characteristic: ENA-CHECKLIST

text: European Molecular Biology Laboratory

text: killed

characteristic: INSDC status

text: E-MTAB-2180:4C_CRM_eya_meso_eya_(1)_MESO_6-8h_2

text: ArrayExpress

text: fruit fly

text: Protocols: 1g of frozen embryos were dounce-homogenized, 20 times with a loose pestle and 10 times with a tight pestle, in 10 ml of chilled HB buffer (15 mM Tris-HCl (pH 7.4), 0.34 M sucrose, 15 mM NaCl, 60 mM KCl, 0.2 mM EDTA and 0.2 mM EGTA) on ice. The lysate was filtered through 2 layers of Miracloth and spun at 3,500g for 10 min to pellet the nuclei. The nuclei were then washed in 10 ml of chilled HB buffer, spun at 3,500g for 10 min and resuspended in 3 ml of PBTB buffer (5% (wt/vol) BSA, 0.1% (vol/vol) Triton X-100 in PBS). The nuclei were dissociated by passing them ten times through a 20-G needle and then ten times through a 22-G needle using a 5-ml syringe, and filtered through a 20-μm Sefar Nitex membrane. The nuclei were stained with a mouse anti-SBP antibody at 1:100 for 1 h, nutating at 4 μC. Primary antibody was washed by adding 6 ml of PBTB, spining for 10 min at 1,000g and discarding the supernatant. The niclei were then stained with an anti-mouse Alexa488 antibody at 1:100 in 3 ml of PBTB and incubated for 1 h while nutating at 4 μC. Secondary antibody was washed by adding 6 ml of PBTB, spining for 10 min at 1,000g and discarding the supernatant. The nuclei were resuspended in 3 ml of PBTB and subjected to FACS sorting. After sorting, the purity was evaluated by microscopy. The nuclei were spun at 3,500g for 15 min, and 30 million nuclei aliquots were frozen in liquid nitrogen. 30 million nuclei were resuspended in 500μl 1.2x restriction buffer (60μl 10x DpnII buffer, 440μl H2O). The nuclei were placed at 37C and 0.3% SDS was added before 1h incubation at 37C, shaking gently. 2% Triton X-100 was added to the nuclei before incubating for an additional 1h at 37C, shaking gently. 400U of the DpnII restriction enzyme were added, and the nuclei where incubated overnight at 37C, shaking gently. The next day, 1.6% SDS was added and the nuclei were incubated for 20 min at 65C, shaking gently. The nuclei were transferred in 5ml of 1.4x ligation buffer with 1% Triton X-100 and incubated 1h at 37C, shaking gently. 100U of ligase were added and the reaction was incubated for 4hrs at 16C, followed by 30min at room temperature. The chromatin was de-crosslinked by adding 300μg of proteinase K and incubating overnight at 65C. The next day, 300μg of RNaseA were added to the reaction before 45min incubation at 37C. The DNA was purified by phenol/chloroform followed by ethanol precipitation, and resuspended in 150μl of Tris pH7.5. Libraries were amplified from 320 ng of 4C template using touchdown PCR (94C 2min; 8 cycles of 94C 15sec, 55C 1min, 68C 5sec; 18 cycles of 94C 15sec, 63C 1min, 63C 5sec + 10sec per cycle; 68C 10sec; 22C forever). 100 libraries were multiplexed in equi-molar ratio and sequenced on two HiSeq2000 lanes using 100 bp single-end reads.

text: stage 10 to 11 embryo

text: wild type

text: egg laying

text: Drosophila melanogaster

characteristic: organism

text: Drosophila melanogaster

text: Drosophila melanogaster

text: mixed sex

text: 6 to 8 hour


status: KILLED

tag: attribute

characteristic: External Id

text: European Molecular Biology Laboratory

characteristic: INSDC center name

characteristic: INSDC last update

text: killed

characteristic: SRA accession

tag: Namespace:European Molecular Biology Laboratory

characteristic: Submitter Id

text: ArrayExpress

characteristic: broker name

text: fruit fly

characteristic: common name

characteristic: description

text: stage 6 to 7 embryo

characteristic: developmental stage

text: wild type

characteristic: genotype

text: egg laying

characteristic: initial time point

text: Drosophila melanogaster

text: Drosophila melanogaster

characteristic: organism part

text: Drosophila melanogaster

text: mixed sex

characteristic: sex

characteristic: strain

text: 3 to 4 hour

characteristic: time

characteristic: title


characteristic: ENA-CHECKLIST

text: European Molecular Biology Laboratory

text: killed

characteristic: INSDC status

text: ArrayExpress

text: fruit fly

text: Protocols: 1g of frozen embryos were dounce-homogenized, 20 times with a loose pestle and 10 times with a tight pestle, in 10 ml of chilled HB buffer (15 mM Tris-HCl (pH 7.4), 0.34 M sucrose, 15 mM NaCl, 60 mM KCl, 0.2 mM EDTA and 0.2 mM EGTA) on ice. The lysate was filtered through 2 layers of Miracloth and spun at 3,500g for 10 min to pellet the nuclei. The nuclei were then washed in 10 ml of chilled HB buffer, spun at 3,500g for 10 min and resuspended in 3 ml of PBTB buffer (5% (wt/vol) BSA, 0.1% (vol/vol) Triton X-100 in PBS). The nuclei were dissociated by passing them ten times through a 20-G needle and then ten times through a 22-G needle using a 5-ml syringe, and filtered through a 20-μm Sefar Nitex membrane. The total number of nuclei was estimated by microscopy, and 30 million nuclei aliquots were frozen in liquid nitrogen. 30 million nuclei were resuspended in 500μl 1.2x restriction buffer (60μl 10x DpnII buffer, 440μl H2O). The nuclei were placed at 37C and 0.3% SDS was added before 1h incubation at 37C, shaking gently. 2% Triton X-100 was added to the nuclei before incubating for an additional 1h at 37C, shaking gently. 400U of the DpnII restriction enzyme were added, and the nuclei where incubated overnight at 37C, shaking gently. The next day, 1.6% SDS was added and the nuclei were incubated for 20 min at 65C, shaking gently. The nuclei were transferred in 5ml of 1.4x ligation buffer with 1% Triton X-100 and incubated 1h at 37C, shaking gently. 100U of ligase were added and the reaction was incubated for 4hrs at 16C, followed by 30min at room temperature. The chromatin was de-crosslinked by adding 300μg of proteinase K and incubating overnight at 65C. The next day, 300μg of RNaseA were added to the reaction before 45min incubation at 37C. The DNA was purified by phenol/chloroform followed by ethanol precipitation, and resuspended in 150μl of Tris pH7.5. Libraries were amplified from 320 ng of 4C template using touchdown PCR (94C 2min; 8 cycles of 94C 15sec, 55C 1min, 68C 5sec; 18 cycles of 94C 15sec, 63C 1min, 63C 5sec + 10sec per cycle; 68C 10sec; 22C forever). 100 libraries were multiplexed in equi-molar ratio and sequenced on two HiSeq2000 lanes using 100 bp single-end reads.

