{"database": "metadata", "table": "run_metadata", "is_view": false, "human_description_en": "where devstage_curation = \"Hatching\" and experiment.platform = \"BGISEQ\"", "rows": [[57271, "SRR12577970", "SRX9064853", "SRS7314026", "SRP279881", "PRJNA612371", "Danio rerio strain:TU Raw sequence reads", "PRJNA612371", "Whole Genome Sequencing", "Hemorrhage stroke is a severe vascular disease of the brain with a high mortality rate in humans. Sodium tanshinone IIA sulfonate STS is a water soluble derivative of tanshinone IIA  which is the main active ingredient of Salvia miltiorrhiza Bge known as Danshen in Chinese and has been approved as a commercial drug for treating cardiovascular disease by the China Food and Drug Administration. In our previous study  we established a HMG COA inhibitor atorvastatin Ator induced zebrafish model of cerebral hemorrhage and found that STS dramatically decreased both the hemorrhage rate and hemorrhage area  although the underlying mechanism was not fully elucidated. Therefore  in the present study  we conducted transcriptome analysis of the protective effect of STS against Ator induced cerebral hemorrhage in zebrafish using RNA Seq technology  and further clarify its underlying molecular mechanisms on HIF 1 and its regulators  i.e.  the PI3K/Akt and MAPK signaling pathways were verified by real time PCR analysis and specific pharmacological inhibitors. We are also able to show that hemoglobin  carbonic anhydrase  Na+/H+ exchanger and HIF 1 genes might be potential biomarkers of Ator induced cerebral hemorrhage in zebrafish  as well as pharmacological targets of STS. This study also provided evidence of bio markers involved in hemorrhage stroke and improved understanding of the effects of HMG COA inhibition on vascular permeability and cerebral hemorrhage.", null, null, null, null, "Ctrl 3 zebrafish", null, "strain:TU|isolate:not collected|breed:not collected|cultivar:not collected|ecotype:not collected|age:2dpf|dev stage:not collected|sex:not applicable|tissue:head|geo loc name:China:Shanghai|sample type:model organism|replicate:replicate=biological replicate 6'|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Ctrl 3 zebrafish", "Ctrl 3 zebrafish", "Ctrl 3 zebrafish", "transcriptome", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "SINGLE", "BGISEQ", "BGISEQ-500", null, "SRP279881", null, null, "Ctrl_3_1.fq.gz", "fastq", 1061227250.0, 21224545.0, "Ctrl 3 1.fq.gz", "0:50", "A:286099732;C:241244619;G:246876865;T:287006034;N:0", 50, null, null, null, 286099732, 241244619, 246876865, 287006034, 0, "SRX9064853", "SRS7314026", "SRA1120721", "Shanghai University of Traditional Chinese Medicine|Longhua Hospital", "Shanghai University of Traditional Chinese Medicine", 1, 0.94563, null, 0.10453, null, 0.70552, null, 0.46655, null, 50, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "China", "2020-09-03", "Hatching", "Embryo", "Head", "Nervous System"], [57272, "SRR12577971", "SRX9064852", "SRS7314025", "SRP279881", "PRJNA612371", "Danio rerio strain:TU Raw sequence reads", "PRJNA612371", "Whole Genome Sequencing", "Hemorrhage stroke is a severe vascular disease of the brain with a high mortality rate in humans. Sodium tanshinone IIA sulfonate STS is a water soluble derivative of tanshinone IIA  which is the main active ingredient of Salvia miltiorrhiza Bge known as Danshen in Chinese and has been approved as a commercial drug for treating cardiovascular disease by the China Food and Drug Administration. In our previous study  we established a HMG COA inhibitor atorvastatin Ator induced zebrafish model of cerebral hemorrhage and found that STS dramatically decreased both the hemorrhage rate and hemorrhage area  although the underlying mechanism was not fully elucidated. Therefore  in the present study  we conducted transcriptome analysis of the protective effect of STS against Ator induced cerebral hemorrhage in zebrafish using RNA Seq technology  and further clarify its underlying molecular mechanisms on HIF 1 and its regulators  i.e.  the PI3K/Akt and MAPK signaling pathways were verified by real time PCR analysis and specific pharmacological inhibitors. We are also able to show that hemoglobin  carbonic anhydrase  Na+/H+ exchanger and HIF 1 genes might be potential biomarkers of Ator induced cerebral hemorrhage in zebrafish  as well as pharmacological targets of STS. This study also provided evidence of bio markers involved in hemorrhage stroke and improved understanding of the effects of HMG COA inhibition on vascular permeability and cerebral hemorrhage.", null, null, null, null, "Ctrl 2 zebrafish", null, "strain:TU|isolate:not collected|breed:not collected|cultivar:not collected|ecotype:not collected|age:2dpf|dev stage:not collected|sex:not applicable|tissue:head|geo loc name:China:Shanghai|sample type:model organism|replicate:replicate=biological replicate 5 prime|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Ctrl 2 zebrafish", "Ctrl 2 zebrafish", "Ctrl 2 zebrafish", "transcriptome", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "SINGLE", "BGISEQ", "BGISEQ-500", null, "SRP279881", null, null, "Ctrl_2_1.fq.gz", "fastq", 1058116700.0, 21162334.0, "Ctrl 2 1.fq.gz", "0:50", "A:287223905;C:238707750;G:244987559;T:287197486;N:0", 50, null, null, null, 287223905, 238707750, 244987559, 287197486, 0, "SRX9064852", "SRS7314025", "SRA1120721", "Shanghai University of Traditional Chinese Medicine|Longhua Hospital", "Shanghai University of Traditional Chinese Medicine", 1, 0.94534, null, 0.11174, null, 0.70104, null, 0.47946, null, 50, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "China", "2020-09-03", "Hatching", "Embryo", "Head", "Nervous System"], [57273, "SRR12577972", "SRX9064851", "SRS7314024", "SRP279881", "PRJNA612371", "Danio rerio strain:TU Raw sequence reads", "PRJNA612371", "Whole Genome Sequencing", "Hemorrhage stroke is a severe vascular disease of the brain with a high mortality rate in humans. Sodium tanshinone IIA sulfonate STS is a water soluble derivative of tanshinone IIA  which is the main active ingredient of Salvia miltiorrhiza Bge known as Danshen in Chinese and has been approved as a commercial drug for treating cardiovascular disease by the China Food and Drug Administration. In our previous study  we established a HMG COA inhibitor atorvastatin Ator induced zebrafish model of cerebral hemorrhage and found that STS dramatically decreased both the hemorrhage rate and hemorrhage area  although the underlying mechanism was not fully elucidated. Therefore  in the present study  we conducted transcriptome analysis of the protective effect of STS against Ator induced cerebral hemorrhage in zebrafish using RNA Seq technology  and further clarify its underlying molecular mechanisms on HIF 1 and its regulators  i.e.  the PI3K/Akt and MAPK signaling pathways were verified by real time PCR analysis and specific pharmacological inhibitors. We are also able to show that hemoglobin  carbonic anhydrase  Na+/H+ exchanger and HIF 1 genes might be potential biomarkers of Ator induced cerebral hemorrhage in zebrafish  as well as pharmacological targets of STS. This study also provided evidence of bio markers involved in hemorrhage stroke and improved understanding of the effects of HMG COA inhibition on vascular permeability and cerebral hemorrhage.", null, null, null, null, "Ctrl 1 zebrafish", null, "strain:TU|isolate:not collected|breed:not collected|cultivar:not collected|ecotype:not collected|age:2dpf|dev stage:not collected|sex:not applicable|tissue:head|geo loc name:China:Shanghai|sample type:model organism|replicate:replicate=biological replicate 4'|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Ctrl 1 zebrafish", "Ctrl 1 zebrafish", "Ctrl 1 zebrafish", "transcriptome", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "SINGLE", "BGISEQ", "BGISEQ-500", null, "SRP279881", null, null, "Ctrl_1_1.fq.gz", "fastq", 1065919600.0, 21318392.0, "Ctrl 1 1.fq.gz", "0:50", "A:295920720;C:242146677;G:242962633;T:284889570;N:0", 50, null, null, null, 295920720, 242146677, 242962633, 284889570, 0, "SRX9064851", "SRS7314024", "SRA1120721", "Shanghai University of Traditional Chinese Medicine|Longhua Hospital", "Shanghai University of Traditional Chinese Medicine", 1, 0.94228, null, 0.15007, null, 0.68028, null, 0.46845, null, 50, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "China", "2020-09-03", "Hatching", "Embryo", "Head", "Nervous System"], [57274, "SRR12577973", "SRX9064850", "SRS7314023", "SRP279881", "PRJNA612371", "Danio rerio strain:TU Raw sequence reads", "PRJNA612371", "Whole Genome Sequencing", "Hemorrhage stroke is a severe vascular disease of the brain with a high mortality rate in humans. Sodium tanshinone IIA sulfonate STS is a water soluble derivative of tanshinone IIA  which is the main active ingredient of Salvia miltiorrhiza Bge known as Danshen in Chinese and has been approved as a commercial drug for treating cardiovascular disease by the China Food and Drug Administration. In our previous study  we established a HMG COA inhibitor atorvastatin Ator induced zebrafish model of cerebral hemorrhage and found that STS dramatically decreased both the hemorrhage rate and hemorrhage area  although the underlying mechanism was not fully elucidated. Therefore  in the present study  we conducted transcriptome analysis of the protective effect of STS against Ator induced cerebral hemorrhage in zebrafish using RNA Seq technology  and further clarify its underlying molecular mechanisms on HIF 1 and its regulators  i.e.  the PI3K/Akt and MAPK signaling pathways were verified by real time PCR analysis and specific pharmacological inhibitors. We are also able to show that hemoglobin  carbonic anhydrase  Na+/H+ exchanger and HIF 1 genes might be potential biomarkers of Ator induced cerebral hemorrhage in zebrafish  as well as pharmacological targets of STS. This study also provided evidence of bio markers involved in hemorrhage stroke and improved understanding of the effects of HMG COA inhibition on vascular permeability and cerebral hemorrhage.", null, null, null, null, "Ator STS 3 zebrafish", null, "strain:TU|isolate:not collected|breed:not collected|cultivar:not collected|ecotype:not collected|age:2dpf|dev stage:not collected|sex:not applicable|tissue:head|geo loc name:China:Shanghai|sample type:model organism|replicate:replicate=biological replicate 3 prime|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Ator STS 3 zebrafish", "Ator STS 3 zebrafish", "Ator STS 3 zebrafish", "transcriptome", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "SINGLE", "BGISEQ", "BGISEQ-500", null, "SRP279881", null, null, "Ator_STS_3_1.fq.gz", "fastq", 1059717350.0, 21194347.0, "Ator STS 3 1.fq.gz", "0:50", "A:287279590;C:239708340;G:245740313;T:286989107;N:0", 50, null, null, null, 287279590, 239708340, 245740313, 286989107, 0, "SRX9064850", "SRS7314023", "SRA1120721", "Shanghai University of Traditional Chinese Medicine|Longhua Hospital", "Shanghai University of Traditional Chinese Medicine", 1, 0.94345, null, 0.10458, null, 0.69686, null, 0.4755, null, 50, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "China", "2020-09-03", "Hatching", "Embryo", "Head", "Nervous System"], [57275, "SRR12577974", "SRX9064849", "SRS7314022", "SRP279881", "PRJNA612371", "Danio rerio strain:TU Raw sequence reads", "PRJNA612371", "Whole Genome Sequencing", "Hemorrhage stroke is a severe vascular disease of the brain with a high mortality rate in humans. Sodium tanshinone IIA sulfonate STS is a water soluble derivative of tanshinone IIA  which is the main active ingredient of Salvia miltiorrhiza Bge known as Danshen in Chinese and has been approved as a commercial drug for treating cardiovascular disease by the China Food and Drug Administration. In our previous study  we established a HMG COA inhibitor atorvastatin Ator induced zebrafish model of cerebral hemorrhage and found that STS dramatically decreased both the hemorrhage rate and hemorrhage area  although the underlying mechanism was not fully elucidated. Therefore  in the present study  we conducted transcriptome analysis of the protective effect of STS against Ator induced cerebral hemorrhage in zebrafish using RNA Seq technology  and further clarify its underlying molecular mechanisms on HIF 1 and its regulators  i.e.  the PI3K/Akt and MAPK signaling pathways were verified by real time PCR analysis and specific pharmacological inhibitors. We are also able to show that hemoglobin  carbonic anhydrase  Na+/H+ exchanger and HIF 1 genes might be potential biomarkers of Ator induced cerebral hemorrhage in zebrafish  as well as pharmacological targets of STS. This study also provided evidence of bio markers involved in hemorrhage stroke and improved understanding of the effects of HMG COA inhibition on vascular permeability and cerebral hemorrhage.", null, null, null, null, "Ator STS 2 zebrafish", null, "strain:TU|isolate:not collected|breed:not collected|cultivar:not collected|ecotype:not collected|age:2dpf|dev stage:not collected|sex:not applicable|tissue:head|geo loc name:China:Shanghai|sample type:model organism|replicate:replicate=biological replicate 2'|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Ator