knock-out Embryonic Stem Cell Derived Macrophages stimulated with Influenza 24 hr

text: Mus musculus


text: mus musculus

text: SC

text: public

text: house mouse

text: Mus musculus

text: Screen 3 IRAK-1 Knock-out Embryonic Stem Cell Derived Macrophages stimulated with Influenza 4 hr

text: Mus musculus


text: mus musculus

text: SC

text: public

text: house mouse

text: Mus musculus

text: Screen 3 IRAK-1 Knock-out Embryonic Stem Cell Derived Macrophages stimulated with Salmonella

text: Mus musculus


text: mus musculus

text: SC

text: public

text: house mouse

text: Mus musculus

text: Screen 3 Unstimulated IRAK-1 Knock-out Embryonic Stem Cell Derived Macrophages 4hr

text: Mus musculus


text: mus musculus

text: SC

text: public

text: house mouse

text: Mus musculus

text: Screen 3 Unstimulated IRAK-1 Knock-out Embryonic Stem Cell Derived Macrophages 24hr

text: Mus musculus


text: Homo sapiens

text: SC

text: public

text: human

text: Homo sapiens

text: Homo sapiens


text: mus musculus

text: SC

text: public

text: house mouse

text: Mus musculus

text: Screen 3 TMEM-165 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 3 TMEM-165 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 3 TMEM-165 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 3 TMEM-165 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 3 TMEM-165 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 3 TMEM-165 Knock-out Embryonic Stem Cell Derived Macrophages stimulated with Influenza 4 hr

text: Mus musculus


text: mus musculus

text: SC

text: public

text: house mouse

text: Mus musculus

text: Screen 3 TMEM-165 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 3 Unstimulated TMEM-165 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 3 Unstimulated TMEM-165 Knock-out Embryonic Stem Cell Derived Macrophages 24hr

text: Mus musculus


characteristic: ArrayExpress-DevelopmentalStage

text: blastocyst

characteristic: ArrayExpress-OrganismPart

text: mus musculus

text: SC

text: public

text: house mouse

text: Mus musculus

text: genomic DNA from blastocyst

text: Mus musculus


text: female

characteristic: ArrayExpress-Sex

text: Mus Musculus

characteristic: ArrayExpress-Species

text: SC

text: public

text: house mouse

text: Mus musculus

text: RNA from MEF

text: Mus musculus


text: female

text: Mus Musculus

text: SC

text: public

text: house mouse

characteristic: common name

text: Mus musculus

text: RNA from ESC

text: Mus musculus


text: female

text: Mus Musculus

characteristic: ENA-FIRST-PUBLIC

text: SC

text: public

text: house mouse

text: Mus musculus

text: RNA from iPSC

text: Mus musculus


text: adult

text: earclip

text: mus musculus

characteristic: ArrayExpress-StrainOrLine

text: SC

text: public

text: house mouse

text: Mus musculus

characteristic: organism

text: genomic DNA from earclips

text: Mus musculus

characteristic: strain


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Uppsala University

text: public

tag: Namespace:Uppsala  University

text: collared flycatcher

text: Sampled on the Baltic island Öland.

characteristic: description

text: Ficedula albicollis

text: Ficedula albicollis

text: Male

characteristic: sex

characteristic: title


characteristic: ENA-CHECKLIST

text: Uppsala University

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: collared flycatcher

text: Sampled on the Baltic island Öland.