text: stage 6 to 7 embryo

text: wild type

text: egg laying

text: Drosophila melanogaster

characteristic: organism

text: Drosophila melanogaster

text: Drosophila melanogaster

text: mixed sex

text: 3 to 4 hour


characteristic: External Id

text: European Molecular Biology Laboratory

characteristic: INSDC center name

characteristic: INSDC last update

text: killed

text: E-MTAB-2180:4C_CRM_eya_meso_eya_(1)_WE_6-8h_1

text: ArrayExpress

text: fruit fly

text: stage 10 to 11 embryo

text: wild type

text: egg laying

text: Drosophila melanogaster

text: Drosophila melanogaster

text: Drosophila melanogaster

text: mixed sex

text: 6 to 8 hour


text: European Molecular Biology Laboratory

text: killed

characteristic: SRA accession

characteristic: Submitter Id

text: ArrayExpress

characteristic: broker name

text: fruit fly

text: stage 10 to 11 embryo

text: wild type

text: egg laying

text: Drosophila melanogaster

text: Drosophila melanogaster

text: Drosophila melanogaster

text: mixed sex

text: 6 to 8 hour


text: European Molecular Biology Laboratory

text: killed

text: ArrayExpress

text: fruit fly

characteristic: common name

characteristic: description

text: stage 10 to 11 embryo

characteristic: developmental stage

text: wild type

text: egg laying

text: Drosophila melanogaster

text: Drosophila melanogaster

text: Drosophila melanogaster

text: mixed sex

text: 6 to 8 hour


text: European Molecular Biology Laboratory

text: killed

text: E-MTAB-2180:4C_CRM_Con_1kb_3prime_WE_3-4h_1

text: ArrayExpress

text: fruit fly

text: stage 6 to 7 embryo

text: wild type

characteristic: genotype

text: egg laying

characteristic: initial time point

text: Drosophila melanogaster

text: Drosophila melanogaster

characteristic: organism part

text: Drosophila melanogaster

text: mixed sex

text: 3 to 4 hour


text: European Molecular Biology Laboratory

text: killed

text: E-MTAB-2180:4C_CRM_Mef2_II-B[L]_NR_MESO_6-8h_2

text: ArrayExpress

text: fruit fly

text: stage 10 to 11 embryo

text: wild type

text: egg laying

text: Drosophila melanogaster

text: Drosophila melanogaster

text: Drosophila melanogaster

text: mixed sex

characteristic: sex

characteristic: strain

text: 6 to 8 hour

characteristic: time


characteristic: ENA-CHECKLIST

text: European Molecular Biology Laboratory

text: killed

characteristic: INSDC status

text: E-MTAB-2180:4C_CRM_pdm2_CE8012_WE_6-8h_1

text: ArrayExpress

text: fruit fly

text: stage 10 to 11 embryo

text: wild type

text: egg laying

text: Drosophila melanogaster

text: Drosophila melanogaster

text: Drosophila melanogaster

text: mixed sex

text: 6 to 8 hour

characteristic: title


characteristic: External Id

text: European Molecular Biology Laboratory

characteristic: INSDC center name

text: killed

text: E-MTAB-2180:4C_CRM_stumps_hbr_DME_MESO_6-8h_2

text: ArrayExpress

text: fruit fly

text: stage 10 to 11 embryo

text: wild type

text: egg laying

text: Drosophila melanogaster

characteristic: organism

text: Drosophila melanogaster

text: Drosophila melanogaster

text: mixed sex

text: 6 to 8 hour


text: European Molecular Biology Laboratory

characteristic: INSDC last update

text: killed

characteristic: SRA accession

text: E-MTAB-2180:4C_CRM_Con_2kb_3prime_MESO_6-8h_2

characteristic: Submitter Id

text: ArrayExpress

text: fruit fly

text: stage 10 to 11 embryo

text: wild type

text: egg laying

text: Drosophila melanogaster

text: Drosophila melanogaster

text: Drosophila melanogaster

text: mixed sex

text: 6 to 8 hour


text: European Molecular Biology Laboratory

text: killed

text: E-MTAB-2180:4C_CRM_Con_2kb_3prime_WE_3-4h_2

text: ArrayExpress

characteristic: broker name

text: fruit fly

characteristic: common name

characteristic: description

text: stage 6 to 7 embryo

text: wild type

text: egg laying

text: Drosophila melanogaster

text: Drosophila melanogaster

text: Drosophila melanogaster

text: mixed sex

text: 3 to 4 hour


text: European Molecular Biology Laboratory

text: killed

text: E-MTAB-2180:4C_CRM_pdm2_CE8012_WE_3-4h_1

text: ArrayExpress

text: fruit fly

text: stage 6 to 7 embryo

characteristic: developmental stage

text: wild type

characteristic: genotype

text: egg laying

characteristic: initial time point

text: Drosophila melanogaster

text: Drosophila melanogaster

text: Drosophila melanogaster

text: mixed sex

text: 3 to 4 hour


text: European Molecular Biology Laboratory

text: killed

text: E-MTAB-2180:4C_CRM_Ubx_BXD-A_MESO_6-8h_2

text: ArrayExpress

text: fruit fly

text: stage 10 to 11 embryo

text: wild type

text: egg laying

text: Drosophila melanogaster

text: Drosophila melanogaster

characteristic: organism part

text: Drosophila melanogaster

text: mixed sex

characteristic: sex

characteristic: strain

text: 6 to 8 hour


characteristic: ENA-CHECKLIST

text: European Molecular Biology Laboratory

text: killed

characteristic: INSDC status

text: E-MTAB-2180:4C_CRM_Con_1kb_3prime_WE_6-8h_1

text: ArrayExpress

text: fruit fly

text: stage 10 to 11 embryo

text: wild type

text: egg laying

text: Drosophila melanogaster

text: Drosophila melanogaster

text: Drosophila melanogaster

text: mixed sex

text: 6 to 8 hour

characteristic: time


characteristic: External Id

text: European Molecular Biology Laboratory

characteristic: INSDC center name

text: killed

text: E-MTAB-2180:4C_CRM_eya_meso_eya_(1)_WE_3-4h_1

text: ArrayExpress

text: fruit fly

text: stage 6 to 7 embryo

text: wild type

text: egg laying

text: Drosophila melanogaster

text: Drosophila melanogaster

text: Drosophila melanogaster

text: mixed sex

text: 3 to 4 hour

characteristic: title


text: European Molecular Biology Laboratory

characteristic: INSDC last update

text: killed

characteristic: SRA accession

text: E-MTAB-2180:4C_CRM_pdm2_CE8012_MESO_6-8h_1

text: ArrayExpress

text: fruit fly

text: stage 10 to 11 embryo

text: wild type

text: egg laying

text: Drosophila melanogaster

characteristic: organism

text: Drosophila melanogaster

text: Drosophila melanogaster

text: mixed sex

text: 6 to 8 hour


text: European Molecular Biology Laboratory

text: killed

text: E-MTAB-2180:4C_CRM_pdm2_CE8012_MESO_6-8h_2

characteristic: Submitter Id

text: ArrayExpress

characteristic: broker name

text: fruit fly

characteristic: common name

text: stage 10 to 11 embryo

text: wild type

text: egg laying

text: Drosophila melanogaster

text: Drosophila melanogaster

text: Drosophila melanogaster

text: mixed sex

text: 6 to 8 hour


text: European Molecular Biology Laboratory

text: killed

text: ArrayExpress

text: fruit fly

characteristic: description

text: stage 6 to 7 embryo

characteristic: developmental stage

text: wild type

characteristic: genotype

text: egg laying

text: Drosophila melanogaster

text: Drosophila melanogaster

text: Drosophila melanogaster

text: mixed sex

text: 3 to 4 hour


text: European Molecular Biology Laboratory

text: killed

text: ArrayExpress

text: fruit fly

text: stage 6 to 7 embryo

text: wild type

text: egg laying

characteristic: initial time point

text: Drosophila melanogaster

text: Drosophila melanogaster

characteristic: organism part

text: Drosophila melanogaster

text: mixed sex

characteristic: sex

text: 3 to 4 hour


characteristic: ENA-CHECKLIST

text: European Molecular Biology Laboratory

text: killed

characteristic: INSDC status

text: E-MTAB-2180:4C_CRM_Con_1kb_3prime_MESO_6-8h_1

text: ArrayExpress

text: fruit fly

text: stage 10 to 11 embryo

text: wild type

text: egg laying

text: Drosophila melanogaster

text: Drosophila melanogaster

text: Drosophila melanogaster

text: mixed sex

characteristic: strain

text: 6 to 8 hour


characteristic: External Id

text: European Molecular Biology Laboratory

characteristic: INSDC center name

text: killed

text: E-MTAB-2180:4C_CRM_stumps_hbr_DME_WE_6-8h_2

text: ArrayExpress

text: fruit fly

text: stage 10 to 11 embryo

text: wild type

text: egg laying

text: Drosophila melanogaster

text: Drosophila melanogaster

text: Drosophila melanogaster

text: mixed sex

text: 6 to 8 hour

characteristic: time


text: European Molecular Biology Laboratory

characteristic: INSDC last update

text: killed

characteristic: SRA accession

text: ArrayExpress

text: fruit fly

text: Protocols: 1g of frozen embryos were dounce-homogenized, 20 times with a loose pestle and 10 times with a tight pestle, in 10 ml of chilled HB buffer (15 mM Tris-HCl (pH 7.4), 0.34 M sucrose, 15 mM NaCl, 60 mM KCl, 0.2 mM EDTA and 0.2 mM EGTA) on ice. The lysate was filtered through 2 layers of Miracloth and spun at 3,500g for 10 min to pellet the nuclei. The nuclei were then washed in 10 ml of chilled HB buffer, spun at 3,500g for 10 min and resuspended in 3 ml of PBTB buffer (5% (wt/vol) BSA, 0.1% (vol/vol) Triton X-100 in PBS). The nuclei were dissociated by passing them ten times through a 20-G needle and then ten times through a 22-G needle using a 5-ml syringe, and filtered through a 20-μm Sefar Nitex membrane. The nuclei were stained with a mouse anti-SBP antibody at 1:100 for 1 h, nutating at 4 μC. Primary antibody was washed by adding 6 ml of PBTB, spining for 10 min at 1,000g and discarding the supernatant. The niclei were then stained with an anti-mouse Alexa488 antibody at 1:100 in 3 ml of PBTB and incubated for 1 h while nutating at 4 μC. Secondary antibody was washed by adding 6 ml of PBTB, spining for 10 min at 1,000g and discarding the supernatant. The nuclei were resuspended in 3 ml of PBTB and subjected to FACS sorting. After sorting, the purity was evaluated by microscopy. The nuclei were spun at 3,500g for 15 min, and 30 million nuclei aliquots were frozen in liquid nitrogen. 30 million nuclei were resuspended in 500μl 1.2x restriction buffer (60μl 10x DpnII buffer, 440μl H2O). The nuclei were placed at 37C and 0.3% SDS was added before 1h incubation at 37C, shaking gently. 2% Triton X-100 was added to the nuclei before incubating for an additional 1h at 37C, shaking gently. 400U of the DpnII restriction enzyme were added, and the nuclei where incubated overnight at 37C, shaking gently. The next day, 1.6% SDS was added and the nuclei were incubated for 20 min at 65C, shaking gently. The nuclei were transferred in 5ml of 1.4x ligation buffer with 1% Triton X-100 and incubated 1h at 37C, shaking gently. 100U of ligase were added and the reaction was incubated for 4hrs at 16C, followed by 30min at room temperature. The chromatin was de-crosslinked by adding 300μg of proteinase K and incubating overnight at 65C. The next day, 300μg of RNaseA were added to the reaction before 45min incubation at 37C. The DNA was purified by phenol/chloroform followed by ethanol precipitation, and resuspended in 150μl of Tris pH7.5. Libraries were amplified from 320 ng of 4C template using touchdown PCR (94C 2min; 8 cycles of 94C 15sec, 55C 1min, 68C 5sec; 18 cycles of 94C 15sec, 63C 1min, 63C 5sec + 10sec per cycle; 68C 10sec; 22C forever). 100 libraries were multiplexed in equi-molar ratio and sequenced on two HiSeq2000 lanes using 100 bp single-end reads.

text: stage 10 to 11 embryo

text: wild type

text: egg laying

text: Drosophila melanogaster

text: Drosophila melanogaster

text: Drosophila melanogaster

text: mixed sex

text: 6 to 8 hour

characteristic: title


text: European Molecular Biology Laboratory

text: killed

characteristic: Submitter Id

text: ArrayExpress

characteristic: broker name

text: fruit fly

text: Protocols: 1g of frozen embryos were dounce-homogenized, 20 times with a loose pestle and 10 times with a tight pestle, in 10 ml of chilled HB buffer (15 mM Tris-HCl (pH 7.4), 0.34 M sucrose, 15 mM NaCl, 60 mM KCl, 0.2 mM EDTA and 0.2 mM EGTA) on ice. The lysate was filtered through 2 layers of Miracloth and spun at 3,500g for 10 min to pellet the nuclei. The nuclei were then washed in 10 ml of chilled HB buffer, spun at 3,500g for 10 min and resuspended in 3 ml of PBTB buffer (5% (wt/vol) BSA, 0.1% (vol/vol) Triton X-100 in PBS). The nuclei were dissociated by passing them ten times through a 20-G needle and then ten times through a 22-G needle using a 5-ml syringe, and filtered through a 20-μm Sefar Nitex membrane. The total number of nuclei was estimated by microscopy, and 30 million nuclei aliquots were frozen in liquid nitrogen. 30 million nuclei were resuspended in 500μl 1.2x restriction buffer (60μl 10x DpnII buffer, 440μl H2O). The nuclei were placed at 37C and 0.3% SDS was added before 1h incubation at 37C, shaking gently. 2% Triton X-100 was added to the nuclei before incubating for an additional 1h at 37C, shaking gently. 400U of the DpnII restriction enzyme were added, and the nuclei where incubated overnight at 37C, shaking gently. The next day, 1.6% SDS was added and the nuclei were incubated for 20 min at 65C, shaking gently. The nuclei were transferred in 5ml of 1.4x ligation buffer with 1% Triton X-100 and incubated 1h at 37C, shaking gently. 100U of ligase were added and the reaction was incubated for 4hrs at 16C, followed by 30min at room temperature. The chromatin was de-crosslinked by adding 300μg of proteinase K and incubating overnight at 65C. The next day, 300μg of RNaseA were added to the reaction before 45min incubation at 37C. The DNA was purified by phenol/chloroform followed by ethanol precipitation, and resuspended in 150μl of Tris pH7.5. Libraries were amplified from 320 ng of 4C template using touchdown PCR (94C 2min; 8 cycles of 94C 15sec, 55C 1min, 68C 5sec; 18 cycles of 94C 15sec, 63C 1min, 63C 5sec + 10sec per cycle; 68C 10sec; 22C forever). 100 libraries were multiplexed in equi-molar ratio and sequenced on two HiSeq2000 lanes using 100 bp single-end reads.