STS 2 zebrafish", "Ator STS 2 zebrafish", "Ator STS 2 zebrafish", "transcriptome", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "SINGLE", "BGISEQ", "BGISEQ-500", null, "SRP279881", null, null, "Ator_STS_2_1.fq.gz", "fastq", 1057950250.0, 21159005.0, "Ator STS 2 1.fq.gz", "0:50", "A:286256354;C:238832868;G:244078781;T:288782247;N:0", 50, null, null, null, 286256354, 238832868, 244078781, 288782247, 0, "SRX9064849", "SRS7314022", "SRA1120721", "Shanghai University of Traditional Chinese Medicine|Longhua Hospital", "Shanghai University of Traditional Chinese Medicine", 1, 0.94307, null, 0.10974, null, 0.69631, null, 0.4703, null, 50, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "China", "2020-09-03", "Hatching", "Embryo", "Head", "Nervous System"], [57276, "SRR12577975", "SRX9064848", "SRS7314021", "SRP279881", "PRJNA612371", "Danio rerio strain:TU Raw sequence reads", "PRJNA612371", "Whole Genome Sequencing", "Hemorrhage stroke is a severe vascular disease of the brain with a high mortality rate in humans. Sodium tanshinone IIA sulfonate STS is a water soluble derivative of tanshinone IIA  which is the main active ingredient of Salvia miltiorrhiza Bge known as Danshen in Chinese and has been approved as a commercial drug for treating cardiovascular disease by the China Food and Drug Administration. In our previous study  we established a HMG COA inhibitor atorvastatin Ator induced zebrafish model of cerebral hemorrhage and found that STS dramatically decreased both the hemorrhage rate and hemorrhage area  although the underlying mechanism was not fully elucidated. Therefore  in the present study  we conducted transcriptome analysis of the protective effect of STS against Ator induced cerebral hemorrhage in zebrafish using RNA Seq technology  and further clarify its underlying molecular mechanisms on HIF 1 and its regulators  i.e.  the PI3K/Akt and MAPK signaling pathways were verified by real time PCR analysis and specific pharmacological inhibitors. We are also able to show that hemoglobin  carbonic anhydrase  Na+/H+ exchanger and HIF 1 genes might be potential biomarkers of Ator induced cerebral hemorrhage in zebrafish  as well as pharmacological targets of STS. This study also provided evidence of bio markers involved in hemorrhage stroke and improved understanding of the effects of HMG COA inhibition on vascular permeability and cerebral hemorrhage.", null, null, null, null, "Ator STS 1 zebrafish", null, "strain:TU|isolate:not collected|breed:not collected|cultivar:not collected|ecotype:not collected|age:2dpf|dev stage:not collected|sex:not applicable|tissue:head|geo loc name:China:Shanghai|sample type:model organism|replicate:replicate=biological replicate 1'|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Ator STS 1 zebrafish", "Ator STS 1 zebrafish", "Ator STS 1 zebrafish", "transcriptome", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "SINGLE", "BGISEQ", "BGISEQ-500", null, "SRP279881", null, null, "Ator_STS_1_1.fq.gz", "fastq", 1070136700.0, 21402734.0, "Ator STS 1 1.fq.gz", "0:50", "A:297601042;C:243837062;G:243583907;T:285114689;N:0", 50, null, null, null, 297601042, 243837062, 243583907, 285114689, 0, "SRX9064848", "SRS7314021", "SRA1120721", "Shanghai University of Traditional Chinese Medicine|Longhua Hospital", "Shanghai University of Traditional Chinese Medicine", 1, 0.94665, null, 0.12219, null, 0.67953, null, 0.46393, null, 50, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "China", "2020-09-03", "Hatching", "Embryo", "Head", "Nervous System"], [57277, "SRR12577976", "SRX9064847", "SRS7314020", "SRP279881", "PRJNA612371", "Danio rerio strain:TU Raw sequence reads", "PRJNA612371", "Whole Genome Sequencing", "Hemorrhage stroke is a severe vascular disease of the brain with a high mortality rate in humans. Sodium tanshinone IIA sulfonate STS is a water soluble derivative of tanshinone IIA  which is the main active ingredient of Salvia miltiorrhiza Bge known as Danshen in Chinese and has been approved as a commercial drug for treating cardiovascular disease by the China Food and Drug Administration. In our previous study  we established a HMG COA inhibitor atorvastatin Ator induced zebrafish model of cerebral hemorrhage and found that STS dramatically decreased both the hemorrhage rate and hemorrhage area  although the underlying mechanism was not fully elucidated. Therefore  in the present study  we conducted transcriptome analysis of the protective effect of STS against Ator induced cerebral hemorrhage in zebrafish using RNA Seq technology  and further clarify its underlying molecular mechanisms on HIF 1 and its regulators  i.e.  the PI3K/Akt and MAPK signaling pathways were verified by real time PCR analysis and specific pharmacological inhibitors. We are also able to show that hemoglobin  carbonic anhydrase  Na+/H+ exchanger and HIF 1 genes might be potential biomarkers of Ator induced cerebral hemorrhage in zebrafish  as well as pharmacological targets of STS. This study also provided evidence of bio markers involved in hemorrhage stroke and improved understanding of the effects of HMG COA inhibition on vascular permeability and cerebral hemorrhage.", null, null, null, null, "Ator 3 zebrafish", null, "strain:TU|isolate:not collected|breed:not collected|cultivar:not collected|ecotype:not collected|age:2dpf|dev stage:not collected|sex:not applicable|tissue:head|geo loc name:China:Shanghai|sample type:model organism|replicate:replicate=biological replicate 3 prime|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Ator 3 zebrafish", "Ator 3 zebrafish", "Ator 3 zebrafish", "transcriptome", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "SINGLE", "BGISEQ", "BGISEQ-500", null, "SRP279881", null, null, "Ator_3_1.fq.gz", "fastq", 1058031900.0, 21160638.0, "Ator 3 1.fq.gz", "0:50", "A:285399527;C:239993172;G:245571467;T:287067734;N:0", 50, null, null, null, 285399527, 239993172, 245571467, 287067734, 0, "SRX9064847", "SRS7314020", "SRA1120721", "Shanghai University of Traditional Chinese Medicine|Longhua Hospital", "Shanghai University of Traditional Chinese Medicine", 1, 0.94536, null, 0.11052, null, 0.6957, null, 0.48195, null, 50, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "China", "2020-09-03", "Hatching", "Embryo", "Head", "Nervous System"], [57278, "SRR12577977", "SRX9064846", "SRS7314019", "SRP279881", "PRJNA612371", "Danio rerio strain:TU Raw sequence reads", "PRJNA612371", "Whole Genome Sequencing", "Hemorrhage stroke is a severe vascular disease of the brain with a high mortality rate in humans. Sodium tanshinone IIA sulfonate STS is a water soluble derivative of tanshinone IIA  which is the main active ingredient of Salvia miltiorrhiza Bge known as Danshen in Chinese and has been approved as a commercial drug for treating cardiovascular disease by the China Food and Drug Administration. In our previous study  we established a HMG COA inhibitor atorvastatin Ator induced zebrafish model of cerebral hemorrhage and found that STS dramatically decreased both the hemorrhage rate and hemorrhage area  although the underlying mechanism was not fully elucidated. Therefore  in the present study  we conducted transcriptome analysis of the protective effect of STS against Ator induced cerebral hemorrhage in zebrafish using RNA Seq technology  and further clarify its underlying molecular mechanisms on HIF 1 and its regulators  i.e.  the PI3K/Akt and MAPK signaling pathways were verified by real time PCR analysis and specific pharmacological inhibitors. We are also able to show that hemoglobin  carbonic anhydrase  Na+/H+ exchanger and HIF 1 genes might be potential biomarkers of Ator induced cerebral hemorrhage in zebrafish  as well as pharmacological targets of STS. This study also provided evidence of bio markers involved in hemorrhage stroke and improved understanding of the effects of HMG COA inhibition on vascular permeability and cerebral hemorrhage.", null, null, null, null, "Ator 2 zebrafish", null, "strain:TU|isolate:not collected|breed:not collected|cultivar:not collected|ecotype:not collected|age:2dpf|dev stage:not collected|sex:not applicable|tissue:head|geo loc name:China:Shanghai|sample type:model organism|replicate:replicate=biological replicate 2'|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Ator 2 zebrafish", "Ator 2 zebrafish", "Ator 2 zebrafish", "transcriptome", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "SINGLE", "BGISEQ", "BGISEQ-500", null, "SRP279881", null, null, "Ator_2_1.fq.gz", "fastq", 1059618400.0, 21192368.0, "Ator 2 1.fq.gz", "0:50", "A:283429136;C:243023053;G:248904818;T:284261393;N:0", 50, null, null, null, 283429136, 243023053, 248904818, 284261393, 0, "SRX9064846", "SRS7314019", "SRA1120721", "Shanghai University of Traditional Chinese Medicine|Longhua Hospital", "Shanghai University of Traditional Chinese Medicine", 1, 0.94743, null, 0.09493, null, 0.70218, null, 0.475, null, 50, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "China", "2020-09-03", "Hatching", "Embryo", "Head", "Nervous System"], [57279, "SRR12577978", "SRX9064845", "SRS7314018", "SRP279881", "PRJNA612371", "Danio rerio strain:TU Raw sequence reads", "PRJNA612371", "Whole Genome Sequencing", "Hemorrhage stroke is a severe vascular disease of the brain with a high mortality rate in humans. Sodium tanshinone IIA sulfonate STS is a water soluble derivative of tanshinone IIA  which is the main active ingredient of Salvia miltiorrhiza Bge known as Danshen in Chinese and has been approved as a commercial drug for treating cardiovascular disease by the China Food and Drug Administration. In our previous study  we established a HMG COA inhibitor atorvastatin Ator induced zebrafish model of cerebral hemorrhage and found that STS dramatically decreased both the hemorrhage rate and hemorrhage area  although the underlying mechanism was not fully elucidated. Therefore  in the present study  we conducted transcriptome analysis of the protective effect of STS against Ator induced cerebral hemorrhage in zebrafish using RNA Seq technology  and further clarify its underlying molecular mechanisms on HIF 1 and its regulators  i.e.  the PI3K/Akt and MAPK signaling pathways were verified by real time PCR analysis and specific pharmacological inhibitors. We are also able to show that hemoglobin  carbonic anhydrase  Na+/H+ exchanger and HIF 1 genes might be potential biomarkers of Ator induced cerebral hemorrhage in zebrafish  as well as pharmacological targets of STS. This study also provided evidence of bio markers involved in hemorrhage stroke and improved understanding of the effects of HMG COA inhibition on vascular permeability and cerebral hemorrhage.", null, null, null, null, "Ator 1 zebrafish", null, "strain:TU|isolate:not collected|breed:not collected|cultivar:not collected|ecotype:not collected|age:2dpf|dev stage:not collected|sex:not applicable|tissue:head|geo loc name:China:Shanghai|sample type:model organism|replicate:replicate=biological replicate 1'|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Ator 1 zebrafish", "Ator 1 zebrafish", "Ator 1 zebrafish", "transcriptome", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "SINGLE", "BGISEQ", "BGISEQ-500", null, "SRP279881", null, null, "Ator_1_1.fq.gz", "fastq", 1075695950.0, 21513919.0, "Ator 1 1.fq.gz", "0:50", "A:297768036;C:244470267;G:243768925;T:289688722;N:0", 50, null, null, null, 297768036, 244470267, 243768925, 289688722, 0, "SRX9064845", "SRS7314018", "SRA1120721", "Shanghai University of Traditional Chinese Medicine|Longhua Hospital", "Shanghai University of Traditional Chinese Medicine", 1, 0.94468, null, 0.13183, null, 0.68363, null, 0.46288, null, 50, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "China", "2020-09-03", "Hatching", "Embryo", "Head", "Nervous System"], [59480, "SRR11922874", "SRX8468588", "SRS6769276", "SRP265910", "PRJNA637219", "Next Generation Sequencing Facilitates Quantitative Analysis of Wildtype and aldh3a1 /  Zebrafish Embryo Transcriptomes", "GSE151770", "Transcriptome Analysis", "Our previous experiments showed the function of Aldh3a1 was related to pancreas and insulin secretion and knockout of Aldh3a1 led to destoryed pancreas. To understand how the impaired pancreas reflects at the transcriptome level  we performed full genome RNA Seq between aldh3a1+/+ and aldh3a1 /  larvae at 48 hpf.An overview of RNA Seq  including quality control  principal component analysis PCA  volcano plots of regulated genes and Top 20 KEGG pathway analysis showed comparable properties between aldh3a1 mutants and wild type. We found the insulin signalling pathway was reduced significantly via gene set enrichment analysis normalized enrichment score   1.72; p=0.0006. Interestingly  endocrine pancreas but not exocrine pancreas development pathway was significantly down regulated in aldh3a1 mutants . Taken together  these results further suggest Aldh3a1 as an important regulator in the development  morphology and insulin secretion function of primary pancreas. Furthermore  we offers a comprehensive and more accurate quantitative and qualitative evaluation of mRNA content within zebrafish larvae. We conclude that RNA seq based transcriptome characterization would expedite genetic network analyses and permit the dissection of complex biologic functions. Overall design: mRNA expression profiles of wildtype and aldh3a1 /  zebrafish embryo at 48 hpf", null, "pubmed:32980661", null, "zebrafish embryo Aldh3a1 KO rep6", "GSM4590772", null, "source name:zebrafish embryo|genotype:aldh3a1 KO|tissue:embryo|age:48 hpf", "zebrafish embryo Aldh3a1 KO rep6", "trimmed with trim galore version 0.6.4. Parameters:   length 26   phred33 Get raw counts with kallisto quant version 0.4.6. TPM abundance estimates  generated with kallisto quant 0.4.6 Genome build: danRer11 Supplementary files format and content: TPM abundance estimates and raw counts generated with kallisto.", "zebrafish embryo", "Not applicable", "Total RNA was isolated from TGfli1:EGFP zebrafish larvae using the RNeasy Mini Kit following the manufacturer\u2019s protocol Qiagen. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols", "Zebrafish were raised and staged  under standard husbandry environment. Embryos were kept in E3 media at 28.5 \u00b0C with/without xxx 2.5 ml in 25 ml to suppress pigmentation", "genotype:aldh3a1 KO|tissue:embryo|age:48 hpf", "GSM4590772", "GSM4590772: zebrafish embryo Aldh3a1 KO rep6; Danio rerio; RNA Seq", "GSM4590772", null, "1", "Total RNA was isolated from TGfli1:EGFP zebrafish larvae using the RNeasy Mini Kit following the manufacturer's protocol Qiagen. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols", "GEO Accession:GSM4590772", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "BGISEQ", "BGISEQ-500", null, "SRP265910", null, null, "12_aldh3a1----homo-48hpf-6_1.fq.gz 12_aldh3a1----homo-48hpf-6_2.fq.gz", "fastq fastq", 4660603600.0, 46606036.0, "GSM4590772 r1", "0:100 1:100", "A:1396899993;C:924291840;G:902974172;T:1436437595;N:0", 100, 100, null, null, 1396899993, 924291840, 902974172, 1436437595, 0, "SRX8468588", "SRS6769276", "SRA1083013", "GEO", "ZMF, University Heidelberg", 1, 0.90281, null, 0.2525, null, 0.75943, null, 0.62165, null, 100, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Germany", "2020-06-04", "Hatching", "Embryo", "Embryo Imprecise", "All anatomical structures"], [59481, "SRR11922873", "SRX8468587", "SRS6769275", "SRP265910", "PRJNA637219", "Next Generation Sequencing Facilitates Quantitative Analysis of Wildtype and aldh3a1 /  Zebrafish Embryo Transcriptomes", "GSE151770", "Transcriptome Analysis", "Our previous experiments showed the function of Aldh3a1 was related to pancreas and insulin secretion and knockout of Aldh3a1 led to destoryed pancreas. To understand how the impaired pancreas reflects at the transcriptome level  we performed full genome RNA Seq between aldh3a1+/+ and aldh3a1 /  larvae at 48 hpf.An overview of RNA Seq  including quality control  principal component analysis PCA  volcano plots of regulated genes and Top 20 KEGG pathway analysis showed comparable properties between aldh3a1 mutants and wild type. We found the insulin signalling pathway was reduced significantly via gene set enrichment analysis normalized enrichment score   1.72; p=0.0006. Interestingly  endocrine pancreas but not exocrine pancreas development pathway was significantly down regulated in aldh3a1 mutants . Taken together  these results further suggest Aldh3a1 as an important regulator in the development  morphology and insulin secretion function of primary pancreas. Furthermore  we offers a comprehensive and more accurate quantitative and qualitative evaluation of mRNA content within zebrafish larvae. We conclude that RNA seq based transcriptome characterization would expedite genetic network analyses and permit the dissection of complex biologic functions. Overall design: mRNA expression profiles of wildtype and aldh3a1 /  zebrafish embryo at 48 hpf", null, "pubmed:32980661", null, "zebrafish embryo Aldh3a1 KO rep5", "GSM4590771", null, "source name:zebrafish embryo|genotype:aldh3a1 KO|tissue:embryo|age:48 hpf", "zebrafish embryo Aldh3a1 KO rep5", "trimmed with trim galore version 0.6.4. Parameters:   length 26   phred33 Get raw counts with kallisto quant version 0.4.6. TPM abundance estimates  generated with kallisto quant 0.4.6 Genome build: danRer11 Supplementary files format and content: TPM abundance estimates and raw counts generated with kallisto.", "zebrafish embryo", "Not applicable", "Total RNA was isolated from TGfli1:EGFP zebrafish larvae using the RNeasy Mini Kit following the manufacturer\u2019s protocol Qiagen. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols", "Zebrafish were raised and staged  under standard husbandry environment. Embryos were kept in E3 media at 28.5 \u00b0C with/without xxx 2.5 ml in 25 ml to suppress pigmentation", "genotype:aldh3a1 KO|tissue:embryo|age:48 hpf", "GSM4590771", "GSM4590771: zebrafish embryo Aldh3a1 KO rep5; Danio rerio; RNA Seq", "GSM4590771", null, "1", "Total RNA was isolated from TGfli1:EGFP zebrafish larvae using the RNeasy Mini Kit following the manufacturer's protocol Qiagen. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols", "GEO Accession:GSM4590771", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "BGISEQ", "BGISEQ-500", null, "SRP265910", null, null, "11_aldh3a1----homo-48hpf-5_1.fq.gz 11_aldh3a1----homo-48hpf-5_2.fq.gz", "fastq fastq", 3919649800.0, 39196498.0, "GSM4590771 r1", "0:100 1:100", "A:1203194756;C:742776682;G:744133378;T:1229544984;N:0", 100, 100, null, null, 1203194756, 742776682, 744133378, 1229544984, 0, "SRX8468587", "SRS6769275", "SRA1083013", "GEO", "ZMF, University Heidelberg", 1, 0.86745, null, 0.31349, null, 0.76702, null, 0.63864, null, 100, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Germany", "2020-06-04", "Hatching", "Embryo", "Embryo Imprecise", "All anatomical structures"], [59482, "SRR11922872", "SRX8468586", "SRS6769274", "SRP265910", "PRJNA637219", "Next Generation Sequencing Facilitates Quantitative Analysis of Wildtype and aldh3a1 /  Zebrafish Embryo Transcriptomes", "GSE151770", "Transcriptome Analysis", "Our previous experiments showed the function of Aldh3a1 was related to pancreas and insulin secretion and knockout of Aldh3a1 led to destoryed pancreas. To understand how the impaired pancreas reflects at the transcriptome level  we performed full genome RNA Seq between aldh3a1+/+ and aldh3a1 /  larvae at 48 hpf.An overview of RNA Seq  including quality control  principal component analysis PCA  volcano plots of regulated genes and Top 20 KEGG pathway analysis showed comparable properties between aldh3a1 mutants and wild type. We found the insulin signalling pathway was reduced significantly via gene set enrichment analysis normalized enrichment score   1.72; p=0.0006. Interestingly  endocrine pancreas but not exocrine pancreas development pathway was significantly down regulated in aldh3a1 mutants . Taken together  these results further suggest Aldh3a1 as an important regulator in the development  morphology and insulin secretion function of primary pancreas. Furthermore  we offers a comprehensive and more accurate quantitative and qualitative evaluation of mRNA content within zebrafish larvae. We conclude that RNA seq based transcriptome characterization would expedite genetic network analyses and permit the dissection of complex biologic functions. Overall design: mRNA expression profiles of wildtype and aldh3a1 /  zebrafish embryo at 48 hpf", null, "pubmed:32980661", null, "zebrafish embryo Aldh3a1 KO rep4", "GSM4590770", null, "source name:zebrafish embryo|genotype:aldh3a1 KO|tissue:embryo|age:48 hpf", "zebrafish embryo Aldh3a1 KO rep4", "trimmed with trim galore version 0.6.4. Parameters:   length 26   phred33 Get raw counts with kallisto quant version 0.4.6. TPM abundance estimates  generated with kallisto quant 0.4.6 Genome build: danRer11 Supplementary files format and content: TPM abundance estimates and raw counts generated with kallisto.", "zebrafish embryo", "Not applicable", "Total RNA was isolated from TGfli1:EGFP zebrafish larvae using the RNeasy Mini Kit following the manufacturer\u2019s protocol Qiagen. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols", "Zebrafish were raised and staged  under standard husbandry environment. Embryos were kept in E3 media at 28.5 \u00b0C with/without xxx 2.5 ml in 25 ml to suppress pigmentation", "genotype:aldh3a1 KO|tissue:embryo|age:48 hpf", "GSM4590770", "GSM4590770: zebrafish embryo Aldh3a1 KO rep4; Danio rerio; RNA Seq", "GSM4590770", null, "1", "Total RNA was isolated from TGfli1:EGFP zebrafish larvae using the RNeasy Mini Kit following the manufacturer's protocol Qiagen. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols", "GEO Accession:GSM4590770", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "BGISEQ", "BGISEQ-500", null, "SRP265910", null, null, "10_aldh3a1----homo-48hpf-4_2.fq.gz 10_aldh3a1----homo-48hpf-4_1.fq.gz", "fastq fastq", 4549625000.0, 45496250.0, "GSM4590770 r1", "0:100 1:100", "A:1345145181;C:925949636;G:905779914;T:1372750269;N:0", 100, 100, null, null, 1345145181, 925949636, 905779914, 1372750269, 0, "SRX8468586", "SRS6769274", "SRA1083013", "GEO", "ZMF, University Heidelberg", 1, 0.9117, null, 0.23055, null, 0.72545, null, 0.50968, null, 100, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Germany", "2020-06-04", "Hatching", "Embryo", "Embryo Imprecise", "All anatomical structures"], [59483, "SRR11922871", "SRX8468585", "SRS6769273", "SRP265910", "PRJNA637219", "Next Generation Sequencing Facilitates Quantitative Analysis of Wildtype and aldh3a1 /  Zebrafish Embryo Transcriptomes", "GSE151770", "Transcriptome Analysis", "Our previous experiments showed the function of Aldh3a1 was related to pancreas and insulin secretion and knockout of Aldh3a1 led to destoryed pancreas. To understand how the impaired pancreas reflects at the transcriptome level  we performed full genome RNA Seq between aldh3a1+/+ and aldh3a1 /  larvae at 48 hpf.An overview of RNA Seq  including quality control  principal component analysis PCA  volcano plots of regulated genes and Top 20 KEGG pathway analysis showed comparable properties between aldh3a1 mutants and wild type. We found the insulin signalling pathway was reduced significantly via gene set enrichment analysis normalized enrichment score   1.72; p=0.0006. Interestingly  endocrine pancreas but not exocrine pancreas development pathway was significantly down regulated in aldh3a1 mutants . Taken together  these results further suggest Aldh3a1 as an important regulator in the development  morphology and insulin secretion function of primary pancreas. Furthermore  we offers a comprehensive and more accurate quantitative and qualitative evaluation of mRNA content within zebrafish larvae. We conclude that RNA seq based transcriptome characterization would expedite genetic network analyses and permit the dissection of complex biologic functions. Overall design: mRNA expression profiles of wildtype and aldh3a1 /  zebrafish embryo at 48 hpf", null, "pubmed:32980661", null, "zebrafish embryo Aldh3a1 KO rep3", "GSM4590769", null, "source name:zebrafish embryo|genotype:aldh3a1 KO|tissue:embryo|age:48 hpf", "zebrafish embryo Aldh3a1 KO rep3", "trimmed with trim galore version 0.6.4. Parameters:   length 26   phred33 Get raw counts with kallisto quant version 0.4.6. TPM abundance estimates  generated with kallisto quant 0.4.6 Genome build: danRer11 Supplementary files format and content: TPM abundance estimates and raw counts generated with kallisto.", "zebrafish embryo", "Not applicable", "Total RNA was isolated from TGfli1:EGFP zebrafish larvae using the RNeasy Mini Kit following the manufacturer\u2019s protocol Qiagen. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols", "Zebrafish were raised and staged  under standard husbandry environment. Embryos were kept in E3 media at 28.5 \u00b0C with/without xxx 2.5 ml in 25 ml to suppress pigmentation", "genotype:aldh3a1 KO|tissue:embryo|age:48 hpf", "GSM4590769", "GSM4590769: zebrafish embryo Aldh3a1 KO rep3; Danio rerio; RNA Seq", "GSM4590769", null, "1", "Total RNA was isolated from TGfli1:EGFP zebrafish larvae using the RNeasy Mini Kit following the manufacturer's protocol Qiagen. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols", "GEO Accession:GSM4590769", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "BGISEQ", "BGISEQ-500", null, "SRP265910", null, null, "9_aldh3a1----homo-48hpf-3_1.fq.gz 9_aldh3a1----homo-48hpf-3_2.fq.gz", "fastq fastq", 4194991600.0, 41949916.0, "GSM4590769 r1", "0:100 1:100", "A:1258296885;C:833884600;G:816600639;T:1286209476;N:0", 100, 100, null, null, 1258296885, 833884600, 816600639, 1286209476, 0, "SRX8468585", "SRS6769273", "SRA1083013", "GEO", "ZMF, University Heidelberg", 1, 0.89574, null, 0.28139, null, 0.73397, null, 0.56688, null, 100, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Germany", "2020-06-04", "Hatching", "Embryo", "Embryo Imprecise", "All anatomical structures"], [59484, "SRR11922870", "SRX8468584", "SRS6769272", "SRP265910", "PRJNA637219", "Next Generation Sequencing Facilitates Quantitative Analysis of Wildtype and aldh3a1 /  Zebrafish Embryo Transcriptomes", "GSE151770", "Transcriptome Analysis", "Our previous experiments showed the function of Aldh3a1 was related to pancreas and insulin secretion and knockout of Aldh3a1 led to destoryed pancreas. To understand how the impaired pancreas reflects at the transcriptome level  we performed full genome RNA Seq between aldh3a1+/+ and aldh3a1 /  larvae at 48 hpf.An overview of RNA Seq  including quality control  principal component analysis PCA  volcano plots of regulated genes and Top 20 KEGG pathway analysis showed comparable properties between aldh3a1 mutants and wild type. We found the insulin signalling pathway was reduced significantly via gene set enrichment analysis normalized enrichment score   1.72; p=0.0006. Interestingly  endocrine pancreas but not exocrine pancreas development pathway was significantly down regulated in aldh3a1 mutants . Taken together  these results further suggest Aldh3a1 as an important regulator in the development  morphology and insulin secretion function of primary pancreas. Furthermore  we offers a comprehensive and more accurate quantitative and qualitative evaluation of mRNA content within zebrafish larvae. We conclude that RNA seq based transcriptome characterization would expedite genetic network analyses and permit the dissection of complex biologic functions. Overall design: mRNA expression profiles of wildtype and aldh3a1 /  zebrafish embryo at 48 hpf", null, "pubmed:32980661", null, "zebrafish embryo Aldh3a1 KO rep2", "GSM4590768", null, "source name:zebrafish embryo|genotype:aldh3a1 KO|tissue:embryo|age:48 hpf", "zebrafish embryo Aldh3a1 KO rep2", "trimmed with trim galore version 0.6.4. Parameters:   length 26   phred33 Get raw counts with kallisto quant version 0.4.6. TPM abundance estimates  generated with kallisto quant 0.4.6 Genome build: danRer11 Supplementary files format and content: TPM abundance estimates and raw counts generated with kallisto.", "zebrafish embryo", "Not applicable", "Total RNA was isolated from TGfli1:EGFP zebrafish larvae using the RNeasy Mini Kit following the manufacturer\u2019s protocol Qiagen. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols", "Zebrafish were raised and staged  under standard husbandry environment. Embryos were kept in E3 media at 28.5 \u00b0C with/without xxx 2.5 ml in 25 ml to suppress pigmentation", "genotype:aldh3a1 KO|tissue:embryo|age:48 hpf", "GSM4590768", "GSM4590768: zebrafish embryo Aldh3a1 KO rep2; Danio rerio; RNA Seq", "GSM4590768", null, "1", "Total RNA was isolated from TGfli1:EGFP zebrafish larvae using the RNeasy Mini Kit following the manufacturer's protocol Qiagen. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols", "GEO Accession:GSM4590768", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "BGISEQ", "BGISEQ-500", null, "SRP265910", null, null, "8_aldh3a1----homo-48hpf-2_1.fq.gz 8_aldh3a1----homo-48hpf-2_2.fq.gz", "fastq fastq", 5097901600.0, 50979016.0, "GSM4590768 r1", "0:100 1:100", "A:1487281075;C:1055394796;G:1035616985;T:1519608744;N:0", 100, 100, null, null, 1487281075, 1055394796, 1035616985, 1519608744, 0, "SRX8468584", "SRS6769272", "SRA1083013", "GEO", "ZMF, University Heidelberg", 1, 0.92556, null, 0.18622, null, 0.73026, null, 0.5187, null, 100, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Germany", "2020-06-04", "Hatching", "Embryo", "Embryo Imprecise", "All anatomical structures"], [59485, "SRR11922869", "SRX8468583", "SRS6769271", "SRP265910", "PRJNA637219", "Next Generation Sequencing Facilitates Quantitative Analysis of Wildtype and aldh3a1 /  Zebrafish Embryo Transcriptomes", "GSE151770", "Transcriptome Analysis", "Our previous experiments showed the function of Aldh3a1 was related to pancreas and insulin secretion and knockout of Aldh3a1 led to destoryed pancreas. To understand how the impaired pancreas reflects at the transcriptome level  we performed full genome RNA Seq between aldh3a1+/+ and aldh3a1 /  larvae at 48 hpf.An overview of RNA Seq  including quality control  principal component analysis PCA  volcano plots of regulated genes and Top 20 KEGG pathway analysis showed comparable properties between aldh3a1 mutants and wild type. We found the insulin signalling pathway was reduced significantly via gene set enrichment analysis normalized enrichment score   1.72; p=0.0006. Interestingly  endocrine pancreas but not exocrine pancreas development pathway was significantly down regulated in aldh3a1 mutants . Taken together  these results further suggest Aldh3a1 as an important regulator in the development  morphology and insulin secretion function of primary pancreas. Furthermore  we offers a comprehensive and more accurate quantitative and qualitative evaluation of mRNA content within zebrafish larvae. We conclude that RNA seq based transcriptome characterization would expedite genetic network analyses and permit the dissection of complex biologic functions. Overall design: mRNA expression profiles of wildtype and aldh3a1 /  zebrafish embryo at 48 hpf", null, "pubmed:32980661", null, "zebrafish embryo Aldh3a1 KO rep1", "GSM4590767", null, "source name:zebrafish embryo|genotype:aldh3a1 KO|tissue:embryo|age:48 hpf", "zebrafish embryo Aldh3a1 KO rep1", "trimmed with trim galore version 0.6.4. Parameters:   length 26   phred33 Get raw counts with kallisto quant version 0.4.6. TPM abundance estimates  generated with kallisto quant 0.4.6 Genome build: danRer11 Supplementary files format and content: TPM abundance estimates and raw counts generated with kallisto.", "zebrafish embryo", "Not applicable", "Total RNA was isolated from TGfli1:EGFP zebrafish larvae using the RNeasy Mini Kit following the manufacturer\u2019s protocol Qiagen. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols", "Zebrafish were raised and staged  under standard husbandry environment. Embryos were kept in E3 media at 28.5 \u00b0C with/without xxx 2.5 ml in 25 ml to suppress pigmentation", "genotype:aldh3a1 KO|tissue:embryo|age:48 hpf", "GSM4590767", "GSM4590767: zebrafish embryo Aldh3a1 KO rep1; Danio rerio; RNA Seq", "GSM4590767", null, "1", "Total RNA was isolated from TGfli1:EGFP zebrafish larvae using the RNeasy Mini Kit following the manufacturer's protocol Qiagen. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols", "GEO Accession:GSM4590767", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "BGISEQ", "BGISEQ-500", null, "SRP265910", null, null, "7_aldh3a1----homo-48hpf-1_1.fq.gz 7_aldh3a1----homo-48hpf-1_2.fq.gz", "fastq fastq", 5075421000.0, 50754210.0, "GSM4590767 r1", "0:100 1:100", "A:1523744143;C:1008915874;G:985443760;T:1557317223;N:0", 100, 100, null, null, 1523744143, 1008915874, 985443760, 1557317223, 0, "SRX8468583", "SRS6769271", "SRA1083013", "GEO", "ZMF, University Heidelberg", 1, 0.90167, null, 0.27915, null, 0.75879, null, 0.6673, null, 100, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Germany", "2020-06-04", "Hatching", "Embryo", "Embryo Imprecise", "All anatomical structures"], [59486, "SRR11922868", "SRX8468582", "SRS6769270", "SRP265910", "PRJNA637219", "Next Generation Sequencing Facilitates Quantitative Analysis of Wildtype and aldh3a1 /  Zebrafish Embryo Transcriptomes", "GSE151770", "Transcriptome Analysis", "Our previous experiments showed the function of Aldh3a1 was related to pancreas and insulin secretion and knockout of Aldh3a1 led to destoryed pancreas. To understand how the impaired pancreas reflects at the transcriptome level  we performed full genome RNA Seq between aldh3a1+/+ and aldh3a1 /  larvae at 48 hpf.An overview of RNA Seq  including quality control  principal component analysis PCA  volcano plots of regulated genes and Top 20 KEGG pathway analysis showed comparable properties between aldh3a1 mutants and wild type. We found the insulin signalling pathway was reduced significantly via gene set enrichment analysis normalized enrichment score   1.72; p=0.0006. Interestingly  endocrine pancreas but not exocrine pancreas development pathway was significantly down regulated in aldh3a1 mutants . Taken together  these results further suggest Aldh3a1 as an important regulator in the development  morphology and insulin secretion function of primary pancreas. Furthermore  we offers a comprehensive and more accurate quantitative and qualitative evaluation of mRNA content within zebrafish larvae. We conclude that RNA seq based transcriptome characterization would expedite genetic network analyses and permit the dissection of complex biologic functions. Overall design: mRNA expression profiles of wildtype and aldh3a1 /  zebrafish embryo at 48 hpf", null, "pubmed:32980661", null, "zebrafish embryo wildtype rep5", "GSM4590766", null, "source name:zebrafish embryo|genotype:WT|tissue:embryo|age:48 hpf", "zebrafish embryo wildtype rep5", "trimmed with trim galore version 0.6.4. Parameters:   length 26   phred33 Get raw counts with kallisto quant version 0.4.6. TPM abundance estimates  generated with kallisto quant 0.4.6 Genome build: danRer11 Supplementary files format and content: TPM abundance estimates and raw counts generated with kallisto.", "zebrafish embryo", "Not applicable", "Total RNA was isolated from TGfli1:EGFP zebrafish larvae using the RNeasy Mini Kit following the manufacturer\u2019s protocol Qiagen. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols", "Zebrafish were raised and staged  under standard husbandry environment. Embryos were kept in E3 media at 28.5 \u00b0C with/without xxx 2.5 ml in 25 ml to suppress pigmentation", "genotype:WT|tissue:embryo|age:48 hpf", "GSM4590766", "GSM4590766: zebrafish embryo wildtype rep5; Danio rerio; RNA Seq", "GSM4590766", null, "1", "Total RNA was isolated from TGfli1:EGFP zebrafish larvae using the RNeasy Mini Kit following the manufacturer's protocol Qiagen. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols", "GEO Accession:GSM4590766", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "BGISEQ", "BGISEQ-500", null, "SRP265910", null, null, "6_aldh3a1+-+-wt-48hpf-R_1.fq.gz 6_aldh3a1+-+-wt-48hpf-R_2.fq.gz", "fastq fastq", 5097636600.0, 50976366.0, "GSM4590766 r1", "0:100 1:100", "A:1402424015;C:1146863463;G:1121174200;T:1427174922;N:0", 100, 100, null, null, 1402424015, 1146863463, 1121174200, 1427174922, 0, "SRX8468582", "SRS6769270", "SRA1083013", "GEO", "ZMF, University Heidelberg", 1, 0.95115, null, 0.09816, null, 0.69781, null, 0.46194, null, 100, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Germany", "2020-06-04", "Hatching", "Embryo", "Embryo Imprecise", "All anatomical structures"], [59487, "SRR11922867", "SRX8468581", "SRS6769269", "SRP265910", "PRJNA637219", "Next Generation Sequencing Facilitates Quantitative Analysis of Wildtype and aldh3a1 /  Zebrafish Embryo Transcriptomes", "GSE151770", "Transcriptome Analysis", "Our previous experiments showed the function of Aldh3a1 was related to pancreas and insulin secretion and knockout of Aldh3a1 led to destoryed pancreas. To understand how the impaired pancreas reflects at the transcriptome level  we performed full genome RNA Seq between aldh3a1+/+ and aldh3a1 /  larvae at 48 hpf.An overview of RNA Seq  including quality control  principal component analysis PCA  volcano plots of regulated genes and Top 20 KEGG pathway analysis showed comparable properties between aldh3a1 mutants and wild type. We found the insulin signalling pathway was reduced significantly via gene set enrichment analysis normalized enrichment score   1.72; p=0.0006. Interestingly  endocrine pancreas but not exocrine pancreas development pathway was significantly down regulated in aldh3a1 mutants . Taken together  these results further suggest Aldh3a1 as an important regulator in the development  morphology and insulin secretion function of primary pancreas. Furthermore  we offers a comprehensive and more accurate quantitative and qualitative evaluation of mRNA content within zebrafish larvae. We conclude that RNA seq based transcriptome characterization would expedite genetic network analyses and permit the dissection of complex biologic functions. Overall design: mRNA expression profiles of wildtype and aldh3a1 /  zebrafish embryo at 48 hpf", null, "pubmed:32980661", null, "zebrafish embryo wildtype rep4", "GSM4590765", null, "source name:zebrafish embryo|genotype:WT|tissue:embryo|age:48 hpf", "zebrafish embryo wildtype rep4", "trimmed with trim galore version 0.6.4. Parameters:   length 26   phred33 Get raw counts with kallisto quant version 0.4.6. TPM abundance estimates  generated with kallisto quant 0.4.6 Genome build: danRer11 Supplementary files format and content: TPM abundance estimates and raw counts generated with kallisto.", "zebrafish embryo", "Not applicable", "Total RNA was isolated from TGfli1:EGFP zebrafish larvae using the RNeasy Mini Kit following the manufacturer\u2019s protocol Qiagen. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols", "Zebrafish were raised and staged  under standard husbandry environment. Embryos were kept in E3 media at 28.5 \u00b0C with/without xxx 2.5 ml in 25 ml to suppress pigmentation", "genotype:WT|tissue:embryo|age:48 hpf", "GSM4590765", "GSM4590765: zebrafish embryo wildtype rep4; Danio rerio; RNA Seq", "GSM4590765", null, "1", "Total RNA was isolated from TGfli1:EGFP zebrafish larvae using the RNeasy Mini Kit following the manufacturer's protocol Qiagen. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols", "GEO Accession:GSM4590765", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "BGISEQ", "BGISEQ-500", null, "SRP265910", null, null, "4_aldh3a1+-+-wt-48hpf-4_1.fq.gz 4_aldh3a1+-+-wt-48hpf-4_2.fq.gz", "fastq fastq", 4847250800.0, 48472508.0, "GSM4590765 r1", "0:100 1:100", "A:1351516729;C:1070410976;G:1050113082;T:1375210013;N:0", 100, 100, null, null, 1351516729, 1070410976, 1050113082, 1375210013, 0, "SRX8468581", "SRS6769269", "SRA1083013", "GEO", "ZMF, University Heidelberg", 1, 0.94418, null, 0.12404, null, 0.69374, null, 0.49948, null, 100, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Germany", "2020-06-04", "Hatching", "Embryo", "Embryo Imprecise", "All anatomical structures"], [59488, "SRR11922866", "SRX8468580", "SRS6769268", "SRP265910", "PRJNA637219", "Next Generation Sequencing Facilitates Quantitative Analysis of Wildtype and aldh3a1 /  Zebrafish Embryo Transcriptomes", "GSE151770", "Transcriptome Analysis", "Our previous experiments showed the function of Aldh3a1 was related to pancreas and insulin secretion and knockout of Aldh3a1 led to destoryed pancreas. To understand how the impaired pancreas reflects at the transcriptome level  we performed full genome RNA Seq between aldh3a1+/+ and aldh3a1 /  larvae at 48 hpf.An overview of RNA Seq  including quality control  principal component analysis PCA  volcano plots of regulated genes and Top 20 KEGG pathway analysis showed comparable properties between aldh3a1 mutants and wild type. We found the insulin signalling pathway was reduced significantly via gene set enrichment analysis normalized enrichment score   1.72; p=0.0006. Interestingly  endocrine pancreas but not exocrine pancreas development pathway was significantly down regulated in aldh3a1 mutants . Taken together  these results further suggest Aldh3a1 as an important regulator in the development  morphology and insulin secretion function of primary pancreas. Furthermore  we offers a comprehensive and more accurate quantitative and qualitative evaluation of mRNA content within zebrafish larvae. We conclude that RNA seq based transcriptome characterization would expedite genetic network analyses and permit the dissection of complex biologic functions. Overall design: mRNA expression profiles of wildtype and aldh3a1 /  zebrafish embryo at 48 hpf", null, "pubmed:32980661", null, "zebrafish embryo wildtype rep3", "GSM4590764", null, "source name:zebrafish embryo|genotype:WT|tissue:embryo|age:48 hpf", "zebrafish embryo wildtype rep3", "trimmed with trim galore version 0.6.4. Parameters:   length 26   phred33 Get raw counts with kallisto quant version 0.4.6. TPM abundance estimates  generated with kallisto quant 0.4.6 Genome build: danRer11 Supplementary files format and content: TPM abundance estimates and raw counts generated with kallisto.", "zebrafish embryo", "Not applicable", "Total RNA was isolated from TGfli1:EGFP zebrafish larvae using the RNeasy Mini Kit following the manufacturer\u2019s protocol Qiagen. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols", "Zebrafish were raised and staged  under standard husbandry environment. Embryos were kept in E3 media at 28.5 \u00b0C with/without xxx 2.5 ml in 25 ml to suppress pigmentation", "genotype:WT|tissue:embryo|age:48 hpf", "GSM4590764", "GSM4590764: zebrafish embryo wildtype rep3; Danio rerio; RNA Seq", "GSM4590764", null, "1", "Total RNA was isolated from TGfli1:EGFP zebrafish larvae using the RNeasy Mini Kit following the manufacturer's protocol Qiagen. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols", "GEO Accession:GSM4590764", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "BGISEQ", "BGISEQ-500", null, "SRP265910", null, null, "3_aldh3a1+-+-wt-48hpf-3_1.fq.gz 3_aldh3a1+-+-wt-48hpf-3_2.fq.gz", "fastq fastq", 5083417400.0, 50834174.0, "GSM4590764 r1", "0:100 1:100", "A:1375006484;C:1168556107;G:1139277849;T:1400576960;N:0", 100, 100, null, null, 1375006484, 1168556107, 1139277849, 1400576960, 0, "SRX8468580", "SRS6769268", "SRA1083013", "GEO", "ZMF, University Heidelberg", 1, 0.95419, null, 0.09201, null, 0.69209, null, 0.48244, null, 100, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Germany", "2020-06-04", "Hatching", "Embryo", "Embryo Imprecise", "All anatomical structures"], [59489, "SRR11922865", "SRX8468579", "SRS6769267", "SRP265910", "PRJNA637219", "Next Generation Sequencing Facilitates Quantitative Analysis of Wildtype and aldh3a1 /  Zebrafish Embryo Transcriptomes", "GSE151770", "Transcriptome Analysis", "Our previous experiments showed the function of Aldh3a1 was related to pancreas and insulin secretion and knockout of Aldh3a1 led to destoryed pancreas. To understand how the impaired pancreas reflects at the transcriptome level  we performed full genome RNA Seq between aldh3a1+/+ and aldh3a1 /  larvae at 48 hpf.An overview of RNA Seq  including quality control  principal component analysis PCA  volcano plots of regulated genes and Top 20 KEGG pathway analysis showed comparable properties between aldh3a1 mutants and wild type. We found the insulin signalling pathway was reduced significantly via gene set enrichment analysis normalized enrichment score   1.72; p=0.0006. Interestingly  endocrine pancreas but not exocrine pancreas development pathway was significantly down regulated in aldh3a1 mutants . Taken together  these results further suggest Aldh3a1 as an important regulator in the development  morphology and insulin secretion function of primary pancreas. Furthermore  we offers a comprehensive and more accurate quantitative and qualitative evaluation of mRNA content within zebrafish larvae. We conclude that RNA seq based transcriptome characterization would expedite genetic network analyses and permit the dissection of complex biologic functions. Overall design: mRNA expression profiles of wildtype and aldh3a1 /  zebrafish embryo at 48 hpf", null, "pubmed:32980661", null, "zebrafish embryo wildtype rep2", "GSM4590763", null, "source name:zebrafish embryo|genotype:WT|tissue:embryo|age:48 hpf", "zebrafish embryo wildtype rep2", "trimmed with trim galore version 0.6.4. Parameters:   length 26   phred33 Get raw counts with kallisto quant version 0.4.6. TPM abundance estimates  generated with kallisto quant 0.4.6 Genome build: danRer11 Supplementary files format and content: TPM abundance estimates and raw counts generated with kallisto.", "zebrafish embryo", "Not applicable", "Total RNA was isolated from TGfli1:EGFP zebrafish larvae using the RNeasy Mini Kit following the manufacturer\u2019s protocol Qiagen. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols", "Zebrafish were raised and staged  under standard husbandry environment. Embryos were kept in E3 media at 28.5 \u00b0C with/without xxx 2.5 ml in 25 ml to suppress pigmentation", "genotype:WT|tissue:embryo|age:48 hpf", "GSM4590763", "GSM4590763: zebrafish embryo wildtype rep2; Danio rerio; RNA Seq", "GSM4590763", null, "1", "Total RNA was isolated from TGfli1:EGFP zebrafish larvae using the RNeasy Mini Kit following the manufacturer's protocol Qiagen. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols", "GEO Accession:GSM4590763", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "BGISEQ", "BGISEQ-500", null, "SRP265910", null, null, "2_aldh3a1+-+-wt-48hpf-2_1.fq.gz 2_aldh3a1+-+-wt-48hpf-2_2.fq.gz", "fastq fastq", 5089646400.0, 50896464.0, "GSM4590763 r1", "0:100 1:100", "A:1384714450;C:1161015785;G:1138313445;T:1405602720;N:0", 100, 100, null, null, 1384714450, 1161015785, 1138313445, 1405602720, 0, "SRX8468579", "SRS6769267", "SRA1083013", "GEO", "ZMF, University Heidelberg", 1, 0.95309, null, 0.09301, null, 0.69798, null, 0.48524, null, 100, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Germany", "2020-06-04", "Hatching", "Embryo", "Embryo Imprecise", "All anatomical structures"], [59490, "SRR11922864", "SRX8468578", "SRS6769266", "SRP265910", "PRJNA637219", "Next Generation Sequencing Facilitates Quantitative Analysis of Wildtype and aldh3a1 /  Zebrafish Embryo Transcriptomes", "GSE151770", "Transcriptome Analysis", "Our previous experiments showed the function of Aldh3a1 was related to pancreas and insulin secretion and knockout of Aldh3a1 led to destoryed pancreas. To understand how the impaired pancreas reflects at the transcriptome level  we performed full genome RNA Seq between aldh3a1+/+ and aldh3a1 /  larvae at 48 hpf.An overview of RNA Seq  including quality control  principal component analysis PCA  volcano plots of regulated genes and Top 20 KEGG pathway analysis showed comparable properties between aldh3a1 mutants and wild type. We found the insulin signalling pathway was reduced significantly via gene set enrichment analysis normalized enrichment score   1.72; p=0.0006. Interestingly  endocrine pancreas but not exocrine pancreas development pathway was significantly down regulated in aldh3a1 mutants . Taken together  these results further suggest Aldh3a1 as an important regulator in the development  morphology and insulin secretion function of primary pancreas. Furthermore  we offers a comprehensive and more accurate quantitative and qualitative evaluation of mRNA content within zebrafish larvae. We conclude that RNA seq based transcriptome characterization would expedite genetic network analyses and permit the dissection of complex biologic functions. Overall design: mRNA expression profiles of wildtype and aldh3a1 /  zebrafish embryo at 48 hpf", null, "pubmed:32980661", null, "zebrafish embryo wildtype rep1", "GSM4590762", null, "source name:zebrafish embryo|genotype:WT|tissue:embryo|age:48 hpf", "zebrafish embryo wildtype rep1", "trimmed with trim galore version 0.6.4. Parameters:   length 26   phred33 Get raw counts with kallisto quant version 0.4.6. TPM abundance estimates  generated with kallisto quant 0.4.6 Genome build: danRer11 Supplementary files format and content: TPM abundance estimates and raw counts generated with kallisto.", "zebrafish embryo", "Not applicable", "Total RNA was isolated from TGfli1:EGFP zebrafish larvae using the RNeasy Mini Kit following the manufacturer\u2019s protocol Qiagen. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols", "Zebrafish were raised and staged  under standard husbandry environment. Embryos were kept in E3 media at 28.5 \u00b0C with/without xxx 2.5 ml in 25 ml to suppress pigmentation", "genotype:WT|tissue:embryo|age:48 hpf", "GSM4590762", "GSM4590762: zebrafish embryo wildtype rep1; Danio rerio; RNA Seq", "GSM4590762", null, "1", "Total RNA was isolated from TGfli1:EGFP zebrafish larvae using the RNeasy Mini Kit following the manufacturer's protocol Qiagen. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols", "GEO Accession:GSM4590762", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "BGISEQ", "BGISEQ-500", null, "SRP265910", null, null, "1_aldh3a1+-+-wt-48hpf-1_1.fq.gz 1_aldh3a1+-+-wt-48hpf-1_2.fq.gz", "fastq fastq", 5098267400.0, 50982674.0, "GSM4590762 r1", "0:100 1:100", "A:1406329756;C:1147290302;G:1118206731;T:1426440611;N:0", 100, 100, null, null, 1406329756, 1147290302, 1118206731, 1426440611, 0, "SRX8468578", "SRS6769266", "SRA1083013", "GEO", "ZMF, University Heidelberg", 1, 0.95039, null, 0.10482, null, 0.69641, null, 0.47979, null, 100, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Germany", "2020-06-04", "Hatching", "Embryo", "Embryo Imprecise", "All anatomical structures"], [60605, "SRR12435896", "SRX8931591", "SRS7187999", "SRP277167", "PRJNA656771", "CTCF knockout in zebrafish induces alterations in regulatory landscapes and developmental gene expression [RNA seq]", "GSE156094", "Transcriptome Analysis", "CTCF is an 11 zinc finger DNA binding protein that acts as a transcriptional repressor and insulator  as well as an architectural protein required for 3D genome folding. CTCF mediates long range chromatin looping and is enriched at the boundaries of topologically associating domains TADs  which are sub megabase chromatin structures composed of genomic regions with high contact frequency. Although CTCF is essential for cycling cells and developing embryos  its in vitro removal has only modest effects over gene expression  challenging the generally accepted idea that TADs facilitate enhancer promoter interactions within gene regulatory landscapes. However  the effects of an altered CTCF mediated chromatin structure on gene regulation in vivo are poorly understood. Here  we have generated a ctcf knockout mutant in zebrafish that allows us to monitor the effect of CTCF loss of function during embryo patterning and organogenesis. CTCF absence leads to a loss of chromatin structure in zebrafish embryos and affects the expression of thousands of genes  among them many developmental genes. In addition  we show that chromatin accessibility  both at CTCF sites and at developmental cis regulatory elements CREs  is severely compromised in ctcf mutants. Probing chromatin interactions from developmental genes at high resolution  we further demonstrate that promoters fail to fully establish long range contacts with their associated regulatory landscapes  leading to altered gene expression patterns during development. Therefore  