text: Ficedula albicollis

text: Ficedula albicollis

text: Female


text: Homo sapiens

text: SC

text: public

characteristic: SRA accession

characteristic: Submitter Id

text: human

text: Homo sapiens

text: B-cell lymphoma

characteristic: sample description

text: Homo sapiens


E-MTAB-2962:Sample 2

characteristic: ENA-FIRST-PUBLIC

text: public

text: E-MTAB-2962:Sample 2

tag: Namespace:St. Giles Laboratory of Human Genetics of Infectious Diseases

text: ArrayExpress

characteristic: broker name

text: human

characteristic: common name

text: Protocols: Agilent SureSelect Human All Exon 71Mb

text: normal

characteristic: disease

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens

text: Sample 2


E-MTAB-2962:Sample 1

characteristic: ENA-LAST-UPDATE

text: St. Giles Laboratory of Human Genetics of Infectious Diseases

text: public

text: E-MTAB-2962:Sample 1

text: ArrayExpress

text: human

text: Combined immunodeficiency

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: Homo sapiens

text: Sample 1


E-MTAB-2962:Sample 3

characteristic: External Id

text: public

text: E-MTAB-2962:Sample 3

text: ArrayExpress

text: human

characteristic: description

text: normal

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens

text: Sample 3


text: Uppsala University

text: public

text: collared flycatcher

text: Ficedula albicollis

text: Ficedula albicollis

text: Male

characteristic: sex

characteristic: title


characteristic: ENA-CHECKLIST

text: Uppsala University

characteristic: INSDC center name

text: public

text: collared flycatcher

text: Ficedula albicollis

text: Ficedula albicollis

text: Female


characteristic: INSDC first public

characteristic: INSDC last update

text: public

tag: Namespace:Systems Biology Ireland School of Medicine and Medical Sciences

text: ArrayExpress

text: MCF 10A

characteristic: cell line

text: human

text: Protocols: Monolayer cells were maintained in T75 (10ml) or T175 (20ml) culture flasks, with the following media per flask: 500ml DMEM/F12 (Hyclone), 5% horse serum (Sigma), 0.5ug/ml hydrocortisone (Sigma, stock 1mg/ml in ethanol), 100ng/ul cholera toxin (Sigma, stock 1mg/ml in water), 10ug/ml insulin (Sigma) and 5ml Penicillin/Streptomycin (Pen/Strep) (Gibco, Invitrogen). The media mixture was finally sterilised using a 0.2um filter (Stericup, Millipore). 20ng/ml epidermal growth factor (Sigma) was added freshly to growth media after each cell splitting procedure. For the work performed in MCF10A 3D culture, cells were cultured on a laminin-rich extracellular matrix (ECM) Matrigel (Corning) to form acini. Cold Matrigel was applied to dishes or slides with a sterile pipette and spread evenly using an inoculation loop. Dishes or slides were then placed at 37C for at least 30 minutes to allow the matrix solidify. Prior to seeding of MCF10A cells onto laminin-coated tissue culture plastic/glass slides, cells were treated with Trypsin and detached from plastic flasks as described above, then resuspended in assay medium (containing 2% horse serum). In order to perform cell counting, an aliquot of cells was taken and mixed at a 1:1 ratio with Trypan Blue Stain (Invitrogen). Cells were then counted using a Countess Automated Cell Counter (Invitrogen). For RNA or protein extraction, cells were counted and seeded at a density of 200,000cells/6cm plastic dish (Greiner) pre-coated with 150ul of Matrigel.For all assays performed in 3D, medium was supplemented with 2% Matrigel and 5ng/ml EGF. RNA was harvested from dishes using the RNeasy Kit (Qiagen) or TRI Reagent (Sigma) according to manufacturers protocol. DNA was digested with the DNA-free Kit (Applied Biosystems). RNA concentrations were measured using a Nanodrop2000 (Thermo Scientific) and RNA quality was verified on a 2100 Bioanalyser (Agilent) using a Eukaryote Total RNA Nano Chip (version 2.6). Sequencing libraries were generated from 2ug of total RNA per sample with TruSeq RNA sample preparation Kit v2 (Illumina) according to manufacturers protocol. Size and purity of the libraries were analysed on a Bioanalyser High Sensitivity DNA chip (Agilent).