text: stage 10 to 11 embryo

text: wild type

text: egg laying

text: Drosophila melanogaster

characteristic: organism

text: Drosophila melanogaster

text: Drosophila melanogaster

text: mixed sex

text: 6 to 8 hour


text: European Molecular Biology Laboratory

text: killed

text: E-MTAB-2180:4C_CRM_Mef2_II-B[L]_NR_WE_6-8h_1

text: ArrayExpress

text: fruit fly

characteristic: common name

characteristic: description

text: stage 10 to 11 embryo

characteristic: developmental stage

text: wild type

text: egg laying

text: Drosophila melanogaster

text: Drosophila melanogaster

text: Drosophila melanogaster

text: mixed sex

text: 6 to 8 hour


text: European Molecular Biology Laboratory

text: killed

text: E-MTAB-2180:4C_CRM_stumps_hbr_DME_MESO_6-8h_1

text: ArrayExpress

text: fruit fly

text: stage 10 to 11 embryo

text: wild type

characteristic: genotype

text: egg laying

characteristic: initial time point

text: Drosophila melanogaster

text: Drosophila melanogaster

characteristic: organism part

text: Drosophila melanogaster

text: mixed sex

text: 6 to 8 hour


characteristic: ENA-CHECKLIST

text: European Molecular Biology Laboratory

text: killed

characteristic: INSDC status

text: E-MTAB-2180:4C_CRM_pdm2_CE8012_WE_6-8h_2

text: ArrayExpress

text: fruit fly

text: stage 10 to 11 embryo

text: wild type

text: egg laying

text: Drosophila melanogaster

text: Drosophila melanogaster

text: Drosophila melanogaster

text: mixed sex

characteristic: sex

text: 6 to 8 hour


characteristic: External Id

text: European Molecular Biology Laboratory

characteristic: INSDC center name

text: killed

text: E-MTAB-2180:4C_CRM_stumps_hbr_DME_WE_3-4h_1

text: ArrayExpress

text: fruit fly

text: stage 6 to 7 embryo

text: wild type

text: egg laying

text: Drosophila melanogaster

text: Drosophila melanogaster

text: Drosophila melanogaster

text: mixed sex

characteristic: strain

text: 3 to 4 hour


text: European Molecular Biology Laboratory

characteristic: INSDC last update

text: killed

characteristic: SRA accession

text: E-MTAB-2180:4C_CRM_eya_meso_eya_(1)_WE_6-8h_2

text: ArrayExpress

text: fruit fly

text: stage 10 to 11 embryo

text: wild type

text: egg laying

text: Drosophila melanogaster

text: Drosophila melanogaster

text: Drosophila melanogaster

text: mixed sex

text: 6 to 8 hour

characteristic: time


text: European Molecular Biology Laboratory

text: killed

text: E-MTAB-2180:4C_CRM_ap_ApME680_MESO_6-8h_2

characteristic: Submitter Id

text: ArrayExpress

characteristic: broker name

text: fruit fly

text: stage 10 to 11 embryo

text: wild type

text: egg laying

text: Drosophila melanogaster

text: Drosophila melanogaster

text: Drosophila melanogaster

text: mixed sex

text: 6 to 8 hour

characteristic: title


text: European Molecular Biology Laboratory

text: killed

text: E-MTAB-2180:4C_CRM_Mef2_II-B[L]_NR_WE_6-8h_2

text: ArrayExpress

text: fruit fly

characteristic: common name

characteristic: description

text: stage 10 to 11 embryo

text: wild type

text: egg laying

text: Drosophila melanogaster

characteristic: organism

text: Drosophila melanogaster

text: Drosophila melanogaster

text: mixed sex

text: 6 to 8 hour


text: European Molecular Biology Laboratory

text: killed

text: E-MTAB-2180:4C_CRM_stumps_hbr_DME_WE_3-4h_2

text: ArrayExpress

text: fruit fly

text: stage 6 to 7 embryo

characteristic: developmental stage

text: wild type

characteristic: genotype

text: egg laying

characteristic: initial time point

text: Drosophila melanogaster

text: Drosophila melanogaster

text: Drosophila melanogaster

text: mixed sex

text: 3 to 4 hour


characteristic: ENA-CHECKLIST

text: European Molecular Biology Laboratory

text: killed

characteristic: INSDC status

text: E-MTAB-2180:4C_CRM_pdm2_CE8012_WE_3-4h_2

text: ArrayExpress

text: fruit fly

text: stage 6 to 7 embryo

text: wild type

text: egg laying

text: Drosophila melanogaster

text: Drosophila melanogaster

characteristic: organism part

text: Drosophila melanogaster

text: mixed sex

text: 3 to 4 hour


characteristic: External Id

text: European Molecular Biology Laboratory

characteristic: INSDC center name

text: killed

text: E-MTAB-2180:4C_CRM_Con_1kb_3prime_WE_6-8h_2

text: ArrayExpress

text: fruit fly

text: stage 10 to 11 embryo

text: wild type

text: egg laying

text: Drosophila melanogaster

text: Drosophila melanogaster

text: Drosophila melanogaster

text: mixed sex

characteristic: sex

text: 6 to 8 hour


text: European Molecular Biology Laboratory

characteristic: INSDC last update

text: killed

characteristic: SRA accession

text: E-MTAB-2180:4C_CRM_ap_ApME680_MESO_6-8h_1

text: ArrayExpress

text: fruit fly

text: stage 10 to 11 embryo

text: wild type

text: egg laying

text: Drosophila melanogaster

text: Drosophila melanogaster

text: Drosophila melanogaster

text: mixed sex

characteristic: strain

text: 6 to 8 hour


text: European Molecular Biology Laboratory

text: killed

text: E-MTAB-2180:4C_CRM_Ubx_BXD-A_MESO_6-8h_1

characteristic: Submitter Id

text: ArrayExpress

characteristic: broker name

text: fruit fly

text: stage 10 to 11 embryo

text: wild type

text: egg laying

text: Drosophila melanogaster

text: Drosophila melanogaster

text: Drosophila melanogaster

text: mixed sex

text: 6 to 8 hour

characteristic: time


text: European Molecular Biology Laboratory

text: killed

text: ArrayExpress

text: fruit fly

characteristic: common name

characteristic: description

text: stage 6 to 7 embryo

text: wild type

text: egg laying

text: Drosophila melanogaster

text: Drosophila melanogaster

text: Drosophila melanogaster

text: mixed sex

text: 3 to 4 hour

characteristic: title


text: European Molecular Biology Laboratory

text: killed

text: E-MTAB-2180:4C_CRM_Mef2_II-B[L]_NR_WE_3-4h_1

text: ArrayExpress

text: fruit fly

text: stage 6 to 7 embryo

characteristic: developmental stage

text: wild type

characteristic: genotype

text: egg laying

text: Drosophila melanogaster

characteristic: organism

text: Drosophila melanogaster

text: Drosophila melanogaster

text: mixed sex

text: 3 to 4 hour


characteristic: ENA-CHECKLIST

text: European Molecular Biology Laboratory

text: killed

characteristic: INSDC status

text: ArrayExpress

text: fruit fly

text: stage 6 to 7 embryo

text: wild type

text: egg laying

characteristic: initial time point

text: Drosophila melanogaster

text: Drosophila melanogaster

text: Drosophila melanogaster

text: mixed sex

text: 3 to 4 hour


characteristic: External Id

text: European Molecular Biology Laboratory

characteristic: INSDC center name

text: killed

text: ArrayExpress

text: fruit fly

text: stage 10 to 11 embryo

text: wild type

text: egg laying

text: Drosophila melanogaster

text: Drosophila melanogaster

characteristic: organism part

text: Drosophila melanogaster

text: mixed sex

text: 6 to 8 hour


text: European Molecular Biology Laboratory

characteristic: INSDC last update

text: killed

characteristic: SRA accession

text: ArrayExpress

text: fruit fly

text: stage 10 to 11 embryo

text: wild type

text: egg laying

text: Drosophila melanogaster

text: Drosophila melanogaster

text: Drosophila melanogaster

text: mixed sex

characteristic: sex

text: 6 to 8 hour


text: European Molecular Biology Laboratory

text: killed

text: E-MTAB-2180:4C_CRM_Mef2_II-B[L]_NR_WE_3-4h_2

characteristic: Submitter Id

text: ArrayExpress

characteristic: broker name

text: fruit fly

text: stage 6 to 7 embryo

text: wild type

text: egg laying

text: Drosophila melanogaster

text: Drosophila melanogaster

text: Drosophila melanogaster

text: mixed sex

characteristic: strain

text: 3 to 4 hour


text: European Molecular Biology Laboratory

text: killed

text: E-MTAB-2180:4C_CRM_eya_meso_eya_(1)_MESO_6-8h_1

text: ArrayExpress

text: fruit fly

characteristic: common name

characteristic: description

text: stage 10 to 11 embryo

text: wild type

text: egg laying

text: Drosophila melanogaster

text: Drosophila melanogaster

text: Drosophila melanogaster

text: mixed sex

text: 6 to 8 hour

characteristic: time


text: European Molecular Biology Laboratory

text: killed

text: E-MTAB-2180:4C_CRM_Mef2_II-B[L]_NR_MESO_6-8h_1

text: ArrayExpress

text: fruit fly

text: Protocols: 1g of frozen embryos were dounce-homogenized, 20 times with a loose pestle and 10 times with a tight pestle, in 10 ml of chilled HB buffer (15 mM Tris-HCl (pH 7.4), 0.34 M sucrose, 15 mM NaCl, 60 mM KCl, 0.2 mM EDTA and 0.2 mM EGTA) on ice. The lysate was filtered through 2 layers of Miracloth and spun at 3,500g for 10 min to pellet the nuclei. The nuclei were then washed in 10 ml of chilled HB buffer, spun at 3,500g for 10 min and resuspended in 3 ml of PBTB buffer (5% (wt/vol) BSA, 0.1% (vol/vol) Triton X-100 in PBS). The nuclei were dissociated by passing them ten times through a 20-G needle and then ten times through a 22-G needle using a 5-ml syringe, and filtered through a 20-μm Sefar Nitex membrane. The nuclei were stained with a mouse anti-SBP antibody at 1:100 for 1 h, nutating at 4 μC. Primary antibody was washed by adding 6 ml of PBTB, spining for 10 min at 1,000g and discarding the supernatant. The niclei were then stained with an anti-mouse Alexa488 antibody at 1:100 in 3 ml of PBTB and incubated for 1 h while nutating at 4 μC. Secondary antibody was washed by adding 6 ml of PBTB, spining for 10 min at 1,000g and discarding the supernatant. The nuclei were resuspended in 3 ml of PBTB and subjected to FACS sorting. After sorting, the purity was evaluated by microscopy. The nuclei were spun at 3,500g for 15 min, and 30 million nuclei aliquots were frozen in liquid nitrogen. 30 million nuclei were resuspended in 500μl 1.2x restriction buffer (60μl 10x DpnII buffer, 440μl H2O). The nuclei were placed at 37C and 0.3% SDS was added before 1h incubation at 37C, shaking gently. 2% Triton X-100 was added to the nuclei before incubating for an additional 1h at 37C, shaking gently. 400U of the DpnII restriction enzyme were added, and the nuclei where incubated overnight at 37C, shaking gently. The next day, 1.6% SDS was added and the nuclei were incubated for 20 min at 65C, shaking gently. The nuclei were transferred in 5ml of 1.4x ligation buffer with 1% Triton X-100 and incubated 1h at 37C, shaking gently. 100U of ligase were added and the reaction was incubated for 4hrs at 16C, followed by 30min at room temperature. The chromatin was de-crosslinked by adding 300μg of proteinase K and incubating overnight at 65C. The next day, 300μg of RNaseA were added to the reaction before 45min incubation at 37C. The DNA was purified by phenol/chloroform followed by ethanol precipitation, and resuspended in 150μl of Tris pH7.5. Libraries were amplified from 320 ng of 4C template using touchdown PCR (94C 2min; 8 cycles of 94C 15sec, 55C 1min, 68C 5sec; 18 cycles of 94C 15sec, 63C 1min, 63C 5sec + 10sec per cycle; 68C 10sec; 22C forever). 100 libraries were multiplexed in equi-molar ratio and sequenced on two HiSeq2000 lanes using 100 bp single-end reads.