our results demonstrate that CTCF and TADs are essential to finetune gene expression during embryonic development  providing the structural basis for the establishment of developmental gene regulatory landscapes. Overall design: RNA seq assays in wild type and ctcf zebrafish mutants  at developmental stages 24 hpf and 48 hpf  with and without xxx of tp53 morpholino", "parent bioproject:PRJNA656767", "pubmed:34518536", null, "RNA seq in zebrafish wild type embryos at 48hpf  replicate 2", "GSM4724538", null, "tissue:whole embryo|developmental stage:48 hpf|genotype:WT", "RNA seq in zebrafish wild type embryos at 48hpf  replicate 2", "Reads were aligned against reference genome using STAR software Read counts per gene were calculated using htseq count script from HTSeq tools software package Genome build: Zebrafish September 2014 GRCz10/danRer10 Supplementary files format and content: Individual counts files reads per gene", "whole embryo", "Injection of tp53 morpholino was performed at 1 cell stage", "RNA was extracted using TRIsure Bioline and treated with TURBO DNA free kit Invitrogen", "Embryos were grown at 28\u00b0C in E3 medium until desired developmental stage", "developmental stage:48 hpf|genotype:WT", "GSM4724538", "GSM4724538: RNA seq in zebrafish wild type embryos at 48hpf  replicate 2; Danio rerio; RNA Seq", "GSM4724538", null, "1", "RNA was extracted using TRIsure Bioline and treated with TURBO DNA free kit Invitrogen", "GEO Accession:GSM4724538", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "BGISEQ", "BGISEQ-500", null, "SRP277167", null, null, "RNAseq_48h_wt_rep2_1.fq.gz", "fastq", 2857833100.0, 57156662.0, "GSM4724538 r1", "0:50 1:0", "A:833205284;C:613960566;G:684040839;T:726626411;N:0", 50, 0, null, null, 833205284, 613960566, 684040839, 726626411, 0, "SRX8931591", "SRS7187999", "SRA1111981", "GEO", "CABD, Universidad Pablo de Olavide-CSIC", 1, 0.94607, null, 0.13254, null, 0.683, null, 0.47253, null, 50, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Spain", "2020-08-12", "Hatching", "Embryo", "Whole Organism", "All anatomical structures"], [60606, "SRR12435895", "SRX8931590", "SRS7187998", "SRP277167", "PRJNA656771", "CTCF knockout in zebrafish induces alterations in regulatory landscapes and developmental gene expression [RNA seq]", "GSE156094", "Transcriptome Analysis", "CTCF is an 11 zinc finger DNA binding protein that acts as a transcriptional repressor and insulator  as well as an architectural protein required for 3D genome folding. CTCF mediates long range chromatin looping and is enriched at the boundaries of topologically associating domains TADs  which are sub megabase chromatin structures composed of genomic regions with high contact frequency. Although CTCF is essential for cycling cells and developing embryos  its in vitro removal has only modest effects over gene expression  challenging the generally accepted idea that TADs facilitate enhancer promoter interactions within gene regulatory landscapes. However  the effects of an altered CTCF mediated chromatin structure on gene regulation in vivo are poorly understood. Here  we have generated a ctcf knockout mutant in zebrafish that allows us to monitor the effect of CTCF loss of function during embryo patterning and organogenesis. CTCF absence leads to a loss of chromatin structure in zebrafish embryos and affects the expression of thousands of genes  among them many developmental genes. In addition  we show that chromatin accessibility  both at CTCF sites and at developmental cis regulatory elements CREs  is severely compromised in ctcf mutants. Probing chromatin interactions from developmental genes at high resolution  we further demonstrate that promoters fail to fully establish long range contacts with their associated regulatory landscapes  leading to altered gene expression patterns during development. Therefore  our results demonstrate that CTCF and TADs are essential to finetune gene expression during embryonic development  providing the structural basis for the establishment of developmental gene regulatory landscapes. Overall design: RNA seq assays in wild type and ctcf zebrafish mutants  at developmental stages 24 hpf and 48 hpf  with and without xxx of tp53 morpholino", "parent bioproject:PRJNA656767", "pubmed:34518536", null, "RNA seq in zebrafish wild type embryos at 48hpf  replicate 1", "GSM4724537", null, "tissue:whole embryo|developmental stage:48 hpf|genotype:WT", "RNA seq in zebrafish wild type embryos at 48hpf  replicate 1", "Reads were aligned against reference genome using STAR software Read counts per gene were calculated using htseq count script from HTSeq tools software package Genome build: Zebrafish September 2014 GRCz10/danRer10 Supplementary files format and content: Individual counts files reads per gene", "whole embryo", "Injection of tp53 morpholino was performed at 1 cell stage", "RNA was extracted using TRIsure Bioline and treated with TURBO DNA free kit Invitrogen", "Embryos were grown at 28\u00b0C in E3 medium until desired developmental stage", "developmental stage:48 hpf|genotype:WT", "GSM4724537", "GSM4724537: RNA seq in zebrafish wild type embryos at 48hpf  replicate 1; Danio rerio; RNA Seq", "GSM4724537", null, "1", "RNA was extracted using TRIsure Bioline and treated with TURBO DNA free kit Invitrogen", "GEO Accession:GSM4724537", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "BGISEQ", "BGISEQ-500", null, "SRP277167", null, null, "RNAseq_48h_wt_rep1_1.fq.gz", "fastq", 1780117200.0, 35602344.0, "GSM4724537 r1", "0:50 1:0", "A:515966090;C:381813611;G:432619671;T:449717828;N:0", 50, 0, null, null, 515966090, 381813611, 432619671, 449717828, 0, "SRX8931590", "SRS7187998", "SRA1111981", "GEO", "CABD, Universidad Pablo de Olavide-CSIC", 1, 0.95016, null, 0.1291, null, 0.68546, null, 0.47379, null, 50, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Spain", "2020-08-12", "Hatching", "Embryo", "Whole Organism", "All anatomical structures"], [60607, "SRR12435894", "SRX8931589", "SRS7187997", "SRP277167", "PRJNA656771", "CTCF knockout in zebrafish induces alterations in regulatory landscapes and developmental gene expression [RNA seq]", "GSE156094", "Transcriptome Analysis", "CTCF is an 11 zinc finger DNA binding protein that acts as a transcriptional repressor and insulator  as well as an architectural protein required for 3D genome folding. CTCF mediates long range chromatin looping and is enriched at the boundaries of topologically associating domains TADs  which are sub megabase chromatin structures composed of genomic regions with high contact frequency. Although CTCF is essential for cycling cells and developing embryos  its in vitro removal has only modest effects over gene expression  challenging the generally accepted idea that TADs facilitate enhancer promoter interactions within gene regulatory landscapes. However  the effects of an altered CTCF mediated chromatin structure on gene regulation in vivo are poorly understood. Here  we have generated a ctcf knockout mutant in zebrafish that allows us to monitor the effect of CTCF loss of function during embryo patterning and organogenesis. CTCF absence leads to a loss of chromatin structure in zebrafish embryos and affects the expression of thousands of genes  among them many developmental genes. In addition  we show that chromatin accessibility  both at CTCF sites and at developmental cis regulatory elements CREs  is severely compromised in ctcf mutants. Probing chromatin interactions from developmental genes at high resolution  we further demonstrate that promoters fail to fully establish long range contacts with their associated regulatory landscapes  leading to altered gene expression patterns during development. Therefore  our results demonstrate that CTCF and TADs are essential to finetune gene expression during embryonic development  providing the structural basis for the establishment of developmental gene regulatory landscapes. Overall design: RNA seq assays in wild type and ctcf zebrafish mutants  at developmental stages 24 hpf and 48 hpf  with and without xxx of tp53 morpholino", "parent bioproject:PRJNA656767", "pubmed:34518536", null, "RNA seq in zebrafish wild type embryos at 48hpf  injected with morpholino against tp53  replicate 2", "GSM4724536", null, "tissue:whole embryo|developmental stage:48 hpf|genotype:WT|treatment:tp53 morpholino", "RNA seq in zebrafish wild type embryos at 48hpf  injected with morpholino against tp53  replicate 2", "Reads were aligned against reference genome using STAR software Read counts per gene were calculated using htseq count script from HTSeq tools software package Genome build: Zebrafish September 2014 GRCz10/danRer10 Supplementary files format and content: Individual counts files reads per gene", "whole embryo", "Injection of tp53 morpholino was performed at 1 cell stage", "RNA was extracted using TRIsure Bioline and treated with TURBO DNA free kit Invitrogen", "Embryos were grown at 28\u00b0C in E3 medium until desired developmental stage", "developmental stage:48 hpf|genotype:WT|treatment:tp53 morpholino", "GSM4724536", "GSM4724536: RNA seq in zebrafish wild type embryos at 48hpf  injected with morpholino against tp53  replicate 2; Danio rerio; RNA Seq", "GSM4724536", null, "1", "RNA was extracted using TRIsure Bioline and treated with TURBO DNA free kit Invitrogen", "GEO Accession:GSM4724536", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "BGISEQ", "BGISEQ-500", null, "SRP277167", null, null, "RNAseq_48h_wt_p53MO_rep2_1.fq.gz", "fastq", 1604734300.0, 32094686.0, "GSM4724536 r1", "0:50", "A:420858899;C:372944640;G:386038616;T:424892145;N:0", 50, null, null, null, 420858899, 372944640, 386038616, 424892145, 0, "SRX8931589", "SRS7187997", "SRA1111981", "GEO", "CABD, Universidad Pablo de Olavide-CSIC", 1, 0.9522, null, 0.09133, null, 0.68885, null, 0.47214, null, 50, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Spain", "2020-08-12", "Hatching", "Embryo", "Whole Organism", "All anatomical structures"], [60608, "SRR12435893", "SRX8931588", "SRS7187996", "SRP277167", "PRJNA656771", "CTCF knockout in zebrafish induces alterations in regulatory landscapes and developmental gene expression [RNA seq]", "GSE156094", "Transcriptome Analysis", "CTCF is an 11 zinc finger DNA binding protein that acts as a transcriptional repressor and insulator  as well as an architectural protein required for 3D genome folding. CTCF mediates long range chromatin looping and is enriched at the boundaries of topologically associating domains TADs  which are sub megabase chromatin structures composed of genomic regions with high contact frequency. Although CTCF is essential for cycling cells and developing embryos  its in vitro removal has only modest effects over gene expression  challenging the generally accepted idea that TADs facilitate enhancer promoter interactions within gene regulatory landscapes. However  the effects of an altered CTCF mediated chromatin structure on gene regulation in vivo are poorly understood. Here  we have generated a ctcf knockout mutant in zebrafish that allows us to monitor the effect of CTCF loss of function during embryo patterning and organogenesis. CTCF absence leads to a loss of chromatin structure in zebrafish embryos and affects the expression of thousands of genes  among them many developmental genes. In addition  we show that chromatin accessibility  both at CTCF sites and at developmental cis regulatory elements CREs  is severely compromised in ctcf mutants. Probing chromatin interactions from developmental genes at high resolution  we further demonstrate that promoters fail to fully establish long range contacts with their associated regulatory landscapes  leading to altered gene expression patterns during development. Therefore  our results demonstrate that CTCF and TADs are essential to finetune gene expression during embryonic development  providing the structural basis for the establishment of developmental gene regulatory landscapes. Overall design: RNA seq assays in wild type and ctcf zebrafish mutants  at developmental stages 24 hpf and 48 hpf  with and without xxx of tp53 morpholino", "parent bioproject:PRJNA656767", "pubmed:34518536", null, "RNA seq in zebrafish wild type embryos at 48hpf  injected with morpholino against tp53  replicate 1", "GSM4724535", null, "tissue:whole embryo|developmental stage:48 hpf|genotype:WT|treatment:tp53 morpholino", "RNA seq in zebrafish wild type embryos at 48hpf  injected with morpholino against tp53  replicate 1", "Reads were aligned against reference genome using STAR software Read counts per gene were calculated using htseq count script from HTSeq tools software package Genome build: Zebrafish September 2014 GRCz10/danRer10 Supplementary files format and content: Individual counts files reads per gene", "whole embryo", "Injection of tp53 morpholino was performed at 1 cell stage", "RNA was extracted using TRIsure Bioline and treated with TURBO DNA free kit Invitrogen", "Embryos were grown at 28\u00b0C in E3 medium until desired developmental stage", "developmental stage:48 hpf|genotype:WT|treatment:tp53 morpholino", "GSM4724535", "GSM4724535: RNA seq in zebrafish