text: 3D in matrigel for 36h

characteristic: growth condition

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens


text: Systems Biology Ireland School of Medicine and Medical Sciences

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: ArrayExpress

text: MCF 10A

text: human

text: 3D in matrigel for 48h

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens


characteristic: ENA-FIRST-PUBLIC

text: public

text: ArrayExpress

characteristic: broker name

text: MCF 10A

text: human

characteristic: common name

text: 3D in matrigel for 36h

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens


characteristic: ENA-LAST-UPDATE

text: public

text: ArrayExpress

text: MCF 10A

text: human

text: 3D in matrigel for 24h

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: Homo sapiens


characteristic: External Id

text: public

text: ArrayExpress

text: MCF 10A

text: human

characteristic: description

text: 3D in matrigel for 34h

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens


text: public

text: ArrayExpress

text: MCF 10A

text: human

text: 3D in matrigel for 38h

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens

characteristic: title


E-MTAB-2969:Control 2

characteristic: ENA-CHECKLIST

text: public

text: E-MTAB-2969:Control 2

text: ArrayExpress

text: MCF 10A

text: human

text: monolayer

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens

text: Control 2


E-MTAB-2969:Control 1

characteristic: INSDC center name

text: public

text: E-MTAB-2969:Control 1

text: ArrayExpress

text: MCF 10A

text: human

text: monolayer

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens

text: Control 1


text: CEA, Evry

characteristic: INSDC first public

text: public

tag: Namespace:CEA, Evry

text: ArrayExpress

text: baker's yeast

text: Protocols: All strains were grown in YPD rich medium at 30 degrees C to 0.6 OD600, then shifted at 37 degrees C for 45min. The cultures were cross-linked with 1% formaldehyde for 10 min The cell pellets are resuspended in 1 ml of FA/SDS/PMSF buffer (50 mM HEPES-KOH, pH 7.5, 150 mM NaCl, 1 mM EDTA, 1% Triton X100, 0.1% sodium deoxycholate, 0.1% SDS, 1 mM PMSF) and transferred to 1.5 mL Eppendorf tubes. 0.75 mL glass beads (425-600 um, Sigma) are then added to each tube, and the yeast cells were lysed at 4 degrees C for 15 min by vortexing. Pierce the bottom of a 12 ml Greiner tube with a hot needle (0.7x30 mm or 0.5x15 mm) and place in a Falcon50 with a pierced cap. The lysates are transfered in the pierced tubes. Wash each Epp with twice 1 ml of FA/SDS/PMSF buffer (4 ml per extract). Spin down 1 min/2000 rpm. Gently resuspend the pellet with a 5 ml pipet and transfer in a sterile 15 ml Corex tube. Spin down 20 min / 12000 rpm / 4 degrees C in a JA17 rotor (Beckmann). Vacuum the supernatant. The cross-linked chromatin appears as a transparent layer around the pellet. Transfer the pellet in a 2 ml Epp with a burned Pasteur pipet. Add 0.8 ml of FA/SDS/PMSF buffer in the Corex and resuspend with the Pasteur pipet. Transfer in the Epp. Wash the Corex with 0.8 ml FA/SDS/PMSF buffer. Homogenize the Epp with the Pasteur pipet and ihncubate on a rotating wheal at 4 degrees C for 1 to 2 hours.Spin down 20 min / 12000 rpm / 4 degrees C. Vacuum the supernatant and resuspend in 1.6 ml FA/SDS/PMSF buffer with a burned Pasteur pipet.Place the tubes in a mix water / ice / NaCl. Sonicator settings: Pulse-60%-Power 4. Sonicate 3 times 40 sec with 20 sec intervals. Split in 200ul aliquots and performe an additional sonication step with Bioruptor (Diagenode), 6 cycles of 30s with medium intensity setting. Average size of fragments obtained is 200bp.Transfer in a 12 ml Greiner tube and add 0.5 ml FA/SDS/PMSF buffer. Incubate on a rotating wheal for 30 min to 1 hour at 4 degrees C. Spin down 30 min / 10000 rpm / 4 degrees C on a JA20 rotor (Beckmann).Transfer the supernatant in a new tube. Aliquot the supernatant (the chromatin is now soluble). Aliquots of 650 ul and freeze in liquid nitrogen.Chromatin fragment control: Take an aliquot of 100 ul of chromatin and add 25 ul Pronase buffer 5X and 6.25 ul of Pronase (20 mg/ml in H20). Incubate 1 hour at 37 degrees C and O/N at 65 degrees C (digestproteins and reverse crosslink). Add 3.5 ul of RNaseA 1mg/ml and incubate 1 hour at 37 degrees C. Purify on a Quiagen PCR purification column (Elute wih 50 ul Tris 10 mM pH8.5). Load on gel (1.5% in TAE-100V).Immunoprecipitation:Wash 50 ul of Dynabeads Ig 4 times with 500 ul PBS BSA 0.1% buffer. Resuspend in 100 ul PBS BSA 0.1 % buffer. Add antibody (5ul 8WG16 or 1ul 12CA5). Incubate 30 min at 1300 rpm in an Eppendorf shaker at 30 degrees C. Wash 2X 500 ul PBS BSA 0.1%. Wash 1X 500 ul PBS BSA 0.1% with shaking 10 min at 1300 rpm / 30 degrees C. Wash 1X 500 ul PBS BSA 0.1%.Spin down the chromatin from the -80 degrees C for 15 min / 12000 rpm / 4 degrees C. Add 50 ul of PBS BSA 10mg/ml to the beads and then 500 ul of chromatin.Incubate 2h at 21 degrees C in an Eppendorf shaker (1300 rpm). Resuspend with 500 ul FA/SDS and change tube. Wash 2X 1 ml FA/SDS + NaCl (final concentration 500 mM). Wash 1X 1 ml FA/SDS + NaCl with shaking 10 min at 1300 rpm / 21 degrees C. Wash 1X with 500 ul IP buffer (Tris pH7.5 125 mM, EDTA 25 mM, SDS 2.5%). Wash 1X with 500 ul TE. Elute with 125 ul Pronase Buffer 1X for 20 min at 65 degrees C in an Eppendorf shaker at 600 rpm. Cool down at RT. Add 6.25 ul Pronase to the supernatant. Incubate 1h at 37 degrees C and O/N at 65 degrees C. Add 25 ul of Pronase buffer 5X and 6.25 ul of Pronase to 100 ul of chromatin remaining from the initial tube (total DNA).Incubate 1h at 37 degrees C and O/N at 65 degrees C. Add 3.5 ul RNAseA (1mg/ml) and incubate 1h at 37 degrees C. Purify DNA on a Qiagen PCR purification column.