text: stage 10 to 11 embryo

characteristic: developmental stage

text: wild type

characteristic: genotype

text: egg laying

text: Drosophila melanogaster

text: Drosophila melanogaster

text: Drosophila melanogaster

text: mixed sex

text: 6 to 8 hour

characteristic: title


characteristic: ENA-CHECKLIST

text: European Molecular Biology Laboratory

text: killed

characteristic: INSDC status

text: E-MTAB-2180:4C_CRM_eya_meso_eya_(1)_WE_3-4h_2

text: ArrayExpress

text: fruit fly

text: Protocols: 1g of frozen embryos were dounce-homogenized, 20 times with a loose pestle and 10 times with a tight pestle, in 10 ml of chilled HB buffer (15 mM Tris-HCl (pH 7.4), 0.34 M sucrose, 15 mM NaCl, 60 mM KCl, 0.2 mM EDTA and 0.2 mM EGTA) on ice. The lysate was filtered through 2 layers of Miracloth and spun at 3,500g for 10 min to pellet the nuclei. The nuclei were then washed in 10 ml of chilled HB buffer, spun at 3,500g for 10 min and resuspended in 3 ml of PBTB buffer (5% (wt/vol) BSA, 0.1% (vol/vol) Triton X-100 in PBS). The nuclei were dissociated by passing them ten times through a 20-G needle and then ten times through a 22-G needle using a 5-ml syringe, and filtered through a 20-μm Sefar Nitex membrane. The total number of nuclei was estimated by microscopy, and 30 million nuclei aliquots were frozen in liquid nitrogen. 30 million nuclei were resuspended in 500μl 1.2x restriction buffer (60μl 10x DpnII buffer, 440μl H2O). The nuclei were placed at 37C and 0.3% SDS was added before 1h incubation at 37C, shaking gently. 2% Triton X-100 was added to the nuclei before incubating for an additional 1h at 37C, shaking gently. 400U of the DpnII restriction enzyme were added, and the nuclei where incubated overnight at 37C, shaking gently. The next day, 1.6% SDS was added and the nuclei were incubated for 20 min at 65C, shaking gently. The nuclei were transferred in 5ml of 1.4x ligation buffer with 1% Triton X-100 and incubated 1h at 37C, shaking gently. 100U of ligase were added and the reaction was incubated for 4hrs at 16C, followed by 30min at room temperature. The chromatin was de-crosslinked by adding 300μg of proteinase K and incubating overnight at 65C. The next day, 300μg of RNaseA were added to the reaction before 45min incubation at 37C. The DNA was purified by phenol/chloroform followed by ethanol precipitation, and resuspended in 150μl of Tris pH7.5. Libraries were amplified from 320 ng of 4C template using touchdown PCR (94C 2min; 8 cycles of 94C 15sec, 55C 1min, 68C 5sec; 18 cycles of 94C 15sec, 63C 1min, 63C 5sec + 10sec per cycle; 68C 10sec; 22C forever). 100 libraries were multiplexed in equi-molar ratio and sequenced on two HiSeq2000 lanes using 100 bp single-end reads.

text: stage 6 to 7 embryo

text: wild type

text: egg laying

text: Drosophila melanogaster

characteristic: organism

text: Drosophila melanogaster

text: Drosophila melanogaster

text: mixed sex

text: 3 to 4 hour


characteristic: External Id

text: European Molecular Biology Laboratory

characteristic: INSDC center name

text: killed

text: E-MTAB-2180:4C_CRM_stumps_hbr_DME_WE_6-8h_1

text: ArrayExpress

text: fruit fly

text: stage 10 to 11 embryo

text: wild type

text: egg laying

characteristic: initial time point

text: Drosophila melanogaster

text: Drosophila melanogaster

text: Drosophila melanogaster

text: mixed sex

text: 6 to 8 hour


text: European Molecular Biology Laboratory

characteristic: INSDC last update

text: killed

characteristic: SRA accession

text: E-MTAB-2180:4C_CRM_eya_meso_eya_(1)_MESO_6-8h_2

text: ArrayExpress

text: fruit fly

text: stage 10 to 11 embryo

text: wild type

text: egg laying

text: Drosophila melanogaster

text: Drosophila melanogaster

characteristic: organism part

text: Drosophila melanogaster

text: mixed sex

text: 6 to 8 hour


text: European Molecular Biology Laboratory

text: killed

text: E-MTAB-2180:4C_CRM_eya_meso_eya_(1)_WE_6-8h_1

characteristic: Submitter Id

text: ArrayExpress

characteristic: broker name

text: fruit fly

text: stage 10 to 11 embryo

text: wild type

text: egg laying

text: Drosophila melanogaster

text: Drosophila melanogaster

text: Drosophila melanogaster

text: mixed sex

characteristic: sex

text: 6 to 8 hour


text: European Molecular Biology Laboratory

text: killed

text: E-MTAB-2180:4C_CRM_Con_1kb_3prime_WE_3-4h_1

text: ArrayExpress

text: fruit fly

characteristic: common name

characteristic: description

text: stage 6 to 7 embryo

text: wild type

text: egg laying

text: Drosophila melanogaster

text: Drosophila melanogaster

text: Drosophila melanogaster

text: mixed sex

characteristic: strain

text: 3 to 4 hour


text: European Molecular Biology Laboratory

text: killed

text: E-MTAB-2180:4C_CRM_Mef2_II-B[L]_NR_MESO_6-8h_2

text: ArrayExpress

text: fruit fly

text: stage 10 to 11 embryo

characteristic: developmental stage

text: wild type

characteristic: genotype

text: egg laying

text: Drosophila melanogaster

text: Drosophila melanogaster

text: Drosophila melanogaster

text: mixed sex

text: 6 to 8 hour

characteristic: time


characteristic: ENA-CHECKLIST

text: European Molecular Biology Laboratory

text: killed

characteristic: INSDC status

text: E-MTAB-2180:4C_CRM_pdm2_CE8012_WE_6-8h_1

text: ArrayExpress

text: fruit fly

text: stage 10 to 11 embryo

text: wild type

text: egg laying

text: Drosophila melanogaster

text: Drosophila melanogaster

text: Drosophila melanogaster

text: mixed sex

text: 6 to 8 hour

characteristic: title


status: PUBLIC

text: Adult

characteristic: ArrayExpress-DevelopmentalStage

text: F1 hybred

characteristic: ArrayExpress-Genotype

text: Normal

characteristic: ArrayExpress-GrowthCondition

text: Brain

characteristic: ArrayExpress-OrganismPart

text: female

characteristic: ArrayExpress-Sex

text: Mus musculus

characteristic: ArrayExpress-Species

text: F1 hybred

characteristic: ArrayExpress-StrainOrLine

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: SC

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: house mouse

text: Mus musculus

characteristic: organism

text: RNA from MOE of the brain of S-cross

characteristic: sample description

text: Mus musculus

text: F1 hybred


text: Adult

text: F1 hybred

text: Normal

text: Brain

text: female

text: Mus musculus

text: F1 hybred

characteristic: ENA-CHECKLIST

text: SC

characteristic: INSDC last update

text: public

characteristic: SRA accession

characteristic: Submitter Id

text: house mouse

characteristic: common name

text: Mus musculus

text: RNA from OB of the brain of S- cross

text: Mus musculus

text: F1 hybred

characteristic: strain


text: Adult

characteristic: ArrayExpress-DevelopmentalStage

text: F1 hybred

characteristic: ArrayExpress-Genotype

text: Normal

characteristic: ArrayExpress-GrowthCondition

text: Brain

characteristic: ArrayExpress-OrganismPart

text: female

text: Mus musculus

text: F1 hybred

text: SC

text: public

characteristic: INSDC status

text: house mouse

text: Mus musculus

text: RNA from MOE of the brain of M-cross

text: Mus musculus

text: F1 hybred


text: Adult

text: F1 hybred

text: Normal

text: Brain

text: female

characteristic: ArrayExpress-Sex

text: Mus musculus

characteristic: ArrayExpress-Species

text: F1 hybred

characteristic: ArrayExpress-StrainOrLine

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: SC

text: public

text: house mouse

text: Mus musculus

text: RNA from OB of the brain of M-cross

text: Mus musculus

text: F1 hybred


text: Plasmodium falciparum

characteristic: External Id

text: SC

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: malaria parasite P. falciparum

text: Plasmodium falciparum

characteristic: organism

characteristic: sample description

text: Plasmodium falciparum


characteristic: ENA-CHECKLIST

text: UOY

characteristic: INSDC last update

text: public

characteristic: SRA accession

characteristic: Submitter Id

text: harbor seal

characteristic: common name

text: harbour seal

characteristic: description

text: Phoca vitulina

text: Phoca vitulina

text: RAD HFC samples

characteristic: title

type: has member


text: GSC

text: public

characteristic: INSDC status

text: thale cress

text: A description of each epiRIL can be found in Colome-Tatche et al, PNAS 2012.

text: Arabidopsis thaliana

text: Arabidopsis thaliana


text: Normal

characteristic: ArrayExpress-Phenotype

text: Homo sapiens

characteristic: ArrayExpress-Species

text: SC

text: public

text: human

text: Homo sapiens

text: aDNA from archaeological specimen

text: Homo sapiens


characteristic: ArrayExpress-CellType

text: Mus musculus

characteristic: ENA-FIRST-PUBLIC

text: SC

text: public

text: house mouse

text: Mus musculus

text: Pilot Study 2 Unstimulated Wild type Embryonic Stem Cell Derived Macrophages

text: Mus musculus


text: Mus musculus

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: SC

text: public

text: house mouse

text: Mus musculus

text: Pilot Study 2 Wild type Embryonic Stem Cell Derived Macrophages stimulated with Influenza

text: Mus musculus


text: Mus musculus

text: SC

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: house mouse

text: Mus musculus

text: Pilot Study 2 Wild type Embryonic Stem Cell Derived Macrophages stimulated with Plasmodium berghei infected red blood cells

text: Mus musculus


text: Mus musculus

text: SC

text: public

text: house mouse

text: Mus musculus

characteristic: organism

text: Pilot Study 2 Wild type Embryonic Stem Cell Derived Macrophages stimulated with R848 (Toll-like receptor agonist)

characteristic: sample description

text: Mus musculus


text: Mus musculus

characteristic: ENA-CHECKLIST

text: SC

characteristic: INSDC last update

text: public

text: house mouse

text: Mus musculus

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

text: Mus musculus


text: Mus musculus

text: SC

text: public

characteristic: SRA accession

characteristic: Submitter Id

text: house mouse

text: Mus musculus

text: Pilot Study 2 Wild type Embryonic Stem Cell Derived Macrophages stimulated with IFNg (cytokine)

text: Mus musculus


text: Mus musculus

text: SC

text: public

text: house mouse

characteristic: common name

text: Mus musculus

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

text: Mus musculus


text: Mus musculus

text: SC

text: public

text: house mouse

text: Mus musculus

text: Pilot Study 2 Wild type Embryonic Stem Cell Derived Macrophages stimulated with CpG (Toll-like receptor agonist)

text: Mus musculus


text: Mus musculus

text: SC

text: public

text: house mouse

text: Mus musculus

text: Pilot Study 2 Wild type Embryonic Stem Cell Derived Macrophages stimulated with Flagelin (Toll-like receptor agonist)

text: Mus musculus


text: Mus musculus

text: SC

text: public

text: house mouse

text: Mus musculus

text: Pilot Study 2 Wild type Embryonic Stem Cell Derived Macrophages stimulated with Tri-Dap (Toll-like receptor agonist) + LPS 1ng/ml

text: Mus musculus


text: Mus musculus

text: SC

text: public

text: house mouse

text: Mus musculus

text: Pilot Study 2 Wild type Embryonic Stem Cell Derived Macrophages stimulated with murine Interleukin-4 (cytokine)

text: Mus musculus


text: Mus musculus

text: SC

text: public

text: house mouse

text: Mus musculus

text: Pilot Study 3 Unstimulated Wild type Embryonic Stem Cell Derived Macrophages

text: Mus musculus


text: Mus musculus

text: SC

text: public

text: house mouse

text: Mus musculus

text: Pilot Study 3 Wild type Embryonic Stem Cell Derived Macrophages stimulated with Influenza

text: Mus musculus


text: Mus musculus

text: SC

text: public

text: house mouse

text: Mus musculus

text: Pilot Study 3 Wild type Embryonic Stem Cell Derived Macrophages stimulated with Plasmodium berghei infected red blood cells

text: Mus musculus


text: Mus musculus

text: SC

text: public

text: house mouse

text: Mus musculus

text: Pilot Study 3 Wild type Embryonic Stem Cell Derived Macrophages stimulated with R848 (Toll-like receptor agonist)