wild type embryos at 48hpf  injected with morpholino against tp53  replicate 1; Danio rerio; RNA Seq", "GSM4724535", null, "1", "RNA was extracted using TRIsure Bioline and treated with TURBO DNA free kit Invitrogen", "GEO Accession:GSM4724535", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "BGISEQ", "BGISEQ-500", null, "SRP277167", null, null, "RNAseq_48h_wt_p53MO_rep1_1.fq.gz", "fastq", 2384014500.0, 47680290.0, "GSM4724535 r1", "0:50", "A:625164876;C:552875690;G:576784849;T:629189085;N:0", 50, null, null, null, 625164876, 552875690, 576784849, 629189085, 0, "SRX8931588", "SRS7187996", "SRA1111981", "GEO", "CABD, Universidad Pablo de Olavide-CSIC", 1, 0.94749, null, 0.09167, null, 0.67978, null, 0.48327, null, 50, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Spain", "2020-08-12", "Hatching", "Embryo", "Whole Organism", "All anatomical structures"], [60609, "SRR12435892", "SRX8931587", "SRS7187995", "SRP277167", "PRJNA656771", "CTCF knockout in zebrafish induces alterations in regulatory landscapes and developmental gene expression [RNA seq]", "GSE156094", "Transcriptome Analysis", "CTCF is an 11 zinc finger DNA binding protein that acts as a transcriptional repressor and insulator  as well as an architectural protein required for 3D genome folding. CTCF mediates long range chromatin looping and is enriched at the boundaries of topologically associating domains TADs  which are sub megabase chromatin structures composed of genomic regions with high contact frequency. Although CTCF is essential for cycling cells and developing embryos  its in vitro removal has only modest effects over gene expression  challenging the generally accepted idea that TADs facilitate enhancer promoter interactions within gene regulatory landscapes. However  the effects of an altered CTCF mediated chromatin structure on gene regulation in vivo are poorly understood. Here  we have generated a ctcf knockout mutant in zebrafish that allows us to monitor the effect of CTCF loss of function during embryo patterning and organogenesis. CTCF absence leads to a loss of chromatin structure in zebrafish embryos and affects the expression of thousands of genes  among them many developmental genes. In addition  we show that chromatin accessibility  both at CTCF sites and at developmental cis regulatory elements CREs  is severely compromised in ctcf mutants. Probing chromatin interactions from developmental genes at high resolution  we further demonstrate that promoters fail to fully establish long range contacts with their associated regulatory landscapes  leading to altered gene expression patterns during development. Therefore  our results demonstrate that CTCF and TADs are essential to finetune gene expression during embryonic development  providing the structural basis for the establishment of developmental gene regulatory landscapes. Overall design: RNA seq assays in wild type and ctcf zebrafish mutants  at developmental stages 24 hpf and 48 hpf  with and without xxx of tp53 morpholino", "parent bioproject:PRJNA656767", "pubmed:34518536", null, "RNA seq in zebrafish ctcf mutant embryos at 48hpf  replicate 2", "GSM4724534", null, "tissue:whole embryo|developmental stage:48 hpf|genotype:ctcf  / ", "RNA seq in zebrafish ctcf mutant embryos at 48hpf  replicate 2", "Reads were aligned against reference genome using STAR software Read counts per gene were calculated using htseq count script from HTSeq tools software package Genome build: Zebrafish September 2014 GRCz10/danRer10 Supplementary files format and content: Individual counts files reads per gene", "whole embryo", "Injection of tp53 morpholino was performed at 1 cell stage", "RNA was extracted using TRIsure Bioline and treated with TURBO DNA free kit Invitrogen", "Embryos were grown at 28\u00b0C in E3 medium until desired developmental stage", "developmental stage:48 hpf|genotype:ctcf  / ", "GSM4724534", "GSM4724534: RNA seq in zebrafish ctcf mutant embryos at 48hpf  replicate 2; Danio rerio; RNA Seq", "GSM4724534", null, "1", "RNA was extracted using TRIsure Bioline and treated with TURBO DNA free kit Invitrogen", "GEO Accession:GSM4724534", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "BGISEQ", "BGISEQ-500", null, "SRP277167", null, null, "RNAseq_48h_ctcf_rep2_1.fq.gz", "fastq", 2142745700.0, 42854914.0, "GSM4724534 r1", "0:50 1:0", "A:622717093;C:460353664;G:518363295;T:541311648;N:0", 50, 0, null, null, 622717093, 460353664, 518363295, 541311648, 0, "SRX8931587", "SRS7187995", "SRA1111981", "GEO", "CABD, Universidad Pablo de Olavide-CSIC", 1, 0.94287, null, 0.14736, null, 0.69199, null, 0.47986, null, 50, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Spain", "2020-08-12", "Hatching", "Embryo", "Whole Organism", "All anatomical structures"], [60610, "SRR12435891", "SRX8931586", "SRS7187994", "SRP277167", "PRJNA656771", "CTCF knockout in zebrafish induces alterations in regulatory landscapes and developmental gene expression [RNA seq]", "GSE156094", "Transcriptome Analysis", "CTCF is an 11 zinc finger DNA binding protein that acts as a transcriptional repressor and insulator  as well as an architectural protein required for 3D genome folding. CTCF mediates long range chromatin looping and is enriched at the boundaries of topologically associating domains TADs  which are sub megabase chromatin structures composed of genomic regions with high contact frequency. Although CTCF is essential for cycling cells and developing embryos  its in vitro removal has only modest effects over gene expression  challenging the generally accepted idea that TADs facilitate enhancer promoter interactions within gene regulatory landscapes. However  the effects of an altered CTCF mediated chromatin structure on gene regulation in vivo are poorly understood. Here  we have generated a ctcf knockout mutant in zebrafish that allows us to monitor the effect of CTCF loss of function during embryo patterning and organogenesis. CTCF absence leads to a loss of chromatin structure in zebrafish embryos and affects the expression of thousands of genes  among them many developmental genes. In addition  we show that chromatin accessibility  both at CTCF sites and at developmental cis regulatory elements CREs  is severely compromised in ctcf mutants. Probing chromatin interactions from developmental genes at high resolution  we further demonstrate that promoters fail to fully establish long range contacts with their associated regulatory landscapes  leading to altered gene expression patterns during development. Therefore  our results demonstrate that CTCF and TADs are essential to finetune gene expression during embryonic development  providing the structural basis for the establishment of developmental gene regulatory landscapes. Overall design: RNA seq assays in wild type and ctcf zebrafish mutants  at developmental stages 24 hpf and 48 hpf  with and without xxx of tp53 morpholino", "parent bioproject:PRJNA656767", "pubmed:34518536", null, "RNA seq in zebrafish ctcf mutant embryos at 48hpf  replicate 1", "GSM4724533", null, "tissue:whole embryo|developmental stage:48 hpf|genotype:ctcf  / ", "RNA seq in zebrafish ctcf mutant embryos at 48hpf  replicate 1", "Reads were aligned against reference genome using STAR software Read counts per gene were calculated using htseq count script from HTSeq tools software package Genome build: Zebrafish September 2014 GRCz10/danRer10 Supplementary files format and content: Individual counts files reads per gene", "whole embryo", "Injection of tp53 morpholino was performed at 1 cell stage", "RNA was extracted using TRIsure Bioline and treated with TURBO DNA free kit Invitrogen", "Embryos were grown at 28\u00b0C in E3 medium until desired developmental stage", "developmental stage:48 hpf|genotype:ctcf  / ", "GSM4724533", "GSM4724533: RNA seq in zebrafish ctcf mutant embryos at 48hpf  replicate 1; Danio rerio; RNA Seq", "GSM4724533", null, "1", "RNA was extracted using TRIsure Bioline and treated with TURBO DNA free kit Invitrogen", "GEO Accession:GSM4724533", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "BGISEQ", "BGISEQ-500", null, "SRP277167", null, null, "RNAseq_48h_ctcf_rep1_1.fq.gz", "fastq", 1858500400.0, 37170008.0, "GSM4724533 r1", "0:50 1:0", "A:544611701;C:398699344;G:449892006;T:465297349;N:0", 50, 0, null, null, 544611701, 398699344, 449892006, 465297349, 0, "SRX8931586", "SRS7187994", "SRA1111981", "GEO", "CABD, Universidad Pablo de Olavide-CSIC", 1, 0.94363, null, 0.14349, null, 0.69089, null, 0.48114, null, 50, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Spain", "2020-08-12", "Hatching", "Embryo", "Whole Organism", "All anatomical structures"], [60611, "SRR12435890", "SRX8931585", "SRS7187993", "SRP277167", "PRJNA656771", "CTCF knockout in zebrafish induces alterations in regulatory landscapes and developmental gene expression [RNA seq]", "GSE156094", "Transcriptome Analysis", "CTCF is an 11 zinc finger DNA binding protein that acts as a transcriptional repressor and insulator  as well as an architectural protein required for 3D genome folding. CTCF mediates long range chromatin looping and is enriched at the boundaries of topologically associating domains TADs  which are sub megabase chromatin structures composed of genomic regions with high contact frequency. Although CTCF is essential for cycling cells and developing embryos  its in vitro removal has only modest effects over gene expression  challenging the generally accepted idea that TADs facilitate enhancer promoter interactions within gene regulatory landscapes. However  the effects of an altered CTCF mediated chromatin structure on gene regulation in vivo are poorly understood. Here  we have generated a ctcf knockout mutant in zebrafish that allows us to monitor the effect of CTCF loss of function during embryo patterning and organogenesis. CTCF absence leads to a loss of chromatin structure in zebrafish embryos and affects the expression of thousands of genes  among them many developmental genes. In addition  we show that chromatin accessibility  both at CTCF sites and at developmental cis regulatory elements CREs  is severely compromised in ctcf mutants. Probing chromatin interactions from developmental genes at high resolution  we further demonstrate that promoters fail to fully establish long range contacts with their associated regulatory landscapes  leading to altered gene expression patterns during development. Therefore  our results demonstrate that CTCF and TADs are essential to finetune gene expression during embryonic development  providing the structural basis for the establishment of developmental gene regulatory landscapes. Overall design: RNA seq assays in wild type and ctcf zebrafish mutants  at developmental stages 24 hpf and 48 hpf  with and without xxx of tp53 morpholino", "parent bioproject:PRJNA656767", "pubmed:34518536", null, "RNA seq in zebrafish ctcf mutant embryos at 48hpf  injected with morpholino against tp53  replicate 2", "GSM4724532", null, "tissue:whole embryo|developmental stage:48 hpf|genotype:ctcf  / |treatment:tp53 morpholino", "RNA seq in zebrafish ctcf mutant embryos at 48hpf  injected with morpholino against tp53  replicate 2", "Reads were aligned against reference genome using STAR software Read counts per gene were calculated using htseq count script from HTSeq tools software package Genome build: Zebrafish September 2014 GRCz10/danRer10 Supplementary files format and content: Individual counts files reads per gene", "whole embryo", "Injection of tp53 morpholino was performed at 1 cell stage", "RNA was extracted using TRIsure Bioline and treated with TURBO DNA free kit Invitrogen", "Embryos were grown at 28\u00b0C in E3 medium until desired developmental stage", "developmental stage:48 hpf|genotype:ctcf  / |treatment:tp53 morpholino", "GSM4724532", "GSM4724532: RNA seq in zebrafish ctcf mutant embryos at 48hpf  injected with morpholino against tp53  replicate 2; Danio rerio; RNA Seq", "GSM4724532", null, "1", "RNA was extracted using TRIsure Bioline and treated with TURBO DNA free kit Invitrogen", "GEO Accession:GSM4724532", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "BGISEQ", "BGISEQ-500", null, "SRP277167", null, null, "RNAseq_48h_ctcf_p53MO_rep2_1.fq.gz", "fastq", 2622498950.0, 52449979.0, "GSM4724532 r1", "0:50", "A:683425987;C:612438973;G:639683260;T:686950730;N:0", 50, null, null, null, 683425987, 612438973, 639683260, 686950730, 0, "SRX8931585", "SRS7187993", "SRA1111981", "GEO", "CABD, Universidad Pablo de Olavide-CSIC", 1, 0.94822, null, 0.10163, null, 0.69954, null, 0.4758, null, 50, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Spain", "2020-08-12", "Hatching", "Embryo", "Whole Organism", "All anatomical structures"], [60612, "SRR12435889", "SRX8931584", "SRS7187992", "SRP277167", "PRJNA656771", "CTCF knockout in zebrafish induces alterations in regulatory landscapes and developmental gene expression [RNA seq]", "GSE156094", "Transcriptome Analysis", "CTCF is an 11 zinc finger DNA binding protein that acts as a transcriptional repressor and insulator  as well as an architectural protein required for 3D genome folding. CTCF mediates long range chromatin looping and is enriched at the