text: tagging

characteristic: genetic modification

text: MATa ura3-52 his3-delta200 ade2-101uaa trp1-delta63 lys2-801uag leu2-delta1 LEU2::3HA::SPT15 med17::KanMX6 // med17-504 CEN TRP3

characteristic: genotype

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae


text: CEA, Evry

characteristic: INSDC last update

text: public

text: ArrayExpress

text: baker's yeast

text: tagging

text: MATa ura3-52 his3-delta200 ade2-101uaa trp1-delta63 lys2-801uag leu2-delta1 LEU2::3HA::SPT15 med17::KanMX6 // med17-444 CEN TRP2

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae


text: CEA, Evry

text: public

characteristic: INSDC status

text: ArrayExpress

text: baker's yeast

text: tagging

text: MATa ura3-52 his3-delta200 ade2-101uaa trp1-delta63 lys2-801uag leu2-delta1 MED15::3HA::HIS3 med17::KanMX6 // med17-444 CEN TRP1

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae


text: CEA, Evry

text: public

characteristic: SRA accession

text: ArrayExpress

text: baker's yeast

text: tagging

text: MATa ura3-52 his3-delta200 ade2-101uaa trp1-delta63 lys2-801uag leu2-delta1 MED5::3HA::HIS3 med17::KanMX6 // med17-444 CEN TRP1

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae


text: CEA, Evry

text: public

characteristic: Submitter Id

text: ArrayExpress

text: baker's yeast

text: tagging

text: MATa ura3-52 his3-delta200 ade2-101uaa trp1-delta63 lys2-801uag leu2-delta1 RAD3::3HA::HIS3 med17::KanMX6 // med17-444 CEN TRP1

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae


characteristic: ENA-FIRST-PUBLIC

text: CEA, Evry

text: public

text: ArrayExpress

text: baker's yeast

text: tagging

text: MATa ura3-52 his3-delta200 ade2-101uaa trp1-delta63 lys2-801uag leu2-delta1 MED5::3HA::HIS3 med17::KanMX6 // med17-504 CEN TRP1

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae


text: CEA, Evry

text: public

text: ArrayExpress

characteristic: broker name

text: baker's yeast

text: tagging

text: MATa ura3-52 his3-delta200 ade2-101uaa trp1-delta63 lys2-801uag leu2-delta1 KIN28::3HA::HIS3 med17::KanMX6 // med17-670 CEN TRP1

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae


text: CEA, Evry

text: public

text: ArrayExpress

text: baker's yeast

characteristic: common name

text: tagging

text: MATa ura3-52 his3-delta200 ade2-101uaa trp1-delta63 lys2-801uag leu2-delta1 KIN28::3HA::HIS3 med17::KanMX6 // med17-504 CEN TRP1

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae


characteristic: ENA-LAST-UPDATE

text: CEA, Evry

text: public

text: ArrayExpress

text: baker's yeast

text: tagging

text: MATa ura3-52 his3-delta200 ade2-101uaa trp1-delta63 lys2-801uag leu2-delta1 MED15::3HA::HIS3 med17::KanMX6 // med17-98 CEN TRP1