text: Mus musculus


text: Mus musculus

text: SC

text: public

text: house mouse

text: Mus musculus

text: Pilot Study 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: Pilot Study 3 Wild type Embryonic Stem Cell Derived Macrophages stimulated with IFNg (cytokine)

text: Mus musculus


text: Mus musculus

text: SC

text: public

text: house mouse

text: Mus musculus

text: Pilot Study 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: Pilot Study 3 Wild type Embryonic Stem Cell Derived Macrophages stimulated with CpG (Toll-like receptor agonist)

text: Mus musculus


text: Mus musculus

text: SC

text: public

text: house mouse

text: Mus musculus

text: Pilot Study 3 Wild type Embryonic Stem Cell Derived Macrophages stimulated with Flagelin (Toll-like receptor agonist)

text: Mus musculus


text: Mus musculus

text: SC

text: public

text: house mouse

text: Mus musculus

text: Pilot Study 3 Wild type Embryonic Stem Cell Derived Macrophages stimulated with Tri-Dap (Toll-like receptor agonist) + LPS 1ng/ml

text: Mus musculus


text: Mus musculus

text: SC

text: public

text: house mouse

text: Mus musculus

text: Pilot Study 3 Wild type Embryonic Stem Cell Derived Macrophages stimulated with murine Interleukin-4 (cytokine)

text: Mus musculus


text: Wildtype

characteristic: ArrayExpress-Genotype

text: INPUT

characteristic: ArrayExpress-Immunoprecipitate

text: Lin- bone marrow cells

characteristic: ArrayExpress-OrganismPart

text: wt

text: male

characteristic: ArrayExpress-Sex

text: Mus Musculus

text: SC

text: public

text: house mouse

text: Mus musculus

text: Lin- bone marrow cells

text: Mus musculus


text: Wildtype

text: Lin- bone marrow cells

text: wt

characteristic: ArrayExpress-Phenotype

text: male

text: Mus Musculus

characteristic: ArrayExpress-Species

text: SC

text: public

characteristic: INSDC status

text: house mouse

text: Mus musculus

text: Lin- bone marrow cells

text: Mus musculus


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: CAS-MPG PICB

text: public

tag: Namespace:CAS-MPG PICB

text: ArrayExpress

characteristic: broker name

text: zebrafish

text: Protocols: Zebrafish embryos in HANKS embryo buffer Around 5hpf, sham puncture the controls (SP) with hamilton syringe system. Trizol RNA extraction of whole embryos Truseq RNA Sample preparation Kits V2

characteristic: description

text: embryo stage

characteristic: developmental stage

text: wild type genotype

characteristic: genotype

text: Danio rerio

text: Danio rerio

text: Danio rerio

text: fresh specimen

characteristic: specimen with known storage state

text: tb

characteristic: strain

characteristic: title


characteristic: ENA-CHECKLIST

text: CAS-MPG PICB

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: SRA accession

characteristic: Submitter Id

text: ArrayExpress

text: zebrafish

characteristic: common name

text: Protocols: Zebrafish embryos in HANKS embryo buffer Removed yolk around 5hpf (YD) with hamilton syringe system. Trizol RNA extraction of whole embryos Truseq RNA Sample preparation Kits V2

text: embryo stage

text: wild type genotype

text: Danio rerio

characteristic: organism

text: Danio rerio

text: Danio rerio

text: fresh specimen

text: tb


text: Homo sapiens

characteristic: ArrayExpress-Species

characteristic: ArrayExpress-TimePoint

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: SC

text: public

characteristic: INSDC status

text: human

text: Homo sapiens

text: RNA from TPH1

characteristic: sample description

text: Homo sapiens


characteristic: External Id

text: GSC

text: public

text: thale cress

text: A description of each epiRIL can be found in Colome-Tatche et al, PNAS 2012.

characteristic: description

text: Arabidopsis thaliana

text: Arabidopsis thaliana


text: GSC

text: public

text: thale cress

text: Arabidopsis thaliana

text: Arabidopsis thaliana

text: epiRiL_344 ; Bisulfite sequencing

characteristic: title


characteristic: ENA-CHECKLIST

text: GSC

text: public

text: thale cress

text: Arabidopsis thaliana

text: Arabidopsis thaliana

text: epiRiL_260 ; Bisulfite sequencing


text: GSC

characteristic: INSDC center name

text: public

text: thale cress

text: Arabidopsis thaliana

text: Arabidopsis thaliana

text: epiRiL_98 ; Bisulfite sequencing


text: GSC

characteristic: INSDC first public

text: public

text: thale cress

text: Arabidopsis thaliana

text: Arabidopsis thaliana

text: epiRiL_480 ; Bisulfite sequencing


text: GSC

characteristic: INSDC last update

text: public

text: thale cress

text: Arabidopsis thaliana

text: Arabidopsis thaliana

text: epiRiL_60 ; Bisulfite sequencing


text: Danio rerio

text: mixed

characteristic: ArrayExpress-StrainOrLine

text: SC

text: public

characteristic: SRA accession

text: sox10_t3_36hpf__clutch_1_mutant_1-sc-1818581

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from a single morphologically abnormal embryo from sox10, allele t3 clutch 1. A 8 base indexing sequence (ATCACGTT) is bases 13 to 20 of read 1 followed by polyT.

text: Danio rerio

text: mixed

characteristic: strain


text: Danio rerio

text: mixed

text: SC

text: public

text: sox10_t3_36hpf__clutch_1_sibling_1-sc-1818582

characteristic: Submitter Id

text: zebrafish

characteristic: common name

text: Danio rerio

characteristic: organism

text: 3' end enriched mRNA from a single morphologically normal embryo from sox10, allele t3 clutch 1. A 8 base indexing sequence (CGATGTTT) is bases 13 to 20 of read 1 followed by polyT.

text: Danio rerio

text: mixed


text: Danio rerio

characteristic: ArrayExpress-Species

text: mixed

characteristic: ENA-FIRST-PUBLIC

text: SC

text: public

text: sox10_t3_36hpf__clutch_1_mutant_2-sc-1818583

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from a single morphologically abnormal embryo from sox10, allele t3 clutch 1. A 8 base indexing sequence (TTAGGCAT) is bases 13 to 20 of read 1 followed by polyT.

text: Danio rerio

text: mixed


text: Danio rerio

text: mixed

characteristic: ENA-LAST-UPDATE

text: SC

text: public

characteristic: INSDC status

text: sox10_t3_36hpf__clutch_1_sibling_2-sc-1818584

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from a single morphologically normal embryo from sox10, allele t3 clutch 1. A 8 base indexing sequence (TGACCACT) is bases 13 to 20 of read 1 followed by polyT.

text: Danio rerio

text: mixed


text: Danio rerio

text: mixed

characteristic: External Id

text: SC

text: public

text: sox10_t3_36hpf__clutch_1_mutant_3-sc-1818585

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from a single morphologically abnormal embryo from sox10, allele t3 clutch 1. A 8 base indexing sequence (ACAGTGGT) is bases 13 to 20 of read 1 followed by polyT.

characteristic: sample description

text: Danio rerio

text: mixed


text: Danio rerio

text: mixed

text: SC

text: public

text: sox10_t3_36hpf__clutch_1_sibling_3-sc-1818586

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from a single morphologically normal embryo from sox10, allele t3 clutch 1. A 8 base indexing sequence (GCCAATGT) is bases 13 to 20 of read 1 followed by polyT.

text: Danio rerio

text: mixed


text: Danio rerio

text: mixed

text: SC

text: public

text: sox10_t3_36hpf__clutch_1_mutant_4-sc-1818587

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from a single morphologically abnormal embryo from sox10, allele t3 clutch 1. A 8 base indexing sequence (CAGATCTG) is bases 13 to 20 of read 1 followed by polyT.

text: Danio rerio

text: mixed


text: Danio rerio

text: mixed

text: SC

text: public

text: sox10_t3_36hpf__clutch_1_sibling_4-sc-1818588

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from a single morphologically normal embryo from sox10, allele t3 clutch 1. A 8 base indexing sequence (ACTTGATG) is bases 13 to 20 of read 1 followed by polyT.

text: Danio rerio

text: mixed


text: Danio rerio

text: mixed

text: SC

text: public

text: sox10_t3_36hpf__clutch_1_mutant_5-sc-1818589

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from a single morphologically abnormal embryo from sox10, allele t3 clutch 1. A 8 base indexing sequence (GATCAGCG) is bases 13 to 20 of read 1 followed by polyT.

text: Danio rerio

text: mixed


text: Danio rerio

text: mixed

text: SC

text: public

text: sox10_t3_36hpf__clutch_1_sibling_5-sc-1818590

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from a single morphologically normal embryo from sox10, allele t3 clutch 1. A 8 base indexing sequence (TAGCTTGT) is bases 13 to 20 of read 1 followed by polyT.

text: Danio rerio

text: mixed


text: Danio rerio

text: mixed

text: SC

text: public

text: sox10_t3_36hpf__clutch_1_mutant_6-sc-1818591

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from a single morphologically abnormal embryo from sox10, allele t3 clutch 1. A 8 base indexing sequence (GGCTACAG) is bases 13 to 20 of read 1 followed by polyT.

text: Danio rerio

text: mixed


text: Danio rerio

text: mixed

text: SC

text: public

text: sox10_t3_36hpf__clutch_1_sibling_6-sc-1818592

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from a single morphologically normal embryo from sox10, allele t3 clutch 1. A 8 base indexing sequence (CTTGTACT) is bases 13 to 20 of read 1 followed by polyT.

text: Danio rerio

text: mixed


text: Danio rerio

text: mixed

text: SC

text: public

text: sox10_t3_36hpf__clutch_1_mutant_7-sc-1818593

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from a single morphologically abnormal embryo from sox10, allele t3 clutch 1. A 8 base indexing sequence (TGGTTGTT) is bases 13 to 20 of read 1 followed by polyT.

text: Danio rerio

text: mixed


text: Danio rerio

text: mixed

text: SC

text: public

text: sox10_t3_36hpf__clutch_1_sibling_7-sc-1818594

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from a single morphologically normal embryo from sox10, allele t3 clutch 1. A 8 base indexing sequence (TCTCGGTT) is bases 13 to 20 of read 1 followed by polyT.

text: Danio rerio

text: mixed


text: Danio rerio

text: mixed

text: SC

text: public

text: sox10_t3_36hpf__clutch_1_mutant_8-sc-1818595

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from a single morphologically abnormal embryo from sox10, allele t3 clutch 1. A 8 base indexing sequence (TAAGCGTT) is bases 13 to 20 of read 1 followed by polyT.

text: Danio rerio

text: mixed


text: Danio rerio

text: mixed

text: SC

text: public

text: sox10_t3_36hpf__clutch_1_sibling_8-sc-1818596

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from a single morphologically normal embryo from sox10, allele t3 clutch 1. A 8 base indexing sequence (TCCGTCTT) is bases 13 to 20 of read 1 followed by polyT.

text: Danio rerio

text: mixed


text: Danio rerio

text: mixed

text: SC

text: public

text: sox10_t3_36hpf__clutch_1_mutant_9-sc-1818597

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from a single morphologically abnormal embryo from sox10, allele t3 clutch 1. A 8 base indexing sequence (TGTACCTT) is bases 13 to 20 of read 1 followed by polyT.

text: Danio rerio

text: mixed


text: Danio rerio

text: mixed

text: SC

text: public

text: sox10_t3_36hpf__clutch_1_sibling_9-sc-1818598

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from a single morphologically normal embryo from sox10, allele t3 clutch 1. A 8 base indexing sequence (TTCTGTGT) is bases 13 to 20 of read 1 followed by polyT.

text: Danio rerio

text: mixed


text: Danio rerio

text: mixed

text: SC

text: public

text: sox10_t3_36hpf__clutch_1_mutant_10-sc-1818599

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from a single morphologically abnormal embryo from sox10, allele t3 clutch 1. A 8 base indexing sequence (TCTGCTGT) is bases 13 to 20 of read 1 followed by polyT.

text: Danio rerio

text: mixed


text: Danio rerio

text: mixed

text: SC

text: public

text: sox10_t3_36hpf__clutch_1_sibling_10-sc-1818600

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from a single morphologically normal embryo from sox10, allele t3 clutch 1. A 8 base indexing sequence (TTGGAGGT) is bases 13 to 20 of read 1 followed by polyT.

text: Danio rerio

text: mixed


text: Danio rerio

text: mixed

text: SC

text: public

text: sox10_t3_36hpf__clutch_1_mutant_11-sc-1818601

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from a single morphologically abnormal embryo from sox10, allele t3 clutch 1. A 8 base indexing sequence (TCGAGCGT) is bases 13 to 20 of read 1 followed by polyT.

text: Danio rerio

text: mixed


text: Danio rerio

text: mixed

text: SC

text: public

text: sox10_t3_36hpf__clutch_1_sibling_11-sc-1818602

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from a single morphologically normal embryo from sox10, allele t3 clutch 1. A 8 base indexing sequence (TGATACGT) is bases 13 to 20 of read 1 followed by polyT.

text: Danio rerio

text: mixed


text: Danio rerio

text: mixed

text: SC

text: public

text: sox10_t3_36hpf__clutch_1_mutant_12-sc-1818603

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from a single morphologically abnormal embryo from sox10, allele t3 clutch 1. A 8 base indexing sequence (TGCATAGT) is bases 13 to 20 of read 1 followed by polyT.

text: Danio rerio

text: mixed


text: Danio rerio

text: mixed

text: SC

text: public

text: sox10_t3_36hpf__clutch_1_sibling_12-sc-1818604

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from a single morphologically normal embryo from sox10, allele t3 clutch 1. A 8 base indexing sequence (TTGACTCT) is bases 13 to 20 of read 1 followed by polyT.

text: Danio rerio

text: mixed


text: Danio rerio

text: mixed

text: SC

text: public

text: sox10_t3_48hpf_clutch1_mutant_1-sc-1818605

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from a single morphologically abnormal embryo from sox10, allele t3 clutch 1. A 8 base indexing sequence (TGCGATCT) is bases 13 to 20 of read 1 followed by polyT.

text: Danio rerio

text: mixed


text: Danio rerio

text: mixed

text: SC

text: public

text: sox10_t3_48hpf_clutch_1_sibling_1-sc-1818606

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from a single morphologically normal embryo from sox10, allele t3 clutch 1. A 8 base indexing sequence (TTCCTGCT) is bases 13 to 20 of read 1 followed by polyT.

text: Danio rerio

text: mixed


text: Danio rerio

text: mixed

text: SC

text: public

text: sox10_t3_48hpf_clutch_1_mutant_2-sc-1818607

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from a single morphologically abnormal embryo from sox10, allele t3 clutch 1. A 8 base indexing sequence (TAGTGACT) is bases 13 to 20 of read 1 followed by polyT.

text: Danio rerio

text: mixed


text: Danio rerio

text: mixed

text: SC

text: public

text: sox10_t3_48hpf_clutch_1_sibling_2-sc-1818608

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from a single morphologically normal embryo from sox10, allele t3 clutch 1. A 8 base indexing sequence (TACAGGAT) is bases 13 to 20 of read 1 followed by polyT.

text: Danio rerio

text: mixed


text: Danio rerio

text: mixed

text: SC

text: public

text: sox10_t3_48hpf_clutch_1_mutant_3-sc-1818609

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from a single morphologically abnormal embryo from sox10, allele t3 clutch 1. A 8 base indexing sequence (TCCTCAAT) is bases 13 to 20 of read 1 followed by polyT.

text: Danio rerio

text: mixed


text: Danio rerio

text: mixed

text: SC

text: public

text: sox10_t3_48hpf_clutch_1_sibling_3-sc-1818610

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from a single morphologically normal embryo from sox10, allele t3 clutch 1. A 8 base indexing sequence (TGTGGTTG) is bases 13 to 20 of read 1 followed by polyT.

text: Danio rerio

text: mixed


text: Danio rerio

text: mixed

text: SC

text: public

text: sox10_t3_48hpf_clutch_1_mutant_4-sc-1818611

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from a single morphologically abnormal embryo from sox10, allele t3 clutch 1. A 8 base indexing sequence (TAGTCTTG) is bases 13 to 20 of read 1 followed by polyT.

text: Danio rerio

text: mixed


text: Danio rerio

text: mixed

text: SC

text: public

text: sox10_t3_48hpf_clutch_1_sibling_4-sc-1818612

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from a single morphologically normal embryo from sox10, allele t3 clutch 1. A 8 base indexing sequence (TTCCATTG) is bases 13 to 20 of read 1 followed by polyT.

text: Danio rerio

text: mixed


text: Danio rerio

text: mixed

text: SC

text: public

text: sox10_t3_48hpf_clutch_1_mutant_5-sc-1818613

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from a single morphologically abnormal embryo from sox10, allele t3 clutch 1. A 8 base indexing sequence (TCGAAGTG) is bases 13 to 20 of read 1 followed by polyT.

text: Danio rerio

text: mixed


text: Danio rerio

text: mixed

text: SC

text: public

text: sox10_t3_48hpf_clutch_1_sibling_5-sc-1818614

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from a single morphologically normal embryo from sox10, allele t3 clutch 1. A 8 base indexing sequence (TAACGCTG) is bases 13 to 20 of read 1 followed by polyT.

text: Danio rerio

text: mixed


text: Danio rerio

text: mixed

text: SC

text: public

text: sox10_t3_48hpf_clutch_1_mutant_6-sc-1818615

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from a single morphologically abnormal embryo from sox10, allele t3 clutch 1. A 8 base indexing sequence (TTGGTATG) is bases 13 to 20 of read 1 followed by polyT.

text: Danio rerio

text: mixed


text: Danio rerio

text: mixed

text: SC

text: public

text: sox10_t3_48hpf_clutch_1_sibling_6-sc-1818616

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from a single morphologically normal embryo from sox10, allele t3 clutch 1. A 8 base indexing sequence (TGAACTGG) is bases 13 to 20 of read 1 followed by polyT.

text: Danio rerio

text: mixed


text: Danio rerio

text: mixed

text: SC

text: public

text: sox10_t3_48hpf_clutch_1_mutant_7-sc-1818617

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from a single morphologically abnormal embryo from sox10, allele t3 clutch 1. A 8 base indexing sequence (TACTTCGG) is bases 13 to 20 of read 1 followed by polyT.

text: Danio rerio

text: mixed


text: Danio rerio

text: mixed

text: SC

text: public

text: sox10_t3_48hpf_clutch_1_mutant_8-sc-1818618

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from a single morphologically abnormal embryo from sox10, allele t3 clutch 1. A 8 base indexing sequence (TCTCACGG) is bases 13 to 20 of read 1 followed by polyT.

text: Danio rerio

text: mixed


text: Danio rerio

text: mixed

text: SC

text: public

text: sox10_t3_48hpf_clutch_1_sibling_8-sc-1818619

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from a single morphologically normal embryo from sox10, allele t3 clutch 1. A 8 base indexing sequence (TCAGGAGG) is bases 13 to 20 of read 1 followed by polyT.

text: Danio rerio

text: mixed


text: Danio rerio

text: mixed

text: SC

text: public

text: sox10_t3_48hpf_clutch_1_mutant_9-sc-1818620

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from a single morphologically abnormal embryo from sox10, allele t3 clutch 1. A 8 base indexing sequence (TAAGTTCG) is bases 13 to 20 of read 1 followed by polyT.

text: Danio rerio

text: mixed


text: Danio rerio

text: mixed

text: SC

text: public

text: sox10_t3_48hpf_clutch_1_mutant_10-sc-1818621

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from a single morphologically abnormal embryo from sox10, allele t3 clutch 1. A 8 base indexing sequence (TCCAGTCG) is bases 13 to 20 of read 1 followed by polyT.

text: Danio rerio

text: mixed


text: Danio rerio

text: mixed

text: SC

text: public

text: sox10_t3_48hpf_clutch_1_sibling_10-sc-1818622

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from a single morphologically normal embryo from sox10, allele t3 clutch 1. A 8 base indexing sequence (TGTATGCG) is bases 13 to 20 of read 1 followed by polyT.

text: Danio rerio

text: mixed


text: Danio rerio

text: mixed

text: SC

text: public

text: sox10_t3_48hpf_clutch_1_mutant_11-sc-1818623

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from a single morphologically abnormal embryo from sox10, allele t3 clutch 1. A 8 base indexing sequence (TCATTGAG) is bases 13 to 20 of read 1 followed by polyT.

text: Danio rerio

text: mixed


text: Danio rerio

text: mixed

text: SC

text: public

text: sox10_t3_48hpf_clutch_1_sibling_11-sc-1818624

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from a single morphologically normal embryo from sox10, allele t3 clutch 1. A 8 base indexing sequence (TGGCTCAG) is bases 13 to 20 of read 1 followed by polyT.

text: Danio rerio

text: mixed


text: Danio rerio

text: mixed

text: SC

text: public

text: sox10_t3_48hpf_clutch_1_mutant_12-sc-1818625

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from a single morphologically abnormal embryo from sox10, allele t3 clutch 1. A 8 base indexing sequence (TATGCCAG) is bases 13 to 20 of read 1 followed by polyT.

text: Danio rerio

text: mixed


text: Danio rerio

text: mixed

text: SC

text: public

text: sox10_t3_48hpf_clutch_1_sibling_12-sc-1818626

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from a single morphologically normal embryo from sox10, allele t3 clutch 1. A 8 base indexing sequence (TCAGATTC) is bases 13 to 20 of read 1 followed by polyT.

text: Danio rerio

text: mixed


text: Danio rerio

text: mixed

text: SC

text: public

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from a single morphologically abnormal embryo from ZMP phenotype 35 clutch 1. A 8 base indexing sequence (TACTAGTC) is bases 13 to 20 of read 1 followed by 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_ph35

text: Danio rerio

text: mixed


text: Danio rerio

text: mixed

text: SC

text: public

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from a single morphologically abnormal embryo from ZMP phenotype 35 clutch 1. A 8 base indexing sequence (TTCAGCTC) is bases 13 to 20 of read 1 followed by 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_ph35

text: Danio rerio

text: mixed


text: Danio rerio

text: mixed

text: SC

text: public

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from a single morphologically normal embryo from ZMP phenotype 35 clutch 1. A 8 base indexing sequence (TGTCTATC) is bases 13 to 20 of read 1 followed by 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_ph35

text: Danio rerio

text: mixed


text: Danio rerio

text: mixed

text: SC

text: public

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from a single morphologically abnormal embryo from ZMP phenotype 35 clutch 1. A 8 base indexing sequence (TATGTGGC) is bases 13 to 20 of read 1 followed by 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_ph35

text: Danio rerio

text: mixed


text: Danio rerio

text: mixed

text: SC

text: public

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from a single morphologically normal embryo from ZMP phenotype 35 clutch 1. A 8 base indexing sequence (TTACTCGC) is bases 13 to 20 of read 1 followed by 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_ph35

text: Danio rerio

text: mixed


text: Danio rerio

text: mixed

text: SC

text: public

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from a single morphologically abnormal embryo from ZMP phenotype 35 clutch 1. A 8 base indexing sequence (TCGTTAGC) is bases 13 to 20 of read 1 followed by 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_ph35

text: Danio rerio

text: mixed


text: Danio rerio

text: mixed

text: SC

text: public

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from a single morphologically normal embryo from ZMP phenotype 35 clutch 1. A 8 base indexing sequence (TACCGAGC) is bases 13 to 20 of read 1 followed by 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_ph35

text: Danio rerio

text: mixed


text: Danio rerio

text: mixed

text: SC

text: public

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from a single morphologically abnormal embryo from ZMP phenotype 35 clutch 1. A 8 base indexing sequence (TGTTCTCC) is bases 13 to 20 of read 1 followed by 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_ph35

text: Danio rerio

text: mixed


text: Danio rerio

text: mixed

text: SC

text: public

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from a single morphologically normal embryo from ZMP phenotype 35 clutch 1. A 8 base indexing sequence (TTCGCACC) is bases 13 to 20 of read 1 followed by 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_ph35

text: Danio rerio

text: mixed


text: Danio rerio

text: mixed

text: SC

text: public

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from a single morphologically abnormal embryo from ZMP phenotype 35 clutch 1. A 8 base indexing sequence (TTGCGTAC) is bases 13 to 20 of read 1 followed by 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_ph35

text: Danio rerio

text: mixed


text: Danio rerio

text: mixed

text: SC

text: public

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from a single morphologically normal embryo from ZMP phenotype 35 clutch 1. A 8 base indexing sequence (TCTACGAC) is bases 13 to 20 of read 1 followed by 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_ph35

text: Danio rerio

text: mixed


text: Danio rerio

text: mixed

text: SC

text: public

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from a single morphologically abnormal embryo from ZMP phenotype 35 clutch 1. A 8 base indexing sequence (TGACAGAC) is bases 13 to 20 of read 1 followed by 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_ph35

text: Danio rerio

text: mixed


text: Danio rerio

text: mixed

text: SC

text: public

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from a single morphologically normal embryo from ZMP phenotype 35 clutch 1. A 8 base indexing sequence (TAGAACAC) is bases 13 to 20 of read 1 followed by 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_ph35

text: Danio rerio

text: mixed


text: Danio rerio

text: mixed

text: SC

text: public

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from a single morphologically abnormal embryo from ZMP phenotype 35 clutch 1. A 8 base indexing sequence (TCATCCTA) is bases 13 to 20 of read 1 followed by 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_ph35

text: Danio rerio

text: mixed


text: Danio rerio

text: mixed

text: SC

text: public

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from a single morphologically normal embryo from ZMP phenotype 35 clutch 1. A 8 base indexing sequence (TGCTGATA) is bases 13 to 20 of read 1 followed by 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_ph35

text: Danio rerio

text: mixed


text: Danio rerio

text: mixed

text: SC

text: public

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from a single morphologically normal embryo from ZMP phenotype 35 clutch 1. A 8 base indexing sequence (TAGACGGA) is bases 13 to 20 of read 1 followed by 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_ph35

text: Danio rerio

text: mixed


text: Danio rerio

text: mixed

text: SC

text: public

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from a single morphologically abnormal embryo from ZMP phenotype 35 clutch 1. A 8 base indexing sequence (TGTGAAGA) is bases 13 to 20 of read 1 followed by 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_ph35

text: Danio rerio

text: mixed


text: Danio rerio

text: mixed

text: SC

text: public

text: ZMP_phenotype_35_1_sibling_10-sc-1818644

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from a single morphologically normal embryo from ZMP phenotype 35 clutch 1. A 8 base indexing sequence (TCTCTTCA) is bases 13 to 20 of read 1 followed by 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_ph35

text: Danio rerio

text: mixed


text: Danio rerio

text: mixed

text: SC

text: public

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from a single morphologically abnormal embryo from ZMP phenotype 35 clutch 1. A 8 base indexing sequence (TTGTTCCA) is bases 13 to 20 of read 1 followed by 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_ph35

text: Danio rerio

text: mixed


text: Danio rerio

text: mixed

text: SC

text: public

text: ZMP_phenotype_35_1_sibling_11-sc-1818646

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from a single morphologically normal embryo from ZMP phenotype 35 clutch 1. A 8 base indexing sequence (TGAAGCCA) is bases 13 to 20 of read 1 followed by 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_ph35

text: Danio rerio

text: mixed


text: Danio rerio

text: mixed

text: SC

text: public

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from a single morphologically abnormal embryo from ZMP phenotype 35 clutch 1. A 8 base indexing sequence (TACCACCA) is bases 13 to 20 of read 1 followed by 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_ph35

text: Danio rerio

text: mixed


text: Danio rerio

text: mixed

text: SC

text: public

text: ZMP_phenotype_35_1_sibling_12-sc-1818648

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from a single morphologically normal embryo from ZMP phenotype 35 clutch 1. A 8 base indexing sequence (TGCGTGAA) is bases 13 to 20 of read 1 followed by 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_ph35

text: Danio rerio

text: mixed


text: public

tag: Namespace:Bioinformatics Program, Boston University, Boston, MA, United States of America

text: 46 year

characteristic: age

text: ArrayExpress

characteristic: broker name

text: human

text: Protocols: Frozen brain tissue from prefrontal cortex Brodmann Area 9 (BA9) was obtained and stored in -80 degree refrigerator Total RNA for all samples was isolated using QIAzol Lysis Reagent and purified using miRNeasy MinElute Cleanup columns (Qiagen Sciences Inc, Germantown, MD) For each brain sample, 1 ug of RNA was used to construct sequencing libraries using Illumina's TruSeq Small RNA Sample Prep Kit, according to the manufacturer's protocol (Illumina, San Diego, CA).

characteristic: description

text: normal

characteristic: disease

characteristic: individual

text: Homo sapiens

text: Homo sapiens

text: Prefrontal Cortex, Brodmann Area 9

characteristic: organism part

text: Homo sapiens

text: male

characteristic: sex

text: frozen specimen

characteristic: specimen with known storage state

characteristic: title


characteristic: ENA-CHECKLIST

text: Bioinformatics Program, Boston University, Boston, MA, United States of America

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: SRA accession

characteristic: Submitter Id

text: 43 year

text: ArrayExpress

text: human

characteristic: common name

text: Huntington's disease

text: Homo sapiens

text: Homo sapiens

text: Prefrontal Cortex, Brodmann Area 9

text: Homo sapiens

text: male

text: frozen specimen


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: public

characteristic: INSDC status

text: 55 year

text: ArrayExpress

text: human

text: Huntington's disease

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: Prefrontal Cortex, Brodmann Area 9

text: Homo sapiens

text: male

text: frozen specimen


text: public

text: 72 year

characteristic: age

text: ArrayExpress

characteristic: broker name

text: human

characteristic: description

text: Huntington's disease

characteristic: disease

characteristic: individual

text: Homo sapiens

text: Homo sapiens

text: Prefrontal Cortex, Brodmann Area 9

text: Homo sapiens

text: male

text: frozen specimen


characteristic: ENA-CHECKLIST

text: public

text: 68 year

text: ArrayExpress

text: human

text: Huntington's disease

text: Homo sapiens

text: Homo sapiens

text: Prefrontal Cortex, Brodmann Area 9

characteristic: organism part

text: Homo sapiens

text: male

characteristic: sex

text: frozen specimen

characteristic: specimen with known storage state

characteristic: title


characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: SRA accession

characteristic: Submitter Id

text: 40 year

text: ArrayExpress

text: human

text: Huntington's disease

text: Homo sapiens

text: Homo sapiens

text: Prefrontal Cortex, Brodmann Area 9

text: Homo sapiens

text: male

text: frozen specimen


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: public

characteristic: INSDC status

text: 79 year

text: ArrayExpress

text: human

characteristic: common name

text: normal

text: Homo sapiens

text: Homo sapiens

text: Prefrontal Cortex, Brodmann Area 9

text: Homo sapiens

text: male

text: frozen specimen


text: public

text: 80 year

characteristic: age

text: ArrayExpress

characteristic: broker name

text: human

characteristic: description

text: normal

characteristic: disease

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: Prefrontal Cortex, Brodmann Area 9

text: Homo sapiens

text: male

text: frozen specimen


characteristic: ENA-CHECKLIST

text: public

text: 43 year

text: ArrayExpress

text: human

text: normal

characteristic: individual

text: Homo sapiens

text: Homo sapiens

text: Prefrontal Cortex, Brodmann Area 9

characteristic: organism part

text: Homo sapiens

text: male

characteristic: sex

text: frozen specimen

characteristic: specimen with known storage state


characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: SRA accession

text: 53 year

text: ArrayExpress

text: human

text: normal

text: Homo sapiens

text: Homo sapiens

text: Prefrontal Cortex, Brodmann Area 9

text: Homo sapiens

text: male

text: frozen specimen

characteristic: title


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: public

characteristic: INSDC status

characteristic: Submitter Id

text: 48 year

text: ArrayExpress

text: human

text: Huntington's disease

text: Homo sapiens

text: Homo sapiens

text: Prefrontal Cortex, Brodmann Area 9

text: Homo sapiens

text: male

text: frozen specimen


text: public

text: 44 year

characteristic: age

text: ArrayExpress

characteristic: broker name

text: human

characteristic: common name

characteristic: description

text: normal

characteristic: disease

text: Homo sapiens

text: Homo sapiens

text: Prefrontal Cortex, Brodmann Area 9

text: Homo sapiens

text: male

text: frozen specimen


characteristic: ENA-CHECKLIST

text: public

text: 71 year

text: ArrayExpress

text: human

text: Huntington's disease

characteristic: individual

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: Prefrontal Cortex, Brodmann Area 9

characteristic: organism part

text: Homo sapiens

text: male

characteristic: sex

text: frozen specimen


characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: SRA accession

text: 93 year

text: ArrayExpress

text: human

text: normal

text: Homo sapiens

text: Homo sapiens

text: Prefrontal Cortex, Brodmann Area 9

text: Homo sapiens

text: male

text: frozen specimen

characteristic: specimen with known storage state


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: public

characteristic: INSDC status

text: 57 year

text: ArrayExpress

text: human

text: Huntington's disease

text: Homo sapiens

text: Homo sapiens

text: Prefrontal Cortex, Brodmann Area 9

text: Homo sapiens

text: male

text: frozen specimen

characteristic: title


text: public

characteristic: Submitter Id

text: 57 year

characteristic: age

text: ArrayExpress

characteristic: broker name

text: human

characteristic: common name

characteristic: description

text: normal

text: Homo sapiens

text: Homo sapiens

text: Prefrontal Cortex, Brodmann Area 9

text: Homo sapiens

text: male

text: frozen specimen


characteristic: ENA-CHECKLIST

text: public

text: 40 year

text: ArrayExpress

text: human

text: normal

characteristic: disease

characteristic: individual

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: Prefrontal Cortex, Brodmann Area 9

characteristic: organism part

text: Homo sapiens

text: male

text: frozen specimen


characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: SRA accession

text: 69 year

text: ArrayExpress

text: human

text: Huntington's disease

text: Homo sapiens

text: Homo sapiens

text: Prefrontal Cortex, Brodmann Area 9

text: Homo sapiens

text: male

characteristic: sex

text: frozen specimen


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: public

characteristic: INSDC status

text: 76 year

text: ArrayExpress

text: human

text: normal

text: Homo sapiens

text: Homo sapiens

text: Prefrontal Cortex, Brodmann Area 9

text: Homo sapiens

text: male

text: frozen specimen

characteristic: specimen with known storage state


text: public

characteristic: Submitter Id

text: 59 year

characteristic: age

text: ArrayExpress

characteristic: broker name

text: human

characteristic: common name

text: Huntington's disease

text: Homo sapiens

text: Homo sapiens

text: Prefrontal Cortex, Brodmann Area 9

text: Homo sapiens

text: male

text: frozen specimen

characteristic: title


text: female

characteristic: ArrayExpress-Sex

text: Mus musculus

characteristic: ArrayExpress-Species

characteristic: ENA-CHECKLIST

text: SC

text: public

text: house mouse

text: Mus musculus

characteristic: organism

text: cDNA from PB Granulcoytes

characteristic: sample description

text: Mus musculus


text: male

text: Mus musculus

text: SC

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: SRA accession

text: house mouse

text: Mus musculus

text: cDNA from PB Granulcoytes

text: Mus musculus


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: MMRI

text: public

text: human

text: Homo sapiens

text: Homo sapiens


text: MMRI

text: public

characteristic: INSDC status

characteristic: Submitter Id

text: human

text: Homo sapiens

text: Homo sapiens

type: derived from


FB

text: MMRI

text: public

text: FB

text: human

text: Homo sapiens

text: Homo sapiens

text: FB


text: Danio rerio

text: SC

text: public

text: zebrafish

text: Danio rerio

text: genomic DNA

text: Danio rerio


text: Mus Musculus

text: SC

text: public

text: house mouse

text: Mus musculus

text: mESC

text: Mus musculus


text: ERASMUSMC

text: public

text: ArrayExpress

characteristic: broker name

characteristic: cell line

text: myeloblast

characteristic: cell type

characteristic: chromosome aberration

text: human

text: Protocols: Cell lines were cultured using media conditions as follows. MUTZ-3: 60% alpha-MEM (Life Technologies), 20% FBS (PAA), 20% conditioned medium of cell line 5637, and 10 ng/ml hrGM-CSF (Amgen); K562, MOLM-1, and U937: 90% RPMI and 10% FBS. All cultures contained 50 U/ml penicillin and 50 μg/ml streptomycin (Sigma). JQ1 sensitivity was measured by mitochondrial dehydrogenase (MTT assay) after 6, 24, 48, and 72 h of exposure with JQ1 (5, 50, 500, or 1,000 nM) or vehicle control (DMSO, 0.05%). The cell line MOLM1 was treated for 6 hours with 1,000 nM of JQ1. Subsequently, a BRD4 Chip-Seq was performed on these cells to determine the effect of JQ1 treatment of enhancers and super enhancers. Immunoprecipitated material was de-crosslinked and was amplified using a Whole Genome Amplification kit (WGA2/WGA3; Sigma-Aldrich, Zwijndrecht, The Netherlands). Subsequently, the fragments were sheared by a Covaris shearing device (Covaris S2) and size selected by an agrose gel. ChIP experiments were performed as previously described (Bindels et al., 2012; doi: http://dx.doi.org/10.1182/blood-2011-11-393827). Immunoprecipitation of cross-linked chromatin was performed with antibodies directed against Histone H3K4me1, H3K4me3, H3K27ac, p300, and BRD4, or an equal amount of isotype IgG as background control. Three independent experiments were performed and the amount of immunoprecipitated DNA was represented relative to cross-linked input DNA.

characteristic: description

text: wild type

characteristic: genotype

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens

text: male

characteristic: sex

text: frozen specimen

characteristic: specimen with known storage state


characteristic: ENA-CHECKLIST

text: ERASMUSMC

characteristic: INSDC center name

text: public

text: ArrayExpress

text: myeloblast

text: human

characteristic: common name

text: wild type

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: Homo sapiens

text: male

text: frozen specimen

characteristic: title


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: ERASMUSMC

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: SRA accession

text: ArrayExpress

text: myeloblast

text: human

text: wild type

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens

text: female

text: frozen specimen


characteristic: External Id

text: ERASMUSMC

text: public

characteristic: INSDC status

text: E-MTAB-2224:MOLM1_INPUT_H3K27AC_P300_H3K4ME3

characteristic: Submitter Id

text: ArrayExpress

characteristic: broker name

characteristic: cell line

text: myeloblast

text: human

text: wild type

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens

text: male

text: frozen specimen


text: ERASMUSMC

text: public

text: ArrayExpress

text: myeloblast

characteristic: cell type

characteristic: chromosomal aberration

text: human

text: Protocols: Cell lines were cultured using media conditions as follows. MUTZ-3: 60% alpha-MEM (Life Technologies), 20% FBS (PAA), 20% conditioned medium of cell line 5637, and 10 ng/ml hrGM-CSF (Amgen); F-36P, Kasumi-3, and UCSD-AML1: 80% RPMI 1640 (Life Technologies), 20% FBS, and 10 ng/ml GM-CSF; SB1690CB: 60% alpha-MEM, 20% FBS, 20% conditioned medium of cell line 5637; MOLM-1, and U937: 90% RPMI and 10% FBS. All cultures contained 50 U/ml penicillin and 50 μg/ml streptomycin (Sigma). Total sample RNA was extracted with phenol chloroform and reverse transcribed using Superscript II RT (Invitrogen). The cDNA was sheared with the Covaris device (Covaris S2) and further processed according to the TruSeq RNA Sample Preparation v2 Guide (Illumina).

characteristic: description

text: High

characteristic: evi1 overexpression

text: wild type

characteristic: genotype

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens

text: male

characteristic: sex

text: frozen specimen


characteristic: ENA-CHECKLIST

text: ERASMUSMC

characteristic: INSDC center name

text: public

text: ArrayExpress

text: myeloblast

text: -3, no apparent 3q abnormality

text: human

characteristic: common name

text: Medium

text: wild type

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: Homo sapiens

text: male

text: frozen specimen

characteristic: specimen with known storage state

characteristic: title


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: ERASMUSMC

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: SRA accession

text: ArrayExpress

text: myeloblast

text: no apparent 3q abnormality

text: human

text: Low to none

text: wild type

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens

text: male

text: frozen specimen


text: ERASMUSMC

text: public

characteristic: INSDC status

characteristic: Submitter Id

text: ArrayExpress

characteristic: broker name

characteristic: cell line

text: myeloblast

characteristic: cell type

characteristic: chromosomal aberration

text: human

text: High

text: wild type

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens

text: female

text: frozen specimen


E-MTAB-2226:pool of nine mice

characteristic: ENA-CHECKLIST

characteristic: INSDC center name

text: public

text: E-MTAB-2226:pool of nine mice

text: 8 week

characteristic: age

text: ArrayExpress

text: Immunized with NP-CGG (chicken gamma globulin (CGG) conjugated to 4-hydroxy-3-nitrophenylacetyl)

characteristic: clinical information

text: house mouse

text: Protocols: All animal experiments were performed under the guidelines and protocols approved by the Basel-Stadt cantonal veterinary office (Basel-Stadt Kantonales Veterin_ramt Tierversuchsbewilligung #2582). Female BALB/c mice (n=9, Charles Rivers Laboratories) 6 to 8 weeks old were housed under specific pathogen-free conditions and were maintained on a normal chow diet. Nine BALB/c mice (8-10 weeks old, Charles River, specific-pathogen free) were immunized with 50 ug alum-precipitated chicken gamma globulin (CGG) conjugated to 4-hydroxy-3-nitrophenylacetyl (NP, NP-CGG, BioCat). Mice were sacrificed 14 days post-immunization (dpi) and their spleens and bone marrow (from femurs and tibia) were harvested. Antibody-secreting CD138-positive cells were enriched from spleen and bone marrow 14 dpi as previously described (Reddy et al., 2007, Nat Biotech) Total RNA extraction from the pooled ASC population was performed using the TRIzol Plus RNA Purification Kit (Life Technologies), according to the manufacturer's protocol and concentration was determined on a Nanodrop 2000c Spectrophotometer. Enriched total RNA was homogeneously mixed, aliquoted and stored at -80 degrees C Direct Addition method: The Illumina TruSeq Universal Adapter constituted the 5' portion of the forward primers, while the IgG-reverse primer contained the Illumina index primer (Index 4 [Replicate DA1] and 5[Replicate DA2]), thereby directly adding Illumina adapter sequences to PCR products (Fig. 1). 10 PCR reactions were run in parallel with the standard PCR conditions mentioned above, which is equivalent to 500 ng total RNA. Thusly prepared libraries were concentrated and purified as stated above.

characteristic: description

text: Mus musculus

text: Mus musculus

text: spleen, bone marrow

characteristic: organism part

text: Mus musculus

text: fresh specimen

text: BALB/c

characteristic: strain

text: pool of nine mice


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: GSC

text: public

text: thale cress

characteristic: common name

text: A description of each epiRIL can be found in Colome-Tatche et al, PNAS 2012.

text: Arabidopsis thaliana

characteristic: organism

text: Arabidopsis thaliana

text: epiRiL_202 ; Bisulfite sequencing

characteristic: title


text: MMRI

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: human

text: Homo sapiens

text: Homo sapiens


characteristic: ENA-CHECKLIST

characteristic: INSDC center name

text: public

tag: Namespace:MRC Clinical Sciences Centre, Imperial College London, Du Cane Road, London W12 0NN, UK

text: ArrayExpress

characteristic: broker name

text: fission yeast

text: Protocols: S. pombe cells were grown in EMM medium supplemented with 20 ug/ml Thiamine at 30C for 10 hours (final OD600: 0.5-0.6). Cells were harvested and fixed for 20 minutes with 1% formaldehyde (Larochelle et al. NAR 2012, 40:10240) Whole cell extract from fixed cells was prepared as described in (Larochelle et al. NAR 2012, 40:10240) ChIP experiments were performed as described in (Larochelle et al. NAR 2012, 40:10240). For ChIP-seq experiments, chromatin immunoprecipitation was done as described above with the following modifications. We scaled up the reactions to obtain larger amount of chromatin for library preparation. Chromatin was immunoprecipitated with Pan mouse IgG Dynabeads (Invitrogen) coated with antibody against the HA tag (12CA5, Roche). Libraries were prepared using the NEBNext ChIP-Seq Library Prep Master Mix Set for Illumina kit (New England BioLabs) according to the manufacturer instructions.

text: h- rpb3-3HA::KanMX6

characteristic: genotype

text: Schizosaccharomyces pombe

text: Schizosaccharomyces pombe

text: Schizosaccharomyces pombe

characteristic: sex


text: MRC Clinical Sciences Centre, Imperial College London, Du Cane Road, London W12 0NN, UK

text: public

text: ArrayExpress

text: fission yeast

text: Protocols: S. pombe cells were grown in EMM medium supplemented with 20 ug/ml Thiamine at 30C for 10 hours (final OD600: 0.5-0.6). Total RNA was isolated from S. pombe cells using a hot phenol method followed by phenol-chloroform extractions, and precipitation as described (Lyne et al., 2003, BMC Genomics 4, 27.). 10ug total RNA was used as starting material for strand-specific RNA-seq library preparation using an unreleased early version provided by Illumina of the Illumina TruSeq Small RNA Sample Prep Kit. Briefly: poly(A)+ RNA was enriched by two rounds of poly(dT) Sera-Mag magnetic beads purification. Enriched poly(A)+ RNA was then fragmented to an average size of ~200nt. Fragmented RNA was 3' de-phosphorylated with Antartic phosphatase and 5' phosphorylated with polynucleotide kinase this treatment prepares RNA fragments for subsequent ligation of Illumina RNA adaptors to their 5' and 3' ends using a 3' RNA ligase and a T4 RNA ligase, respectively. First strand cDNA was produced using a primer specific for the Illumina 3' adaptor. The library was finally amplified with 15 cycles of PCR using primers specific for the Illumina adaptors and purified using SPRI-beads (Agencourt, Beckman Coulter). Libraries size distributions and concentrations were determined on an Agilent Bioanalyzer

characteristic: description

text: h? ade6? leu1-32 ura4-D18 his3-D1 p81nmt1::kanMX6-dis3

text: Schizosaccharomyces pombe

text: Schizosaccharomyces pombe

text: Schizosaccharomyces pombe

characteristic: strain


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: public

text: ArrayExpress

text: fission yeast

text: h? ade6-M21? leu1-32 ura4-D18 his3-D1 p81nmt1::kanMX6-rrp41

text: Schizosaccharomyces pombe

text: Schizosaccharomyces pombe

text: Schizosaccharomyces pombe