boundaries of topologically associating domains TADs  which are sub megabase chromatin structures composed of genomic regions with high contact frequency. Although CTCF is essential for cycling cells and developing embryos  its in vitro removal has only modest effects over gene expression  challenging the generally accepted idea that TADs facilitate enhancer promoter interactions within gene regulatory landscapes. However  the effects of an altered CTCF mediated chromatin structure on gene regulation in vivo are poorly understood. Here  we have generated a ctcf knockout mutant in zebrafish that allows us to monitor the effect of CTCF loss of function during embryo patterning and organogenesis. CTCF absence leads to a loss of chromatin structure in zebrafish embryos and affects the expression of thousands of genes  among them many developmental genes. In addition  we show that chromatin accessibility  both at CTCF sites and at developmental cis regulatory elements CREs  is severely compromised in ctcf mutants. Probing chromatin interactions from developmental genes at high resolution  we further demonstrate that promoters fail to fully establish long range contacts with their associated regulatory landscapes  leading to altered gene expression patterns during development. Therefore  our results demonstrate that CTCF and TADs are essential to finetune gene expression during embryonic development  providing the structural basis for the establishment of developmental gene regulatory landscapes. Overall design: RNA seq assays in wild type and ctcf zebrafish mutants  at developmental stages 24 hpf and 48 hpf  with and without xxx of tp53 morpholino", "parent bioproject:PRJNA656767", "pubmed:34518536", null, "RNA seq in zebrafish ctcf mutant embryos at 48hpf  injected with morpholino against tp53  replicate 1", "GSM4724531", null, "tissue:whole embryo|developmental stage:48 hpf|genotype:ctcf  / |treatment:tp53 morpholino", "RNA seq in zebrafish ctcf mutant embryos at 48hpf  injected with morpholino against tp53  replicate 1", "Reads were aligned against reference genome using STAR software Read counts per gene were calculated using htseq count script from HTSeq tools software package Genome build: Zebrafish September 2014 GRCz10/danRer10 Supplementary files format and content: Individual counts files reads per gene", "whole embryo", "Injection of tp53 morpholino was performed at 1 cell stage", "RNA was extracted using TRIsure Bioline and treated with TURBO DNA free kit Invitrogen", "Embryos were grown at 28\u00b0C in E3 medium until desired developmental stage", "developmental stage:48 hpf|genotype:ctcf  / |treatment:tp53 morpholino", "GSM4724531", "GSM4724531: RNA seq in zebrafish ctcf mutant embryos at 48hpf  injected with morpholino against tp53  replicate 1; Danio rerio; RNA Seq", "GSM4724531", null, "1", "RNA was extracted using TRIsure Bioline and treated with TURBO DNA free kit Invitrogen", "GEO Accession:GSM4724531", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "BGISEQ", "BGISEQ-500", null, "SRP277167", null, null, "RNAseq_48h_ctcf_p53MO_rep1_1.fq.gz", "fastq", 2421682100.0, 48433642.0, "GSM4724531 r1", "0:50", "A:625808320;C:568572947;G:596940410;T:630360423;N:0", 50, null, null, null, 625808320, 568572947, 596940410, 630360423, 0, "SRX8931584", "SRS7187992", "SRA1111981", "GEO", "CABD, Universidad Pablo de Olavide-CSIC", 1, 0.94893, null, 0.09731, null, 0.71476, null, 0.48546, null, 50, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Spain", "2020-08-12", "Hatching", "Embryo", "Whole Organism", "All anatomical structures"]], "truncated": false, "filtered_table_rows_count": 28, "expanded_columns": [], "expandable_columns": [], "columns": ["rowid", "run.accession", "experiment.accession", "sample.accession", "study.accession", "bioproject", "study.title", "study.alias", "study.type", "study.abstract", "study.attributes", "study.PMIDs", "sample.description", "sample.title", "sample.alias", "sample.centername", "sample.attributes", "GEOsample.title", "GEOsample.dataprocessing", "GEOsample.source", "GEOsample.treatmentprotocol", "GEOsample.extractprotocol", "GEOsample.growthprotocol", "GEOsample.characteristics", "GEOsample.accession", "experiment.title", "experiment.alias", "experiment.library_name", "experiment.design_description", "experiment.library_construction_protocol", "experiment.attributes", "experiment.library_strategy", "experiment.library_source", "experiment.library_selection", "experiment.library_layout", "experiment.platform", "experiment.instrument_model", "experiment.spot_descriptor", "experiment.study_ref", "run.title", "run.attributes", "run.filename", "run.semantic_name", "run.total_bases", "run.total_spots", "run.alias", "run.read_lengths", "run.base_counts", "run.r1_length", "run.r2_length", "run.r3_length", "run.r4_length", "run.Acount", "run.Ccount", "run.Gcount", "run.Tcount", "run.Ncount", "run.experiment", "run.pool_member", "submission.accession", "submission.srasource", "submission.bioprojectsource", "seqdetective.n_mates", "seqdetective.mapping_rate.mate1", "seqdetective.mapping_rate.mate2", "seqdetective.nofeature_rate.mate1", "seqdetective.nofeature_rate.mate2", "seqdetective.sparsity.mate1", "seqdetective.sparsity.mate2", "seqdetective.pos_strand_rate.mate1", "seqdetective.pos_strand_rate.mate2", "seqdetective.readlen.mate1", "seqdetective.readlen.mate2", "seqdetective.judgement.mate1", "seqdetective.judgement.mate2", "seqdetective.judgement.reason", "platform_family", "instrument_generation", "read_bias", "selection_class", "prep_kit", "sc_or_bulk", "tech_class", "technology", "tech_variant", "submission.bioprojectsource.country", "earliest_date", "devstage_curation", "devstage_curation_coarse", "tissue_curation", "tissue_curation_coarse"], "primary_keys": [], "units": {}, "query": {"sql": "select rowid, [run.accession], [experiment.accession], [sample.accession], [study.accession], bioproject, [study.title], [study.alias], [study.type], [study.abstract], [study.attributes], [study.PMIDs], [sample.description], [sample.title], [sample.alias], [sample.centername], [sample.attributes], [GEOsample.title], [GEOsample.dataprocessing], [GEOsample.source], [GEOsample.treatmentprotocol], [GEOsample.extractprotocol], [GEOsample.growthprotocol], [GEOsample.characteristics], [GEOsample.accession], [experiment.title], [experiment.alias], [experiment.library_name], [experiment.design_description], [experiment.library_construction_protocol], [experiment.attributes], [experiment.library_strategy], [experiment.library_source], [experiment.library_selection], [experiment.library_layout], [experiment.platform], [experiment.instrument_model], [experiment.spot_descriptor], [experiment.study_ref], [run.title], [run.attributes], [run.filename], [run.semantic_name], [run.total_bases], [run.total_spots], [run.alias], [run.read_lengths], [run.base_counts], [run.r1_length], [run.r2_length], [run.r3_length], [run.r4_length], [run.Acount], [run.Ccount], [run.Gcount], [run.Tcount], [run.Ncount], [run.experiment], [run.pool_member], [submission.accession], [submission.srasource], [submission.bioprojectsource], [seqdetective.n_mates], [seqdetective.mapping_rate.mate1], [seqdetective.mapping_rate.mate2], [seqdetective.nofeature_rate.mate1], [seqdetective.nofeature_rate.mate2], [seqdetective.sparsity.mate1], [seqdetective.sparsity.mate2], [seqdetective.pos_strand_rate.mate1], [seqdetective.pos_strand_rate.mate2], [seqdetective.readlen.mate1], [seqdetective.readlen.mate2], [seqdetective.judgement.mate1], [seqdetective.judgement.mate2], [seqdetective.judgement.reason], platform_family, instrument_generation, read_bias, selection_class, prep_kit, sc_or_bulk, tech_class, technology, tech_variant, [submission.bioprojectsource.country], earliest_date, devstage_curation, devstage_curation_coarse, tissue_curation, tissue_curation_coarse from run_metadata where \"devstage_curation\" = :p0 and \"experiment.platform\" = :p1 order by rowid limit 101", "params": {"p0": "Hatching", "p1": "BGISEQ"}}, "facet_results": {"experiment.library_strategy": {"name": "experiment.library_strategy", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?devstage_curation=Hatching&experiment.platform=BGISEQ", "results": [{"value": "RNA-Seq", "label": "RNA-Seq", "count": 28, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation=Hatching&experiment.platform=BGISEQ&experiment.library_strategy=RNA-Seq", "selected": false}], "truncated": false}, "experiment.library_source": {"name": "experiment.library_source", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?devstage_curation=Hatching&experiment.platform=BGISEQ", "results": [{"value": "TRANSCRIPTOMIC", "label": "TRANSCRIPTOMIC", "count": 28, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation=Hatching&experiment.platform=BGISEQ&experiment.library_source=TRANSCRIPTOMIC", "selected": false}], "truncated": false}, "experiment.library_selection": {"name": "experiment.library_selection", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?devstage_curation=Hatching&experiment.platform=BGISEQ", "results": [{"value": "cDNA", "label": "cDNA", "count": 19, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation=Hatching&experiment.platform=BGISEQ&experiment.library_selection=cDNA", "selected": false}, {"value": "Oligo-dT", "label": "Oligo-dT", "count": 9, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation=Hatching&experiment.platform=BGISEQ&experiment.library_selection=Oligo-dT", "selected": false}], "truncated": false}, "experiment.library_layout": {"name": "experiment.library_layout", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?devstage_curation=Hatching&experiment.platform=BGISEQ", "results": [{"value": "SINGLE", "label": "SINGLE", "count": 17, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation=Hatching&experiment.platform=BGISEQ&experiment.library_layout=SINGLE", "selected": false}, {"value": "PAIRED", "label": "PAIRED", "count": 11, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation=Hatching&experiment.platform=BGISEQ&experiment.library_layout=PAIRED", "selected": false}], "truncated": false}, "experiment.platform": {"name": "experiment.platform", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?devstage_curation=Hatching&experiment.platform=BGISEQ", "results": [{"value": "BGISEQ", "label": "BGISEQ", "count": 28, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation=Hatching", "selected": true}], "truncated": false}, "devstage_curation_coarse": {"name": "devstage_curation_coarse", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?devstage_curation=Hatching&experiment.platform=BGISEQ", "results": [{"value": "Embryo", "label": "Embryo", "count": 28, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation=Hatching&experiment.platform=BGISEQ&devstage_curation_coarse=Embryo", "selected": false}], "truncated": false}, "devstage_curation": {"name": "devstage_curation", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?devstage_curation=Hatching&experiment.platform=BGISEQ", "results": [{"value": "Hatching", "label": "Hatching", "count": 28, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.platform=BGISEQ", "selected": true}], "truncated": false}, "tissue_curation_coarse": {"name": "tissue_curation_coarse", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?devstage_curation=Hatching&experiment.platform=BGISEQ", "results": [{"value": "All anatomical structures", "label": "All anatomical structures", "count": 19, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation=Hatching&experiment.platform=BGISEQ&tissue_curation_coarse=All+anatomical+structures", "selected": false}, {"value": "Nervous System", "label": "Nervous System", "count": 9, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation=Hatching&experiment.platform=BGISEQ&tissue_curation_coarse=Nervous+System", "selected": false}], "truncated": false}, "tissue_curation": {"name": "tissue_curation", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?devstage_curation=Hatching&experiment.platform=BGISEQ", "results": [{"value": "Embryo Imprecise", "label": "Embryo Imprecise", "count": 11, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation=Hatching&experiment.platform=BGISEQ&tissue_curation=Embryo+Imprecise", "selected": false}, {"value": "Head", "label": "Head", "count": 9, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation=Hatching&experiment.platform=BGISEQ&tissue_curation=Head", "selected": false}, {"value": "Whole Organism", "label": "Whole Organism", "count": 8, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation=Hatching&experiment.platform=BGISEQ&tissue_curation=Whole+Organism", "selected": false}], "truncated": false}, "technology": {"name": "technology", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?devstage_curation=Hatching&experiment.platform=BGISEQ", "results": [{"value": "unknown", "label": "unknown", "count": 28, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation=Hatching&experiment.platform=BGISEQ&technology=unknown", "selected": false}], "truncated": false}}, "suggested_facets": [], "next": null, "next_url": null, "private": false, "allow_execute_sql": true, "query_ms": 63.310030000138795}