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae


text: CEA, Evry

text: public

text: ArrayExpress

text: baker's yeast

text: tagging

text: MATa ura3-52 his3-delta200 ade2-101uaa trp1-delta63 lys2-801uag leu2-delta1 deltamed17::KanMX6 / MED17 CEN TRP1 MED5::3HA::HIS3

text: Saccharomyces cerevisiae

characteristic: organism

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae


characteristic: External Id

text: CEA, Evry

text: public

text: ArrayExpress

text: baker's yeast

text: tagging

text: MATa ura3-52 his3-delta200 ade2-101uaa trp1-delta63 lys2-801uag leu2-delta1 RAD3::3HA::HIS3 med17::KanMX6 // MED17 CEN TRP1

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae


text: CEA, Evry

text: public

text: ArrayExpress

text: baker's yeast

characteristic: description

text: tagging

text: MATa ura3-52 his3-delta200 ade2-101uaa trp1-delta63 lys2-801uag leu2-delta1 MED15::3HA::HIS3 med17::KanMX6 // med17-504 CEN TRP1

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae


text: CEA, Evry

text: public

text: ArrayExpress

text: baker's yeast

text: tagging

text: MATa ura3-52 his3-delta200 ade2-101uaa trp1-delta63 lys2-801uag leu2-delta1 MED5::3HA::HIS3 med17::KanMX6 // MED17 CEN TRP1

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

characteristic: title


characteristic: ENA-CHECKLIST

text: CEA, Evry

text: public

text: ArrayExpress

text: baker's yeast

text: tagging

text: MATa ura3-52 his3-delta200 ade2-101uaa trp1-delta63 lys2-801uag leu2-delta1 LEU2::3HA::SPT15 med17::KanMX6 // MED17 CEN TRP1

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae


text: CEA, Evry

characteristic: INSDC center name

text: public

text: ArrayExpress

text: baker's yeast

text: tagging

text: MATa ura3-52 his3-delta200 ade2-101uaa trp1-delta63 lys2-801uag leu2-delta1 KIN28::3HA::HIS3 med17::KanMX6 // med17-444 CEN TRP1

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae


text: CEA, Evry

characteristic: INSDC first public

text: public

text: ArrayExpress

text: baker's yeast

text: tagging

text: MATa ura3-52 his3-delta200 ade2-101uaa trp1-delta63 lys2-801uag leu2-delta1 RAD3::3HA::HIS3 med17::KanMX6 // med17-504 CEN TRP1

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae


text: CEA, Evry

text: public

text: ArrayExpress

text: baker's yeast

text: Protocols: All strains were grown in YPD rich medium at 30 degrees C to 0.6 OD600, then shifted at 37 degrees C for 45min. The cultures were cross-linked with 1% formaldehyde for 10 min The cell pellets are resuspended in 1 ml of FA/SDS/PMSF buffer (50 mM HEPES-KOH, pH 7.5, 150 mM NaCl, 1 mM EDTA, 1% Triton X100, 0.1% sodium deoxycholate, 0.1% SDS, 1 mM PMSF) and transferred to 1.5 mL Eppendorf tubes. 0.75 mL glass beads (425-600 um, Sigma) are then added to each tube, and the yeast cells were lysed at 4 degrees C for 15 min by vortexing. Pierce the bottom of a 12 ml Greiner tube with a hot needle (0.7x30 mm or 0.5x15 mm) and place in a Falcon50 with a pierced cap. The lysates are transfered in the pierced tubes. Wash each Epp with twice 1 ml of FA/SDS/PMSF buffer (4 ml per extract). Spin down 1 min/2000 rpm. Gently resuspend the pellet with a 5 ml pipet and transfer in a sterile 15 ml Corex tube. Spin down 20 min / 12000 rpm / 4 degrees C in a JA17 rotor (Beckmann). Vacuum the supernatant. The cross-linked chromatin appears as a transparent layer around the pellet. Transfer the pellet in a 2 ml Epp with a burned Pasteur pipet. Add 0.8 ml of FA/SDS/PMSF buffer in the Corex and resuspend with the Pasteur pipet. Transfer in the Epp. Wash the Corex with 0.8 ml FA/SDS/PMSF buffer. Homogenize the Epp with the Pasteur pipet and ihncubate on a rotating wheal at 4 degrees C for 1 to 2 hours.Spin down 20 min / 12000 rpm / 4 degrees C. Vacuum the supernatant and resuspend in 1.6 ml FA/SDS/PMSF buffer with a burned Pasteur pipet.Place the tubes in a mix water / ice / NaCl. Sonicator settings: Pulse-60%-Power 4. Sonicate 3 times 40 sec with 20 sec intervals. Split in 200ul aliquots and performe an additional sonication step with Bioruptor (Diagenode), 6 cycles of 30s with medium intensity setting. Average size of fragments obtained is 200bp.Transfer in a 12 ml Greiner tube and add 0.5 ml FA/SDS/PMSF buffer. Incubate on a rotating wheal for 30 min to 1 hour at 4 degrees C. Spin down 30 min / 10000 rpm / 4 degrees C on a JA20 rotor (Beckmann).Transfer the supernatant in a new tube. Aliquot the supernatant (the chromatin is now soluble). Aliquots of 650 ul and freeze in liquid nitrogen.Chromatin fragment control: Take an aliquot of 100 ul of chromatin and add 25 ul Pronase buffer 5X and 6.25 ul of Pronase (20 mg/ml in H20). Incubate 1 hour at 37 degrees C and O/N at 65 degrees C (digestproteins and reverse crosslink). Add 3.5 ul of RNaseA 1mg/ml and incubate 1 hour at 37 degrees C. Purify on a Quiagen PCR purification column (Elute wih 50 ul Tris 10 mM pH8.5). Load on gel (1.5% in TAE-100V).Immunoprecipitation:Wash 50 ul of Dynabeads Ig 4 times with 500 ul PBS BSA 0.1% buffer. Resuspend in 100 ul PBS BSA 0.1 % buffer. Add antibody (5ul 8WG16 or 1ul 12CA5). Incubate 30 min at 1300 rpm in an Eppendorf shaker at 30 degrees C. Wash 2X 500 ul PBS BSA 0.1%. Wash 1X 500 ul PBS BSA 0.1% with shaking 10 min at 1300 rpm / 30 degrees C. Wash 1X 500 ul PBS BSA 0.1%.Spin down the chromatin from the -80 degrees C for 15 min / 12000 rpm / 4 degrees C. Add 50 ul of PBS BSA 10mg/ml to the beads and then 500 ul of chromatin.Incubate 2h at 21 degrees C in an Eppendorf shaker (1300 rpm). Resuspend with 500 ul FA/SDS and change tube. Wash 2X 1 ml FA/SDS + NaCl (final concentration 500 mM). Wash 1X 1 ml FA/SDS + NaCl with shaking 10 min at 1300 rpm / 21 degrees C. Wash 1X with 500 ul IP buffer (Tris pH7.5 125 mM, EDTA 25 mM, SDS 2.5%). Wash 1X with 500 ul TE. Elute with 125 ul Pronase Buffer 1X for 20 min at 65 degrees C in an Eppendorf shaker at 600 rpm. Cool down at RT. Add 6.25 ul Pronase to the supernatant. Incubate 1h at 37 degrees C and O/N at 65 degrees C. Add 25 ul of Pronase buffer 5X and 6.25 ul of Pronase to 100 ul of chromatin remaining from the initial tube (total DNA).Incubate 1h at 37 degrees C and O/N at 65 degrees C. Add 3.5 ul RNAseA (1mg/ml) and incubate 1h at 37 degrees C. Purify DNA on a Qiagen PCR purification column.

text: tagging

characteristic: genetic modification

text: MATa ura3-52 his3-delta200 ade2-101uaa trp1-delta63 lys2-801uag leu2-delta1 KIN28::3HA::HIS3 med17::KanMX6 // MED17 CEN TRP1

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae


text: CEA, Evry

text: public

text: ArrayExpress

text: baker's yeast

text: tagging

text: MATa ura3-52 his3-delta200 ade2-101uaa trp1-delta63 lys2-801uag leu2-delta1 LEU2::3HA::SPT15 med17::KanMX6 // med17-504 CEN TRP3

characteristic: genotype

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae


text: CEA, Evry

characteristic: INSDC last update

text: public

text: ArrayExpress

text: baker's yeast

text: tagging

text: MATa ura3-52 his3-delta200 ade2-101uaa trp1-delta63 lys2-801uag leu2-delta1 MED5::3HA::HIS3 med17::KanMX6 // med17-670 CEN TRP1

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae


text: CEA, Evry

text: public

characteristic: INSDC status

text: ArrayExpress

text: baker's yeast

text: tagging

text: MATa ura3-52 his3-delta200 ade2-101uaa trp1-delta63 lys2-801uag leu2-delta1 deltamed17::KanMX6 / MED17 CEN TRP1 MED15::3HA::HIS3

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae